@article {rihtman_coordinated_2024,
	title = {Coordinated transcriptional response to environmental stress by a \textit{Synechococcus virus},
	journal = {The ISME Journal},
	year = {2024},
	month = {mar},
	pages = {wrae032},
	abstract = {Viruses are a major control on populations of microbes. Often, their virulence is examined in controlled laboratory conditions. Yet, in nature, environmental conditions lead to changes in host physiology and fitness that may impart both costs and benefits on viral success.},
	keywords = {rcc752},
	issn = {1751-7362, 1751-7370},
	doi = {10.1093/ismejo/wrae032},
	url = {https://academic.oup.com/ismej/advance-article/doi/10.1093/ismejo/wrae032/7618445},
	author = {Rihtman, Branko and Torcello-Requena, Alberto and Mikhaylina, Alevtina and Puxty, Richard J and Clokie, Martha R J and Millard, Andrew D and Scanlan, David J}
}
@article {dufour_differential_2024,
	title = {Differential acclimation kinetics of the two forms of type IV chromatic acclimaters occurring in marine Synechococcus cyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {15},
	year = {2024},
	pages = {1349322},
	abstract = {Synechococcus , the second most abundant marine phytoplanktonic organism, displays the widest variety of pigment content of all marine oxyphototrophs, explaining its ability to colonize all spectral niches occurring in the upper lit layer of oceans. Seven Synechococcus pigment types (PTs) have been described so far based on the phycobiliprotein composition and chromophorylation of their light-harvesting complexes, called phycobilisomes. The most elaborate and abundant PT (3d) in the open ocean consists of cells capable of type IV chromatic acclimation (CA4), i.e., to reversibly modify the ratio of the blue light-absorbing phycourobilin (PUB) to the green light-absorbing phycoerythrobilin (PEB) in phycobilisome rods to match the ambient light color. Two genetically distinct types of chromatic acclimaters, so-called PTs 3dA and 3dB, occur at similar global abundance in the ocean, but the precise physiological differences between these two types and the reasons for their complementary niche partitioning in the field remain obscure. Here, photoacclimation experiments in different mixes of blue and green light of representatives of these two PTs demonstrated that they differ by the ratio of blue-to-green light required to trigger the CA4 process. Furthermore, shift experiments between 100\% blue and 100\% green light, and vice-versa , revealed significant discrepancies between the acclimation pace of the two types of chromatic acclimaters. This study provides novel insights into the finely tuned adaptation mechanisms used by Synechococcus cells to colonize the whole underwater light field.},
	keywords = {RCC2319, RCC2369, RCC2374, RCC2533, RCC2553, RCC2571, RCC515, rcc555, RCC751},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2024.1349322},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2024.1349322/full},
	author = {Dufour, Louison and Garczarek, Laurence and Gouriou, Bastian and Clairet, Julia and Ratin, Morgane and Partensky, Fr{\'e}d{\'e}ric}
}
@booklet {cock_evolutionary_2024,
	title = {Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems \textbar bioRxiv},
	year = {2024},
	doi = {10.1101/2024.02.19.579948},
	url = {https://www.biorxiv.org/content/10.1101/2024.02.19.579948v1},
	author = {Cock, J Mark}
}
@article {cho_genomic_2024,
	title = {Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses},
	journal = {PLOS Genetics},
	volume = {20},
	number = {4},
	year = {2024},
	note = {Publisher: Public Library of Science},
	pages = {e1011218},
	abstract = {Symbiomonas scintillans Guillou et Chr{\'e}tiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC247, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.},
	keywords = {Eukaryota, Gene prediction, genomics, metagenomics, RCC24, RCC257, Shotgun sequencing, Transcriptome analysis, Viral genomics, Whole genome amplification},
	issn = {1553-7404},
	doi = {10.1371/journal.pgen.1011218},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011218},
	author = {Cho, Anna and Lax, Gordon and Livingston, Samuel J. and Masukagami, Yumiko and Naumova, Mariia and Millar, Olivia and Husnik, Filip and Keeling, Patrick J.}
}
@article {chauhan_size-dependent_2024,
	title = {Size-dependent dynamics of the internal carbon pool drive isotopic vital effects in calcifying phytoplankton},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {373},
	year = {2024},
	pages = {35{\textendash}51},
	abstract = {Isotopic offsets in biogenic calcite from equilibrium values can provide unique insights into the physiology and mechanisms of carbon regulation in calcifying phytoplankton. This study examines the impact of varying CO2 (controlled via pH) on five coccolithophore species chosen for varied cell sizes, physiology, and calcification. The study investigates isotopic offsets in coccolith calcite and organic matter, in relation to carbon demand and supply ({\textmu}/CO2). Species-specific CO2 and/or pH optima for growth ({\textmu}opt) were derived from variations in growth rates with varying CO2 concentrations. Growth rates for all species declined with rising CO2 (decreasing pH) due to H+-driven inhibition. C. braarudii and C. leptoporus exhibited {\textmu}opt at high CO2 concentrations (suggesting high carbon-demand) and limited growth under low CO2 (high pH) suggesting carbon limitation. Under low CO2 supply, when growth rates were CO2-limited, both species exhibited coincident isotopic depletion in calcite and organic matter as a consequence of CO2 diffusion into the cell that experienced no equilibration as a result of a highly depleted internal carbon pool. In these two species, isotopic values in calcite remained unaffected by growth rates and CO2 concentration ({\textmu}/CO2) when CO2 was sufficient for optimal growth. G. huxleyi and G. oceanica displayed optima for growth ({\textmu}opt) at low CO2 concentrations and showed no growth limitation under low CO2 (indicating low carbon-demand). Both species experienced depleted (negative) vital effects caused by an excess of CO2 diffusioninto the small internal carbon pool of the cell when diffusive carbon supply outpaced low demand (low {\textmu}/CO2). Enriched (positive) vital effects were observed under low carbon supply and high demand, likely due to increased HCO3{\textendash} uptake and diffusive CO2 loss from the intracellular carbon pooldue to a lower intracellular pH than the seawater pH. C. carterae exhibited a {\textmu}opt at intermediate CO2 concentrations and isotopically equilibrated intracellular carbon pool such that δ13C values in calcite and organic matter suggested a shared carbon pool. This study illustrates that pH and CO2 driven vital effects and fractionation into organic matter indicate the residence time for carbon in the intracellular carbon pool, where the size of the pool is proportional to cell size. Due to the increased buffering afforded by a larger pool, C. leptoporus and C. carterae may have elevated intracellular pH which minimises CO2 leakage, whereas vital effects in G. huxleyi and G. oceanica are caused by CO2 diffusion in or out of their small internal carbon pool with limited buffering capacity owing to its small size.},
	keywords = {Carbon demand and supply, Carbon residence time, coccolithophores, Internal carbon pool, RCC1130, RCC1198, RCC1314, Vital effects},
	issn = {0016-7037},
	doi = {10.1016/j.gca.2024.03.033},
	url = {https://www.sciencedirect.com/science/article/pii/S0016703724001571},
	author = {Chauhan, Nishant and Rickaby, Rosalind E. M.}
}
@article {strauss_bay_2023,
	title = {The Bay of Bengal exposes abundant photosynthetic picoplankton and newfound diversity along salinity-driven gradients},
	journal = {Environmental Microbiology},
	year = {2023},
	abstract = {The Bay of Bengal (BoB) is a 2,600,000 km2 expanse in the Indian Ocean upon which many humans rely. However, the primary producers underpinning food chains here remain poorly characterized. We examined phytoplankton abundance and diversity along strong BoB latitudinal and vertical salinity gradients-which have low temperature variation (27-29{\textdegree}C) between the surface and subsurface chlorophyll maximum (SCM). In surface waters, Prochlorococcus averaged 11.7 {\textpm} 4.4 {\texttimes} 104  cells ml-1 , predominantly HLII, whereas LLII and {\textquoteright}rare{\textquoteright} ecotypes, HLVI and LLVII, dominated in the SCM. Synechococcus averaged 8.4 {\textpm} 2.3 {\texttimes} 104  cells ml-1 in the surface, declined rapidly with depth, and population structure of dominant Clade II differed between surface and SCM; Clade X was notable at both depths. Across all sites, Ostreococcus Clade OII dominated SCM eukaryotes whereas communities differentiated strongly moving from Arabian Sea-influenced high salinity (southerly; prasinophytes) to freshwater-influenced low salinity (northerly; stramenopiles, specifically, diatoms, pelagophytes, and dictyochophytes, plus the prasinophyte Micromonas) surface waters. Eukaryotic phytoplankton peaked in the south (1.9 {\texttimes} 104  cells ml-1 , surface) where a novel Ostreococcus was revealed, named here Ostreococcus bengalensis. We expose dominance of a single picoeukaryote and hitherto {\textquoteright}rare{\textquoteright} picocyanobacteria at depth in this complex ecosystem where studies suggest picoplankton are replacing larger phytoplankton due to climate change.},
	keywords = {RCC393, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.16431},
	author = {Strauss, Jan and Choi, Chang Jae and Grone, Jonathan and Wittmers, Fabian and Jimenez, Valeria and Makareviciute-Fichtner, Kriste and Bachy, Charles and Jaeger, Gualtiero Spiro and Poirier, Camille and Eckmann, Charlotte and Spezzano, Rachele and L{\"o}scher, Carolin R. and Sarma, V. V. S. S. and Mahadevan, Amala and Worden, Alexandra Z.}
}
@article {churakova_biogenic_2023,
	title = {Biogenic silica accumulation in picoeukaryotes: Novel players in the marine silica cycle},
	journal = {Environmental Microbiology Reports},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.13144},
	abstract = {It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2{\textendash}3 μm), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 μM). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell-1. Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.},
	keywords = {RCC4221, RCC827},
	issn = {1758-2229},
	doi = {10.1111/1758-2229.13144},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.13144},
	author = {Churakova, Yelena and Aguilera, Anabella and Charalampous, Evangelia and Conley, Daniel J. and Lundin, Daniel and Pinhassi, Jarone and Farnelid, Hanna}
}
@article {cruz_bioprospecting_2023,
	title = {Bioprospecting for industrially relevant exopolysaccharide-producing cyanobacteria under Portuguese simulated climate},
	journal = {Scientific Reports},
	volume = {13},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {13561},
	abstract = {Cyanobacterial exopolysaccharides (EPS) are potential candidates for the production of sustainable biopolymers. Although the bioactive and physicochemical properties of cyanobacterial-based EPS are attractive, their commercial exploitation is limited by the high production costs. Bioprospecting and characterizing novel EPS-producing strains for industrially relevant conditions is key to facilitate their implementation in various biotechnological applications and fields. In the present work, we selected twenty-five Portuguese cyanobacterial strains from a diverse taxonomic range (including some genera studied for the first time) to be grown in diel light and temperature, simulating the Portuguese climate conditions, and evaluated their growth performance and proximal composition of macronutrients. Synechocystis and Cyanobium genera, from marine and freshwater origin, were highlighted as fast-growing (0.1{\textendash}0.2~g~L-1~day-1) with distinct biomass composition. Synechocystis sp. LEGE 07367 and Chroococcales cyanobacterium LEGE 19970, showed a production of 0.3 and 0.4~g~L-1 of released polysaccharides (RPS). These were found to be glucan-based polymers with high molecular weight and a low number of monosaccharides than usually reported for cyanobacterial EPS. In addition, the absence of known cyanotoxins in these two RPS producers was also confirmed. This work provides the initial steps for the development of cyanobacterial EPS bioprocesses under the Portuguese climate.},
	keywords = {Biochemistry, Biotechnology, Microbiology, rcc2380},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-40542-6},
	url = {https://www.nature.com/articles/s41598-023-40542-6},
	author = {Cruz, Jos{\'e} Diogo and Delattre, C{\'e}dric and Felpeto, Aldo Barreiro and Pereira, Hugo and Pierre, Guillaume and Morais, Jo{\~a}o and Petit, Emmanuel and Silva, Joana and Azevedo, Joana and Elboutachfaiti, Redouan and Maia, In{\^e}s B. and Dubessay, Pascal and Michaud, Philippe and Vasconcelos, Vitor}
}
@booklet {clark_coccolithophorids_2023,
	title = {Coccolithophorids precipitate carbonate in clumped isotope equilibrium with seawater},
	year = {2023},
	month = {nov},
	publisher = {EGUsphere},
	type = {preprint},
	abstract = {Numerous recent studies have tested the clumped isotope (Δ47) thermometer on a variety of biogenic carbonates such as foraminifera and bivalves and showed that all follow a common calibration. While the sample size requirements for a reliable Δ47 measurement have decreased over the years, the availability and preservation of many biogenic carbonates is still 10 limited and/or require substantial time to be extracted from sediments in sufficient amounts. We thus determined the Δ47temperature relationship for coccolith carbonate, which is abundant and often well-preserved in sediments. The carbon and oxygen isotopic compositions of coccolith calcite have limited use in palaeoenvironmental reconstructions due to physiological effects that cause variability in the carbon and oxygen isotopic values. However, the relatively limited data available suggest that clumped isotopes may not be influenced by these effects. We cultured three species of coccolithophores in well15 constrained carbonate system conditions with a CO2(aq) between 5 and 45 μM and temperatures between 6{\textdegree}C and 27{\textdegree}C.},
	keywords = {RCC1130, RCC1303, RCC3370},
	doi = {10.5194/egusphere-2023-2581},
	url = {https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2581/},
	author = {Clark, Alexander J. and Torres-Romero, Ismael and Jaggi, Madalina and Bernasconi, Stefano M. and Stoll, Heather M.}
}
@article {edullantes_comparison_2023,
	title = {Comparison of thermal traits between non-toxic and potentially toxic marine phytoplankton: Implications to their responses to ocean warming},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {562},
	year = {2023},
	pages = {151883},
	abstract = {Understanding the effect of temperature on growth in marine phytoplankton is crucial in predicting the biogeography and phenology of algal blooms in the warming ocean. Here, we investigated the temperature dependence of the growth of non-toxic and potentially toxic marine phytoplankton. Using non-toxic strains (Prorocentrum sp. NRR 188, Prorocentrum micans CCAP 1136/15, and Alexandrium tamutum PARALEX 242) and potentially toxic strains (Prorocentrum minimum Poulet, Prorocentrum lima CCAP 1136/11, and Alexandrium minutum PARALEX 246) of dinoflagellates as test organisms, we measured their growth rates along a wide temperature gradient and estimated their maximum growth rates, thermal traits (e.g. thermal optima (Topt), critical thermal minima (CTmin), critical thermal maximum (CTmax), fundamental thermal niche (FTN), and skewness), thermal sensitivity, and warming vulnerability. To allow a comparison of these traits with an adequate number of observations, we independently analyzed datasets compiled from published laboratory experiments. Our experiments revealed that the temperature traits were independent of the toxicity of phytoplankton, except for Topt and CTmax. Also, the results of the analysis of the published datasets showed that maximum growth rates and thermal traits were comparable between non-toxic and potentially toxic phytoplankton. Our findings suggest that non-toxic and potentially toxic phytoplankton have generally comparable temperature traits that they can use to respond to climate change. However, depending on the climate scenario, non-toxic phytoplankton may be more vulnerable to warming than potentially toxic phytoplankton. Further studies are needed to improve our understanding of the response of marine phytoplankton to temperature, which can advance our ability to predict algal blooms in response to ongoing climate change.},
	keywords = {Growth experiment, Growth models, Microalgal ecophysiology, RCC2649, RCC291, RCC3034, Thermal performance, Thermal physiology, Toxic microalgae},
	issn = {0022-0981},
	doi = {10.1016/j.jembe.2023.151883},
	url = {https://www.sciencedirect.com/science/article/pii/S0022098123000151},
	author = {Edullantes, Brisneve and Low-Decarie, Etienne and Steinke, Michael and Cameron, Tom}
}
@article {coello-camba_design_2023,
	title = {Design and use of a new primer pair for the characterization of the cyanobacteria Synechococcus and Prochlorococcus communities targeting petB gene through metabarcoding approaches.},
	journal = {MethodsX},
	year = {2023},
	month = {oct},
	pages = {102444},
	abstract = {During the last years, the application of next-generation sequencing (NGS) technologies to search for specific genetic markers has become a crucial method for the characterization of microbial communities. Illumina MiSeq, likely the most widespread NGS platform for metabarcoding experiments and taxonomic classification, allows processing shorter reads than the classical SANGER sequencing method and therefore requires specific primer pairs that produce shorter amplicons. Specifically, for the analysis of the commonly studied Prochlorococcus and Synechococcus communities, the petB marker gene has recently stood out as able to provide deep coverage to determine the microdiversity of the community.. However, current petB primer set produce a 597 bp amplicon that is not suitable for MiSeq chemistry. Here, we designed and tested a petB primer pair that targets both Prochlorococcus and Synechococcus communities producing an appropriate amplicon to be used with state-of-the-art Illumina MiSeq. This new primer set allows the classification of both groups to a low taxonomic level and is therefore suitable for high throughput experiments using MiSeq technologies, therefore constituting a useful, novel tool to facilitate further studies on Prochlorococcus and Synechococcus communities. {\textbullet} This work describes the de novo design of a Prochlorococcus and Synechococcus-specific petB primer pair, allowing the characterization of both populations to a low taxonomic level. {\textbullet} This primer pair is suitable for widespread Illumina MiSeq sequencing technologies. {\textbullet} petB was confirmed as an adequate target for the characterization of both picocyanobacteria.},
	keywords = {cyanobacteria, Illumina MiSeq, RCC156, rcc162, RCC2319, RCC2372, RCC2378, RCC2383, RCC2384, RCC2455, RCC2529, RCC2531, RCC2554, RCC3377, RCC407, RCC408, sequencing},
	issn = {2215-0161},
	doi = {10.1016/j.mex.2023.102444},
	url = {https://www.sciencedirect.com/science/article/pii/S2215016123004405},
	author = {Coello-Camba, Alexandra and D{\'\i}az-R{\'u}a, Rub{\'e}n and Agusti, Susana}
}
@article {ruan_different_2023,
	title = {Different photosynthetic responses of haploid and diploid Emiliania huxleyi (Prymnesiophyceae) to high light and ultraviolet radiation},
	journal = {Bioresources and Bioprocessing},
	volume = {10},
	number = {1},
	year = {2023},
	month = {jul},
	pages = {40},
	abstract = {Solar radiation varies quantitatively and qualitatively while penetrating through the seawater column and thus is one of the most important environmental factors shaping the vertical distribution pattern of phytoplankton. The haploid and diploid life-cycle phases of coccolithophores might have different vertical distribution preferences. Therefore, the two phases respond differently to high solar photosynthetically active radiation (PAR, 400{\textendash}700~nm) and ultraviolet radiation (UVR, 280{\textendash}400~nm). To test this, the haploid and diploid Emiliania huxleyi were exposed to oversaturating irradiance. In the presence of PAR alone, the effective quantum yield was reduced by 10\% more due to the higher damage rate of photosystem II in haploid cells than in diploid cells. The addition of UVR resulted in further inhibition of the quantum yield for both haploid and diploid cells in the first 25~min, partly because of the increased damage of photosystem II. Intriguingly, this UVR-induced inhibition of the haploid cells completely recovered half an hour later. This recovery was confirmed by the comparable maximum quantum yields, maximum relative electron transport rates and yields of the haploid cells treated with PAR and PAR + UVR. Our data indicated that photosynthesis of the haploid phase was more sensitive to high visible light than the diploid phase but resistant to UVR-induced inhibition, reflecting the ecological niches to which this species adapts.},
	keywords = {Diploid phase, Effective quantum yield, Emiliania huxleyi, Haploid phase, rcc1217, Ultraviolet radiation (UVR)},
	issn = {2197-4365},
	doi = {10.1186/s40643-023-00660-5},
	url = {https://doi.org/10.1186/s40643-023-00660-5},
	author = {Ruan, Zuoxi and Lu, Meifang and Lin, Hongmin and Chen, Shanwen and Li, Ping and Chen, Weizhou and Xu, Huijuan and Qiu, Dajun}
}
@article {yu_does_2023,
	title = {Does the life cycle stage matter for distinguishing phytoplankton via fluoro-electrochemical microscopy?},
	journal = {Cell Reports Physical Science},
	year = {2023},
	pages = {101223},
	abstract = {Phytoplankton have species-specific responses toward electrogenerated oxidants, allowing high-throughput species analysis. Herein, a fluoro-electrochemical method is used to expose single Chlamydomonas concordia vegetative cells at different points within their life cycle to electro-generated oxidants from seawater. The resulting decay in fluorescence from chlorophyll-a is measured as a function of time and drops to zero for phytoplankton adjacent to the electrode over a period of a few seconds. The chlorophyll-a transient timescale allows mother cells, which are distinctively larger and require a larger quantity of oxidants, to be distinguished from either zoospores or {\textquotedblleft}growing{\textquotedblright} cells, while all the cells show the same intrinsic susceptibility modulated only by the size of the phytoplankton. These observations are essential for the future automated characterization of the speciation of phytoplankton populations as they show that there is no need to manually identify the life cycle stage.},
	keywords = {electrogenerated radicals, fluoro-electrochemistry, Green algae, life cycle, marine phytoplankton, oxidative damage, RCC1, remote sensing, susceptibility library},
	issn = {2666-3864},
	doi = {10.1016/j.xcrp.2022.101223},
	url = {https://www.sciencedirect.com/science/article/pii/S2666386422005410},
	author = {Yu, Jiahao and Yang, Minjun and Batchelor-McAuley, Christopher and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {coleman_fine-tuning_2023,
	title = {Fine-tuning the flavor of Tetraselmis chuii by modifying nitrogen supply},
	journal = {Algal Research},
	year = {2023},
	pages = {103208},
	abstract = {Dried Tetraselmis chuii biomass has potential as flavoring agent for the development of plant-based seafood alternatives because of its seafood-like aroma and strong umami taste. Depending on the cultivation conditions, microalgae can adapt their metabolism, resulting in a change in biochemical composition. The aim of this study was to assess if the flavor of T. chuii could be modified by changing the nitrogen (N) supply in the cultivation medium in order to maximize the potential of T. chuii as flavoring agent. The sensory evaluation by a trained panel showed that the T. chuii biomass obtained from N starved cultivation conditions (N-deplete) is characterized by a significantly stronger odor intensity and earthy-like off-odor compared to T. chuii biomass obtained from N sufficient cultivation conditions (N-replete). The analysis of volatile organic compounds (VOCs) using SPME-GC{\textendash}MS showed that these odor features of N-deplete biomass are attributed to an increased formation of odor-active VOCs including 2,3-butanedione, 3-methylbutanal, 3-methylbutanol and sulfur-containing dimethyl sulfide and dimethyl disulfide. In contrast, the T. chuii N-replete biomass possessed a significantly stronger taste intensity, umami and salty taste compared to the T. chuii N-deplete biomass. The higher umami is attributed to the significantly higher free glutamic acid (Glu) and adenosine monophosphate (AMP) concentrations in N-replete biomass compared to N-deplete biomass. This study illustrates that flavor and palatability of microalgae biomass is strongly affected by cultivating conditions and modifying these conditions can be an important tool in the development of plant-based seafood alternatives.},
	keywords = {Microalgae, Nitrogen starvation, RCC128, Sensory evaluation, Umami, Volatile organic compounds},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103208},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423002412},
	author = {Coleman, Bert and Van Poucke, Christof and Dewitte, Bavo and Casciaro, Valentina and Moerdijk-Poortvliet, Tanja and Muylaert, Koenraad and Robbens, Johan}
}
@article {sands_genetic_2023,
	title = {Genetic and physiological responses to light quality in a deep ocean ecotype of Ostreococcus, an ecologically important photosynthetic picoeukaryote},
	journal = {Journal of Experimental Botany},
	year = {2023},
	pages = {erad347},
	abstract = {Abstract Phytoplankton are exposed to dramatic variations in light quality when cells are carried by upwelling or downwelling currents or encounter sediment. We investigated the potential impact of light quality changes in Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue light. The clade B species RCC809, isolated from the deep euphotic zone of the tropical Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves and by increasing the relative level of blue-light absorbing pigments. RCC809 responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originates from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. This was associated with the loss of candidate lightquality responsive promoter motifs identified in RCC809 genes. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning.},
	keywords = {Rcc141, RCC4221, RCC745, RCC809},
	issn = {0022-0957, 1460-2431},
	doi = {10.1093/jxb/erad347},
	url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erad347/7258950},
	author = {Sands, Elizabeth and Davies, Sian and Puxty, Richard John and Verg{\'e}, Val{\'e}rie and Bouget, Fran{\c c}ois-Yves and Scanlan, David John and Carr{\'e}, Isabelle Alice}
}
@article {lopez-pacheco_growth_2023,
	title = {Growth Behavior, Biomass Composition and Fatty Acid Methyl Esters (FAMEs) Production Potential of Chlamydomonas reinhardtii, and Chlorella vulgaris Cultures},
	journal = {Marine Drugs},
	volume = {21},
	number = {8},
	year = {2023},
	month = {aug},
	pages = {450},
	abstract = {The production of biomolecules by microalgae has a wide range of applications in the development of various materials and products, such as biodiesel, food supplements, and cosmetics. Microalgae biomass can be produced using waste and in a smaller space than other types of crops (e.g., soja, corn), which shows microalgae{\textquoteright}s great potential as a source of biomass. Among the produced biomolecules of greatest interest are carbohydrates, proteins, lipids, and fatty acids. In this study, the production of these biomolecules was determined in two strains of microalgae (Chlamydomonas reinhardtii and Chlorella vulgaris) when exposed to different concentrations of nitrogen, phosphorus, and sulfur. Results show a significant microalgal growth (3.69 g L-1) and carbohydrates (163 mg g-1) increase in C. reinhardtii under low nitrogen concentration. Also, higher lipids content was produced under low sulfur concentration (246 mg g-1). It was observed that sulfur variation could affect in a negative way proteins production in C. reinhardtii culture. In the case of C. vulgaris, a higher biomass production was obtained in the standard culture medium (1.37 g L-1), and under a low-phosphorus condition, C. vulgaris produced a higher lipids concentration (248 mg g-1). It was observed that a low concentration of nitrogen had a better effect on the accumulation of fatty acid methyl esters (FAMEs) (C16-C18) in both microalgae. These results lead us to visualize the effects that the variation in macronutrients can have on the growth of microalgae and their possible utility for the production of microalgae-based subproducts.},
	keywords = {RCC2488},
	issn = {1660-3397},
	doi = {10.3390/md21080450},
	url = {https://www.mdpi.com/1660-3397/21/8/450},
	author = {L{\'o}pez-Pacheco, Itzel Y. and Ayala-Moreno, Victoria Guadalupe and Mejia-Melara, Catherinne Arlette and Rodr{\'\i}guez-Rodr{\'\i}guez, Jos{\'e} and Cuellar-Bermudez, Sara P. and Gonz{\'a}lez-Gonz{\'a}lez, Reyna Berenice and Coronado-Apodaca, Karina G. and Farfan-Cabrera, Leonardo I. and Gonz{\'a}lez-Meza, Georgia Mar{\'\i}a and Iqbal, Hafiz M. N. and Parra-Sald{\'\i}var, Roberto}
}
@article {groussman_marferret_2023,
	title = {MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes},
	journal = {Scientific Data},
	volume = {10},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {926},
	abstract = {Metatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.},
	keywords = {Classification and taxonomy, Microbial genetics, transcriptomics},
	issn = {2052-4463},
	doi = {10.1038/s41597-023-02842-4},
	url = {https://www.nature.com/articles/s41597-023-02842-4},
	author = {Groussman, R. D. and Blaskowski, S. and Coesel, S. N. and Armbrust, E. V.}
}
@article {mertens_morpho-molecular_2023,
	title = {Morpho-molecular analysis of podolampadacean dinoflagellates (Dinophyceae), with the description of two new genera},
	journal = {Phycologia},
	year = {2023},
	note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/00318884.2022.2158281},
	month = {feb},
	pages = {1{\textendash}19},
	abstract = {Sequences were obtained for 58 podolampadacean single cells from France, Reunion Island (French territories) and Japan (6 SSU rDNA only, 40 SSU+LSU and 12 LSU only). The sequenced taxa belong to five of the eight described genera: Podolampas, Blepharocysta, Lissodinium, Gaarderiella and Mysticella. Two new genera, Alatosphaera and Pseudalatosphaera, were erected to accommodate {\textquoteleft}Blepharocysta{\textquoteright} hermosillae and {\textquoteleft}Blepharocysta{\textquoteright} denticulata. Most genera are well supported by concatenated LSU{\textendash}SSU rDNA phylogenies, with the least support for Lissodinium. Metabarcoding of podolampadaceans using the V4 region of SSU rDNA showed a resolution too low to discriminate genera or species. Roscoffia and Cabra are here considered podolampadaceans, whilst Lessardia is considered to belong in a separate family. The relationship of Rhinodinium to the Podolampadaceae needs further study. Desmoschisis was recorded for the first time in Alatosphaera and Pseudalatosphaera. Several ribotypes need further study to attribute a species name to them.},
	keywords = {Alatosphaera, Blepharocysta, desmoschisis, Gaarderiella, Lissodinium, LSU rDNA, Mysticella, Podolampas, Pseudalatosphaera, SSU rDNA},
	issn = {0031-8884},
	doi = {10.1080/00318884.2022.2158281},
	url = {https://doi.org/10.1080/00318884.2022.2158281},
	author = {Mertens, Kenneth Neil and Carbonell-Moore, M. Consuelo and Chom{\'e}rat, Nicolas and Bilien, Gwenael and Boulben, Sylviane and Guillou, Laure and Romac, Sarah and Probert, Ian and Ishikawa, Akira and N{\'e}zan, Elisabeth}
}
@booklet {wang_novel_2023,
	title = {Novel dimethylsulfoniopropionate biosynthesis enzymes in diverse marine bacteria, cyanobacteria and abundant algae},
	year = {2023},
	month = {mar},
	publisher = {In Review},
	type = {preprint},
	abstract = {Abstract Dimethylsulfoniopropionate (DMSP) is an abundant marine organosulfur compound[1] with roles in stress protection[2, 3], chemotaxis[4], nutrient and sulfur cycling[5] and, potentially, climate regulation[6, 7]. Marine algae and bacteria are considered significant DMSP producers, but many diverse representatives lack known DMSP synthesis genes/enzymes[8, 9]. Here, new DMSP biosynthesis enzymes were identified that considerably increase the number and diversity of potential DMSP-producing organisms, inferring new and significant global DMSP producers. A novel bifunctional DMSP biosynthesis enzyme, DsyGD, identified in the rhizobacterium Gynuella sunshinyii, produces DMSP at levels higher than any other bacterium from methylthiohydroxybutyrate (MTHB) via an N-terminal MTHB S-methyltransferase domain (termed DsyG) and a C-terminal dimethylsulfoniohydroxybutyrate (DMSHB) decarboxylase domain (termed DsyD, which is the first reported enzyme with this activity). DsyGD is also found in some filamentous cyanobacteria, not previously known to produce DMSP. Regulation of DMSP production and dsyGD transcription was consistent with their role in osmoprotection. Indeed, cloned dsyGD conferred osmotolerance to bacteria deficient in osmolyte production, something not previously demonstrated for any known DMSP synthesis gene, and which could be exploited for biotechnology e.g., engineering salt tolerance. DsyGD characterisation led to identification of phylogenetically distinct DsyG-like proteins, termed DSYE, with MTHB S-methyltransferase activity, in diverse and environmentally abundant Chlorophyta, Chlorachniophyta, Ochraphyta, Haptophyta and Bacillariophyta algae. These algae comprise a mix of low, high and previously unknown DMSP producers[10]. Algae containing DSYE, particularly bloom-forming Pelagophyceae species, which we showed to accumulate medium-high intracellular DMSP levels, were globally more abundant DMSP producers than Haptophyta, Dinophyta and Bacillariophyta with DSYB and/or TpMMT. This highlights the potential importance of Pelagophyceae and other DSYE containing algae in global DMSP production and sulfur cycling.},
	keywords = {RCC100, RCC2956, RCC4094, RCC4422, RCC6172},
	doi = {10.21203/rs.3.rs-2678769/v1},
	url = {https://www.researchsquare.com/article/rs-2678769/v1},
	author = {Wang, Jinyan and Zhou, Shun and Curson, Andrew and Vieira, Ana and Walsham, Keanu and Monaco, Serena and Li, Chun-Yang and Rivera, Peter Paolo and Wang, Xiao-Di and Hanwell, Libby and Zhu, Xiao-Yu and Le{\~a}o, Pedro and Lea-Smith, David J. and Zhang, Yuzhong and Zhang, Xiaohua and Todd, Jonathan}
}
@article {concordio-reis_novel_2023,
	title = {Novel exopolysaccharide produced by the marine dinoflagellate Heterocapsa AC210: Production, characterization, and biological properties},
	journal = {Algal Research},
	volume = {70},
	year = {2023},
	pages = {103014},
	abstract = {Marine microalgae are promising sources of novel valuable biomolecules such as polysaccharides. In this study, the dinoflagellate Heterocapsa sp. AC210 was described as a new exopolysaccharide (EPS) producer. The cultivation and EPS production in bioreactor was evaluated for the first time in detail. The EPS was composed of seven different sugar monomers, including fucose and glucosamine, which are quite rare and have never been reported in dinoflagellates{\textquoteright} EPS. Moreover, the EPS had a high content of sulphate, which is often associated with biological properties. Cytotoxicity was accessed and the results showed that the EPS did not reduce cell viability for concentrations up to 1~g~L-1. Additionally, antioxidant and anti-inflammatory assays demonstrated that the EPS reduced by 18~\% the intracellular reactive oxygen species and decreased up to 79.3~\% and 46.2~\% of IL-8 and IL-6 secretion in keratinocytes, which supports its potential application in the cosmeceutical and biomedical fields.},
	keywords = {Anti-inflammatory, Cytotoxicity, Dinoflagellates, Exopolysaccharide production, Marine microalgae, RCC1514, sp. AC210},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103014},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423000474},
	author = {Conc{\'o}rdio-Reis, Patr{\'\i}cia and Cardeira, Martim and Macedo, Ana Catarina and Ferreira, S{\'o}nia S. and Serra, Ana Teresa and Coimbra, Manuel A. and Amorim, Ana and Reis, Maria A. M. and Freitas, Filomena}
}
@booklet {barton_novel_2023,
	title = {A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton},
	year = {2023},
	month = {apr},
	publisher = {Life Sciences},
	type = {preprint},
	abstract = {<p>To broaden our understanding of pelagic ecosystem responses to environmental change, it is essential that we improve the spatio-temporal resolution of in situ monitoring of phytoplankton communities. A key challenge for existing methods is in classifying and quantifying cells within the nanophytoplankton size range (2-20{\textmu}m). This is particularly difficult when there are similarities in morphology, making visual differentiation difficult for both trained taxonomists and machine learning based approaches. Here we present a rapid fluoro-electrochemical technique for classifying nanophytoplankton, and using a library of 52 diverse strains of nanophytoplankton we assess the accuracy of this technique based on two measurements at the individual level: charge required to reduce per cell chlorophyll a fluorescence by 50\%, and cell radius. We demonstrate a high degree of accuracy overall (\&gt;90\%) in categorising cells belonging to widely recognised key functional groups, however this is reduced when we consider the broader diversity of {\textquotedblleft}nano-phytoflagellates{\textquotedblright}. Notably, we observe that some groups, for example calcifying Isochrysidales, have much greater resilience to electrochemically driven oxidative conditions relative to others of a similar size, making them more easily categorised by the technique. The findings of this study present a promising step forward in advancing our toolkit for monitoring phytoplankton communities. We highlight that, for improved categorisation accuracy, future iterations of the method can be enhanced by measuring additional predictor variables with minimal adjustments to the set-up. In doing so, we foresee this technique being highly applicable, and potentially invaluable, for in situ classification and enumeration of the nanophytoplankton size fraction.</p>
},
	keywords = {RCC1, rcc1084, RCC1130, RCC1150, RCC1178, RCC1185, RCC1198, RCC1216, rcc1217, RCC1242, RCC1314, RCC1346, RCC1489, RCC1511, RCC1546, RCC1557, RCC1614, rcc1731, RCC191, RCC2570, RCC3598, RCC3696, RCC3776, RCC3780, RCC4207, RCC4221, RCC4273, RCC4657, RCC4660, RCC6, RCC623, RCC6516, RCC656, RCC678, RCC69, RCC74, RCC76, RCC8, RCC80, RCC81, RCC88, RCC911, RCC950},
	doi = {10.1002/lom3.10572},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10572},
	author = {Barton, Samuel and Yang, Minjun and Chen, Haotian and Batchelor-McAuley, Christopher and Compton, Richard and Bouman, Heather and Rickaby, Rosalind}
}
@article {cho_phylogenomic_2023,
	title = {Phylogenomic position of genetically diverse phagotrophic stramenopile flagellates in the sediment-associated MAST-6 lineage and a potentially halotolerant placididean},
	journal = {Molecular Phylogenetics and Evolution},
	year = {2023},
	month = {nov},
	pages = {107964},
	abstract = {Unlike morphologically conspicuous ochrophytes, many flagellates belonging to basally branching stramenopiles are small and often overlooked. As a result, many of these lineages are known only through molecular surveys and identified as MArine STramenopiles (MAST), and remain largely uncharacterized at the cellular or genomic level. These likely phagotrophic flagellates are not only phylogenetically diverse, but also extremely abundant in some environments, making their characterization all the more important. MAST-6 is one example of a phylogenetically distinct group that has been known to be associated with sediments, but little else is known about it. Indeed, until the present study, only a single species from this group, Pseudophyllomitus vesiculosus (Pseudophyllomitidae), has been both formally described and associated with genomic information. Here, we describe four new species including two new genera of sediment-dwelling MAST-6, Vomastramonas tehuelche gen. et sp. nov., Mastreximonas tlaamin gen. et sp. nov., one undescribed Pseudophyllomitus sp., BSC2, and a new species belonging to Placididea, the potentially halotolerant Haloplacidia sinai sp. nov. We also provide two additional bikosian transcriptomes from a public culture collection, to allow for better phylogenetic reconstructions of deep-branching stramenopiles. With the SSU rRNA sequences of the new MAST-6 species, we investigate the phylogenetic diversity of the MAST-6 group and show a high relative abundance of MAST-6 related to M. tlaamin in samples across various depths and geographical locations. Using the new MAST-6 species, we also update the phylogenomic tree of stramenopiles, particularly focusing on the paraphyly of Bigyra.},
	keywords = {benthic protists, Bigyra, MAST-6, phylogenomics, Placididea, RCC1078, RCC257, Stramenopile},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2023.107964},
	url = {https://www.sciencedirect.com/science/article/pii/S1055790323002646},
	author = {Cho, Anna and Tikhonenkov, Denis V. and Lax, Gordon and Prokina, Kristina I. and Keeling, Patrick J.}
}
@article {zhang_stimulating_2023,
	title = {Stimulating and toxic effect of chromium on growth and photosynthesis of a marine chlorophyte},
	journal = {New Phytologist},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19376},
	abstract = {Marine phytoplankton can interchange trace metals in various biochemical functions, particularly under metal-limiting conditions. Here, we investigate the stimulating and toxicity effect of chromium (Cr) on a marine Chlorophyceae Osetreococcus tauri under Fe-replete and Fe-deficient conditions. We determined the growth, photosynthesis, and proteome expressions of Osetreococcus tauri cultured under different Cr and Fe concentrations. In Fe-replete conditions, the presence of Cr(VI) stimulated significantly the growth rate and the maximum yield of photochemistry of photosystem II (Fv/Fm) of the phytoplankton, while the functional absorption cross-section of photosystem II (σPSII) did not change. Minor additions of Cr(VI) partially rescued phytoplankton growth under Fe-limited conditions. Proteomic analysis of this alga grown in Fe-replete normal and Fe-replete with Cr addition media (10 μM Cr) showed that the presence of Cr significantly decreased the expression of phosphate-transporting proteins and photosynthetic proteins, while increasing the expression of proteins related to carbon assimilation. Cr can stimulate the growth and photosynthesis of O. tauri, but the effects are dependent on both the Cr(VI) concentration and the availability of Fe. The proteomic results further suggest that Cr(VI) addition might significantly increase starch production and carbon fixation.},
	keywords = {chromium, Photosynthesis, phytoplankton, proteomics, RCC1, RCC1242, trace metal},
	issn = {1469-8137},
	doi = {10.1111/nph.19376},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19376},
	author = {Zhang, Qiong and Charles, Philip D. and Bendif, El Mahdi and Hester, Svenja S. and Mohammad, Shabaz and Rickaby, Rosalind E. M.}
}
@article {storti_tailoring_2023,
	title = {Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution},
	journal = {Cell Reports Methods},
	year = {2023},
	pages = {100568},
	abstract = {Photoautotrophs{\textquoteright} environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy.},
	keywords = {rcc1383},
	issn = {26672375},
	doi = {10.1016/j.crmeth.2023.100568},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126},
	author = {Storti, Mattia and Hsine, Haythem and Uwizeye, Clarisse and Bastien, Olivier and Yee, Daniel P. and Chevalier, Fabien and Decelle, Johan and Giustini, C{\'e}cile and B{\'e}al, Daniel and Curien, Gilles and Finazzi, Giovanni and Tolleter, Dimitri}
}
@article {alonso-saez_transcriptional_2023,
	title = {Transcriptional Mechanisms of Thermal Acclimation in \textit{Prochlorococcus},
	journal = {mBio},
	year = {2023},
	pages = {e03425{\textendash}22},
	abstract = {Low temperature limits the growth and the distribution of the key oceanic primary producer Prochlorococcus, which does not proliferate above a latitude of ca. 40{\textdegree}. Yet, the molecular basis of thermal acclimation in this cyanobacterium remains unexplored. We analyzed the transcriptional response of the Prochlorococcus marinus strain MIT9301 in long-term acclimations and in natural Prochlorococcus populations along a temperature range enabling its growth (17 to 30{\textdegree}C). MIT9301 upregulated mechanisms of the global stress response at the temperature minimum (17{\textdegree}C) but maintained the expression levels of genes involved in essential metabolic pathways (e.g., ATP synthesis and carbon fixation) along the whole thermal niche. Notably, the declining growth of MIT9301 from the optimum to the minimum temperature was coincident with a transcriptional suppression of the photosynthetic apparatus and a dampening of its circadian expression patterns, indicating a loss in their regulatory capacity under cold conditions. Under warm conditions, the cellular transcript inventory of MIT9301 was strongly streamlined, which may also induce regulatory imbalances due to stochasticity in gene expression. The daytime transcriptional suppression of photosynthetic genes at low temperature was also observed in metatranscriptomic reads mapping to MIT9301 across the global ocean, implying that this molecular mechanism may be associated with the restricted distribution of Prochlorococcus to temperate zones.},
	keywords = {RCC3377},
	issn = {2150-7511},
	doi = {10.1128/mbio.03425-22},
	url = {https://journals.asm.org/doi/10.1128/mbio.03425-22},
	author = {Alonso-S{\'a}ez, Laura and Palacio, Antonio S. and Cabello, Ana M. and Robaina-Est{\'e}vez, Semid{\'a}n and Gonz{\'a}lez, Jos{\'e} M. and Garczarek, Laurence and L{\'o}pez-Urrutia, {\'A}ngel},
	editor = {Martiny, Jennifer B. H.}
}
@article {bordiga_unexpected_2023,
	title = {Unexpected silicon localization in calcium carbonate exoskeleton of cultured and fossil coccolithophores},
	journal = {Scientific Reports},
	volume = {13},
	number = {1},
	year = {2023},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {may},
	pages = {7417},
	abstract = {Coccolithophores, marine calcifying phytoplankton, are important primary producers impacting the global carbon cycle at different timescales. Their biomineral structures, the calcite containing coccoliths, are among the most elaborate hard parts of any organism. Understanding the morphogenesis of coccoliths is not only relevant in the context of coccolithophore eco-physiology but will also inform biomineralization and crystal design research more generally. The recent discovery of a silicon (Si) requirement for crystal shaping in some coccolithophores has opened up a new avenue of biomineralization research. In order to develop a mechanistic understanding of the role of Si, the presence and localization of this chemical element in coccoliths needs to be known. Here, we document for the first time the uneven Si distribution in Helicosphaera carteri coccoliths through three synchrotron-based techniques employing X-ray Fluorescence and Infrared Spectromicroscopy. The enrichment of Si in specific areas of the coccoliths point to a targeted role of this element in the coccolith formation. Our findings mark a key step in biomineralization research because it opens the door for a detailed mechanistic understanding of the role Si plays in shaping coccolith crystals.},
	keywords = {Biogeochemistry, Marine biology, Palaeontology, RCC1323},
	issn = {2045-2322},
	doi = {10.1038/s41598-023-34003-3},
	url = {https://www.nature.com/articles/s41598-023-34003-3},
	author = {Bordiga, M. and Lupi, C. and Langer, G. and Gianoncelli, A. and Birarda, G. and Pollastri, S. and Bonanni, V. and Bedolla, D. E. and Vaccari, L. and Gariani, G. and Cerino, F. and Cabrini, M. and Beran, A. and Zuccotti, M. and Fiorentino, G. and Zanoni, M. and Garagna, S. and Cobianchi, M. and Di Giulio, A.}
}
@article {walde_viral_2023,
	title = {Viral infection impacts the 3D subcellular structure of the abundant marine diatom Guinardia delicatula},
	journal = {Frontiers in Marine Science},
	volume = {9},
	year = {2023},
	abstract = {Viruses are key players in marine ecosystems where they infect abundant marine microbes. RNA viruses are emerging as key members of the marine virosphere. They have recently been identified as a potential source of mortality in diatoms, a group of microalgae that accounts for roughly 40\% of the primary production in the ocean. Despite their likely importance, their impacts on host populations and ecosystems remain difficult to assess. In this study, we introduce an innovative approach that combines automated 3D confocal microscopy with quantitative image analysis and physiological measurements to expand our understanding of viral infection. We followed different stages of infection of the bloom-forming diatom Guinardia delicatula by the RNA virus GdelRNAV-04 until the complete lysis of the host. From 20h after infection, we observed quantifiable changes in subcellular host morphology and biomass. Our microscopy monitoring also showed that viral infection of G. delicatula induced the formation of auxospores as a probable defense strategy against viruses. Our method enables the detection of discriminative morphological features on the subcellular scale and at high throughput for comparing populations, making it a promising approach for the quantification of viral infections in the field in the future.},
	keywords = {RCC3083, RCC5812},
	issn = {2296-7745},
	doi = {10.3389/fmars.2022.1034235},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2022.1034235},
	author = {Walde, Marie and Camplong, Cyprien and de Vargas, Colomban and Baudoux, Anne-claire and Simon, Nathalie}
}
@article {ferrieux_comparative_2022,
	title = {Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	abstract = {Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.},
	keywords = {RCC2374, RCC2385, RCC2533, RCC2534, RCC2571, RCC515, rcc539, rcc791},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.893413},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.893413},
	author = {Ferrieux, Mathilde and Dufour, Louison and Dor{\'e}, Hugo and Ratin, Morgane and Gu{\'e}neugu{\`e}s, Audrey and Chasselin, L{\'e}o and Marie, Dominique and Rigaut-jalabert, Fabienne and Le Gall, Florence and Sciandra, Th{\'e}o and Monier, Garance and Hoebeke, Mark and Corre, Erwan and Xia, Xiaomin and Liu, Hongbin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {fernandes_effects_2022,
	title = {Effects of phosphorus-induced changes on the growth, nitrogen uptake, and biochemical composition of Pavlova pinguis and Hemiselmis cf. andersenii},
	journal = {Journal of Applied Phycology},
	year = {2022},
	abstract = {The understanding of the phosphorus-induced changes in the biochemical composition of microalgae is of great importance for achieving efficiency in high-value lipid production. To study the chemoplasticity of Pavlova pinguis (Haptophyceae) and Hemiselmis cf. andersenii (Cryptophyceae), their growth, carotenoid and chlorophyll a content, and their monosaccharide and lipid profiles were analyzed against several phosphorus (P) regimes: low (LP), medium (MP), and high (HP). For both microalgal cultures, increasing initial P concentrations showed a positive effect on biomass productivities. Carbon-rich pools presented significant differences (p< 0.05) for P. pinguis against P treatments, in contrast to H. cf. andersenii. Differential responses to P-induced changes in microalgae monosaccharide and lipid profile were observed. Hemiselmis cf. andersenii increased its proportion in galactose (up to 3 times) from LP to HP conditions, whereas P. pinguis decreased (up to 20\%) its glucose proportion from LP to HP conditions. For P. pinguis, the lowest amount (13.12 mg g-1 dw) of sterols was observed at LP conditions, in contrast to its carotenoid content (4.32 mg g-1 dw). P-replete conditions were the most effective in inducing high-value lipid accumulation. Non-targeted lipid analysis revealed which samples would need to be processed to fully exploit its high-value lipids, namely H. cf andersenii under MP and HP conditions. This study demonstrated that P played an important role in carbon allocation, nitrogen uptake, and lipid regulation on P. pinguis and H. cf. andersenii, and that P-replete conditions could be useful for optimizing high-value lipids with potential for nutraceutical and pharmaceutical fields.},
	keywords = {RCC1539},
	issn = {1573-5176},
	doi = {10.1007/s10811-021-02662-2},
	url = {https://doi.org/10.1007/s10811-021-02662-2},
	author = {Fernandes, Tom{\'a}sia and Cordeiro, Nereida}
}
@article {ebenezer_elemental_2022,
	title = {Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes},
	journal = {Limnology and Oceanography},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12013},
	abstract = {Chloropicophyceae (Prasinophyte Clade VII) are small nonmotile coccoid cells with cell diameters ranging from 1 to 3 μm. Molecular surveys indicate they are relatively high in abundance in moderately oligotrophic oceanic waters and may substantively contribute to biogeochemical cycling in the sea. Here, we quantify the elemental and macromolecular composition of three subtropical Chloropicophyceae strains: Chloropicon mariensis, Chloropicon maureeniae, and Chloropicon roscoffensis under nutrient-sufficient exponential growth and nitrate starvation. Under nutrient-sufficient conditions the Chloropicophyceae are high in C : N and quite low in C : P and N : P relative to the canonical Redfield ratio, reflecting their relatively high nucleic acid composition compared to many other phytoplankton taxa. Nitrate starvation causes increases in C : N and C : P and decreases in N : P, primarily due to increases in carbohydrate and lipid and decreases in protein and RNA. There is genetic evidence that unlike most other green algae, Chloropicophyceae are diploid. The high nucleic acid content in the Chloropicon is consistent with the hypothesis that the nucleus, as a nonscalable component, takes up a larger and substantial proportion of cell mass in diploid picoeukaryotes. The elemental and macromolecular composition of these Chloropicophyceae, and relatively homeostatic response to N-starvation compared to diatoms, provides some insight into their success in the moderately oligotrophic ocean.},
	keywords = {RCC138, RCC3374, RCC3375},
	issn = {1939-5590},
	doi = {10.1002/lno.12013},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12013},
	author = {Ebenezer, Vinitha and Hu, Yingyu and Carnicer, Olga and Irwin, Andrew J. and Follows, Michael J. and Finkel, Zoe V.}
}
@article {guerin_genomic_2022,
	title = {Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},
	journal = {Communications Biology},
	volume = {5},
	number = {1},
	year = {2022},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {1{\textendash}14},
	abstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.},
	keywords = {Biogeography, comparative genomics, metagenomics, RCC100, Water microbiology},
	issn = {2399-3642},
	doi = {10.1038/s42003-022-03939-z},
	url = {https://www.nature.com/articles/s42003-022-03939-z},
	author = {Gu{\'e}rin, Nina and Ciccarella, Marta and Flamant, Elisa and Fr{\'e}mont, Paul and Mangenot, Sophie and Istace, Benjamin and Noel, Benjamin and Belser, Caroline and Bertrand, Laurie and Labadie, Karine and Cruaud, Corinne and Romac, Sarah and Bachy, Charles and Gachenot, Martin and Pelletier, Eric and Alberti, Adriana and Jaillon, Olivier and Wincker, Patrick and Aury, Jean-Marc and Carradec, Quentin}
}
@article {dore_global_2022,
	title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts},
	journal = {mSystems},
	year = {2022},
	note = {Publisher: American Society for Microbiology},
	pages = {e00656{\textendash}22},
	abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of {\textquotedblleft}who is where{\textquotedblright} by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.},
	keywords = {RCC1086, RCC1695, RCC2369, rcc2380, RCC2553, RCC2556, RCC2570, rcc791},
	doi = {10.1128/msystems.00656-22},
	url = {https://journals.asm.org/doi/full/10.1128/msystems.00656-22},
	author = {Dor{\'e}, Hugo and Leconte, Jade and Guyet, Ulysse and Breton, Sol{\`e}ne and Farrant, Gregory K. and Demory, David and Ratin, Morgane and Hoebeke, Mark and Corre, Erwan and Pitt, Frances D. and Ostrowski, Martin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Garczarek, Laurence}
}
@article {vazquez_high-co2_2022,
	title = {High-CO2 Levels Rather than Acidification Restrict Emiliania huxleyi Growth and Performance},
	journal = {Microbial Ecology},
	year = {2022},
	abstract = {The coccolithophore Emiliania huxleyi shows a variety of responses to ocean acidification (OA) and to high-CO2 concentrations, but there is still controversy on differentiating between these two factors when using different strains and culture methods. A heavily calcified type A strain isolated from the Norwegian Sea was selected and batch cultured in order to understand whether acclimation to OA was mediated mainly by CO2 or H+, and how it impacted cell growth performance, calcification, and physiological stress management. Emiliania huxleyi responded differently to each acidification method. CO2-enriched aeration (1200 {\textmu}atm, pH 7.62) induced a negative effect on the cells when compared to acidification caused by decreasing pH alone (pH 7.60). The growth rates of the coccolithophore were more negatively affected by high pCO2 than by low pH without CO2 enrichment with respect to the control (400 {\textmu}atm, pH 8.1). High CO2 also affected cell viability and promoted the accumulation of reactive oxygen species (ROS), which was not observed under low pH. This suggests a possible metabolic imbalance induced by high CO2 alone. In contrast, the affinity for carbon uptake was negatively affected by both low pH and high CO2. Photochemistry was only marginally affected by either acidification method when analysed by PAM fluorometry. The POC and PIC cellular quotas and the PIC:POC ratio shifted along the different phases of the cultures; consequently, calcification did not follow the same pattern observed in cell stress and growth performance. Specifically, acidification by HCl addition caused a higher proportion of severely deformed coccoliths, than CO2 enrichment. These results highlight the capacity of CO2 rather than acidification itself to generate metabolic stress, not reducing calcification.},
	keywords = {Calcification, coccolithophores, Emiliania huxleyi, Ocean acidification, pCO2, Photochemistry, phytoplankton, rcc1226, Stress},
	issn = {1432-184X},
	doi = {10.1007/s00248-022-02035-3},
	url = {https://doi.org/10.1007/s00248-022-02035-3},
	author = {V{\'a}zquez, V{\'\i}ctor and Le{\'o}n, Pablo and Gordillo, Francisco J. L. and Jim{\'e}nez, Carlos and Concepci{\'o}n, I{\~n}iguez and Mackenzie, Kevin and Bresnan, Eileen and Segovia, Mar{\'\i}a}
}
@article {fernandes_high-value_2022,
	title = {High-value lipids accumulation by Pavlova pinguis as a response to nitrogen-induced changes},
	journal = {Biomass and Bioenergy},
	volume = {158},
	year = {2022},
	month = {mar},
	pages = {106341},
	abstract = {The challenges of exploring the potential of microalgal strains for biotechnological applications include the optimization of their cell growth and chemical composition. To overcome this, it is essential to understand the mechanisms that lead to the accumulation of desired products within microalgal cells. In this study, a gradient of nitrogen as nitrate (NO3{\textendash}N) concentrations was used for the preparation of P. pinguis growth medium. The algal growth dynamics, pigments, nutrient uptake, and detailed lipid composition across treatments were assessed. Increasing the NO3{\textendash}N level led to higher lipid content (21\%), a higher cell uptake rate (0.20 pg NO3{\textendash}N cell-1 d-1) and more accumulation of chlorophylls, carotenoids, and high-value lipids. Eicosapentaenoic acid, essential fatty acids, phytol and stigmasterol were the key high-value lipids that were positively influenced by higher NO3{\textendash}N levels. High NO3{\textendash}N conditions induced an increase of 54\% in total sterol content, while low NO3{\textendash}N conditions resulted in increased proportions of saturated fatty acids (66\% more) and decreased proportions of polyunsaturated fatty acids (14\% less). The low NO3{\textendash}N level also led to higher amounts of monoglyceride (1.60 mg g-1; 64\% more). The analysis of P. pinguis lipids before and after hydrolysis provided an insight into the composition of the esterified lipids across treatments. NO3{\textendash}N supplementation was revealed to be an effective strategy for enhancing P. pinguis lipid composition, for nutraceutical and pharmaceutical industries (high NO3{\textendash}N level). A greater understanding of the NO3{\textendash}N uptake and the use efficiency by P. pinguis was reached, showing its potential for further biotechnological applications.},
	keywords = {Biotechnological application, High-value lipids, RCC1359, supply},
	issn = {0961-9534},
	doi = {10.1016/j.biombioe.2022.106341},
	url = {https://www.sciencedirect.com/science/article/pii/S0961953422000022},
	author = {Fernandes, Tom{\'a}sia and Cordeiro, Nereida}
}
@article {falciatore_light-driven_2022,
	title = {Light-driven processes: key players of the functional biodiversity in microalgae},
	journal = {Comptes Rendus. Biologies},
	volume = {345},
	number = {2},
	year = {2022},
	pages = {1{\textendash}24},
	doi = {10.5802/crbiol.80},
	url = {https://comptes-rendus.academie-sciences.fr/biologies/articles/10.5802/crbiol.80/},
	author = {Falciatore, Angela and Bailleul, Benjamin and Boulouis, Alix and Bouly, Jean-Pierre and Bujaldon, Sandrine and Cheminant-Navarro, Soizic and Choquet, Yves and Vitry, Catherine de and Eberhard, Stephan and Jaubert, Marianne and Kuras, Richard and Lafontaine, Ingrid and Landier, Sophie and Selles, Julien and Vallon, Olivier and Wostrikoff, Katia}
}
@article {castejon_limpet_2022,
	title = {Limpet larvae (Patella aspera R{\"o}ding, 1798), obtained by gonad dissection and fecundation in vitro, settled and metamorphosed on crustose coralline algae},
	journal = {Journal of the Marine Biological Association of the United Kingdom},
	year = {2022},
	note = {Publisher: Cambridge University Press},
	month = {feb},
	pages = {1{\textendash}12},
	abstract = {<p>The limpet Patella aspera R{\"o}ding, 1798, is a native species from the Macaronesian region whose fishing is regulated. The early life of limpets, including the settlement process, is poorly known thus far. The current study evaluated different substrates to induce settlement in P. aspera, including microalgae strains (Halamphora coffeaeformis, Navicula incerta and Pavlova sp.) and crustose coralline algae (CCA) obtained from limpet shells. The results showed that gametes obtained by dissection and matured artificially using alkalinized seawater baths can produce viable larvae able to metamorphose to juveniles. Feeding was not required during larval development, suggesting lecithotrophy. Early postlarvae were identified by the shedding of the velum, and juveniles were identified by teleoconch and active grazing behaviour. The presence of CCA shortened the timing for settlement and increased the ratio of juveniles. The type and abundance of CCA can influence settlement success. Moreover, the results suggested that settlement and metamorphosis in true limpets (Patellogastropoda) might be triggered by a two-step mechanism, i.e. a first cue influencing the shift between swimming and crawling activity and a second cue determining settlement and metamorphosis to early postlarvae and juveniles.</p>
},
	keywords = {Early postlarvae, lecithotrophy, metamorphosis, oocyte alkalinization, pediveliger larvae, RCC3458, settlement},
	issn = {0025-3154, 1469-7769},
	doi = {10.1017/S0025315421000916},
	author = {Castej{\'o}n, Diego and Nogueira, Natacha and Andrade, Carlos A. P.}
}
@article {gomez_molecular_2022,
	title = {Molecular phylogeny of the spiny-surfaced species of the dinoflagellate Prorocentrum with the description of P. Thermophilum sp. nov. and P. criophilum sp. nov. (Prorocentrales, Dinophyceae)},
	journal = {Journal of Phycology},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13298},
	abstract = {Spiny-surfaced species of Prorocentrum forms harmful algal blooms, and its taxonomic identity is obscure due to the size and shape variability. Molecular phylogenies reveal two major clades: one for P. cordatum with sequences mainly retrieved as P. minimum, and other for P. shikokuense with sequences also retrieved as P. dentatum and P. donghaiense. Several closely related clades still need to be characterized. Here, we provide SSU- and LSU rRNA, and ITS gene sequences of the strain CCMP3122 isolated from Florida (initially named P. donghaiense) and strains Prorocentrum sp. RCC6871{\textendash}2 from the Ross Sea, Antarctica. We describe Prorocentrum thermophilum sp. nov. based on the strain CCMP3122, a species also distributed in the open waters of Gulf of Mexico, New Zealand and the Arabian Gulf; and Prorocentrum criophilum sp. nov. based on the strain RCC6872, which is distributed in the Antarctic Ocean and the Arctic Sea. Prorocentrum thermophilum is roundish ( 14 μm long, 12 μm wide), with an inconspicuous anterior spine-like prolongation under light microscopy, valves with tiny, short knobs (5{\textendash}7 per μm2), and several (<7) large trichocyst pores ( 0.3 μm) in the right valve, as well as smaller pores ( 0.15 μm). Prorocentrum criophilum is round in valve view ( 11 μm long, 10 μm wide) and asymmetrically roundish in lateral view, the periflagellar area was not discernible under light microscopy, valves with very tiny, short knobs (6{\textendash}10 per μm2), and at least twelve large pores in the right valve. Other potentially undescribed species of spiny-surfaced Prorocentrum are discussed},
	keywords = {Dinophyta, HABs, harmful algae blooms, molecular phylogenetics, new species, Prorocentraceae, RCC6871, RCC6872, taxonomy},
	issn = {1529-8817},
	doi = {10.1111/jpy.13298},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13298},
	author = {G{\'o}mez, Fernando and Gourvil, Priscillia and Li, Tangcheng and Huang, Yulin and Zhang, Huan and Courcot, Lucie and Artigas, Luis F. and Soler On{\'\i}s, Emilio and Gutierrez-Rodriguez, Andres and Lin, Senjie}
}
@article {lacour_photoacclimation_2022,
	title = {Photoacclimation of the polar diatom Chaetoceros neogracilis at low temperature},
	journal = {PLOS ONE},
	volume = {17},
	number = {9},
	year = {2022},
	note = {Publisher: Public Library of Science},
	month = {sep},
	pages = {e0272822},
	abstract = {Polar microalgae face two major challenges: 1- growing at temperatures (-1.7 to 5{\textdegree}C) that limit enzyme kinetics; and 2- surviving and exploiting a wide range of irradiance. The objective of this study is to understand the adaptation of an Arctic diatom to its environment by studying its ability to acclimate to changes in light and temperature. We acclimated the polar diatom Chaetoceros neogracilis to various light levels at two different temperatures and studied its growth and photosynthetic properties using semi-continuous cultures. Rubisco content was high, to compensate for low catalytic rates, but did not change detectably with growth temperature. Contrary to what is observed in temperate species, in C. neogracilis, carbon fixation rate (20 min 14C incorporation) equaled net growth rate (μ) suggesting very low or very rapid (<20 min) re-oxidation of the newly fixed carbon. The comparison of saturation irradiances for electron transport, oxygen net production and carbon fixation revealed alternative electron pathways that could provide energy and reducing power to the cell without consuming organic carbon which is a very limiting product at low temperatures. High protein contents, low re-oxidation of newly fixed carbon and the use of electron pathways alternative to carbon fixation may be important characteristics allowing efficient growth under those extreme environmental conditions.},
	keywords = {5-bisphosphate carboxylase oxygenase, Carbon fixation, diatoms, Fluorescence, Light, Photons, Photosynthesis, pigments, RCC2278, Ribulose-1},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0272822},
	url = {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0272822},
	author = {Lacour, Thomas and Larivi{\`e}re, Jade and Ferland, Joannie and Morin, Philippe-Isra{\"e}l and Grondin, Pierre-Luc and Donaher, Natalie and Cockshutt, Amanda and Campbell, Douglas A. and Babin, Marcel}
}
@article {carrigee_phycoerythrobilin_2022,
	title = {The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	pages = {1011189},
	abstract = {Marine Synechococcus efficiently harvest available light for photosynthesis using complex antenna systems, called phycobilisomes, composed of an allophycocyanin core surrounded by rods, which in the open ocean are always constituted of phycocyanin and two phycoerythrin (PE) types: PEI and PEII. These cyanobacteria display a wide pigment diversity primarily resulting from differences in the ratio of the two chromophores bound to PEs, the green-light absorbing phycoerythrobilin and the blue-light absorbing phycourobilin. Prior to phycobiliprotein assembly, bilin lyases post-translationally catalyze the ligation of phycoerythrobilin to conserved cysteine residues on α- or β-subunits, whereas the closely related lyase-isomerases isomerize phycoerythrobilin to phycourobilin during the attachment reaction. MpeV was recently shown in Synechococcus sp. RS9916 to be a lyase-isomerase which doubly links phycourobilin to two cysteine residues (C50 and C61; hereafter C50, 61) on the β-subunit of both PEI and PEII. Here we show that Synechococcus sp. WH8020, which belongs to the same pigment type as RS9916, contains MpeV that demonstrates lyase-isomerase activity on the PEII β-subunit but only lyase activity on the PEI β-subunit. We also demonstrate that occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916, prevents the isomerization activity by WH8020 MpeV, showing for the first time that both the substrate and the enzyme play a role in the isomerization reaction. We propose a structural-based mechanism for the role of H141 in blocking isomerization. More generally, the knowledge of the amino acid present at position 141 of the β-subunits may be used to predict which phycobilin is bound at C50, 61 of both PEI and PEII from marine Synechococcus strains.},
	keywords = {RCC2437, RCC307, RCC751},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.1011189},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011189/full},
	author = {Carrigee, Lyndsay A. and Frick, Jacob P. and Liu, Xindi and Karty, Jonathan A. and Trinidad, Jonathan C. and Tom, Irin P. and Yang, Xiaojing and Dufour, Louison and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M.}
}
@article {akita_providing_2022,
	title = {Providing a phylogenetic framework for trait-based analyses in brown algae: Phylogenomic tree inferred from 32 nuclear protein-coding sequences},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {168},
	year = {2022},
	month = {mar},
	pages = {107408},
	abstract = {In the study of the evolution of biological complexity, a reliable phylogenetic framework is needed. Many attempts have been made to resolve phylogenetic relationships between higher groups (i.e., interordinal) of brown algae (Phaeophyceae) based on molecular evidence, but most of these relationships remain unclear. Analyses based on small multi-gene data (including chloroplast, mitochondrial and nuclear sequences) have yielded inconclusive and sometimes contradictory results. To address this problem, we have analyzed 32 nuclear protein-coding sequences in 39 Phaeophycean species belonging to eight orders. The resulting nuclear-based phylogenomic trees provide virtually full support for the phylogenetic relationships within the studied taxa, with few exceptions. The relationships largely confirm phylogenetic trees based on nuclear, chloroplast and mitochondrial sequences, except for the placement of the Sphacelariales with weak bootstrap support. Our study indicates that nuclear protein-coding sequences provide significant support to conclusively resolve phylogenetic relationships among Phaeophyceae, and may be a powerful approach to fully resolve interordinal relationships with increased taxon sampling.},
	keywords = {Ectocarpales, genomics, Heterokontophytes, Phaeoexplorer, Phaeophyceae, RCC4962, RCC7086, RCC7088, RCC7090, RCC7092, RCC7094, RCC7096, RCC7098, RCC7101, RCC7104, RCC7107, RCC7108, RCC7109, RCC7112, RCC7115, RCC7116, RCC7117, RCC7120, RCC7123, RCC7124, RCC7125, RCC7127, RCC7129, RCC7131, RCC7134, RCC7137, RCC7138, RCC7139, stramenopiles},
	issn = {1055-7903},
	doi = {10.1016/j.ympev.2022.107408},
	url = {https://www.sciencedirect.com/science/article/pii/S1055790322000215},
	author = {Akita, Shingo and Vieira, Christophe and Hanyuda, Takeaki and Rousseau, Florence and Cruaud, Corinne and Couloux, Arnaud and Heesch, Svenja and Cock, J. Mark and Kawai, Hiroshi}
}
@article {fan_quantifying_2022,
	title = {Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter},
	journal = {Analytical Chemistry},
	year = {2022},
	month = {sep},
	pages = {acs.analchem.2c01971},
	abstract = {Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is nearuniversally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores�single cells encrusted with biogenic calcite�to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a singlespecies coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.},
	keywords = {RCC1198, RCC1216, RCC1314},
	issn = {0003-2700, 1520-6882},
	doi = {10.1021/acs.analchem.2c01971},
	url = {https://pubs.acs.org/doi/10.1021/acs.analchem.2c01971},
	author = {Fan, Xinmeng and Batchelor-McAuley, Christopher and Yang, Minjun and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {pilatova_revisiting_2022,
	title = {Revisiting biocrystallization: purine crystalline inclusions are widespread in eukaryotes},
	journal = {The ISME Journal},
	year = {2022},
	month = {jun},
	keywords = {RCC1350, RCC745},
	issn = {1751-7362, 1751-7370},
	doi = {10.1038/s41396-022-01264-1},
	url = {https://www.nature.com/articles/s41396-022-01264-1},
	author = {Pil{\'a}tov{\'a}, Jana and P{\'a}nek, Tom{\'a}{\v s} and Obornik, Miroslav and {\v C}epi{\v c}ka, Ivan and Mojze{\v s}, Peter}
}
@article {de_la_broise_scale-up_2022,
	title = {Scale-Up to Pilot of a Non-Axenic Culture of Thraustochytrids Using Digestate from Methanization as Nitrogen Source},
	journal = {Marine Drugs},
	volume = {20},
	number = {8},
	year = {2022},
	month = {aug},
	pages = {499},
	abstract = {The production of non-fish based docosahexaenoic acid (DHA) for feed and food has become a critical need in our global context of over-fishing. The industrial-scale production of DHA{\textendash}rich Thraustochytrids could be an alternative, if costs turned out to be competitive. In order to reduce production costs, this study addresses the feasibility of the non-axenic (non-sterile) cultivation of Aurantiochytrium mangrovei on industrial substrates (as nitrogen and mineral sources and glucose syrup as carbon and energy sources), and its scale-up from laboratory (250 mL) to 500 L cultures. Pilot-scale reactors were airlift cylinders. Batch and fed-batch cultures were tested. Cultures over 38 to 62 h achieved a dry cell weight productivity of 3.3 to 5.5 g.L-1.day-1, and a substrate to biomass yield of up to 0.3. DHA productivity ranged from 10 to 0.18 mg.L-1.day-1. Biomass productivity appears linearly related to oxygen transfer rate. Bacterial contamination of cultures was low enough to avoid impacts on fatty acid composition of the biomass. A specific work on microbial risks assessment (in supplementary files) showed that the biomass can be securely used as feed. However, to date, there is a law void in EU legislation regarding the recycling of nitrogen from digestate from animal waste for microalgae biomass and its usage in animal feed. Overall, the proposed process appears similar to the industrial yeast production process (non-axenic heterotrophic process, dissolved oxygen supply limiting growth, similar cell size). Such similarity could help in further industrial developments.},
	keywords = {RCC893},
	issn = {1660-3397},
	doi = {10.3390/md20080499},
	url = {https://www.mdpi.com/1660-3397/20/8/499},
	author = {de la Broise, Denis and Ventura, Mariana and Chauchat, Luc and Guerreiro, Maurean and Michez, Teo and Vinet, Thibaud and Gautron, Nicolas and Le Grand, Fabienne and Bideau, Antoine and Go{\"\i}c, Nelly Le and Bidault, Adeline and Lambert, Christophe and Soudant, Philippe}
}
@article {croteau_shifts_2022,
	title = {Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic},
	journal = {Journal of Ecology},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.13874},
	abstract = {1. Diatoms of the Arctic Ocean annually experience extreme changes of light environment linked to photoperiodic cycles and seasonal variations of the snow and sea-ice cover extent and thickness which attenuate light penetration in the water column. Arctic diatom communities exploit this complex seasonal dynamic through a well-documented species succession during spring, beginning in sea-ice and culminating in massive phytoplankton blooms underneath sea-ice and in the marginal ice zone. The pattern of diatom taxa sequentially dominating this succession is relatively well conserved interannually, and taxonomic shifts seem to align with habitat transitions. 2. To understand whether differential photoadaptation strategies among diatom taxa explain these recurring succession sequences, we coupled lab experiments with field work in Baffin Bay at 67.5{\textdegree}N. Based on field data, we selected five diatom species typical of different ecological niches and measured their growth rates under light intensity ranges representative of their natural habitats. To characterize their photoacclimative responses, we sampled pigments and total particulate carbon, and conducted 14C-uptake photosynthesis response curves and variable fluorescence measurements. 3. We documented a gradient in species respective light intensity for maximal growth suggesting divergent light response plasticity, which for the most part align with species sequential dominance. Other photophysiological parameters supported this ecophysiological framing, although contrasts were always clear only between succession endmembers, Nitzschia frigida and Chaetoceros neogracilis. To validate that these photoacclimative responses are representative of in situ dynamics, we compared them to the chlorophyll a-specific light-limited slope (α*) and saturated rate of photosynthesis (P*M), monitored in Baffin Bay on sea-ice and planktonic communities. This complementary approach confirmed that unusual responses in α* and P*M as a function of light history intensity are similar between sentinel sympagic species N. frigida and natural ice-core communities. While no light-history-dependent trends were observed in planktonic communities, their α* and P*M values were in the range of measurements from our monospecific cultures. 4. Synthesis. Our results suggest that Arctic diatoms species photoadaptation strategy is tuned to the light environment of the habitats in which they dominate and indeed drives the seasonal taxonomic succession.},
	keywords = {Arctic Ocean, diatoms, Ecophysiology, photoacclimation, photoadaptation, primary production, RCC2046, RCC2278, seasonal species succession, spring bloom},
	issn = {1365-2745},
	doi = {10.1111/1365-2745.13874},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.13874},
	author = {Croteau, D. and Lacour, T. and Schiffrine, N. and Morin, P.-I. and Forget, M.-H. and Bruyant, F. and Ferland, J. and Lafond, A. and Campbell, D. A. and Tremblay, J.-E. and Babin, M. and Lavaud, J.}
}
@article {calo_tor_2022,
	title = {TOR signaling in the green picoalga Ostreococcus tauri},
	journal = {Plant Science},
	volume = {323},
	year = {2022},
	month = {oct},
	pages = {111390},
	abstract = {Target of rapamycin (TOR) is a master regulator that controls growth and metabolism by integrating external and internal signals. Although there was a great progress in the study of TOR in plants and in the model alga Chlamydomonas, scarce data are available in other green algae. Thus, in this work we studied TOR signaling in Ostreococcus tauri, the smallest free-living eukaryote described to date. This picoalga is particularly important because it has a key site at the base of the green lineage and is part of the marine phytoplankton, contributing to global photosynthesis. We investigated OtTOR complex in silico and experimentally, by using first- and second-generation TOR inhibitors, such as rapamycin and PP242. We analyzed the effect of TOR down-regulation on cell growth and on the accumulation of carbon reserves. The results showed that O. tauri responds to TOR inhibitors more similarly to plants than to Chlamydomonas, being PP242 a valuable tool to study this pathway. Besides, Ottor expression analysis revealed that the kinase is dynamically regulated under nutritional stress. Our data indicate that TOR signaling is conserved in O. tauri and we propose this alga as a good and simple model for studying TOR kinase and its regulation.},
	keywords = {Carbon reserves, Green algae, Growth, Nitrogen deprivation, RCC745, TOR inhibitors, TOR kinase},
	issn = {0168-9452},
	doi = {10.1016/j.plantsci.2022.111390},
	url = {https://www.sciencedirect.com/science/article/pii/S016894522200214X},
	author = {Cal{\'o}, Gonzalo and De Marco, Mar{\'\i}a Agustina and Salerno, Graciela Lidia and Mart{\'\i}nez-No{\"e}l, Giselle Mar{\'\i}a Astrid}
}
@article {stewart_altitudinal_2021,
	title = {Altitudinal Zonation of Green Algae Biodiversity in the French Alps},
	journal = {Frontiers in Plant Science},
	volume = {12},
	year = {2021},
	pages = {1066},
	abstract = {Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.},
	keywords = {rcc, RCC1055, RCC130, RCC1563, RCC2501, RCC2960, RCC3402, RCC443, RCC4743, RCC537, RCC581, RCC6, RCC7, RCC891},
	issn = {1664-462X},
	doi = {10.3389/fpls.2021.679428},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.679428},
	author = {Stewart, Adeline and Rioux, Delphine and Boyer, Fr{\'e}deric and Gielly, Ludovic and Pompanon, Fran{\c c}ois and Saillard, Am{\'e}lie and Thuiller, Wilfried and Valay, Jean-Gabriel and Mar{\'e}chal, {\'E}ric and Coissac, Eric}
}
@article {Trefaut2020,
	title = {Annual phytoplankton dynamics in coastal waters from fildes bay, western antarctic peninsula},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {tex.mendeley-tags: RCC2265,RCC2289,RCC4582,RCC4586,RCC5152},
	month = {dec},
	pages = {1368},
	abstract = {Year-round reports of phytoplankton dynamics in the West Antarctic Peninsula are rare and mainly limited to microscopy and/or pigment-based studies. We analyzed the phytoplankton community from coastal waters of Fildes Bay in the West Antarctic Peninsula between January 2014 and 2015 using metabarcoding of the nuclear and plastidial 18/16S rRNA gene from both size-fractionated and flow cytometry sorted samples. Overall 14 classes of photosynthetic eukaryotes were present in our samples with the following dominating: Bacillariophyta (diatoms), Pelagophyceae and Dictyochophyceae for division Ochrophyta, Mamiellophyceae and Pyramimonadophyceae for division Chlorophyta, Haptophyta and Cryptophyta. Each metabarcoding approach yielded a different image of the phytoplankton community with for example Prymnesiophyceae more prevalent in plastidial metabarcodes and Mamiellophyceae in nuclear ones. Diatoms were dominant in the larger size fractions and during summer, while Prymnesiophyceae and Cryptophyceae were dominant in colder seasons. Pelagophyceae were particularly abundant towards the end of autumn (May). In addition of Micromonas polaris and Micromonas sp. clade B3, both previously reported in Arctic waters, we detected a new Micromonas 18S rRNA sequence signature, close to, but clearly distinct from M. polaris , which potentially represents a new clade specific of the Antarctic. These results highlight the need for complementary strategies as well as the importance of year-round monitoring for a comprehensive description of phytoplankton communities in Antarctic coastal waters.},
	keywords = {RCC2265, RCC2289, RCC4582, RCC4586, RCC5152},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-80568-8},
	url = {http://biorxiv.org/content/early/2020/10/27/2020.10.27.356600.abstract http://www.nature.com/articles/s41598-020-80568-8},
	author = {Trefault, Nicole and de la Iglesia, Rodrigo and Moreno-Pino, Mario and Lopes dos Santos, Adriana and G{\'e}rikas Ribeiro, Catherine and Parada-Pozo, G{\'e}nesis and Cristi, Antonia and Marie, Dominique and Vaulot, Daniel}
}
@article {roux_bacteria_2021,
	title = {Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {1{\textendash}15},
	abstract = {High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity.},
	keywords = {RCC1489},
	issn = {2045-2322},
	doi = {10.1038/s41598-021-84253-2},
	url = {http://www.nature.com/articles/s41598-021-84253-2},
	author = {Roux, Pauline and Siano, Raffaele and Collin, Karine and Bilien, Gwenael and Sinquin, Corinne and Marchand, Laetitia and Zykwinska, Agata and Delbarre-Ladrat, Christine and Schapira, Mathilde}
}
@article {pollara_bacterial_2021,
	title = {Bacterial Quorum-Sensing Signal Arrests Phytoplankton Cell Division and Impacts Virus-Induced Mortality},
	journal = {mSphere},
	volume = {6},
	number = {3},
	year = {2021},
	pages = {e00009{\textendash}21, /msphere/6/3/mSph.00009{\textendash}21.atom},
	abstract = {Interactions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems by controlling primary production, structuring marine food webs, mediating carbon export, and influencing global climate. Phytoplankton-bacterium interactions are facilitated by secreted compounds; however, linking these chemical signals, their mechanisms of action, and their resultant ecological consequences remains a fundamental challenge. The bacterial quorumsensing signal 2-heptyl-4-quinolone (HHQ) induces immediate, yet reversible, cellular stasis (no cell division or mortality) in the coccolithophore Emiliania huxleyi; however, the mechanism responsible remains unknown. Using transcriptomic and proteomic approaches in combination with diagnostic biochemical and fluorescent cell-based assays, we show that HHQ exposure leads to prolonged S-phase arrest in phytoplankton coincident with the accumulation of DNA damage and a lack of repair despite the induction of the DNA damage response (DDR). While this effect is reversible, HHQ-exposed phytoplankton were also protected from viral mortality, ascribing a new role of quorum-sensing signals in regulating multitrophic interactions. Furthermore, our data demonstrate that in situ measurements of HHQ coincide with areas of enhanced micro- and nanoplankton biomass. Our results suggest bacterial communication signals as emerging players that may be one of the contributing factors that help structure complex microbial communities throughout the ocean.},
	keywords = {rcc1731},
	issn = {2379-5042},
	doi = {10.1128/mSphere.00009-21},
	url = {https://msphere.asm.org/content/6/3/e00009-21},
	author = {Pollara, Scott B. and Becker, Jamie W. and Nunn, Brook L. and Boiteau, Rene and Repeta, Daniel and Mudge, Miranda C. and Downing, Grayton and Chase, Davis and Harvey, Elizabeth L. and Whalen, Kristen E.},
	editor = {McMahon, Katherine}
}
@article {thomy_combining_2021,
	title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri},
	journal = {Cells},
	volume = {10},
	number = {3},
	year = {2021},
	pages = {664},
	abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.},
	keywords = {RCC1115, RCC7079, RCC7080, RCC7081, RCC7082, RCC7083, RCC7084, RCC7085},
	issn = {2073-4409},
	doi = {10.3390/cells10030664},
	url = {https://www.mdpi.com/2073-4409/10/3/664},
	author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree}
}
@booklet {thomy_combining_2021,
	title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri},
	year = {2021},
	month = {feb},
	publisher = {LIFE SCIENCES},
	type = {preprint},
	abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration appears to be random, occurring mainly at a single locus, and thus confirming the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci, and often within the vector sequence itself. From these observations, we speculate that a non-homologous end joining-like mechanism is required during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in ecologically important marine algae.},
	keywords = {RCC1115},
	doi = {10.20944/preprints202102.0506.v1},
	url = {https://www.preprints.org/manuscript/202102.0506/v1},
	author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree}
}
@article {fernandes_comparative_2021,
	title = {Comparative lipidomic analysis of Chlorella stigmatophora and Hemiselmis cf. andersenii in response to nitrogen-induced changes},
	journal = {Algal Research},
	volume = {58},
	year = {2021},
	pages = {102417},
	abstract = {The current focus of algae biotechnology is the production of high-value lipids, and its improvement by employing abiotic perturbations such as nitrogen-induced changes. In the present study, the growth dynamics, nitrogen uptake, pigments, and lipid composition of Chlorellla stigmatophora and Hemiselmis cf. andersenii were studied, in response to low (LN), medium (MN) and high (HN) nitrogen supplementations. Both microalgae responded to increased nitrogen levels by increasing their nitrogen uptake rate and pigment content. However, for lipid accumulation, C. stigmatophora presented a different pattern (LN: 16.56\% > MN: 11.51\% > HN: 10.95\%) to that of H. cf. andersenii (MN: 15.37\% > HN: 13.06\% > LN: 6.71\%). Untargeted gas chromatography{\textendash}mass spectrometry analysis allowed the visualization of the biochemical diversity of C. stigmatophora and H. cf. andersenii, as well as differences in lipid regulation upon nitrogen-induced changes among species. For instance, glycosyl sterols were only detected for C. stigmatophora samples grown under MN and HN conditions. Moreover, lipid analysis of H. cf. andersenii, before and after alkaline hydrolysis, suggests that wax esters play a key role in the response of this microalga to high nitrogen levels. The cultivation of H. cf. andersenii at MN and HN was shown to be ideal for providing a rich source of ω3 and polyunsaturated fatty acids for nutraceutical purposes. The hierarchical cluster analysis showed the differential intra- and interspecific effects of nitrogen on lipid composition. The diverse ways by which both microalgae responded to nitrogen-induced changes highlighted the influence of phylogeny on the carbon flux through metabolic networks, and accumulation.},
	keywords = {cf., Lipidome analysis, Nitrogen supplementation, Nutraceutical lipids, rcc, RCC661},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2021.102417},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926421002368},
	author = {Fernandes, Tom{\'a}sia and Ferreira, Artur and Cordeiro, Nereida}
}
@article {croteau_contrasting_2021,
	title = {Contrasting nonphotochemical quenching patterns under high light and darkness aligns with light niche occupancy in Arctic diatoms},
	journal = {Limnology and Oceanography},
	volume = {66},
	number = {S1},
	year = {2021},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11587},
	pages = {S231{\textendash}S245},
	abstract = {Over the seasons, Arctic diatom species occupy shifting habitats defined by contrasting light climates, constrained by snow and ice cover dynamics interacting with extreme photoperiod and solar angle variations. How Arctic diatom photoadaptation strategies differ across their heterogeneous light niches remains a poorly documented but crucial missing link to anticipate Arctic Ocean responses to shrinking sea-ice and increasing light. To address this question, we selected five Arctic diatom species with diverse life traits, representative of distinct light niches across the seasonal light environment continuum: from snow-covered dimly lit bottom ice to summer stratified waters. We studied their photoacclimation plasticity to two growth light levels and the subsequent responses of their nonphotochemical quenching (NPQ) and xanthophyll cycle to both dark incubations and light shifts. We deciphered NPQ and xanthophyll cycle tuning in darkness and their light-dependent induction kinetics, which aligned with species{\textquoteright} light niche occupancy. In ice-related species, NPQ was sustained in darkness and its induction was more reactive to moderate light shifts. Open-water species triggered strong NPQ induction in darkness and reached higher maximal NPQ under high light. Marginal ice zone species showed strong adaptation to light fluctuations with a dark response fine-tuned depending upon light history. We argue these traits are anchored in diverging photoadaption strategies fostering Arctic diatom success in their respective light niches.},
	keywords = {RCC2046, RCC2278, RCC5318},
	issn = {1939-5590},
	doi = {10.1002/lno.11587},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11587},
	author = {Croteau, Dany and Gu{\'e}rin, S{\'e}bastien and Bruyant, Flavienne and Ferland, Joannie and Campbell, Douglas A. and Babin, Marcel and Lavaud, Johann}
}
@inbook {Paredes2021,
	title = {Cryopreservation of algae},
	booktitle = {Cryopreservation and freeze-drying protocols},
	volume = {2180},
	year = {2021},
	pages = {607{\textendash}621},
	publisher = {Springer Science+Business Media, LLC},
	organization = {Springer Science+Business Media, LLC},
	keywords = {cryopreservation, macroalgae, Microalgae},
	isbn = {978-1-07-160783-1},
	doi = {10.1007/978-1-0716-0783-1_32},
	url = {http://link.springer.com/10.1007/978-1-0716-0783-1_32},
	author = {Paredes, Estefania and Ward, Angela and Probert, Ian and Gouhier, L{\'e}na and Campbell, Christine N.},
	editor = {Wolkers, Willem F. and Oldenhof, Harriette}
}
@article {uwizeye_cytoklepty_2021,
	title = {Cytoklepty in the plankton: A host strategy to optimize the bioenergetic machinery of endosymbiotic algae},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {27},
	year = {2021},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	month = {jul},
	abstract = {Endosymbioses have shaped the evolutionary trajectory of life and remain ecologically important. Investigating oceanic photosymbioses can illuminate how algal endosymbionts are energetically exploited by their heterotrophic hosts and inform on putative initial steps of plastid acquisition in eukaryotes. By combining three-dimensional subcellular imaging with photophysiology, carbon flux imaging, and transcriptomics, we show that cell division of endosymbionts (Phaeocystis) is blocked within hosts (Acantharia) and that their cellular architecture and bioenergetic machinery are radically altered. Transcriptional evidence indicates that a nutrient-independent mechanism prevents symbiont cell division and decouples nuclear and plastid division. As endosymbiont plastids proliferate, the volume of the photosynthetic machinery volume increases 100-fold in correlation with the expansion of a reticular mitochondrial network in close proximity to plastids. Photosynthetic efficiency tends to increase with cell size, and photon propagation modeling indicates that the networked mitochondrial architecture enhances light capture. This is accompanied by 150-fold higher carbon uptake and up-regulation of genes involved in photosynthesis and carbon fixation, which, in conjunction with a ca.15-fold size increase of pyrenoids demonstrates enhanced primary production in symbiosis. Mass spectrometry imaging revealed major carbon allocation to plastids and transfer to the host cell. As in most photosymbioses, microalgae are contained within a host phagosome (symbiosome), but here, the phagosome invaginates into enlarged microalgal cells, perhaps to optimize metabolic exchange. This observation adds evidence that the algal metamorphosis is irreversible. Hosts, therefore, trigger and benefit from major bioenergetic remodeling of symbiotic microalgae with potential consequences for the oceanic carbon cycle. Unlike other photosymbioses, this interaction represents a so-called cytoklepty, which is a putative initial step toward plastid acquisition.},
	keywords = {3D electron microscopy, oceanic plankton, Photosynthesis, rcc, rcc1383, single-cell transcriptomics, symbiosis},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.2025252118},
	url = {https://www.pnas.org/content/118/27/e2025252118},
	author = {Uwizeye, Clarisse and Brisbin, Margaret Mars and Gallet, Benoit and Chevalier, Fabien and LeKieffre, Charlotte and Schieber, Nicole L. and Falconet, Denis and Wangpraseurt, Daniel and Schertel, Lukas and Stryhanyuk, Hryhoriy and Musat, Niculina and Mitarai, Satoshi and Schwab, Yannick and Finazzi, Giovanni and Decelle, Johan}
}
@booklet {marc_dinophyceae_2021,
	title = {Dinophyceae use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	month = {jan},
	pages = {2021.01.05.425281},
	abstract = {Parasites of the genus Amoebophrya sp. are important contributors to marine ecosystems and can be determining factors in the demise of blooms of Dinophyceae, including microalgae commonly responsible for toxic red tides. Yet they rarely lead to the total collapse of Dinophyceae blooms. The addition of resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or their exudate into a well-established host-parasite culture (Scrippsiella acuminata-Amoebophrya sp.) mitigated the success of the parasite and increased the survival of the sensitive host. Effect were mediated via water-borne molecules without the need of a physical contact. Severity of the anti-parasitic defenses fluctuated depending on the species, the strain and its concentration, but never totally prevented the parasite transmission. The survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. The progeny drastically decreased with both species. Integrity of the membrane of dinospores was altered by A. minutum which provided a first indication on the mode of action of these anti-parasitic molecules. These results demonstrate that extracellular defenses are an effective strategy against parasites that does not only protect the resistant cells but also have the potential to affect the whole surrounding community.},
	keywords = {rcc, RCC1627, RCC4383, RCC4714, RCC749},
	doi = {10.1101/2021.01.05.425281},
	url = {https://www.biorxiv.org/content/10.1101/2021.01.05.425281v1},
	author = {Marc, Long and Dominique, Marie and Jeremy, Szymczak and Jordan, Toullec and Estelle, Bigeard and Marc, Sourisseau and Mickael, Le Gac and Laure, Guillou and C{\'e}cile, Jauzein}
}
@article {bock_experimental_2021,
	title = {Experimental identification and in silico prediction of bacterivory in green algae},
	journal = {The ISME Journal},
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	month = {mar},
	pages = {1{\textendash}14},
	abstract = {While algal phago-mixotrophs play a major role in aquatic microbial food webs, their diversity remains poorly understood. Recent studies have indicated several species of prasinophytes, early diverging green algae, to be able to consume bacteria for nutrition. To further explore the occurrence of phago-mixotrophy in green algae, we conducted feeding experiments with live fluorescently labeled bacteria stained with CellTracker Green CMFDA, heat-killed bacteria stained with 5-(4,6-dichlorotriazin-2-yl) aminofluorescein (DTAF), and magnetic beads. Feeding was detected via microscopy and/or flow cytometry in five strains of prasinophytes when provided with live bacteria: Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, and Dolichomastix tenuilepis CCMP3274. No feeding was detected when heat-killed bacteria or magnetic beads were provided, suggesting a strong preference for live prey in the strains tested. In parallel to experimental assays, green algal bacterivory was investigated using a gene-based prediction model. The predictions agreed with the experimental results and suggested bacterivory potential in additional green algae. Our observations underline the likelihood of widespread occurrence of phago-mixotrophy among green algae, while additionally highlighting potential biases introduced when using prey proxy to evaluate bacterial ingestion by algal cells.},
	keywords = {RCC180, RCC3375, RCC369, RCC618},
	issn = {1751-7370},
	doi = {10.1038/s41396-021-00899-w},
	url = {http://www.nature.com/articles/s41396-021-00899-w},
	author = {Bock, Nicholas A. and Charvet, Sophie and Burns, John and Gyaltshen, Yangtsho and Rozenberg, Andrey and Duhamel, Solange and Kim, Eunsoo}
}
@article {geffroy_sxta4_2021,
	title = {From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	pages = {613199},
	abstract = {Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9{\textendash}187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.},
	keywords = {RCC2644, RCC2645, RCC3327, RCC4871, RCC4872, RCC4890, RCC7037, RCC7038, RCC7039},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.613199},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.613199/full},
	author = {Geffroy, Sol{\`e}ne and Lechat, Marc-Marie and Le Gac, Micka{\"e}l and Rovillon, Georges-Augustin and Marie, Dominique and Bigeard, Estelle and Malo, Florent and Amzil, Zouher and Guillou, Laure and Caruana, Amandine M. N.}
}
@article {Wang2021,
	title = {Group 2i Isochrysidales produce characteristic alkenones reflecting sea ice distribution},
	journal = {Nature Communications},
	volume = {12},
	number = {1},
	year = {2021},
	note = {Publisher: Springer US tex.mendeley-tags: RCC107,RCC1195,RCC1334,RCC5486},
	month = {dec},
	pages = {15},
	abstract = {Alkenones are biomarkers produced solely by algae in the order Isochrysidales that have been used to reconstruct sea surface temperature (SST) since the 1980s. However, alkenone-based SST reconstructions in the northern high latitude oceans show significant bias towards warmer temperatures in core-tops, diverge from other SST proxies in down core records, and are often accompanied by anomalously high relative abundance of the C 37 tetra-unsaturated methyl alkenone (\%C 37:4 ). Elevated \%C 37:4 is widely interpreted as an indicator of low sea surface salinity from polar water masses, but its biological source has thus far remained elusive. Here we identify a lineage of Isochrysidales that is responsible for elevated C 37:4 methyl alkenone in the northern high latitude oceans through next-generation sequencing and lab-culture experiments. This Isochrysidales lineage co-occurs widely with sea ice in marine environments and is distinct from other known marine alkenone-producers, namely Emiliania huxleyi and Gephyrocapsa oceanica . More importantly, the \%C 37:4 in seawater filtered particulate organic matter and surface sediments is significantly correlated with annual mean sea ice concentrations. In sediment cores from the Svalbard region, the \%C 37:4 concentration aligns with the Greenland temperature record and other qualitative regional sea ice records spanning the past 14 kyrs, reflecting sea ice concentrations quantitatively. Our findings imply that \%C 37:4 is a powerful proxy for reconstructing sea ice conditions in the high latitude oceans on thousand- and, potentially, on million-year timescales.},
	keywords = {RCC107, RCC1195, RCC1334, RCC5486},
	issn = {2041-1723},
	doi = {10.1038/s41467-020-20187-z},
	url = {http://dx.doi.org/10.1038/s41467-020-20187-z http://www.nature.com/articles/s41467-020-20187-z},
	author = {Wang, Karen Jiaxi and Huang, Yongsong and Majaneva, Markus and Belt, Simon T. and Liao, Sian and Novak, Joseph and Kartzinel, Tyler R. and Herbert, Timothy D. and Richter, Nora and Cabedo-Sanz, Patricia}
}
@article {schapira_les_2021,
	title = {Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : D{\'e}terminisme et cons{\'e}quences sur la qualit{\'e} des masses d{\textquoteright}eau c{\^o}ti{\`e}res},
	year = {2021},
	abstract = {Ce projet, organis{\'e} en trois actions, avait pour objectif de mieux {\'e}valuer les risques d{\textquoteright}eaux color{\'e}es vertes se produisant sur le secteur c{\^o}tier situ{\'e} au large de la Loire et de la Vilaine, en termes (i) de fr{\'e}quence de ces {\'e}pisodes, (ii) d{\textquoteright}abondance et (iii) de localisation des zones {\`a} risque. Action 1 : Am{\'e}lioration du recensement des eaux vertes {\`a} L. chlorophorum Action 2 : Optimisation de l{\textquoteright}estimation des abondances de L. chlorophorum Action 3 : Identification des zones {\`a} risque au large de la Loire et de la Vilaine.},
	keywords = {? No DOI found, rcc, RCC1489},
	url = {https://archimer.ifremer.fr/doc/00724/83598/},
	author = {Schapira, Mathilde and Roux, Pauline and Andre, Coralie and Mertens, Kenneth and Bilien, Gwenael and Terre Terrillon, Aouregan and Le Gac-Abernot, Chantal and Siano, Raffaele and Qu{\'e}r{\'e}, Julien and Bizzozero, Lucie and Bonneau, Francoise and Bouget, Jean-Francois and Cochennec-Laureau, Nathalie and Collin, Karine and Fortune, Mireille and Gabellec, Raoul and Le Merrer, Yoann and Manach, Soazig and Pierre-Duplessix, Olivier and Retho, Michael and Schmitt, Anne and Souchu, Philippe and Stachowski-Haberkorn, Sabine}
}
@article {six_marine_2021,
	title = {Marine Synechococcus  picocyanobacteria: Light utilization across latitudes},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {38},
	year = {2021},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	abstract = {<p>The most ubiquitous cyanobacteria, Synechococcus, have colonized different marine thermal niches through the evolutionary specialization of lineages adapted to different ranges of temperature seawater. We used the strains of Synechococcus temperature ecotypes to study how light utilization has evolved in the function of temperature. The tropical Synechococcus (clade II) was unable to grow under 16 {\textdegree}C but, at temperatures \&gt;25 {\textdegree}C, induced very high growth rates that relied on a strong synthesis of the components of the photosynthetic machinery, leading to a large increase in photosystem cross-section and electron flux. By contrast, the Synechococcus adapted to subpolar habitats (clade I) grew more slowly but was able to cope with temperatures \&lt;10 {\textdegree}C. We show that growth at such temperatures was accompanied by a large increase of the photoprotection capacities using the orange carotenoid protein (OCP). Metagenomic analyzes revealed that Synechococcus natural communities show the highest prevalence of the ocp genes in low-temperature niches, whereas most tropical clade II Synechococcus have lost the gene. Moreover, bioinformatic analyzes suggested that the OCP variants of the two cold-adapted Synechococcus clades I and IV have undergone evolutionary convergence through the adaptation of the molecular flexibility. Our study points to an important role of temperature in the evolution of the OCP. We, furthermore, discuss the implications of the different metabolic cost of these physiological strategies on the competitiveness of Synechococcus in a warming ocean. This study can help improve the current hypotheses and models aimed at predicting the changes in ocean carbon fluxes in response to global warming.</p>
},
	keywords = {?? Invalid DOI, RCC2035, rcc2382, RCC2385, RCC2421, RCC2527, RCC2535, RCC2553, RCC2570, RCC515, rcc539, rcc752, rcc791, to add},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.2111300118},
	url = {http://www.pnas.org/content/118/38/e2111300118},
	author = {Six, Christophe and Ratin, Morgane and Marie, Dominique and Corre, Erwan}
}
@article {wang_moderating_2021,
	title = {The moderating role of population succession in the adaptive responses of Synechococcus assemblages: evidence from light intensity simulation experiment},
	journal = {Photosynthetica},
	volume = {59},
	number = {4},
	year = {2021},
	pages = {587{\textendash}599},
	abstract = {Synechococcus is one of the most abundant photoautotrophic picoplankton in the marine ecosystem. However, it is not clear how Synechococcus assemblages respond to light intensity variation in a genus group. Here, enriched Synechococcus assemblages from in situ coastal seawater were subjected to light intensity simulation experiments in a range of 9-243 μmol(photon) m{\textendash}2 s{\textendash}1. Characteristics concerning physiology, genomics, and metatranscriptomics were analyzed. Physiologically, the fitting model predicted photosynthesis indications and pigment contents increased with different trends following the light intensity. Genomic sequencing demonstrated that both the phylogenetic and phenotypic compositions of Synechococcus assemblage exhibited population succession. Especially, the proportion of Synechococcus pigment type 2 was changed significantly. In metatranscriptomics, most genes were downregulated in the high-light intensity group, while photosynthesis-related genes were entirely upregulated. The high upregulation of photosynthesis-related genes, such as psbO, psbA, apcB, and cpcB, corresponded to the succession of Synechococcus genotype and was responsible for the physiological shift in response to light intensity.},
	issn = {03003604, 15739058},
	doi = {10.32615/ps.2021.050},
	url = {http://ps.ueb.cas.cz/doi/10.32615/ps.2021.050.html},
	author = {Wang, T. and Chen, X. and Li, J.L. and Qin, S. and Cui, Y.L. and Xu, F.}
}
@article {grebert_molecular_2021,
	title = {Molecular bases of an alternative dual-enzyme system for light color acclimation of marine \textit{Synechococcus cyanobacteria},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {118},
	number = {9},
	year = {2021},
	pages = {e2019715118},
	abstract = {<p>Marine Synechococcus cyanobacteria owe their ubiquity in part to the wide pigment diversity of their light-harvesting complexes. In open ocean waters, cells predominantly possess sophisticated antennae with rods composed of phycocyanin and two types of phycoerythrins (PEI and PEII). Some strains are specialized for harvesting either green or blue light, while others can dynamically modify their light absorption spectrum to match the dominant ambient color. This process, called type IV chromatic acclimation (CA4), has been linked to the presence of a small genomic island occurring in two configurations (CA4-A and CA4-B). While the CA4-A process has been partially characterized, the CA4-B process has remained an enigma. Here we characterize the function of two members of the phycobilin lyase E/F clan, MpeW and MpeQ, in Synechococcus sp. strain A15-62 and demonstrate their critical role in CA4-B. While MpeW, encoded in the CA4-B island and up-regulated in green light, attaches the green light-absorbing chromophore phycoerythrobilin to cysteine-83 of the PEII α-subunit in green light, MpeQ binds phycoerythrobilin and isomerizes it into the blue light-absorbing phycourobilin at the same site in blue light, reversing the relationship of MpeZ and MpeY in the CA4-A strain RS9916. Our data thus reveal key molecular differences between the two types of chromatic acclimaters, both highly abundant but occupying distinct complementary ecological niches in the ocean. They also support an evolutionary scenario whereby CA4-B island acquisition allowed former blue light specialists to become chromatic acclimaters, while former green light specialists would have acquired this capacity by gaining a CA4-A island.</p>
},
	keywords = {RCC2374, to add},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.2019715118},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.2019715118},
	author = {Gr{\'e}bert, Th{\'e}ophile and Nguyen, Adam A. and Pokhrel, Suman and Joseph, Kes Lynn and Ratin, Morgane and Dufour, Louison and Chen, Bo and Haney, Allissa M. and Karty, Jonathan A. and Trinidad, Jonathan C. and Garczarek, Laurence and Schluchter, Wendy M. and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric}
}
@article {uwizeye_morphological_2021,
	title = {Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging},
	journal = {Nature Communications},
	volume = {12},
	number = {1},
	year = {2021},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {feb},
	pages = {1{\textendash}12},
	abstract = {Phytoplankton account for a large proportion of global primary production and comprise a number of phylogenetically distinct lineages. Here, Uwizeye et al. use FIB-SEM to study ultrastructural plasticity of 7 distinct taxa and describe how subcellular organisation is linked to energy metabolism.},
	keywords = {RCC100, RCC4014, RCC827, RCC909},
	issn = {2041-1723},
	doi = {10.1038/s41467-021-21314-0},
	url = {http://www.nature.com/articles/s41467-021-21314-0},
	author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Flori, Serena and Gallet, Benoit and Keck, Jean-baptiste and Bo, Davide Dal and Moriscot, Christine and Seydoux, Claire and Chevalier, Fabien and Schieber, Nicole L. and Templin, Rachel and Allorent, Guillaume and Courtois, Florence and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C. and Falconet, Denis and Finazzi, Giovanni}
}
@article {harada_novel_2021,
	title = {A novel characteristic of a phytoplankton as a potential source of straight-chain alkanes},
	journal = {Scientific Reports},
	volume = {11},
	number = {1},
	year = {2021},
	note = {Bandiera_abtest: a Cc_license_type: cc_by Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Biofuels;Biological techniques Subject_term_id: biofuels;biological-techniques},
	pages = {14190},
	abstract = {Biosynthesis of hydrocarbons is a promising approach for the production of alternative sources of energy because of the emerging need to reduce global consumption of fossil fuels. However, the suitability of biogenic hydrocarbons as fuels is limited because their range of the number of carbon atoms is small, and/or they contain unsaturated carbon bonds. Here, we report that a marine phytoplankton, Dicrateria rotunda, collected from the western Arctic Ocean, can synthesize a series of saturated hydrocarbons (n-alkanes) from C10H22 to C38H78, which are categorized as petrol (C10{\textendash}C15), diesel oils (C16{\textendash}C20), and fuel oils (C21{\textendash}C38). The observation that these n-alkanes were also produced by ten other cultivated strains of Dicrateria collected from the Atlantic and Pacific oceans suggests that this capability is a common characteristic of Dicrateria. We also identified that the total contents of the n-alkanes in the Arctic D. rotunda strain increased under dark and nitrogen-deficient conditions. The unique characteristic of D. rotunda could contribute to the development of a new approach for the biosynthesis of n-alkanes.},
	keywords = {RCC3437, RCC4217, RCC4577, RCC4578, RCC5635, RCC5639},
	issn = {2045-2322},
	doi = {10.1038/s41598-021-93204-w},
	url = {http://www.nature.com/articles/s41598-021-93204-w},
	author = {Harada, Naomi and Hirose, Yuu and Chihong, Song and Kurita, Hirofumi and Sato, Miyako and Onodera, Jonaotaro and Murata, Kazuyoshi and Itoh, Fumihiro}
}
@article {yang_opto-electrochemical_2021,
	title = {Opto-Electrochemical Dissolution Reveals Coccolith Calcium Carbonate Content},
	journal = {Angewandte Chemie International Edition},
	volume = {60},
	number = {38},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.202108435},
	pages = {20999{\textendash}21006},
	abstract = {Coccoliths are plates of biogenic calcium carbonate secreted by calcifying marine phytoplankton; annually these phytoplankton are responsible for exporting >1 billion tonnes (1015 g) of calcite to the deep ocean. Rapid and reliable methods for assessing the degree of calcification are technically challenging because the coccoliths are micron sized and contain picograms (pg) of calcite. Here we pioneer an opto-eletrochemical acid titration of individual coccoliths which allows 3D reconstruction of each individual coccolith via in situ optical imaging enabling direct inference of the coccolith mass. Coccolith mass ranging from 2 to 400 pg are reported herein, evidencing both inter- and intra-species variation over four different species. We foresee this scientific breakthrough, which is independent of knowledge regarding the species and calibration-free, will allow continuous monitoring and reporting of the degree of coccolith calcification in the changing marine environment.},
	keywords = {analytical methods, calcite dissolution, electrochemistry, global carbonate cycle, marine phytoplankton, RCC1130, RCC1198, RCC1216, RCC1314},
	issn = {1521-3773},
	doi = {10.1002/anie.202108435},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202108435},
	author = {Yang, Minjun and Batchelor-McAuley, Christopher and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {Farhat2021,
	title = {Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.},
	journal = {BMC Biology},
	year = {2021},
	note = {Publisher: BMC Biology tex.mendeley-tags: RCC4383,RCC4398},
	pages = {1{\textendash}21},
	keywords = {Dinoflagellate, genome, Introner elements, Non-canonical introns, parasite, RCC4383, RCC4398},
	doi = {10.1186/s12915-020-00927-9},
	author = {Farhat, Sarah and Le, Phuong and Kayal, Ehsan and Noel, Benjamin and Bigeard, Estelle and Corre, Erwan and Maumus, Florian and Florent, Isabelle and Alberti, Adriana and Aury, Jean-Marc and Barbeyron, Tristan and Cai, Ruibo and Silva, Corinne Da and Istace, Benjamin and Labadie, Karine and Marie, Dominique and Mercier, Jonathan and Rukwavu, Tsinda and Szymczak, Jeremy and Tonon, Thierry and Alves-de-Souza, Catharina and Rouze, Pierre and de Peer, Yves Van and Wincker, Patrick and Rombauts, Stephane and Porcel, Betina M and Guillou, Laure}
}
@article {royer_response_2021,
	title = {Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to oxidative stress in three phytoplankton species},
	journal = {Journal of Plankton Research},
	volume = {43},
	number = {5},
	year = {2021},
	month = {sep},
	pages = {673{\textendash}690},
	abstract = {Several phytoplankton species produce the metabolites dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) but their intracellular roles need to be better understood. To improve the understanding of the DMSP antioxidant function suggested by Sunda et al. (2002), we exposed the diatom Skeletonema costatum, the Prymnesiophyceae Phaeocystis globosa and the dinoflagellate Heterocapsa triquetra to experimental treatments known to cause potential oxidative stress (high light intensities (HL); HL with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU); menadione sodium bisulfite (MSB)). DMSP and DMSO concentrations decreased after 6 h in all treatments indicating an interaction with Reactive Oxygen Species (ROS) produced. DMSP and DMSO-to-cell ratios in control conditions were higher for H. triquetra, while being unable to grow under HL. DMSP and DMSO-to-cell carbon were the highest for P. globosa, while the other species had similar values. During long-term treatment, these ratios were not increased in high-light grown cells of P. globosa and S. costatum. Overall, this illustrates that (1) the DMSP- and DMSO-to-cell or carbon seems to be not indicative of the capability of the species to tolerate an oxidative stress, (2) these molecules could react with ROS and lower their cellular concentration, but no clues demonstrated that these molecules are part of the antioxidant response of the cell.},
	keywords = {rcc, RCC1719, RCC4800},
	issn = {0142-7873},
	doi = {10.1093/plankt/fbab052},
	url = {https://doi.org/10.1093/plankt/fbab052},
	author = {Royer, C and Gypens, N and Cardol, P and Borges, A V and Roberty, S}
}
@article {castillo_seasonal_2021,
	title = {Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH},
	journal = {Environmental Microbiology},
	volume = {n/a},
	number = {n/a},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15504},
	abstract = {Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral{\textendash}host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21\% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. This article is protected by copyright. All rights reserved.},
	keywords = {RCC2590, RCC4221, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.15504},
	url = {http://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15504},
	author = {Castillo, Yaiza M. and Forn, Irene and Yau, Sheree and Mor{\'a}n, Xos{\'e} Anxelu G. and Alonso-S{\'a}ez, Laura and Arandia-Gorostidi, N{\'e}stor and Vaqu{\'e}, Dolors and Sebasti{\'a}n, Marta}
}
@article {decelle_subcellular_2021,
	title = {Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae},
	journal = {bioRxiv},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	pages = {2021.03.13.435225},
	abstract = {Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the {\textquotedblleft}greenhouse-like{\textquotedblright} colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.},
	doi = {10.1101/2021.03.13.435225},
	url = {https://www.biorxiv.org/content/10.1101/2021.03.13.435225v1},
	author = {Decelle, Johan and Veronesi, Giulia and LeKieffre, Charlotte and Gallet, Benoit and Chevalier, Fabien and Stryhanyuk, Hryhoriy and Marro, Sophie and Ravanel, St{\'e}phane and Tucoulou, R{\'e}mi and Schieber, Nicole and Finazzi, Giovanni and Schwab, Yannick and Musat, Niculina}
}
@booklet {roquis_tropical_2021,
	title = {The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching},
	number = {6:195},
	year = {2021},
	note = {Type: article},
	month = {jul},
	publisher = {Wellcome Open Research},
	abstract = {<p>Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2\% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average \textasciitilde90\% of sequence similarities with mice and \textasciitilde96\% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta . The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.</p>
},
	keywords = {chromatin structure, Histone H3 clipping, invertebrate epigenetics, Pocillopora acuta, Pocillopora damicornis, rcc, RCC4017},
	doi = {10.12688/wellcomeopenres.17058.1},
	url = {https://wellcomeopenresearch.org/articles/6-195},
	author = {Roquis, David and Cosseau, C{\'e}line and Raffalli, Kelly Brener and Romans, Pascal and Masanet, Patrick and Mitta, Guillaume and Grunau, Christoph and Vidal-Dupiol, Jeremie}
}
@article {bachy_viruses_2021,
	title = {Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts},
	journal = {The ISME Journal},
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	month = {may},
	pages = {1{\textendash}19},
	abstract = {The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90\% of their proteins, and between 65\% to 83\% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.},
	keywords = {RCC715, RCC716},
	issn = {1751-7370},
	doi = {10.1038/s41396-021-00989-9},
	url = {https://www.nature.com/articles/s41396-021-00989-9},
	author = {Bachy, Charles and Yung, Charmaine C. M. and Needham, David M. and Gazit{\'u}a, Maria Consuelo and Roux, Simon and Limardo, Alexander J. and Choi, Chang Jae and Jorgens, Danielle M. and Sullivan, Matthew B. and Worden, Alexandra Z.}
}
@article {barbeyron_zobellia_2021,
	title = {Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov., two flavobacteria from the epiphytic microbiota of the brown alga Ascophyllum nodosum, and emended description of the genus Zobellia},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	volume = {71},
	number = {8},
	year = {2021},
	abstract = {Four marine bacterial strains were isolated from a thallus of the brown alga Ascophyllum nodosum collected in Roscoff, France. Cells were Gram-s- tain--negative, strictly aerobic, non-f-lagellated, gliding, rod--shaped and grew optimally at 25{\textendash}30 {\textdegree}C, at pH 7{\textendash}8 and with 2{\textendash}4 \% NaCl. Phylogenetic analyses of their 16S rRNA gene sequences showed that the bacteria were affiliated to the genus Zobellia (family Flavobacteriaceae, phylum Bacteroidetes). The four strains exhibited 97.8{\textendash}100 \% 16S rRNA gene sequence similarity values among themselves, 97.9{\textendash}99.1 \% to the type strains of Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T, and less than 99 \% to other species of the genus Zobellia. The DNA G+C content of the four strains ranged from 36.7 to 37.7 mol\%. Average nucleotide identity and digital DNA{\textendash}DNA hybridization calculations between the new strains and other members of the genus Zobellia resulted in values of 76.4{\textendash}88.9 \% and below 38.5 \%, respectively. Phenotypic, phylogenetic and genomic analyses showed that the four strains are distinct from species of the genus Zobellia with validly published names. They represent two novel species of the genus Zobellia, for which the names Zobellia roscoffensis sp. nov. and Zobellia nedashkovskayae sp. nov. are proposed with Asnod1--F08T (RCC6906T=KMM 6823T=CIP 111902T) and Asnod2--B07--BT (RCC6908T=KMM 6825T=CIP 111904T), respectively, as the type strains.},
	keywords = {RCC6906, RCC6907, RCC6908, RCC6909},
	issn = {1466-5026, 1466-5034},
	doi = {10.1099/ijsem.0.004913},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.004913},
	author = {Barbeyron, Tristan and Thi{\'e}baud, Manon and Le Duff, Nolwen and Martin, Marjolaine and Corre, Erwan and Tanguy, Gwenn and Vandenbol, Micheline and Thomas, Fran{\c c}ois}
}
@article {Nissimov2020,
	title = {Aquatic virus culture collection: an absent (but necessary) safety net for environmental microbiologists},
	journal = {Applied Phycology},
	volume = {00},
	number = {00},
	year = {2020},
	note = {Publisher: Taylor \& Francis},
	pages = {1{\textendash}15},
	keywords = {algae, Aquatic viruses, bacteria, biological preservation, community resource, culture collection, genetic and metabolic diversity},
	issn = {2638-8081},
	doi = {10.1080/26388081.2020.1770123},
	url = {https://doi.org/10.1080/26388081.2020.1770123 https://www.tandfonline.com/doi/full/10.1080/26388081.2020.1770123},
	author = {Nissimov, Jozef I and Campbell, Christine N and Probert, Ian and Wilson, William H}
}
@article {Palacio2020,
	title = {Changes in population age-structure obscure the temperature-size rule in marine cyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC2382,RCC3377},
	month = {aug},
	pages = {2059},
	abstract = {The temperature-size Rule (TSR) states that there is a negative relationship between ambient temperature and body size. This rule has been independently evaluated for different phases of the life cycle in multicellular eukaryotes, but mostly for the average population in unicellular organisms. We acclimated two model marine cyanobacterial strains (Prochlorococcus marinus MIT9301 and Synechococcus sp. RS9907) to a gradient of temperatures and measured the changes in population age-structure and cell size along their division cycle. Both strains displayed temperature-dependent diel changes in cell size, and as a result, the relationship between temperature and average cell size varied along the day. We computed the mean cell size of new-born cells in order to test the prediction of the TSR on a single-growth stage. Our work reconciles previous inconsistent results when testing the TSR on unicellular organisms, and shows that when a single-growth stage is considered the predicted negative response to temperature is revealed.},
	keywords = {cell cycle, Cell Division, cell size, Prochlorococcus, rcc2382, RCC3377, Synechococcus, temperature, temperature-size rule},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.02059},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.02059/full},
	author = {Palacio, Antonio S. and Cabello, Ana Mar{\'\i}a and Garc{\'\i}a, Francisca C. and Labban, Abbrar and Mor{\'a}n, Xos{\'e} Anxelu G. and Garczarek, Laurence and Alonso-S{\'a}ez, Laura and L{\'o}pez-Urrutia, {\'A}ngel}
}
@article {Carrigee2020,
	title = {CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I <span class="nocase">α</span>-subunit in marine Synechococcus},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	year = {2020},
	note = {Publisher: Elsevier B.V tex.mendeley-tags: RCC555},
	month = {apr},
	pages = {148215},
	keywords = {rcc555},
	issn = {00052728},
	doi = {10.1016/j.bbabio.2020.148215},
	url = {https://doi.org/10.1016/j.bbamem.2019.183135 https://linkinghub.elsevier.com/retrieve/pii/S0005272820300657},
	author = {Carrigee, Lyndsay A. and Mahmoud, Rania M. and Sanfilippo, Joseph E. and Frick, Jacob P. and Strnat, Johann A. and Karty, Jonathan A. and Chen, Bo and Kehoe, David M. and Schluchter, Wendy M.}
}
@article {Cai2020,
	title = {Cryptic species in the parasitic Amoebophrya species complex revealed by a polyphasic approach},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1627,RCC1720,RCC3018,RCC3043,RCC3044,RCC3047,RCC3048,RCC3049,RCC3145,RCC3278,RCC3596,RCC4381,RCC4382,RCC4383,RCC4384,RCC4385,RCC4386,RCC4387,RCC4388,RCC4389,RCC4390,RCC4391,RCC4392,RCC4393,RCC4394,RCC4395,RCC4396,RCC4397,RCC4398,RCC4399,RCC4400,RCC4401,RCC4402,RCC4403,RCC4404,RCC4405,RCC4406,RCC4407,RCC4408,RCC4409,RCC4410,RCC4411,RCC4412,RCC4413,RCC4414,RCC4415,RCC4416,RCC4711,RCC4712,RCC4713,RCC4715,RCC4716,RCC4722,RCC4723,RCC4726,RCC4728,RCC4729,RCC4732,RCC4733,RCC4734,RCC5984,RCC5985,RCC5986,RCC5987,RCC5988,RCC5989,RCC5990,RCC5991,RCC5992,RCC5993,RCC5994,RCC5995,RCC5997,RCC5998,RCC5999,RCC6000,RCC6001,RCC6002,RCC6003,RCC6004,RCC6005,RCC6006,RCC6007,RCC6008,RCC6009,RCC6010,RCC6079,RCC6080,RCC6081,RCC6082,RCC6083,RCC6084,RCC6085,RCC6087,RCC6088,RCC6094,RCC6096,RCC6100,RCC6101,RCC6102,RCC6103,RCC6104,RCC6105,RCC6106,RCC6107,RCC6108,RCC6109,RCC6110,RCC6111,RCC6112,RCC6113,RCC6115,RCC6116,RCC6117,RCC6118,RCC6119,RCC6120,RCC6121},
	month = {dec},
	pages = {2531},
	keywords = {RCC1627, RCC1720, RCC3018, RCC3043, RCC3044, RCC3047, RCC3048, RCC3049, RCC3145, RCC3278, RCC3596, RCC4381, RCC4382, RCC4383, RCC4384, RCC4385, RCC4386, RCC4387, RCC4388, RCC4389, RCC4390, RCC4391, RCC4392, RCC4393, RCC4394, RCC4395, RCC4396, RCC4397, RCC4398, RCC4399, RCC4400, RCC4401, RCC4402, RCC4403, RCC4404, RCC4405, RCC4406, RCC4407, RCC4408, RCC4409, RCC4410, RCC4411, RCC4412, RCC4413, RCC4414, RCC4415, RCC4416, RCC4711, RCC4712, RCC4713, RCC4715, RCC4716, RCC4722, RCC4723, RCC4726, RCC4728, RCC4729, RCC4732, RCC4733, RCC4734, RCC5984, RCC5985, RCC5986, RCC5987, RCC5988, RCC5989, RCC5990, RCC5991, RCC5992, RCC5993, RCC5994, RCC5995, RCC5997, RCC5998, RCC5999, RCC6000, RCC6001, RCC6002, RCC6003, RCC6004, RCC6005, RCC6006, RCC6007, RCC6008, RCC6009, RCC6010, RCC6079, RCC6080, RCC6081, RCC6082, RCC6083, RCC6084, RCC6085, RCC6087, RCC6088, RCC6094, RCC6096, RCC6100, RCC6101, RCC6102, RCC6103, RCC6104, RCC6105, RCC6106, RCC6107, RCC6108, RCC6109, RCC6110, RCC6111, RCC6112, RCC6113, RCC6115, RCC6116, RCC6117, RCC6118, RCC6119, RCC6120, RCC6121},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-59524-z},
	url = {http://dx.doi.org/10.1038/s41598-020-59524-z http://www.nature.com/articles/s41598-020-59524-z},
	author = {Cai, Ruibo and Kayal, Ehsan and Alves-de-Souza, Catharina and Bigeard, Estelle and Corre, Erwan and Jeanthon, Christian and Marie, Dominique and Porcel, Betina M and Siano, Raffaele and Szymczak, Jeremy and Wolf, Matthias and Guillou, Laure}
}
@article {Connell2020,
	title = {Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre},
	journal = {Aquatic Microbial Ecology},
	volume = {85},
	year = {2020},
	note = {Publisher: Inter-Research Science Center tex.mendeley-tags: RCC80},
	month = {dec},
	pages = {167{\textendash}181},
	abstract = {Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, but it is less clear how the light-dark cycle affects the activities of their consumers. We investigated the relationship between marine picocyanobacteria and nanoplanktonic consumers throughout the diel cycle to determine whether heterotrophic and mixotrophic protists (algae with phagotrophic ability) display significant periodicity in grazing pressure. Carbon biomass of Prochlorococcus and Synechococcus was estimated continuously from abundances and cell size measurements made by flow cytometry. Picocyanobacterial dynamics were then compared to nanoplankton abundances and ingestion of fluorescently labeled bacteria measured every 4 h during a 4 d survey in the North Pacific Subtropical Gyre. Grazing of the labeled bacteria by heterotrophic nanoplankton was significantly greater at night than during the day. The grazing activity of mixotrophic nanoplankton showed no diel periodicity, suggesting that they may feed continuously, albeit at lower rates than heterotrophic nanoplankton, to alleviate nutrient limitation in this oligotrophic environment. Diel changes in Prochlorococcus biomass indicated that they could support substantial growth of nanoplankton if those grazers are the main source of picocyanobacterial mortality, and that grazers may contribute to temporally stable abundances of picocyanobacteria.},
	keywords = {bacterivory, diel cycles, mixotrophy, nanoplankton grazing, picocyanobacteria, RCC80},
	issn = {0948-3055},
	doi = {10.3354/ame01950},
	url = {http://dx.doi.org/10.3354/ame01950 https://www.int-res.com/abstracts/ame/v85/p167-181/},
	author = {Connell, PE and Ribalet, F and Armbrust, EV and White, A and Caron, DA}
}
@article {Wittek2020,
	title = {Dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas variations arising from sea ice shifts of salinity and temperature in the Prymnesiophyceae Phaeocystis antarctica},
	journal = {Environmental Chemistry},
	year = {2020},
	note = {tex.mendeley-tags: RCC4023},
	abstract = {Environmental context. Dimethylsulfoniopropionate and dimethylsulfoxide could have a climatic influence especially in the polar areas. We investigate the effect of sea ice salinity and temperature on the production of these two sulfur metabolites by a polar microalga, and suggest their potential roles of osmoregulator and cryoprotectant. These results bring new information about the sulfur cycle in sea ice that is useful for climate models.. The Southern Ocean, which includes the seasonal ice zone (SIZ), is a source of large sea-air fluxes of dimethylsulfide (DMS), a climate active gas involved in Earth cooling processes. In this area, the prymnesiophyte Phaeocystis antarctica (P. antarctica) is one of the main producers of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO), two metabolites that are precursors of DMS. These algae are also present in sea ice and contribute substantially to the high DMSP and DMSO concentrations observed in this habitat. DMSP and DMSO production in sea ice by P. antarctica is proposed to be promoted by its ability to live in extreme environmental conditions. We designed cell culture experiments to test that hypothesis, focusing on the impact of shifts of temperature and salinity on the DMSP and DMSO cell quotas. Our experiments show an increase in DMSP and DMSO cell quotas following shifts in salinity (34 to 75, at 4 {\textdegree}C), which suggests a potential osmoregulator function for both DMSP and DMSO. Stronger salinity shifts (up to 100) directly impact cell growth and induce a crash of the cultures. Combining the salinity (34 to 75) and temperature (4 {\textdegree}C to {\textendash}2.3 {\textdegree}C) shifts induces higher increases of DMSP and DMSO cell quotas that also suggests an implication of both metabolites in a cryoprotectant system. Experimental cell quotas (including diatom Fragilariopsis cylindrus quotas from a previous study) are then used to reconstruct DMSP and DMSO profiles in sea ice based on the biomass and taxonomy. Finally, the complexity of the transposition of rates obtained in the experimental domain to the real world is discussed.},
	keywords = {RCC4023},
	doi = {10.1071/EN19302},
	url = {https://doi.org/10.1071/EN19302},
	author = {Wittek, Boris and Carnat, Gauthier and Delille, Bruno and Tison, Jean-Louis and Gypens, Nathalie}
}
@article {Altenburger2020,
	title = {Dimorphism in cryptophytes{\textemdash}The case of Teleaulax amphioxeia / Plagioselmis prolonga and its ecological implications},
	journal = {Science Advances},
	volume = {6},
	number = {37},
	year = {2020},
	note = {tex.mendeley-tags: RCC5152},
	month = {sep},
	pages = {eabb1611},
	abstract = {Growing evidence suggests that sexual reproduction might be common in unicellular organisms, but observations are sparse. Limited knowledge of sexual reproduction constrains understanding of protist ecology. Although Teleaulax amphioxeia and Plagioselmis prolonga are common marine cryptophytes worldwide, and are also important plastid donors for some kleptoplastic ciliates and dinoflagellates, the ecology and development of these protists are poorly known. We demonstrate that P. prolonga is the haploid form of the diploid T. amphioxeia and describe the seasonal dynamics of these two life stages. The diploid T. amphioxeia dominates during periods of high dissolved inorganic nitrogen (DIN) and low irradiance, temperature, and grazing (winter and early spring), whereas the haploid P. prolonga becomes more abundant during the summer, when DIN is low and irradiance, temperature, and grazing are high. Dimorphic sexual life cycles might explain the success of this species by fostering high genetic diversity and enabling endurance in adverse conditions.},
	keywords = {RCC5152},
	issn = {2375-2548},
	doi = {10.1126/sciadv.abb1611},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.abb1611},
	author = {Altenburger, A and Blossom, H E and Garcia-Cuetos, L. and Jakobsen, H H and Carstensen, J and Lundholm, N. and Hansen, P. J. and Moestrup, {\O}. and Haraguchi, L.}
}
@article {Kayal2020,
	title = {Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {December},
	year = {2020},
	note = {tex.mendeley-tags: RCC1627,RCC4398},
	month = {dec},
	pages = {1{\textendash}11},
	abstract = {Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.},
	keywords = {amoebophrya, chloroplast, Dinoflagellate, frontiers in microbiology, frontiersin, kleptoplast, marine plankton, org, organelles, parasitism, RCC1627, RCC4398, www},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.600823},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full},
	author = {Kayal, Ehsan and Alves-de-Souza, Catharina and Farhat, Sarah and Velo-Suarez, Lourdes and Monjol, Joanne and Szymczak, Jeremy and Bigeard, Estelle and Marie, Dominique and Noel, Benjamin and Porcel, Betina M and Corre, Erwan and Six, Christophe and Guillou, Laure}
}
@article {Coelho2020,
	title = {Ectocarpus: an evo-devo model for the brown algae},
	journal = {EvoDevo},
	volume = {11},
	number = {1},
	year = {2020},
	note = {ISBN: 1322702000164 Publisher: BioMed Central},
	month = {dec},
	pages = {19},
	keywords = {Brown algae, complex, Complex multicellularity, cycle, Ectocarpus, ectocarpus is a genus, filamentous, Gametophyte, life-cycle, Marine, multicellu-, multicellularity, natural habitat and life, of small, Phaeoviruses, Sex determination, Sporophyte},
	issn = {2041-9139},
	doi = {10.1186/s13227-020-00164-9},
	url = {https://doi.org/10.1186/s13227-020-00164-9 https://evodevojournal.biomedcentral.com/articles/10.1186/s13227-020-00164-9},
	author = {Coelho, Susana M and Peters, Akira F and M{\"u}ller, Dieter and Cock, J Mark}
}
@article {Thorel2020,
	title = {Effect of 10 UV filters on the brine shrimp Artemia salina and themarinemicroalga Tetraselmis sp.},
	journal = {Toxics},
	volume = {8},
	number = {2},
	year = {2020},
	note = {Publisher: MDPI AG tex.mendeley-tags: RCC500},
	month = {jun},
	pages = {29},
	abstract = {The presence of pharmaceutical and personal care product (PPCP) residues in the aquatic environment is an emerging issue due to their uncontrolled release through gray water, and accumulation in the environment that may affect living organisms, ecosystems and public health. The aim of this study is to assess the toxicity of benzophenone-3 (BP-3), bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), butyl methoxydibenzoylmethane (BM), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), 2-ethylhexyl salicylate (ES), diethylaminohydroxybenzoyl hexyl benzoate (DHHB), diethylhexyl butamido triazone (DBT), ethylhexyl triazone (ET), homosalate (HS) and octocrylene (OC) on marine organisms from two major trophic levels, including autotrophs (Tetraselmis sp.) and heterotrophs (Artemia salina). In general, results showed that both HS and OC were the most toxic UV filters for our tested species, followed by a significant effect of BM on Artemia salina due to BM-but only at high concentrations (1 mg/L). ES, BP3 and DHHB affected the metabolic activity of the microalgae at 100 ??g/L. BEMT, DBT, ET, MBBT had no effect on the tested organisms, even at high concentrations (2 mg/L). OC toxicity represents a risk for those species, since concentrations used in this study are 15-90 times greater than those reported in occurrence studies for aquatic environments. For the first time in the literature, we report HS toxicity on a microalgae species at concentrations complementing those found in aquatic environments. These preliminary results could represent a risk in the future if concentrations of OC and HS continue to increase.},
	keywords = {Artemia salina, marine environment, Marine microalgae, RCC500, Toxicity tests, UV-filters},
	issn = {23056304},
	doi = {10.3390/TOXICS8020029},
	url = {www.mdpi.com/journal/toxics},
	author = {Thorel, Evane and Clergeaud, Fanny and Jaugeon, Lucie and Rodrigues, Alice M.S. and Lucas, Julie and Stien, Didier and Lebaron, Philippe}
}
@article {Dore2020,
	title = {Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {September},
	year = {2020},
	note = {tex.mendeley-tags: RCC1084,RCC1085,RCC1086,RCC1087,RCC156,RCC158,RCC162,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2374,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2385,RCC2433,RCC2436,RCC2438,RCC2527,RCC2528,RCC2533,RCC2534,RCC2535,RCC2553,RCC2554,RCC2555,RCC2556,RCC2571,RCC2673,RCC278,RCC296,RCC307,RCC328,RCC3377,RCC407,RCC515,RCC539,RCC555,RCC556,RCC752,RCC753,RCC791},
	month = {sep},
	pages = {1{\textendash}23},
	keywords = {amino-acid substitutions, comparative genomics, evolution, genomic islands, marine cyanobacteria, niche adaptation, Prochlorococcus, rcc1084, RCC1085, RCC1086, RCC1087, RCC156, RCC158, rcc162, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2374, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2385, RCC2433, RCC2436, RCC2438, RCC2527, RCC2528, RCC2533, RCC2534, RCC2535, RCC2553, RCC2554, RCC2555, RCC2556, RCC2571, RCC2673, RCC278, rcc296, RCC307, RCC328, RCC3377, RCC407, RCC515, rcc539, rcc555, RCC556, rcc752, RCC753, rcc791, Synechococcus},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.567431},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full},
	author = {Dor{\'e}, Hugo and Farrant, Gregory K. and Guyet, Ulysse and Haguait, Julie and Humily, Florian and Ratin, Morgane and Pitt, Frances D. and Ostrowski, Martin and Six, Christophe and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Bisch, Antoine and Le Corguill{\'e}, Gildas and Corre, Erwan and Labadie, Karine and Aury, Jean-Marc and Wincker, Patrick and Choi, Dong Han and Noh, Jae Hoon and Eveillard, Damien and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {Belisle2020,
	title = {Genome sequences of synechococcus sp. Strain MIT S9220 and cocultured cyanophage SynMITS9220M01},
	journal = {Microbiology Resource Announcements},
	volume = {9},
	number = {30},
	year = {2020},
	note = {tex.mendeley-tags: RCC2571},
	month = {jul},
	pages = {28{\textendash}30},
	abstract = {Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture.},
	keywords = {RCC2571},
	issn = {2576-098X},
	doi = {10.1128/MRA.00481-20},
	url = {https://mra.asm.org/content/9/30/e00481-20},
	author = {Belisle, B. Shafer and Avila Paz, Andres A. and Carpenter, Angelina R. and Cormier, Tayla C. and Lewis, Adam J. and Menin, Linnea S. and Oliveira, Daniel R and Song, Bukyung and Szeto, Amy and Tchantouridze, Elizabeth I and Watson, Kayleigh A and Yohannes, Mary T and Ahlgren, Nathan A},
	editor = {Putonti, Catherine}
}
@article {Fernandes2020,
	title = {Hemiselmis andersenii and chlorella stigmatophora as new sources of High-value compounds: A lipidomic approach},
	journal = {Journal of Phycology},
	year = {2020},
	note = {Publisher: Blackwell Publishing Inc. tex.mendeley-tags: RCC661},
	month = {aug},
	pages = {jpy.13042},
	abstract = {To unlock the potential of Chlorella stigmatophora (Trebouxiophyceae, Chlorophyta) and Hemiselmis andersenii (Cryptophyceae, Cryptophyta) as natural reactors for biotechnological exploitation, their lipophilic extracts were characterized using Fourier Transform Infrared spectroscopy with Attenuated Total Reflectance (FTIR-ATR) and Gas Chromatography-Mass Spectrometry (GC-MS) before and after alkaline hydrolysis. The GC-MS analysis enabled the identification of 62 metabolites{\textemdash}namely fatty acids (27), aliphatic alcohols (17), monoglycerides (7), sterols (4), and other compounds (7). After alkaline hydrolysis, monounsaturated fatty acids increased by as much as 87\%, suggesting that the esterified compounds were mainly neutral lipids. Hemiselmis andersenii yielded the highest Σω3/Σω6 ratio (7.26), indicating that it is a good source of ω3 fatty acids, in comparison to C. stigmatophora (Σω3/Σω6 = 1.24). Both microalgae presented significant amounts of aliphatic alcohols (6.81{\textendash}10.95 mg ? g dw-1), which are recognized by their cholesterol-lowering properties. The multivariate analysis allowed visualization of the chemical divergence among H. andersenii lipophilic extracts before and after alkaline hydrolysis, as well as species-specific differences. Chlorella stigmatophora showed to be a valuable source of essential fatty acids for nutraceuticals, whereas H. andersenii, due to its high chemical diversity, seems to be suitable for different fields of application.},
	keywords = {Chlorella stigmatophora, GC-MS, Hemiselmis andersenii, lipophilic fraction, Microalgae, RCC661},
	issn = {0022-3646},
	doi = {10.1111/jpy.13042},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13042},
	author = {Fernandes, Tom{\'a}sia and Cordeiro, Nereida},
	editor = {Li, Y.}
}
@article {Carrillo2020,
	title = {Identification and characterization of ChlreSEX4, a novel glucan phosphatase from Chlamydomonas reinhardtii green alga},
	journal = {Archives of Biochemistry and Biophysics},
	volume = {680},
	year = {2020},
	note = {Publisher: Academic Press Inc.},
	month = {feb},
	pages = {108235},
	abstract = {Chlamydomonas reinhardtii is the best known unicellular green alga model which has long been used to investigate all kinds of cellular processes, including starch metabolism. Here we identified and characterized a novel enzyme, ChlreSEX4, orthologous to glucan phosphatase SEX4 from Arabidopsis thaliana, that is capable of binding and dephosphorylating amylopectin in vitro. We also reported that cysteine 224 and tryptophan 305 residues are critical for enzyme catalysis and substrate binding. Furthermore, we verified that ChlreSEX4 gene is expressed in vivo and that glucan phosphatase activity is measurable in Chlamydomonas protein extracts. In view of the results presented, we suggest ChlreSEX4 as a functional phosphoglucan phosphatase from C. reinhardtii. Our data obtained so far contribute to understanding the phosphoglucan phosphatases evolutionary process in the green lineage and their role in starch reversible phosphorylation. In addition, this allows to position Chlamydomonas as a potential tool to obtain starches with different degrees of phosphorylation for industrial or biotechnological purposes.},
	keywords = {Chlamydomonas Reinhardtii, ChlreSEX4, Glucan phosphatase, SEX4, Starch phosphorylation},
	issn = {10960384},
	doi = {10.1016/j.abb.2019.108235},
	author = {Carrillo, Julieta B. and Torresi, Florencia and Morales, Luisina L. and Ricordi, Micaela and Gomez-Casati, Diego F. and Busi, Maria V. and Mart{\'\i}n, Mariana}
}
@article {Uwizeye2020,
	title = {In-cell quantitative structural imaging of phytoplankton using 3D electron microscopy},
	journal = {bioRxiv},
	year = {2020},
	note = {tex.mendeley-tags: RCC100,RCC4014,RCC827,RCC909},
	month = {jan},
	pages = {2020.05.19.104166},
	abstract = {Phytoplankton is a minor fraction of the global biomass playing a major role in primary production and climate. Despite improved understanding of phytoplankton diversity and genomics, we lack nanoscale subcellular imaging approaches to understand their physiology and cell biology. Here, we present a complete Focused Ion Beam - Scanning Electron Microscopy (FIB-SEM) workflow (from sample preparation to image processing) to generate nanometric 3D phytoplankton models. Tomograms of entire cells, representatives of six ecologically-successful phytoplankton unicellular eukaryotes, were used for quantitative morphometric analysis. Besides lineage-specific cellular architectures, we observed common features related to cellular energy management: i) conserved cell-volume fractions occupied by the different organelles; ii) consistent plastid-mitochondria interactions, iii) constant volumetric ratios in these energy-producing organelles. We revealed detailed subcellular features related to chromatin organization and to biomineralization. Overall, this approach opens new perspectives to study phytoplankton acclimation responses to abiotic and biotic factors at a relevant biological scale.Competing Interest StatementThe authors have declared no competing interest.},
	keywords = {RCC100, RCC4014, RCC827, RCC909},
	doi = {10.1101/2020.05.19.104166},
	url = {http://biorxiv.org/content/early/2020/05/20/2020.05.19.104166.abstract},
	author = {Uwizeye, Clarisse and Decelle, Johan and Jouneau, Pierre-Henri and Gallet, Benoit and Keck, Jean-baptiste and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni and Moriscot, Christine and Chevalier, Fabien and Schieber, Nicole L and Templin, Rachel and Curien, Gilles and Schwab, Yannick and Schoehn, Guy and Zeeman, Samuel C and Falconet, Denis and Finazzi, Giovanni}
}
@article {Helliwell2020,
	title = {A novel single-domain Na +-selective voltage-gated channel in photosynthetic eukaryotes},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC1456},
	month = {apr},
	pages = {2020.04.29.068528},
	abstract = {The evolution of Na+-selective four-domain voltage-gated channels (4D-Navs) in animals allowed rapid Na+-dependent electrical excitability, and enabled the development of sophisticated systems for rapid and long-range signalling. Whilst bacteria encode single-domain Na+-selective voltage-gated channels (BacNav), they typically exhibit much slower kinetics than 4D-Navs, and are not thought to have crossed the prokaryote-eukaryote boundary. As such, the capacity for rapid Na+-selective signalling is considered to be confined to certain animal taxa, and absent from photosynthetic eukaryotes. Certainly, in land plants, such as the Venus Flytrap where fast electrical excitability has been described, this is most likely based on fast anion channels. Here, we report a unique class of eukaryotic Na+-selective single-domain channels (EukCatBs) that are present primarily in haptophyte algae, including the ecologically important calcifying coccolithophores. The EukCatB channels exhibit very rapid voltage-dependent activation and inactivation kinetics, and sensitivity to the highly selective 4D-Nav blocker tetrodotoxin. The results demonstrate that the capacity for rapid Na+-based signalling in eukaryotes is not restricted to animals or to the presence of 4D-Navs. The EukCatB channels therefore represent an independent evolution of fast Na+-based electrical signalling in eukaryotes that likely contribute to sophisticated cellular control mechanisms operating on very short time scales in unicellular algae. One Sentence Summary The capacity for rapid Na+-based signalling has evolved in ecologically important coccolithophore species via a novel class of voltage-gated Na+ channels, EukCatBs.},
	keywords = {RCC1456},
	doi = {10.1101/2020.04.29.068528},
	url = {https://doi.org/10.1101/2020.04.29.068528},
	author = {Helliwell, Katherine E and Chrachri, Abdul and Koester, Julie and Wharam, Susan and Wheeler, Glen L and Brownlee, Colin}
}
@article {Calmes2020,
	title = {Parallelisable non-invasive biomass, fitness and growth measurement of macroalgae and other protists with nephelometry},
	journal = {Algal Research},
	volume = {46},
	number = {November 2019},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC149,RCC3088,RCC3510,RCC3553},
	pages = {101762},
	abstract = {With the exponential development of algal aquaculture and blue biotechnology, there is a strong demand for simple, inexpensive, high-throughput, quantitative phenotyping assays to measure the biomass, growth and fertility of algae and other marine protists. Here, we validate nephelometry, a method that relies on measuring the scattering of light by particles in suspension, as a non-invasive tool to measure in real-time the biomass of aquatic micro-organisms, such as microalgae, filamentous algae, as well as non-photosynthetic protists. Nephelometry is equally applicable to optic density and chlorophyll fluorescence measurements for the quantification of some microalgae, but outperforms other spectroscopy methods to quantify the biomass of biofilm-forming and filamentous algae, highly pigmented species and non-photosynthetic eukaryotes. Thanks to its insensitivity to the sample{\textquoteright}s pigmentation, nephelometry is also the method of choice when chlorophyll content varies between samples or time points, for example due to abiotic stress or pathogen infection. As examples, we illustrate how nephelometry can be combined with fluorometry or image analysis to monitor the quantity and time-course of spore release in fertile kelps or the progression of symptoms in diseased algal cultures.},
	keywords = {Algal cultivation, Biomass, Biotechnology, Nephelometry, Phenotyping, RCC149, RCC3088, RCC3510, rcc3553},
	issn = {22119264},
	doi = {10.1016/j.algal.2019.101762},
	url = {https://doi.org/10.1016/j.algal.2019.101762},
	author = {Calmes, Beno{\^\i}t and Strittmatter, Martina and Jacquemin, Bertrand and Perrineau, Marie Mathilde and Rousseau, C{\'e}line and Badis, Yacine and Cock, J. Mark and Destombe, Christophe and Valero, Myriam and Gachon, Claire M.M.}
}
@article {Avilan2020,
	title = {ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC2967},
	month = {mar},
	pages = {2020.03.05.978130},
	abstract = {{\textbullet} Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta-and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. {\textbullet} Here, we studied the function of ppGpp in the diatom P. tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. {\textbullet} We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. {\textbullet} Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.},
	keywords = {chloroplast, diatoms, lipid droplets, Phaeodactylum tricornutum, Photosynthesis, ppGpp, proteome, RCC2967},
	doi = {10.1101/2020.03.05.978130},
	url = {https://doi.org/10.1101/2020.03.05.978130},
	author = {Avilan, Luisana and Lebrun, Regine and Puppo, Carine and Citerne, Sylvie and Cuin{\'e}, Stephane and Li-Beisson, Yonghua and Menand, Benoit and Field, Ben and Gontero, Brigitte}
}
@article {Hepach2020,
	title = {Senescence as the main driver of iodide release from a diverse range of marine phytoplankton},
	journal = {Biogeosciences},
	volume = {17},
	number = {9},
	year = {2020},
	note = {tex.mendeley-tags: RC4512,RCC1164,RCC1210,RCC1318,RCC1725,RCC2366,RCC4024,RCC4208,RCC4560},
	month = {may},
	pages = {2453{\textendash}2471},
	keywords = {RCC1164, rcc1210, RCC1318, RCC1725, RCC2366, RCC4024, RCC4208, RCC4512, RCC4560},
	issn = {1726-4189},
	doi = {10.5194/bg-17-2453-2020},
	url = {https://www.biogeosciences.net/17/2453/2020/},
	author = {Hepach, Helmke and Hughes, Claire and Hogg, Karen and Collings, Susannah and Chance, Rosie}
}
@article {Guyet2020,
	title = {Synergic effects of temperature and irradiance on the physiology of the marine synechococcus strain WH7803},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC752},
	month = {jul},
	pages = {1707},
	abstract = {Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.},
	keywords = {light stress, marine cyanobacteria, rcc752, Synechococcus, temperature stress, transcriptomics, UV radiations},
	issn = {1664302X},
	doi = {10.3389/fmicb.2020.01707},
	url = {www.frontiersin.org},
	author = {Guyet, Ulysse and Nguyen, Ngoc A. and Dor{\'e}, Hugo and Haguait, Julie and Pittera, Justine and Conan, Ma{\"e}l and Ratin, Morgane and Corre, Erwan and Le Corguill{\'e}, Gildas and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Six, Christophe and Steglich, Claudia and Siegel, Anne and Eveillard, Damien and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {Tisserand2020,
	title = {Use of organic exudates from two polar diatoms by bacterial isolates from the Arctic Ocean},
	journal = {Philosophical transactions. Series A, Mathematical, physical, and engineering sciences},
	volume = {378},
	number = {2181},
	year = {2020},
	note = {Publisher: NLM (Medline) tex.mendeley-tags: RCC2278,RCC4289},
	month = {oct},
	pages = {20190356},
	abstract = {Global warming affects primary producers in the Arctic, with potential consequences for the bacterial community composition through the consumption of microalgae-derived dissolved organic matter (DOM). To determine the degree of specificity in the use of an exudate by bacterial taxa, we used simple microalgae-bacteria model systems. We isolated 92 bacterial strains from the sea ice bottom and the water column in spring-summer in the Baffin Bay (Arctic Ocean). The isolates were grouped into 42 species belonging to Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. Forty strains were tested for their capacity to grow on the exudate from two Arctic diatoms. Most of the strains tested (78\%) were able to grow on the exudate from the pelagic diatom Chaetoceros neogracilis, and 33\% were able to use the exudate from the sea ice diatom Fragilariopsis cylindrus. 17.5\% of the strains were not able to grow with any exudate, while 27.5\% of the strains were able to use both types of exudates. All strains belonging to Flavobacteriia (n = 10) were able to use the DOM provided by C. neogracilis, and this exudate sustained a growth capacity of up to 100 times higher than diluted Marine Broth medium, of two Pseudomonas sp. strains and one Sulfitobacter strain. The variable bioavailability of exudates to bacterial strains highlights the potential role of microalgae in shaping the bacterial community composition. This article is part of the theme issue {\textquoteright}The changing Arctic Ocean: consequences for biological communities, biogeochemical processes and ecosystem functioning{\textquoteright}.},
	keywords = {Arctic Ocean, bacterial diversity, bacterial isolation, biodegradation, diatoms, dissolved organic exudates, RCC2278, RCC4289},
	issn = {14712962},
	doi = {10.1098/rsta.2019.0356},
	url = {https://royalsocietypublishing.org/doi/10.1098/rsta.2019.0356},
	author = {Tisserand, Lucas and Dadaglio, La{\"e}titia and Intertaglia, Laurent and Catala, Philippe and Panagiotopoulos, Christos and Obernosterer, Ingrid and Joux, Fabien}
}
@article {Castillo2020,
	title = {Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC4221},
	month = {jul},
	pages = {1559},
	abstract = {One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.},
	keywords = {culture system, marine picoeukaryote, Ostreococcus tauri, Ostreococcus tauri virus 5, RCC4221, virus fluorescence in situ hybridization, virus-host interactions},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.01559},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01559/full},
	author = {Castillo, Yaiza M. and Sebasti{\'a}n, Marta and Forn, Irene and Grimsley, Nigel and Yau, Sheree and Moraru, Cristina and Vaqu{\'e}, Dolors}
}
@article {Helliwell2019,
	title = {Alternative mechanisms for fast na + /ca 2+ signaling in eukaryotes via a novel class of single-domain voltage-gated channels},
	journal = {Current Biology},
	volume = {29},
	number = {9},
	year = {2019},
	note = {tex.mendeley-tags: RCC299},
	pages = {1503{\textendash}1511.e6},
	abstract = {Rapid Na + /Ca 2+ -based action potentials govern essential cellular functions in eukaryotes, from the motile responses of unicellular protists, such as Paramecium [1, 2], to complex animal neuromuscular activity [3]. A key innovation underpinning this fundamental signaling process has been the evolution of four-domain voltage-gated Na + /Ca 2+ channels (4D-Ca v s/Na v s). These channels are widely distributed across eukaryote diversity [4], albeit several eukaryotes, including land plants and fungi, have lost voltage-sensitive 4D-Ca v /Na v s [5{\textendash}7]. Because these lineages appear to lack rapid Na + /Ca 2+ -based action potentials, 4D-Ca v /Na v s are generally considered necessary for fast Na + /Ca 2+ -based signaling [7]. However, the cellular mechanisms underpinning the membrane physiology of many eukaryotes remain unexamined. Eukaryotic phytoplankton critically influence our climate as major primary producers. Several taxa, including the globally abundant diatoms, exhibit membrane excitability [8{\textendash}10]. We previously demonstrated that certain diatom genomes encode 4D-Ca v /Na v s [4] but also proteins of unknown function, resembling prokaryote single-domain, voltage-gated Na + channels (BacNa v s) [4]. Here, we show that single-domain channels are actually broadly distributed across major eukaryote phytoplankton lineages and represent three novel classes of single-domain channels, which we refer collectively to as EukCats. Functional characterization of diatom EukCatAs indicates that they are voltage-gated Na + - and Ca 2+ -permeable channels, with rapid kinetics resembling metazoan 4D-Ca v s/Na v s. In Phaeodactylum tricornutum, which lacks 4D-Ca v /Na v s, EukCatAs underpin voltage-activated Ca 2+ signaling important for membrane excitability, and mutants exhibit impaired motility. EukCatAs therefore provide alternative mechanisms for rapid Na + /Ca 2+ signaling in eukaryotes and may functionally replace 4D-Ca v s/Na v s in pennate diatoms. Marine phytoplankton thus possess unique signaling mechanisms that may be key to environmental sensing in the oceans. Diatoms exhibit fast animal-like action potentials, but many species lack 4D-Ca v /Na v channels that underpin membrane excitability in animals. Diatoms do encode novel 1D voltage-gated channels (EukCatAs). Helliwell, Chrachri et al. show that EukCatAs are fast Na + and Ca 2+ channels that provide alternative mechanisms for rapid signaling in eukaryotes.},
	keywords = {action potentials, BacNa v, calcium channel, diatoms, EukCats, gliding motility, ion selectivity, RCC299, signaling, single-domain channel, voltage-gated channel},
	issn = {09609822},
	doi = {10.1016/j.cub.2019.03.041},
	author = {Helliwell, Katherine E. and Chrachri, Abdul and Koester, Julie A. and Wharam, Susan and Verret, Frederic and Taylor, Alison R. and Wheeler, Glen L. and Brownlee, Colin}
}
@article {Lacour2019,
	title = {Decoupling light harvesting, electron transport and carbon fixation during prolonged darkness supports rapid recovery upon re-illumination in the Arctic diatom Chaetoceros neogracilis},
	journal = {Polar Biology},
	year = {2019},
	note = {ISBN: 0123456789 Publisher: Springer Berlin Heidelberg tex.mendeley-tags: RCC2278},
	month = {may},
	keywords = {Arctic microalgae, Darkness, Diatom, GROWTH RATE, Photosynthesis, Polar night, RCC2278, temperature},
	issn = {0722-4060},
	doi = {10.1007/s00300-019-02507-2},
	url = {https://doi.org/10.1007/s00300-019-02507-2 http://link.springer.com/10.1007/s00300-019-02507-2},
	author = {Lacour, Thomas and Morin, Philippe-Isra{\"e}l and Sciandra, Th{\'e}o and Donaher, Natalie and Campbell, Douglas A. and Ferland, Joannie and Babin, Marcel}
}
@article {Arsenieff2019,
	title = {First viruses infecting the marine diatom guinardia delicatula},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {January},
	year = {2019},
	note = {tex.mendeley-tags: RCC1000,RCC2023,RCC3046,RCC3083,RCC3093,RCC3101,RCC4657,RCC4659,RCC4660,RCC4667,RCC4834,RCC5154,RCC5777,RCC5778,RCC5779,RCC5780,RCC5781,RCC5782,RCC5783,RCC5784,RCC5785,RCC5787,RCC5788,RCC5789,RCC5790,RCC5792,RCC5793,RCC5794,RCC80},
	month = {jan},
	keywords = {diatoms, genomics, host-virus dynamics, RCC1000, RCC2023, RCC3046, RCC3083, RCC3093, RCC3101, RCC4657, RCC4659, RCC4660, RCC4667, RCC4834, RCC5154, RCC5777, RCC5778, RCC5779, RCC5780, RCC5781, RCC5782, RCC5783, RCC5784, RCC5785, RCC5787, RCC5788, RCC5789, RCC5790, RCC5792, RCC5793, RCC5794, RCC80, single-stranded RNA viruses, Western English Channel},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.03235},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.03235/full},
	author = {Arsenieff, Laure and Simon, Nathalie and Rigaut-jalabert, Fabienne and Le Gall, Florence and Chaffron, Samuel and Corre, Erwan and Com, Emmanuelle and Bigeard, Estelle and Baudoux, Anne-claire}
}
@article {Iglesias2019,
	title = {NMR characterization and evaluation of antibacterial and antiobiofilm activity of organic extracts from stationary phase batch cultures of five marine microalgae (Dunaliella sp., D. salina, Chaetoceros calcitrans, C. gracilis and Tisochrysis lutea)},
	journal = {Phytochemistry},
	volume = {164},
	number = {April},
	year = {2019},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC1349,RCC1811,RCC3579,RCC5,RCC5953},
	month = {aug},
	pages = {192{\textendash}205},
	keywords = {Antibacterial, Antibiofilm, Chaetoceros, Dunaliella, Metabolite identification, NMR, RCC1349, RCC1811, RCC3579, RCC5, RCC5953, Tisochrysis},
	issn = {00319422},
	doi = {10.1016/j.phytochem.2019.05.001},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0031942219300184},
	author = {Iglesias, Ma Jos{\'e} and Soengas, Raquel and Probert, Ian and Guilloud, Emilie and Gourvil, Priscillia and Mehiri, Mohamed and L{\'o}pez, Yuly and Cepas, Virginio and Guti{\'e}rrez-del-R{\'\i}o, Ignacio and Redondo-Blanco, Sa{\'u}l and Villar, Claudio J. and Lomb{\'o}, Felipe and Soto, Sara and Ortiz, Fernando L{\'o}pez}
}
@article {bramucci_phaeobacter_2019,
	title = {Phaeobacter inhibens induces apoptosis-like programmed cell death in calcifying Emiliania huxleyi},
	journal = {Scientific Reports},
	volume = {9},
	number = {1},
	year = {2019},
	note = {Number: 1 Publisher: Nature Publishing Group},
	month = {mar},
	pages = {1{\textendash}12},
	abstract = {The model coccolithophore, Emiliania huxleyi, forms expansive blooms dominated by the calcifying cell type, which produce calcite scales called coccoliths. Blooms last several weeks, after which the calcified algal cells rapidly die, descending into the deep ocean. E. huxleyi bloom collapse is attributed to E. huxleyi viruses (EhVs) that infect and kill calcifying cells, while other E. huxleyi pathogens, such as bacteria belonging to the roseobacter clade, are overlooked. EhVs kill calcifying E. huxleyi by inducing production of bioactive viral-glycosphingolipids (vGSLs), which trigger algal programmed cell death (PCD). The roseobacter Phaeobacter inhibens was recently shown to interact with and kill the calcifying cell type of E. huxleyi, but the mechanism of algal death remains unelucidated. Here we demonstrate that P. inhibens kills calcifying E. huxleyi by inducing a highly specific type of PCD called apoptosis-like-PCD (AL-PCD). Host death can successfully be abolished in the presence of a pan-caspase inhibitor, which prevents the activation of caspase-like molecules. This finding differentiates P. inhibens and EhV pathogenesis of E. huxleyi, by demonstrating that bacterial-induced AL-PCD requires active caspase-like molecules, while the viral pathogen does not. This is the first demonstration of a bacterium inducing AL-PCD in an algal host as a killing mechanism.},
	keywords = {RCC1216},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-36847-6},
	url = {http://www.nature.com/articles/s41598-018-36847-6},
	author = {Bramucci, Anna R. and Case, Rebecca J.}
}
@article {Kashiyama2019,
	title = {Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth},
	journal = {The ISME Journal},
	year = {2019},
	note = {Publisher: Springer US tex.mendeley-tags: RCC164,RCC22,RCC24,RCC375,RCC916},
	month = {feb},
	pages = {1},
	abstract = {Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.},
	keywords = {Biochemistry, Biogeochemistry, Cellular microbiology, microbial ecology, RCC164, RCC22, RCC24, RCC375, RCC916},
	issn = {1751-7362},
	doi = {10.1038/s41396-019-0377-0},
	url = {http://www.nature.com/articles/s41396-019-0377-0},
	author = {Kashiyama, Yuichiro and Yokoyama, Akiko and Shiratori, Takashi and Hess, Sebastian and Not, Fabrice and Bachy, Charles and Gutierrez-Rodriguez, Andres and Kawahara, Jun and Suzaki, Toshinobu and Nakazawa, Masami and Ishikawa, Takahiro and Maruyama, Moe and Wang, Mengyun and Chen, Man and Gong, Yingchun and Seto, Kensuke and Kagami, Maiko and Hamamoto, Yoko and Honda, Daiske and Umetani, Takahiro and Shihongi, Akira and Kayama, Motoki and Matsuda, Toshiki and Taira, Junya and Yabuki, Akinori and Tsuchiya, Masashi and Hirakawa, Yoshihisa and Kawaguchi, Akane and Nomura, Mami and Nakamura, Atsushi and Namba, Noriaki and Matsumoto, Mitsufumi and Tanaka, Tsuyoshi and Yoshino, Tomoko and Higuchi, Rina and Yamamoto, Akihiro and Maruyama, Tadanobu and Yamaguchi, Aika and Uzuka, Akihiro and Miyagishima, Shinya and Tanifuji, Goro and Kawachi, Masanobu and Kinoshita, Yusuke and Tamiaki, Hitoshi}
}
@article {Liu2019,
	title = {Transcriptome of thalassicolla nucleata holobiont reveals details of a radiolarian symbiotic relationship},
	journal = {Frontiers in Marine Science},
	volume = {6},
	number = {June},
	year = {2019},
	note = {tex.mendeley-tags: RCC3387},
	month = {jun},
	pages = {1{\textendash}11},
	keywords = {Brandtodinium, holobiont, photosymbiosis, radiolarian, RCC3387, Transcriptome},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00284},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00284/full},
	author = {Liu, Zhenfeng and Mesrop, Lisa Y. and Hu, Sarah K. and Caron, David A.}
}
@article {Pierre2019,
	title = {What is in store for EPS microalgae in the next decade?},
	journal = {Molecules},
	volume = {24},
	number = {23},
	year = {2019},
	month = {nov},
	pages = {4296},
	abstract = {Microalgae and their metabolites have been an El Dorado since the turn of the 21st century. Many scientific works and industrial exploitations have thus been set up. These developments have often highlighted the need to intensify the processes for biomass production in photo-autotrophy and exploit all the microalgae value including ExoPolySaccharides (EPS). Indeed, the bottlenecks limiting the development of low value products from microalgae are not only linked to biology but also to biological engineering problems including harvesting, recycling of culture media, photoproduction, and biorefinery. Even respecting the so-called {\textquotedblleft}Biorefinery Concept{\textquotedblright}, few applications had a chance to emerge and survive on the market. Thus, exploiting EPS from microalgae for industrial applications in some low-value markets such as food is probably not a mature proposition considering the competitiveness of polysaccharides from terrestrial plants, macroalgae, and bacteria. However, it does not imply drawing a line on their uses but rather {\textquotedblleft}thinking them{\textquotedblright} differently. This review provides insights into microalgae, EPS, and their exploitation. Perspectives on issues affecting the future of EPS microalgae are also addressed with a critical point of view.},
	keywords = {application, eps, exopolysaccharides, market, Microalgae},
	issn = {1420-3049},
	doi = {10.3390/molecules24234296},
	url = {https://www.mdpi.com/1420-3049/24/23/4296},
	author = {Pierre, Guillaume and Delattre, C{\'e}dric and Dubessay, Pascal and Jubeau, S{\'e}bastien and Vialleix, Carole and Cadoret, Jean-Paul and Probert, Ian and Michaud, Philippe}
}
@article {Beuvier2019,
	title = {X-ray nanotomography of coccolithophores reveals that coccolith mass and segment number correlate with grid size},
	journal = {Nature Communications},
	volume = {10},
	number = {1},
	year = {2019},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1212,RCC1216,RCC1314,RCC3370,RCC4032,RCC4036},
	month = {dec},
	pages = {751},
	abstract = {Coccolithophores of the No{\"e}laerhabdaceae family are covered by imbricated coccoliths, each composed of multiple calcite crystals radially distributed around the periphery of a grid. The factors that determine coccolith size remain obscure. Here, we used synchrotron-based three-dimensional Coherent X-ray Diffraction Imaging to study coccoliths of 7 species of Gephyrocapsa, Emiliania and Reticulofenestra with a resolution close to 30 nm. Segmentation of 45 coccoliths revealed remarkable size, mass and segment number variations, even within single coccospheres. In particular, we observed that coccolith mass correlates with grid perimeter which scales linearly with crystal number. Our results indirectly support the idea that coccolith mass is determined in the coccolith vesicle by the size of the organic base plate scale (OBPS) around which R-unit nucleation occurs every 110{\textendash}120 nm. The curvation of coccoliths allows inference of a positive correlation between cell nucleus, OBPS and coccolith sizes.},
	keywords = {Biomaterials, Marine biology, rcc1212, RCC1216, RCC1314, RCC3370, RCC4032, RCC4036},
	issn = {2041-1723},
	doi = {10.1038/s41467-019-08635-x},
	url = {http://www.nature.com/articles/s41467-019-08635-x},
	author = {Beuvier, T. and Probert, I. and Beaufort, L. and Such{\'e}ras-Marx, B. and Chushkin, Y. and Zontone, F. and Gibaud, A.}
}
@article {Cheng2018,
	title = {10KP: A phylodiverse genome sequencing plan},
	journal = {GigaScience},
	volume = {7},
	number = {3},
	year = {2018},
	pages = {1{\textendash}9},
	keywords = {10kp, 12 february 2018, 2018, 4, accepted, access article distributed under, and reproduction in any, attribution license, biodiversity, by, c the author, creative commons, creativecommons, Distribution, genome sequencing, genomics, http, licenses, medium, mgiseq, open community, org, phylogenomics, PLANTS, press, published by oxford university, received, s, samples, the terms of the, this is an open, which permits unrestricted reuse},
	issn = {2047-217X},
	doi = {10.1093/gigascience/giy013},
	url = {https://academic.oup.com/gigascience/article/7/3/1/4880447},
	author = {Cheng, Shifeng and Melkonian, Michael and Smith, Stephen A and Brockington, Samuel and Archibald, John M and Delaux, Pierre-Marc and Li, Fay-Wei and Melkonian, Barbara and Mavrodiev, Evgeny V and Sun, Wenjing and Fu, Yuan and Yang, Huanming and Soltis, Douglas E and Graham, Sean W and Soltis, Pamela S and Liu, Xin and Xu, Xun and Wong, Gane Ka-Shu}
}
@article {Meng2018,
	title = {Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network},
	journal = {Molecular Ecology},
	year = {2018},
	note = {tex.mendeley-tags: RCC1491,RCC1516,RCC3387,RCC3468,RCC3507},
	pages = {0{\textendash}2},
	abstract = {Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g. sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56\% and 57\% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization. This article is protected by copyright. All rights reserved.},
	keywords = {Genomics/Proteomics, Microbial Biology, Molecular Evolution, Protists, rcc1491, RCC1516, RCC3387, rcc3468, rcc3507, transcriptomics},
	issn = {09621083},
	doi = {10.1111/mec.14579},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/29624751\%0Ahttp://doi.wiley.com/10.1111/mec.14579},
	author = {Meng, Arnaud and Corre, Erwan and Probert, Ian and Gutierrez-Rodriguez, Andres and Siano, Raffaele and Annamale, Anita and Alberti, Adriana and Da Silva, Corinne and Wincker, Patrick and Le Crom, St{\'e}phane and Not, Fabrice and Bittner, Lucie}
}
@article {Crenn2018,
	title = {Bacterial epibiotic communities of ubiquitous and abundant marine diatoms are distinct in short- and long-term associations},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {December},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC2560,RCC2565,rcc},
	pages = {1{\textendash}12},
	abstract = {Interactions between phytoplankton and bacteria play a central role in mediatingbiogeochemical cycling and food web structure in the ocean. The cosmopolitan diatomsThalassiosiraandChaetocerosoften dominate phytoplankton communities in marinesystems. Past studies of diatom-bacterial associations have employed community-level methods and culture-based or natural diatom populations. Although bacterialassemblages attached to individual diatoms represents tight associations little is knownon their makeup or interactions. Here, we examined the epibiotic bacteria of 436Thalassiosiraand 329Chaetocerossingle cells isolated from natural samples andcollection cultures, regarded here as short- and long-term associations, respectively.Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning-sequencing of 16S rRNA genes obtained from whole-genome amplification products.The prevalence of epibiotic bacteria was higher in cultures and dependent of the hostspecies. Culture approaches demonstrated that both diatoms carry distinct bacterialcommunities in short- and long-term associations. Bacterial epibonts, commonlyassociated with phytoplankton, were repeatedly isolated from cells of diatom collectioncultures but were not recovered from environmental cells. Our results suggest thatin controlled laboratory culture conditions bacterial{\textendash}diatom and bacterial{\textendash}bacterialinteractions select for a simplified, but specific, epibiotic microbiota shaped and adaptedfor long-term associations.},
	keywords = {2018, Chaetoceros, diatoms, diversity, heterotrophic bacteria, interactions, microbiome, rcc, RCC2560, RCC2565, Thalassiosira, Western English Channel},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.02879},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02879/full},
	author = {Crenn, Klervi and Duffieux, Delphine and Jeanthon, Christian}
}
@article {Annunziata2018,
	title = {A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC2967},
	pages = {271445},
	abstract = {Periodic light dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular bases controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we here unveil the key function of a Phaeodactylum tricornutum bHLH-PAS protein, named Pt bHLH1a, in the regulation of light-dependent rhythms. Peak expression of Pt bHLH1a mRNA occurs at the end of the light period and it is adjusted to photoperiod changes. Ectopic over-expression of Pt bHLH1a results in lines with altered cell division and gene expression and showing a phase shift in diurnal responses, compared to the wild-type cells. Reduced oscillations in gene expression are also observed in continuous darkness, showing that the regulation of rhythmicity by Pt bHLH1a is not directly dependent on light inputs and cell division. Pt bHLH1a orthologs are widespread in both pennate and centric diatom genomes, hinting at a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but still underinvestigated branch of the tree of life.},
	keywords = {RCC2967},
	doi = {10.1101/271445},
	url = {https://www.biorxiv.org/content/early/2018/02/25/271445},
	author = {Annunziata, Rossella and Ritter, Andr{\'e}s and Fortunato, Antonio Emidio and Cheminant-Navarro, Soizic and Agier, Nicolas and Huysman, Marie J. J. and Winge, Per and Bones, Atle and Bouget, Fran{\c c}ois-Yves and Lagomarsino, Marco Cosentino and Bouly, Jean Pierre and Falciatore, Angela}
}
@article {Farhat2018,
	title = {Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {October},
	year = {2018},
	note = {tex.mendeley-tags: RCC1627,RCC3596,RCC4383,RCC4398},
	month = {oct},
	pages = {1{\textendash}19},
	keywords = {amoebophrya, Dinoflagellates, Gene Expression, infection, oxidative stress response, parasite, plankton, RCC1627, RCC3596, RCC4383, RCC4398, syndiniales},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.02251},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full},
	author = {Farhat, Sarah and Florent, Isabelle and Noel, Benjamin and Kayal, Ehsan and Da Silva, Corinne and Bigeard, Estelle and Alberti, Adriana and Labadie, Karine and Corre, Erwan and Aury, Jean-Marc and Rombauts, Stephane and Wincker, Patrick and Guillou, Laure and Porcel, Betina M.}
}
@article {Partensky2018,
	title = {Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex},
	journal = {Photosynthesis Research},
	volume = {138},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC752},
	pages = {57{\textendash}71},
	abstract = {The extrinsic PsbU and PsbV proteins are known to play a critical role in stabilizing the Mn4CaO5 cluster of the PSII oxygen-evolving complex (OEC). However, most isolates of the marine cyanobacterium Prochlorococcus naturally miss these proteins, even though they have kept the main OEC protein, PsbO. A structural homology model of the PSII of such a natural deletion mutant strain (P. marinus MED4) did not reveal any obvious compensation mechanism for this lack. To assess the physiological consequences of this unusual OEC, we compared oxygen evolution between Prochlorococcus strains missing psbU and psbV (PCC 9511 and SS120) and two marine strains possessing these genes (Prochlorococcus sp. MIT9313 and Synechococcus sp. WH7803). While the low light-adapted strain SS120 exhibited the lowest maximal O2 evolution rates (Pmax per divinyl-chlorophyll a, per cell or per photosystem II) of all four strains, the high light-adapted strain PCC 9511 displayed even higher PChlmax and PPSIImax at high irradiance than Synechococcus sp. WH7803. Furthermore, thermoluminescence glow curves did not show any alteration in the B-band shape or peak position that could be related to the lack of these extrinsic proteins. This suggests an efficient functional adaptation of the OEC in these natural deletion mutants, in which PsbO alone is seemingly sufficient to ensure proper oxygen evolution. Our study also showed that Prochlorococcus strains exhibit negative net O2 evolution rates at the low irradiances encountered in minimum oxygen zones, possibly explaining the very low O2 concentrations measured in these environments, where Prochlorococcus is the dominant oxyphototroph.},
	keywords = {rcc752},
	issn = {1573-5079},
	doi = {10.1007/s11120-018-0539-3},
	url = {https://doi.org/10.1007/s11120-018-0539-3},
	author = {Partensky, Fr{\'e}d{\'e}ric and Mella-Flores, Daniella and Six, Christophe and Garczarek, Laurence and Czjzek, Mirjam and Marie, Dominique and Kotabov{\'a}, Eva and Felcmanov{\'a}, Kristina and Pr{\'a}{\v s}il, Ond{\v r}ej}
}
@article {Kazamia2018,
	title = {Endocytosis-mediated siderophore uptake as a strategy for Fe acquisition in diatoms},
	journal = {Science Advances},
	volume = {4},
	number = {5},
	year = {2018},
	note = {tex.mendeley-tags: RCC2967},
	month = {may},
	pages = {eaar4536},
	keywords = {RCC2967},
	issn = {2375-2548},
	doi = {10.1126/sciadv.aar4536},
	url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aar4536},
	author = {Kazamia, Elena and Sutak, Robert and Paz-Yepes, Javier and Dorrell, Richard G and Vieira, Fabio Rocha Jimenez and Mach, Jan and Morrissey, Joe and Leon, S{\'e}bastien and Lam, France and Pelletier, Eric and Camadro, Jean-michel and Bowler, Chris and Lesuisse, Emmanuel}
}
@article {Carrillo2018,
	title = {Identification and analysis of OsttaDSP, a phosphoglucan phosphatase from Ostreococcus tauri},
	journal = {PLOS ONE},
	volume = {13},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	month = {jan},
	pages = {e0191621},
	keywords = {RCC745},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0191621},
	url = {http://dx.plos.org/10.1371/journal.pone.0191621},
	author = {Carrillo, Julieta B and Gomez-Casati, Diego F. and Mart{\'\i}n, Mariana and Busi, Maria V.},
	editor = {Permyakov, Eugene A.}
}
@article {Smallwood2018,
	title = {Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	keywords = {? No DOI found, RCC745},
	author = {Smallwood, Authors Chuck R and Chen, Jian-hua and Kumar, Neeraj and Chrisler, William and Samuel, O and Kyle, Jennifer E and Nicora, Carrie D and Boudreau, Rosanne and Ekman, Axel and Kim, K and Moore, Ronald J and Mcdermott, Gerry and Cannon, William R and Evans, James E}
}
@article {Liefer2018,
	title = {Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes},
	journal = {PLOS ONE},
	volume = {13},
	number = {4},
	year = {2018},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC745},
	month = {apr},
	pages = {e0195705},
	abstract = {Nitrogen stress is an important control on the growth of phytoplankton and varying responses to this common condition among taxa may affect their relative success within phytoplankton communities.We analyzed photosynthetic responses to nitrogen (N) stress in two classes of phytoplankton that often dominate their respective size ranges, diatoms and prasinophytes, selecting species of distinct niches within each class. Changes in photosynthetic structures appeared similar within each class during N stress, but photophysiological and growth responses were more species -or niche-specific. In the coastal diatom Thalassiosira pseudonana and the oceanic diatom T. weissflogii, N starvation induced large declines in photosynthetic pigments and Photosystem II (PSII) quantity and activity as well as increases in the effective absorption cross-section of PSII photochemistry (σ{\textquoteright}PSII). These diatoms also increased photoprotection through energy-dependent non-photochemical quenching (NPQ) during N starvation. Resupply of N in diatoms caused rapid recovery of growth and relaxation of NPQ, while recovery of PSII photochemistry was slower. In contrast, the prasinophytes Micromonas sp., an Arctic Ocean species, and Ostreococcus tauri, a temperate coastal eutrophile, showed little change in photosynthetic pigments and structures and a decline or no change, respectively, inσ{\textquoteright}PSII with N starvation. Growth and PSII function recovered quickly in Micromonas sp. after resupply of N while O. tauri failed to recover N-replete levels of electron transfer from PSII and growth, possibly due to their distinct photoprotective strategies. O. tauri induced energy-dependent NPQ for photoprotection that may suit its variable and nutrient-rich habitat. Micromonas sp. relies upon both energy-dependent NPQ and a sustained, energy-independent NPQ mechanism. A strategy in Micromonas sp. that permits photoprotection with little change in photosynthetic structures is consistent with its Arctic niche, where low temperatures and thus low biosynthetic rates create higher opportunity costs to rebuild photosynthetic structures.},
	keywords = {RCC745},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0195705},
	url = {http://dx.plos.org/10.1371/journal.pone.0195705},
	author = {Liefer, Justin D and Garg, Aneri and Campbell, Douglas A and Irwin, Andrew J and Finkel, Zoe V},
	editor = {Ianora, Adrianna}
}
@article {Partensky2018,
	title = {A novel species of the marine cyanobacterium Acaryochloris with a unique pigment content and lifestyle},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC1774},
	month = {dec},
	pages = {9142},
	keywords = {RCC1774},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-27542-7},
	url = {http://www.nature.com/articles/s41598-018-27542-7},
	author = {Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Ratin, Morgane and Garczarek, Laurence and Vaulot, Daniel and Probert, Ian and Calteau, Alexandra and Gourvil, Priscillia and Marie, Dominique and Gr{\'e}bert, Th{\'e}ophile and Bouchier, Christiane and Le Panse, Sophie and Gachenot, Martin and Rodr{\'\i}guez, Francisco and Garrido, Jos{\'e} L.}
}
@article {Mizrachi2018,
	title = {Phenotypic variability in chloroplast redox state predicts cell fate in a marine diatom},
	journal = {bioRxiv},
	year = {2018},
	note = {arXiv: 319517 tex.arxivid: 319517 tex.mendeley-tags: RCC2967},
	keywords = {RCC2967},
	doi = {10.1101/319517},
	author = {Mizrachi, Avia and Graff, Shiri and Creveld, Van and Shapiro, Orr H and Rosenwasser, Shilo}
}
@article {Klinger2018,
	title = {Plastid transcript editing across dinoflagellate lineages shows lineage-specific application but conserved trends},
	journal = {Genome Biology and Evolution},
	volume = {10},
	number = {April},
	year = {2018},
	note = {tex.mendeley-tags: RCC1513},
	pages = {1019{\textendash}1038},
	abstract = {Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with plastids of distinct evolutionary affiliations, including a fucoxanthin pigment-containing plastid of haptophyte origin. Previous studies have described the presence of widespread substitutional RNA editing in peridinin and fucoxanthin plastid genes. Because reports of this process have been limited to manual assessment of individual lineages, global trends concerning this RNA editing and its effect on the biological function of the plastid are largely unknown. Using novel bioinformatic methods, we examine the dynamics and evolution of RNA editing over a large multispecies data set of dinoflagellates, including novel sequence data from the peridinin dinoflagellate Pyrocystis lunula and the fucoxanthin dinoflagellate Karenia mikimotoi. We demonstrate that while most individual RNA editing events in dinoflagellate plastids are restricted to single species, global patterns, and functional consequences of editing are broadly conserved. We find that editing is biased toward specific codon positions and regions of genes, and generally corrects otherwise deleterious changes in the genome prior to translation, though this effect is more prevalent in peridinin than fucoxanthin lineages. Our results support a model for promiscuous editing application subsequently shaped by purifying selection, and suggest the presence of an underlying editing mechanism transferred from the peridinin-containing ancestor into fucoxanthin plastids postendosymbiosis, with remarkably conserved functional consequences in the new lineage.},
	keywords = {constructive neutral evolution, Dinoflagellate, plastid, RCC1513, serial endosymbiosis, transcript editing},
	issn = {1759-6653},
	doi = {10.1093/gbe/evy057},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evy057/4935245},
	author = {Klinger, Christen M and Paoli, Lucas and Newby, Robert J and Wang, Matthew Yu-Wei and Carroll, Hyrum D and Leblond, Jeffrey D and Howe, Christopher J and Dacks, Joel B and Bowler, Chris and Cahoon, A Bruce and Dorrell, Richard G and Richardson, Elisabeth}
}
@article {yau_rapidity_2018,
	title = {Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga},
	journal = {Viruses},
	volume = {10},
	number = {8},
	year = {2018},
	note = {Number: 8 Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {441},
	abstract = {Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10\&minus;3\&ndash;10\&minus;4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.},
	keywords = {adsorption, Chromosome, host range, karyotype, mamiellophyceae, phycodnaviridae, RCC1105, RCC4221, RCC4223, rearrangement, resistance, specificity, \textitOstreococcus tauri},
	doi = {10.3390/v10080441},
	url = {https://www.mdpi.com/1999-4915/10/8/441},
	author = {Yau, Sheree and Caravello, Ga{\"e}tan and Fonvieille, Nad{\`e}ge and Desgranges, Elodie and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Gu2017,
	title = {Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain},
	journal = {Phycologia},
	volume = {57},
	number = {October},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1982,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1{\textendash}13},
	abstract = {The sand-dwelling?1dinoflagellate generaAdenoidesandPseudadenoidesare morphologically very close butdistinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected inintertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic,France). Strain morphology was examined with light and scanning electron microscopy, and both large subunitribosomal DNA (LSU rDNA) and small subunit ribosomal DNA (SSU rDNA) sequences were amplified. Molecularphylogeny, corroborated by morphological examination showing the existence of a ventral pore, confirmed theidentification of the French strain (RCC1982) asAdenoides eludens. The Chinese strains differed fromAdenoides eludensin two additional posterior intercalary plates and differed fromPseudadenoidesin one additional apical plate having theplate formula of Po, Cp, X, 50,600, 4S, 5000, 5p, 10000or alternatively Po, Cp, X, 50,600, 5S, 5000, 3p, 20000. Maximumlikelihood and Bayesian inference carried out with concatenated LSU and SSU sequences demonstrated that the Chinesestrains were closely related but different fromA. eludensand, in corroboration with morphological evidence, supportedtheir classification as a distinct species,Adenoides sinensis sp. nov. Morphological and molecular results confirmed theclose relationship between the two generaAdenoidesandPseudadenoides.},
	keywords = {2017, rcc, RCC1982, sbr?hyto$_\textrmd$ipo},
	doi = {10.2216/17-76.1},
	author = {Gu, Haifeng and Li, Xintian and Chom{\'e}rat, Nicolas and Luo, Zhaohe and Sarno, Diana and Gourvil, Priscillia and Balzano, Sergio and Siano, Raffaele}
}
@article {Ni2016,
	title = {Arctic Micromonas uses protein pools and non-photochemical quenching to cope with temperature restrictions on Photosystem II protein turnover},
	journal = {Photosynthesis Research},
	volume = {131},
	number = {2},
	year = {2017},
	note = {ISBN: 1112001603 Publisher: Springer Netherlands tex.mendeley-tags: 2016,RCC806},
	month = {feb},
	pages = {203{\textendash}220},
	keywords = {2016, {\'a}, Photoinactivation, photoinactivation {\'a} xanthophyll cycle, Photosystem II, Prasinophyte, prasinophyte {\'a} photosystem ii, RCC806, Xanthophyll cycle},
	issn = {0166-8595},
	doi = {10.1007/s11120-016-0310-6},
	url = {http://link.springer.com/10.1007/s11120-016-0310-6},
	author = {Ni, Guangyan and Zimbalatti, Gabrielle and Murphy, Cole D. and Barnett, Audrey B. and Arsenault, Christopher M. and Li, Gang and Cockshutt, Amanda M. and Campbell, Douglas A.}
}
@article {LopesdosSantos2017,
	title = {Chloropicophyceae, a new class of picophytoplanktonic prasinophytes},
	journal = {Scientific Reports},
	volume = {7},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4572,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC887,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo},
	month = {dec},
	pages = {14019},
	keywords = {2017, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4572, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC887, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo},
	issn = {2045-2322},
	doi = {10.1038/s41598-017-12412-5},
	url = {http://www.nature.com/articles/s41598-017-12412-5},
	author = {Lopes dos Santos, Adriana and Pollina, Thibaut and Gourvil, Priscillia and Corre, Erwan and Marie, Dominique and Garrido, Jos{\'e} Luis and Rodr{\'\i}guez, Francisco and No{\"e}l, Mary-H{\'e}l{\`e}ne and Vaulot, Daniel and Eikrem, Wenche}
}
@article {Walter2017,
	title = {Ecogenomics and taxonomy of cyanobacteria phylum},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {November},
	year = {2017},
	note = {tex.mendeley-tags: RCC307},
	month = {nov},
	keywords = {charting biodiversity, ecological niches, genome-based microbial taxonomy, high-throughput sequencing technology, metagenome, microbial ecology, RCC307},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.02132},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02132/full},
	author = {Walter, Juline M. and Coutinho, Felipe H. and Dutilh, Bas E. and Swings, Jean and Thompson, Fabiano L. and Thompson, Cristiane C.}
}
@article {Moutier2017,
	title = {Evolution of the scattering properties of phytoplankton cells from flow cytometry measurements},
	journal = {PLoS ONE},
	volume = {12},
	number = {7},
	year = {2017},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC1,RCC950},
	abstract = {Combining a modern, data-analytic perspective with a focus on applications in the social sciences, the Second Edition of Applied Regression Analysis and Generalized Linear Models provides in-depth coverage of regression analysis, generalized linear models, and closely related methods. Although the text is largely accessible to readers with a modest background in statistics and mathematics, author John Fox also presents more advanced material throughout the book. Key Updates to the Second Edition:Provides greatly enhanced coverage of generalized linear models, with an emphasis on models for categorical and count data Offers new chapters on missing data in regression models and on methods of model selection Includes expanded treatment of robust regression, time-series regression, nonlinear regression, and nonparametric regression Incorporates new examples using larger data sets Includes an extensive Web site at http://www.sagepub.com/fox that presents appendixes, data sets used in the book and for data-analytic exercises, and the data-analytic exercises themselves Intended Audience: This core text will be a valuable resource for graduate students and researchers in the social sciences (particularly sociology, political science, and psychology) and other disciplines that employ linear and related models for data analysis. High Praise for the First Edition: Even though the book is written with social scientists as the target audience, the depth of material and how it is conveyed give it far broader appeal. Indeed, I recommend it as a useful learning text and resource for researchers and students in any field that applies regression or linear models (that is, most everyone), including courses for undergraduate statistics majors.... The author is to be commended for giving us this book, which I trust will find a wide and enduring readership.-JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION [T]his wonderfully comprehensive book focuses on regression analysis and linear models.... We enthusiastically recommend this book {\textemdash} having used it in class, we know that it is thorough and well liked by students. -CHANCE},
	keywords = {RCC1, RCC950},
	issn = {19326203},
	doi = {10.1371/journal.pone.0181180},
	author = {Moutier, William and Dufor{\^e}t-Gaurier, Lucile and Thyssen, M{\'e}lilotus and Loisel, Hubert and M{\'e}riaux, Xavier and Courcot, Lucie and Dessailly, David and R{\^e}ve, Anne H{\'e}l{\`e}ne and Gr{\'e}gori, Gerald and Alvain, S{\'e}verine and Barani, Aude and Brutier, Laurent and Dugenne, Mathilde}
}
@article {Degraeve-Guilbault2017,
	title = {Glycerolipid characterization and nutrient deprivation-associated changes in the green picoalga ostreococcus tauri},
	journal = {Plant Physiology},
	volume = {173},
	number = {4},
	year = {2017},
	note = {tex.mendeley-tags: RCC3401,RCC4222,RCC745,RCC788,RCC789,RCC802,RCC809,RCC834},
	pages = {2060{\textendash}2080},
	abstract = {The picoalga Ostreococcus tauri is a minimal photosynthetic eukaryote that has been used as a model system. O. tauri is known to efficiently produce docosahexaenoic acid (DHA). We provide a comprehensive study of the glycerolipidome of O. tauri and validate this species as model for related picoeukaryotes. O. tauri lipids displayed unique features that combined traits from the green and the chromalveolate lineages. The betaine lipid diacylglyceryl-hydroxymethyl-trimethyl-β-alanine and phosphatidyldimethylpropanethiol, both hallmarks of chromalveolates, were identified as presumed extraplastidial lipids. DHA was confined to these lipids, while plastidial lipids of prokaryotic type were characterized by the overwhelming presence of ω-3 C18 polyunsaturated fatty acids (FAs), 18:5 being restricted to galactolipids. C16:4, an FA typical of green microalgae galactolipids, also was a major component of O. tauri extraplastidial lipids, while the 16:4-coenzyme A (CoA) species was not detected. Triacylglycerols (TAGs) displayed the complete panel of FAs, and many species exhibited combinations of FAs diagnostic for plastidial and extraplastidial lipids. Importantly, under nutrient deprivation, 16:4 and ω-3 C18 polyunsaturated FAs accumulated into de novo synthesized TAGs while DHA-TAG species remained rather stable, indicating an increased contribution of FAs of plastidial origin to TAG synthesis. Nutrient deprivation further severely down-regulated the conversion of 18:3 to 18:4, resulting in obvious inversion of the 18:3/18:4 ratio in plastidial lipids, TAGs, as well as acyl-CoAs. The fine-tuned and dynamic regulation of the 18:3/18:4 ratio suggested an important physiological role of these FAs in photosynthetic membranes. Acyl position in structural and storage lipids together with acyl-CoA analysis further help to determine mechanisms possibly involved in glycerolipid synthesis.},
	keywords = {rcc3401, RCC4222, RCC745, RCC788, RCC789, RCC802, RCC809, RCC834},
	issn = {0032-0889},
	doi = {10.1104/pp.16.01467},
	url = {http://www.plantphysiol.org/lookup/doi/10.1104/pp.16.01467},
	author = {Degraeve-Guilbault, Charlotte and Br{\'e}h{\'e}lin, Claire and Haslam, Richard and Sayanova, Olga and Marie-Luce, Glawdys and Jouhet, Juliette and Corellou, Florence}
}
@article {Monier2017,
	title = {Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton},
	journal = {Proceedings of the National Academy of Sciences},
	year = {2017},
	note = {tex.mendeley-tags: RCC1107,RCC1621,RCC2573,RCC2593,RCC745,RCC809},
	pages = {201708097},
	keywords = {rcc1107, RCC1621, RCC2573, RCC2593, RCC745, RCC809},
	issn = {0027-8424},
	doi = {10.1073/pnas.1708097114},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1708097114},
	author = {Monier, Adam and Chambouvet, Aurelie and Milner, David S. and Attah, Victoria and Terrado, Ram{\'o}n and Lovejoy, Connie and Moreau, Herv{\'e} and Santoro, Alyson E. and Derelle, Evelyne and Richards, Thomas A.}
}
@article {Balzano2017c,
	title = {Morphological and genetic diversity of Beaufort Sea diatoms with high contributions from the Chaetoceros neogracilis species complex},
	journal = {Journal of Phycology},
	volume = {53},
	number = {1},
	year = {2017},
	note = {tex.mendeley-tags: RCC1984,RCC1985,RCC1986,RCC1988,RCC1989,RCC1990,RCC1991,RCC1992,RCC1993,RCC1995,RCC1997,RCC1999,RCC2000,RCC2002,RCC2003,RCC2004,RCC2005,RCC2006,RCC2008,RCC2010,RCC2011,RCC2012,RCC2014,RCC2016,RCC2017,RCC2021,RCC2037,RCC2038,RCC2039,RCC2042,RCC2043,RCC2261,RCC2262,RCC2263,RCC2264,RCC2265,RCC2266,RCC2267,RCC2268,RCC2269,RCC2270,RCC2272,RCC2273,RCC2274,RCC2275,RCC2276,RCC2277,RCC2278,RCC2279,RCC2280,RCC2281,RCC2282,RCC2318,RCC2506,RCC2517,RCC2520,RCC2521,RCC2522},
	month = {feb},
	pages = {161{\textendash}187},
	abstract = {Seventy-five diatom strains isolated from the Beaufort Sea (Canadian Arctic) in the summer of 2009 were characterized by light and electron microscopy (SEM and TEM), as well as 18S and 28S rRNA gene sequencing. These strains group into 20 genotypes and 17 morphotypes and are affiliated with the genera Arcocellulus, Attheya, Chaetoceros, Cylindrotheca, Eucampia, Nitzschia, Porosira, Pseudo-nitzschia, Shionodiscus, Thalassiosira, and Synedropsis. Most of the species have a distribution confined to the northern/polar area. Chaetoceros neogracilis and Chaetoceros gelidus were the most represented taxa. Strains of C. neogracilis were morphologically similar and shared identical 18S rRNA gene sequences, but belonged to four distinct genetic clades based on 28S rRNA, ITS-1 and ITS-2 phylogenies. Secondary structure prediction revealed that these four clades differ in hemi-compensatory base changes (HCBCs) in paired positions of the ITS-2, suggesting their inability to interbreed. Reproductively isolated C. neogracilis genotypes can thus co-occur in summer phytoplankton communities in the Beaufort Sea. C. neogracilis generally occurred as single cells but also formed short colonies. It is phylogenetically distinct from an Antarctic species, erroneously identified in some previous studies as C. neogracilis, but named here as Chaetoceros sp. This work provides taxonomically validated sequences for 20 Arctic diatom taxa, which will facilitate future metabarcoding studies on phytoplankton in this region.},
	keywords = {RCC1984, RCC1985, RCC1986, RCC1988, RCC1989, RCC1990, RCC1991, RCC1992, RCC1993, RCC1995, RCC1997, RCC1999, RCC2000, RCC2002, RCC2003, RCC2004, RCC2005, RCC2006, RCC2008, RCC2010, RCC2011, RCC2012, RCC2014, RCC2016, RCC2017, RCC2021, RCC2037, RCC2038, RCC2039, RCC2042, RCC2043, RCC2261, RCC2262, RCC2263, RCC2264, RCC2265, RCC2266, RCC2267, RCC2268, RCC2269, RCC2270, RCC2272, RCC2273, RCC2274, RCC2275, RCC2276, RCC2277, RCC2278, RCC2279, RCC2280, RCC2281, RCC2282, RCC2318, RCC2506, RCC2517, RCC2520, RCC2521, RCC2522},
	issn = {00223646},
	doi = {10.1111/jpy.12489},
	url = {http://doi.wiley.com/10.1111/jpy.12489},
	author = {Balzano, Sergio and Percopo, Isabella and Siano, Raffaele and Gourvil, Priscillia and Chanoine, M{\'e}lanie and Marie, Dominique and Vaulot, Daniel and Sarno, Diana},
	editor = {Wood, M.}
}
@article {Parks2017,
	title = {Phylogenomics reveals an extensive history of genome duplication in diatoms (Bacillariophyta)},
	journal = {American Journal of Botany},
	volume = {105},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC205,RCC80},
	pages = {1{\textendash}18},
	keywords = {and, b, c, citation, diatoms, e, gene tree, genome duplication, j, n, nakov, paleopolyploidy, parks m, polyploidy, RCC205, RCC80, ruck, synonymous divergence, t, these authors contributed equally, to this work, wickett},
	doi = {10.1101/181115},
	author = {Parks, Matthew and Nakov, Teofil and Ruck, Elizabeth and Wickett, Norman J and Alverson, Andrew J and Rice, Ada L and Conservation, Plant and Botanic, Chicago and Glencoe, Garden}
}
@article {Limardo2017,
	title = {Quantitative biogeography of picoprasinophytes establishes ecotype distributions and significant contributions to marine phytoplankton},
	journal = {Environmental Microbiology},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC715,RCC716,RCC809},
	month = {jun},
	keywords = {RCC1105, RCC715, RCC716, RCC809},
	issn = {14622912},
	doi = {10.1111/1462-2920.13812},
	url = {http://doi.wiley.com/10.1111/1462-2920.13812},
	author = {Limardo, Alexander J. and Sudek, Sebastian and Choi, Chang Jae and Poirier, Camille and Rii, Yoshimi M. and Blum, Marguerite and Roth, Robyn and Goodenough, Ursula and Church, Matthew J. and Worden, Alexandra Z.}
}
@article {Roesler2017,
	title = {Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {6},
	year = {2017},
	note = {tex.mendeley-tags: RCC233,RCC42,RCC834},
	pages = {572{\textendash}585},
	abstract = {Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matchups between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA{\textquoteright}s standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration.},
	keywords = {RCC233, RCC42, RCC834},
	issn = {15415856},
	doi = {10.1002/lom3.10185},
	author = {Roesler, Collin and Uitz, Julia and Claustre, Herv{\'e} and Boss, Emmanuel and Xing, Xiaogang and Organelli, Emanuele and Briggs, Nathan and Bricaud, Annick and Schmechtig, Catherine and Poteau, Antoine and D{\textquoteright}Ortenzio, Fabrizio and Ras, Josephine and Drapeau, Susan and Ha{\"e}ntjens, Nils and Barbieux, Marie}
}
@article {Cuvelier2017,
	title = {Responses of the picoprasinophyte Micromonas commoda to light and ultraviolet stress},
	journal = {PLOS ONE},
	volume = {12},
	number = {3},
	year = {2017},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC299},
	month = {mar},
	pages = {e0172135},
	keywords = {RCC299},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0172135},
	url = {http://dx.plos.org/10.1371/journal.pone.0172135},
	author = {Cuvelier, Marie L and Guo, Jian and Ortiz, Alejandra C. and van Baren, Marijke J. and Tariq, Muhammad Akram and Partensky, Fr{\'e}d{\'e}ric and Worden, Alexandra Z},
	editor = {Cockshutt, Amanda M.}
}
@article {Waltman2016,
	title = {Identifying aspects of the post-transcriptional program governing the proteome of the green alga micromonas pusilla.},
	journal = {PloS one},
	volume = {11},
	number = {7},
	year = {2016},
	note = {ISBN: 10.1371/journal.pone.0155839 Publisher: Public Library of Science tex.mendeley-tags: 2016,RCC,rcc834},
	month = {jan},
	pages = {e0155839},
	abstract = {Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote ({\textexclamdown}2 ??m diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3{\textquoteright} UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.},
	keywords = {2016, rcc, RCC834},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0155839},
	url = {http://dx.doi.org/10.1371/journal.pone.0155839},
	author = {Waltman, Peter H and Guo, Jian and Reistetter, Emily Nahas and Purvine, Samuel and Ansong, Charles K and van Baren, Marijke J and Wong, Chee-Hong and Wei, Chia-Lin and Smith, Richard D and Callister, Stephen J and Stuart, Joshua M and Worden, Alexandra Z}
}
@article {Tragin2016,
	title = {Phylogenetic diversity and ecology of green micro algae in marine systems},
	journal = {Perspectives in Phycology},
	volume = {in press},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo},
	keywords = {2016, ? No DOI found, rcc, sbr?hyto$_\textrmd$ipo},
	author = {Tragin, M and Lopes dos Santos, Adriana and Christen, R. and Vaulot, D.}
}
@article {Coutinho2015,
	title = {Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus},
	journal = {PeerJ},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {e{\textendash}1522},
	keywords = {rcc},
	issn = {2167-8359},
	doi = {10.7717/peerj.1522},
	author = {Coutinho, Felipe and Tschoeke, Diogo Antonio and Thompson, Fabiano and Thomson, Cristiane}
}
@article {Schaum2015,
	title = {Environmental stability affects phenotypic evolution in a globally distributed marine picoplankton},
	journal = {The ISME Journal},
	year = {2015},
	note = {tex.mendeley-tags: oth95,rcc1107,rcc1108,rcc1114,rcc1558,rcc1645,rcc1662,rcc410,rcc422,rcc434,rcc501,rcc675,rcc747,rcc789,rcc809,rcc810},
	pages = {1{\textendash}10},
	abstract = {Marine phytoplankton can evolve rapidly when confronted with aspects of climate change because of their large population sizes and fast generation times. Despite this, the importance of environment fluctuations, a key feature of climate change, has received little attention{\textemdash}selection experiments with marine phytoplankton are usually carried out in stable environments and use single or few representatives of a species, genus or functional group. Here we investigate whether and by how much environmental fluctuations contribute to changes in ecologically important phytoplankton traits such as C:N ratios and cell size, and test the variability of changes in these traits within the globally distributed species Ostreococcus. We have evolved 16 physiologically distinct lineages of Ostreococcus at stable high CO2 (1031{\textpm}87 ??atm CO2 , SH) and fluctuating high CO2 (1012{\textpm}244 ??atm CO2 , FH) for 400 generations.We find that although both fluctuation and high CO2 drive evolution, FH- evolved lineages are smaller, have reduced C:N ratios and respond more strongly to further increases in CO2 than do SH-evolved lineages. This indicates that environmental fluctuations are an important factor to consider when predicting how the characteristics of future phytoplankton populations will have an impact on biogeochemical cycles and higher trophic levels in marine food webs.},
	keywords = {oth95, rcc1107, RCC1108, RCC1114, RCC1558, rcc1645, rcc1662, rcc410, rcc422, RCC434, rcc501, rcc675, rcc747, RCC789, RCC809, rcc810},
	issn = {1751-7362},
	doi = {10.1038/ismej.2015.102},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2015.102},
	author = {Schaum, C-Elisa and Rost, Bj{\"o}rn and Collins, Sin{\'e}ad}
}
@article {Baudoux2015,
	title = {Interplay between the genetic clades of {\textexclamdown}i{\textquestiondown}Micromonas{\textexclamdown}/i{\textquestiondown} and their viruses in the Western English Channel.},
	journal = {Environmental microbiology reports},
	year = {2015},
	note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo},
	month = {jun},
	abstract = {The genus Micromonas comprises distinct genetic clades that commonly dominate eukaryotic phytoplankton community from polar to tropical waters. This phytoplankter is also recurrently infected by abundant and genetically diverse prasinoviruses. Here we report on the interplay between prasinoviruses and Micromonas with regards to the genetic diversity of this host. During one year, we monitored the abundance of 3 clades of Micromonas and their viruses in the Western English Channel both in the environment, using clade-specific probes and flow cytometry, and in the laboratory, using clonal strains of Micromonas clades to assay for their viruses by plaque-forming units. We showed that the seasonal fluctuations of Micromonas clades were closely mirrored by the abundances of their corresponding viruses, indicating that the members of Micromonas genus are susceptible to viral infection, regardless of their genetic affiliation. The characterization of 45 viral isolates revealed that Micromonas clades are attacked by specific virus populations, which exhibit distinctive clade specificity, life strategies, and genetic diversity. However, some viruses can also cross-infect different host clades suggesting a mechanism of horizontal gene transfer within Micromonas genus. This study provides novel insights into the impact of viral infection for the ecology and evolution of the prominent phytoplankter Micromonas.},
	keywords = {2015, rcc, RCC?o?dd, sbr?hyto$_\textrmd$ipo},
	issn = {1758-2229},
	doi = {10.1111/1758-2229.12309},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/26081716},
	author = {Baudoux, A-C and Lebredonchel, H and Dehmer, H and Latimier, M and Edern, R and Rigaut-Jalabert, F and Ge, P and Guillou, L and Foulon, E and Bozec, Y and Cariou, T and Desdevises, Y and Derelle, E and Grimsley, N and Moreau, H and Simon, N}
}
@article {Decelle2015,
	title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy},
	journal = {Molecular Ecology Resources},
	volume = {15},
	number = {6},
	year = {2015},
	note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {1435{\textendash}1445},
	abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.},
	keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1755098X},
	doi = {10.1111/1755-0998.12401},
	url = {http://doi.wiley.com/10.1111/1755-0998.12401},
	author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard}
}
@article {Bombar2014,
	title = {Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria},
	journal = {The ISME Journal},
	volume = {8},
	number = {12},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	pages = {2530{\textendash}2542},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2014.167},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2014.167},
	author = {Bombar, Deniz and Heller, Philip and Sanchez-Baracaldo, Patricia and Carter, Brandon J and Zehr, Jonathan P}
}
@article {Bellec2014,
	title = {Cophylogenetic interactions between marine viruses and eukaryotic picophytoplankton},
	journal = {BMC Evolutionary Biology},
	volume = {14},
	number = {1},
	year = {2014},
	note = {tex.mendeley-tags: RCC1105,RCC1107,RCC1108,RCC1109,RCC114,RCC2482,RCC2483,RCC2484,RCC2485,RCC344,RCC356,RCC373,RCC418,RCC461,RCC464,RCC465,RCC629,RCC658,RCC745,RCC789,RCC834},
	pages = {59},
	abstract = {BACKGROUND:Numerous studies have investigated cospeciation (or cophylogeny) in various host-symbiont systems, and different patterns were inferred, from strict cospeciation where symbiont phylogeny mirrors host phylogeny, to complete absence of correspondence between trees. The degree of cospeciation is generally linked to the level of host specificity in the symbiont species and the opportunity they have to switch hosts. In this study, we investigated cophylogeny for the first time in a microalgae-virus association in the open sea, where symbionts are believed to be highly host-specific but have wide opportunities to switch hosts. We studied prasinovirus-Mamiellales associations using 51 different viral strains infecting 22 host strains, selected from the characterisation and experimental testing of the specificities of 313 virus strains on 26 host strains.RESULTS:All virus strains were restricted to their host genus, and most were species-specific, but some of them were able to infect different host species within a genus. Phylogenetic trees were reconstructed for viruses and their hosts, and their congruence was assessed based on these trees and the specificity data using different cophylogenetic methods, a topology-based approach, Jane, and a global congruence method, ParaFit. We found significant congruence between virus and host trees, but with a putatively complex evolutionary history.CONCLUSIONS:Mechanisms other than true cospeciation, such as host-switching, might explain a part of the data. It has been observed in a previous study on the same taxa that the genomic divergence between host pairs is larger than between their viruses. It implies that if cospeciation predominates in this algae-virus system, this would support the hypothesis that prasinoviruses evolve more slowly than their microalgal hosts, whereas host switching would imply that these viruses speciated more recently than the divergence of their host genera.},
	keywords = {rcc, RCC1105, rcc1107, RCC1108, RCC1109, RCC114, RCC2482, RCC2483, RCC2484, RCC2485, RCC344, RCC356, RCC373, RCC418, RCC461, RCC464, RCC465, RCC629, RCC658, RCC745, RCC789, RCC834, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1186/1471-2148-14-59},
	url = {http://www.biomedcentral.com/1471-2148/14/59},
	author = {Bellec, Laure and Clerissi, Camille and Edern, Roseline and Foulon, Elodie and Simon, Nathalie and Grimsley, Nigel and Desdevises, Yves}
}
@article {Chambouvet2014,
	title = {Diverse molecular signatures for ribosomally {\textquoteright}active{\textquoteright} Perkinsea in marine sediments},
	journal = {BMC Microbiology},
	volume = {14},
	number = {1},
	year = {2014},
	note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?ppo},
	pages = {110},
	abstract = {BACKGROUND:Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples. Only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity {\textquoteright}tag{\textquoteright} sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations.RESULTS:We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27\% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97\% sequence similarity as to suggest this diversity encompasses a range of biologically and ecologically distinct organisms.CONCLUSIONS:These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally {\textquoteright}active{\textquoteright} and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the {\textquoteright}seed bank{\textquoteright} microbial community.},
	keywords = {2014, Biomarks, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1186/1471-2180-14-110},
	url = {http://www.biomedcentral.com/1471-2180/14/110},
	author = {Chambouvet, Aurelie and Berney, Cedric and Romac, Sarah and Audic, St{\'e}phane and Maguire, Finlay and de Vargas, Colomban and Richards, Thomas}
}
@article {Bendif2014,
	title = {Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)},
	journal = {Journal of Phycology},
	volume = {50},
	year = {2014},
	note = {tex.mendeley-tags: 2014,cc3549,rcc,rcc1210,rcc1213,rcc1220,rcc1227,rcc1229,rcc1242,rcc1252,rcc1253,rcc1258,rcc1259,rcc1260,rcc1271,rcc1281,rcc1288,rcc1292,rcc1297,rcc1300,rcc1303,rcc1305,rcc1316,rcc1562,rcc174,rcc1839,rcc3545,rrcc1247,sbr?hyto?ppo},
	pages = {140{\textendash}148},
	keywords = {2014, cc3549, rcc, rcc1210, RCC1213, rcc1220, rcc1227, rcc1229, RCC1242, rcc1252, RCC1253, rcc1258, RCC1259, rcc1260, rcc1271, RCC1281, rcc1288, RCC1292, rcc1297, RCC1300, RCC1303, RCC1305, RCC1316, RCC1562, rcc174, RCC1839, rcc3545, rrcc1247, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/jpy.12147},
	author = {Bendif, El Mahdi and Probert, Ian and Carmichael, Margaux and Romac, Sarah and Hagino, Kyoko and de Vargas, Colomban}
}
@article {Nezan2014,
	title = {Genetic diversity of the harmful family Kareniaceae (Gymnodiniales, Dinophyceae) in France, with the description of {\textexclamdown}i{\textquestiondown}Karlodinium gentienii{\textexclamdown}/i{\textquestiondown} sp. nov.: A new potentially toxic dinoflagellate},
	journal = {Harmful Algae},
	volume = {40},
	year = {2014},
	note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?app},
	pages = {75{\textendash}91},
	abstract = {A B S T R A C T The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1{\textendash}D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.},
	keywords = {2014, rcc, sbr?hyto?app},
	issn = {15689883},
	doi = {10.1016/j.hal.2014.10.006},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1568988314001863},
	author = {N{\'e}zan, Elisabeth and Siano, Raffaele and Boulben, Sylviane and Six, Christophe and Bilien, Gwenael and Ch{\`e}ze, Karine and Duval, Audrey and Le Panse, Sophie and Qu{\'e}r{\'e}, Julien and Chom{\'e}rat, Nicolas}
}
@article {Biller2014,
	title = {Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus},
	journal = {Scientific Data},
	volume = {1},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	month = {sep},
	pages = {1{\textendash}11},
	abstract = {The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity{\textemdash}both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.},
	keywords = {Environmental microbiology, genomics, rcc, RCC?o?dd},
	issn = {2052-4463},
	doi = {10.1038/sdata.2014.34},
	url = {http://www.nature.com/articles/sdata201434},
	author = {Biller, Steven J. and Berube, Paul M. and Berta-Thompson, Jessie W. and Kelly, Libusha and Roggensack, Sara E. and Awad, Lana and Roache-Johnson, Kathryn H. and Ding, Huiming and Giovannoni, Stephen J. and Rocap, Gabrielle and Moore, Lisa R. and Chisholm, Sallie W. and H. and Ding, Huiming and Giovannoni, Stephen J. and Moore, Lisa R. and Chisholm, Sallie W.}
}
@article {Keeling2014,
	title = {The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing},
	journal = {PLoS biology},
	volume = {12},
	number = {6},
	year = {2014},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2014,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e1001889},
	abstract = {Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world{\textquoteright}s oceans},
	keywords = {2014, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pbio.1001889},
	url = {http://dx.doi.org/10.1371\%252Fjournal.pbio.1001889},
	author = {Keeling, Patrick J and Burki, Fabien and Wilcox, Heather M and Allam, Bassem and Allen, Eric E and Amaral-Zettler, Linda A and Armbrust, E Virginia and Archibald, John M and Bharti, Arvind K and Bell, Callum J and Beszteri, Bank and Bidle, Kay D and Cameron, Connor T and Campbell, Lisa and Caron, David A and Cattolico, Rose Ann and Collier, Jackie L and Coyne, Kathryn and Davy, Simon K and Deschamps, Phillipe and Dyhrman, Sonya T and Edvardsen, Bente and Gates, Ruth D and Gobler, Christopher J and Greenwood, Spencer J and Guida, Stephanie M and Jacobi, Jennifer L and Jakobsen, Kjetill S and James, Erick R and Jenkins, Bethany and John, Uwe and Johnson, Matthew D and Juhl, Andrew R and Kamp, Anja and Katz, Laura A and Kiene, Ronald and Kudryavtsev, Alexander and Leander, Brian S and Lin, Senjie and Lovejoy, Connie and Lynn, Denis and Marchetti, Adrian and McManus, George and Nedelcu, Aurora M and Menden-Deuer, Susanne and Miceli, Cristina and Mock, Thomas and Montresor, Marina and Moran, Mary Ann and Murray, Shauna and Nadathur, Govind and Nagai, Satoshi and Ngam, Peter B and Palenik, Brian and Pawlowski, Jan and Petroni, Giulio and Piganeau, Gwenael and Posewitz, Matthew C and Rengefors, Karin and Romano, Giovanna and Rumpho, Mary E and Rynearson, Tatiana and Schilling, Kelly B and Schroeder, Declan C and Simpson, Alastair G B and Slamovits, Claudio H and Smith, David R and Smith, G Jason and Smith, Sarah R and Sosik, Heidi M and Stief, Peter and Theriot, Edward and Twary, Scott N and Umale, Pooja E and Vaulot, Daniel and Wawrik, Boris and Wheeler, Glen L and Wilson, William H and Xu, Yan and Zingone, Adriana and Worden, Alexandra Z}
}
@article {Kashtan2014,
	title = {Single-cell genomics reveals hundreds of coexisting subpopulations in wild prochlorococcus},
	journal = {Science},
	volume = {344},
	number = {6182},
	year = {2014},
	note = {tex.mendeley-tags: RCC278},
	pages = {416{\textendash}420},
	abstract = {Extensive genomic diversity within coexisting members of a microbial species has been revealed through selected cultured isolates and metagenomic assemblies. Yet, the cell-by-cell genomic composition of wild uncultured populations of co-occurring cells is largely unknown. In this work, we applied large-scale single-cell genomics to study populations of the globally abundant marine cyanobacterium Prochlorococcus. We show that they are composed of hundreds of subpopulations with distinct {\textquotedblleft}genomic backbones,{\textquotedblright} each backbone consisting of a different set of core gene alleles linked to a small distinctive set of flexible genes. These subpopulations are estimated to have diverged at least a few million years ago, suggesting ancient, stable niche partitioning. Such a large set of coexisting subpopulations may be a general feature of free-living bacterial species with huge populations in highly mixed habitats.},
	keywords = {RCC278},
	doi = {10.1126/science.1248575},
	url = {http://www.sciencemag.org/content/344/6182/416.abstract},
	author = {Kashtan, Nadav and Roggensack, Sara E and Rodrigue, S{\'e}bastien and Thompson, Jessie W and Biller, Steven J and Coe, Allison and Ding, Huiming and Marttinen, Pekka and Malmstrom, Rex R and Stocker, Roman and Follows, Michael J and Stepanauskas, Ramunas and Chisholm, Sallie W}
}
@article {Clerissi2014,
	title = {Unveiling of the diversity of prasinoviruses (phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-Amplified DNA polymerase and major capsid protein genes},
	journal = {Applied and Environmental Microbiology},
	volume = {80},
	number = {10},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,rcc},
	pages = {3150{\textendash}3160},
	abstract = {Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.},
	keywords = {Micromonas, rcc, TARA-Oceans},
	doi = {10.1128/aem.00123-14},
	url = {http://aem.asm.org/content/80/10/3150.abstract},
	author = {Clerissi, Camille and Grimsley, Nigel and Ogata, Hiroyuki and Hingamp, Pascal and Poulain, Julie and Desdevises, Yves}
}
@article {Rousseau2013,
	title = {Characterization of {\textexclamdown}i{\textquestiondown}Phaeocystis globosa{\textexclamdown}/i{\textquestiondown} (haptophyceae), the blooming species in the southern north sea},
	journal = {Journal of Sea Research},
	volume = {76},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {105{\textendash}113},
	keywords = {2013, ASSEMBLE, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, Souchotheque},
	doi = {10.1016/j.seares.2012.07.011},
	author = {Rousseau, V and Lantoine, F and Rodriguez, F and Le Gall, F and Chr{\'e}tiennot-Dinet, M.-J. and Lancelot, C}
}
@article {chen_genetic_2013,
	title = {Genetic transformation of marine cyanobacterium Synechococcus sp. CC9311 (Cyanophyceae) by electroporation},
	journal = {Chinese Journal of Oceanology and Limnology},
	volume = {31},
	number = {2},
	year = {2013},
	pages = {416{\textendash}420},
	abstract = {Synechococcus sp. CC9311 is a marine cyanobacterium characterized by type IV chromatic acclimation (CA). A genetic transformation system was developed as a first step to elucidate the molecular mechanism of CA. The results show that Synechococcus sp. CC9311 cells were sensitive to four commonly used antibiotics: ampicillin, kanamycin, spectinomycin, and chloramphenicol. An integrative plasmid to disrupt the putative phycoerythrin lyase gene mpeV, using a kanamycin resistance gene as selectable marker, was constructed by recombinant polymerase chain reaction. The plasmid was then transformed into Synechococcus sp. CC9311 via electroporation. High transformation efficiency was achieved at a field strength of 2 kV/cm. DNA analysis showed that mpeV was fully disrupted following challenge of the transformants with a high concentration of kanamycin. In addition, the transformants that displayed poor growth on agar SN medium could be successfully plated on agarose SN medium.},
	keywords = {RCC1086},
	issn = {1993-5005},
	doi = {10.1007/s00343-013-2164-5},
	url = {https://doi.org/10.1007/s00343-013-2164-5},
	author = {Chen, Huaxin and Lin, Hanzhi and Jiang, Peng and Li, Fuchao and Qin, Song}
}
@article {Collen2013,
	title = {Genome structure and metabolic features in the red seaweed Chondrus crispus shed light on evolution of the Archaeplastida},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {110},
	number = {13},
	year = {2013},
	note = {tex.mendeley-tags: RCC299},
	pages = {5247{\textendash}5252},
	abstract = {Red seaweeds are key components of coastal ecosystems and are economically important as food and as a source of gelling agents, but their genes and genomes have received little attention. Here we report the sequencing of the 105-Mbp genome of the florideophyte Chondrus crispus (Irish moss) and the annotation of the 9,606 genes. The genome features an unusual structure characterized by gene-dense regions surrounded by repeat-rich regions dominated by transposable elements. Despite its fairly large size, this genome shows features typical of compact genomes, e.g., on average only 0.3 introns per gene, short introns, low median distance between genes, small gene families, and no indication of large-scale genome duplication. The genome also gives insights into the metabolism of marine red algae and adaptations to the marine environment, including genes related to halogen metabolism, oxylipins, and multicellularity (microRNA processing and transcription factors). Particularly interesting are features related to carbohydrate metabolism, which include a minimalistic gene set for starch biosynthesis, the presence of cellulose synthases acquired before the primary endosymbiosis showing the polyphyly of cellulose synthesis in Archaeplastida, and cellulases absent in terrestrial plants as well as the occurrence of a mannosylglycerate synthase potentially originating from a marine bacterium. To explain the observations on genome structure and gene content, we propose an evolutionary scenario involving an ancestral red alga that was driven by early ecological forces to lose genes, introns, and intergenetic DNA; this loss was followed by an expansion of genome size as a consequence of activity of transposable elements.},
	keywords = {RCC299},
	doi = {10.1073/pnas.1221259110},
	url = {http://www.pnas.org/content/110/13/5247.abstract},
	author = {Collen, Jonas and Porcel, Betina and Carr{\'e}, Wilfrid and Ball, Steven G and Chaparro, Cristian and Tonon, Thierry and Barbeyron, Tristan and Michel, Gurvan and Noel, Benjamin and Valentin, Klaus and Elias, Marek and Artiguenave, Fran{\c c}ois and Arun, Alok and Aury, Jean-Marc and Barbosa-Neto, Jos{\'e} F and Bothwell, John H and Bouget, Fran{\c c}ois-Yves and Brillet, Loraine and Cabello-Hurtado, Francisco and Capella-Guti{\'e}rrez, Salvador and Charrier, B{\'e}n{\'e}dicte and Cladi{\`e}re, Lionel and Cock, J Mark and Coelho, Susana M and Colleoni, Christophe and Czjzek, Mirjam and Da Silva, Corinne and Delage, Ludovic and Denoeud, France and Deschamps, Philippe and Dittami, Simon M and Gabald{\'o}n, Toni and Gachon, Claire M M and Groisillier, Agn{\`e}s and Herv{\'e}, C{\'e}cile and Jabbari, Kamel and Katinka, Michael and Kloareg, Bernard and Kowalczyk, Nathalie and Labadie, Karine and Leblanc, Catherine and Lopez, Pascal J and McLachlan, Deirdre H and Meslet-Cladiere, Laurence and Moustafa, Ahmed and Nehr, Zofia and Nyvall Coll{\'e}n, Pi and Panaud, Olivier and Partensky, Fr{\'e}d{\'e}ric and Poulain, Julie and Rensing, Stefan A and Rousvoal, Sylvie and Samson, Gaelle and Symeonidi, Aikaterini and Weissenbach, Jean and Zambounis, Antonios and Wincker, Patrick and Boyen, Catherine}
}
@article {Chamnansinp2013,
	title = {Global diversity of two widespread, colony-forming diatoms of the marine plankton, Chaetoceros socialis (syn. C. radians ) and Chaetoceros gelidus sp. nov.},
	journal = {Journal of Phycology},
	volume = {49},
	number = {6},
	year = {2013},
	note = {ISBN: 1529-8817 tex.mendeley-tags: RCC3007},
	month = {dec},
	pages = {1128{\textendash}1141},
	keywords = {Arctic, Biogeography, Chaetoceros gelidus sp. nov., Chaetoceros radians, Chaetoceros socialis, Diatom, Distribution, Global, phylogeny, RCC3007},
	issn = {00223646},
	doi = {10.1111/jpy.12121},
	url = {http://doi.wiley.com/10.1111/jpy.12121},
	author = {Chamnansinp, Atchaneey and Li, Yang and Lundholm, Nina and Moestrup, {\O}jvind},
	editor = {Bowler, C.}
}
@article {Guillou2013,
	title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy},
	journal = {Nucleic Acids Research},
	volume = {41},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {D597{\textendash}D604},
	keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1093/nar/gks1160},
	author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard}
}
@article {Balzano2012a,
	title = {Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer},
	journal = {Biogeosciences},
	volume = {9},
	year = {2012},
	note = {tex.mendeley-tags: 2012,macumba,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {4553{\textendash}4571},
	keywords = {2012, ASSEMBLE, MACUMBA, MALINA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.5194/bg-9-4553-2012},
	author = {Balzano, Sergio and Gourvil, Priscillia and Siano, Raffaele and Chanoine, M{\'e}lanie and Marie, Dominique and Lessard, Sylvie and Sarno, Diana and Vaulot, Daniel}
}
@article {Stern2012,
	title = {Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker},
	journal = {PLoS ONE},
	volume = {7},
	year = {2012},
	note = {tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e42780},
	keywords = {2012, ASSEMBLE, Barcoding, ITS, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pone.0042780},
	url = {http://www.plosone.org/article/info\%253Adoi\%252F10.1371\%252Fjournal.pone.0042780},
	author = {Stern, Rowena F and Andersen, Robert A and Jameson, Ian and K{\"u}pper, Frithjof C and Coffroth, Mary-Alice and Vaulot, Daniel and Gall, Florence Le and Veron, Benoit and Brand, Jerry J and Skelton, Hayley and Kasai, Fumai and Lilly, Emily L and Keeling, Patrick J}
}
@article {Giovagnetti2012,
	title = {Growth and photophysiological responses of two picoplanktonic {\textexclamdown}i{\textquestiondown}Minutocellus species{\textexclamdown}/i{\textquestiondown}, strains RCC967 and RCC703 (Bacillariophyceae)},
	journal = {European Journal of Phycology},
	volume = {47},
	number = {4},
	year = {2012},
	note = {ISBN: 0967-0262 tex.mendeley-tags: rcc703,rcc967},
	pages = {408{\textendash}420},
	abstract = {Reaching up to 50\% of the total biomass in oligotrophic waters and armed with a set of ecological and biological properties related to their small size, picophytoplankton ({\textexclamdown}3.0 mm) are a good model to address ecophysiological questions regarding phytoplankton biodiversity. Two picoplanktonic diatoms, one isolated from an upwelling ecosystem in the Pacific Ocean (Minutocellus sp., strain RCC967), and another from oceanic waters in the Indian Ocean (Minutocellus sp., strain RCC703) were used to test hypotheses on the functional relation between ecological niche adaptation and photosynthetic regulation capacity and efficiency. Cultures were subjected to five sine light climates, each one set to peak at a different photon flux density, respectively 10, 50, 100, 250 and 500 mmol photons m(-2) s(-1). Growth rate, photosynthesis, non-photochemical fluorescence quenching, pigment composition, and particulate organic carbon and nitrogen content were followed daily for 5 days. Growth rate and physiological response curves were different in the two species, in agreement with their distinct habitats of origin. Such differences could be related to the diverse photoacclimative strategies displayed by the two species, revealing a clear adaptive divergence despite their close taxonomic relationship. Photoacclimative strategies of the two picoplanktonic diatoms are discussed in the light of functional diversity and ecosystem adaptation.},
	keywords = {carbon, diatoms, elemental stoichiometry, fluctuating light, marine-phytoplankton, non-photochemical fluorescence quenching, phaeodactylum-tricornutum, photoacclimation, photoprotection, photoregulation, Photosynthesis, picoeukaryotes, planktonic diatoms, rcc703, rcc967, RCC?o?dd, violaxanthin cycle, Xanthophyll cycle, xanthophyll-cycle activity},
	doi = {10.1080/09670262.2012.733030},
	author = {Giovagnetti, V and Cataldo, M L and Conversano, F and Brunet, C}
}
@article {Zeng2012,
	title = {Marine viruses exploit their host{\textquoteright}s two-component regulatory system in response to resource limitation},
	journal = {Current Biology},
	year = {2012},
	note = {Publisher: Cell Press tex.mendeley-tags: rcc},
	abstract = {Phosphorus (P) availability, which often limits productivity in marine ecosystems, shapes the P-acquisition gene content of the marine cyanobacteria Prochlorococcus [1 4] and its viruses (cyanophages) [5, 6]. As in other bacteria, in Prochlorococcus these genes are regulated by the PhoR/PhoB two-component regulatory system that is used to sense and respond to P availability and is typical of signal transduction systems found in diverse organisms [7]. Replication of cyanophage genomes requires a significant amount of P, and therefore these phages could gain a fitness advantage by influencing host P acquisition in P-limited environments. Here we show that the transcription of a phage-encoded high-affinity phosphate-binding protein gene (pstS) and alkaline phosphatase gene (phoA) both of which have host orthologs is elevated when the phages are infecting host cells that are P starved, relative to P-replete control cells. We further show that the phage versions of these genes are regulated by the host{\textquoteright}s PhoR/PhoB system. This not only extends this fundamental signaling mechanism to viruses but is also the first example of regulation of lytic phage genes by nutrient limitation in the host. As such, it reveals an important new dimension of the intimate coevolution of phage, host, and environment in the world{\textquoteright}s oceans. {\textordmasculine} Phage production, but not lytic cycle, is reduced in P-starved host cells {\textordmasculine} Transcription of phage P acquisition genes is upregulated in P-starved hosts {\textordmasculine} Phage P-acquisition genes are regulated by the host PhoR/PhoB two-component system {\textordmasculine} This is the first incidence of regulation of virus genes by a two-component system},
	keywords = {NATL2A, rcc, RCC?o?dd},
	doi = {10.1016/j.cub.2011.11.055},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982211013704},
	author = {Zeng, Qinglu and Chisholm, Sallie W}
}
@article {Decelle2012,
	title = {An original mode of symbiosis in open ocean plankton},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	year = {2012},
	note = {tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo},
	pages = {18000{\textendash}18005},
	keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.1212303109},
	author = {Decelle, J and Probert, I and Bittner, L and Desdevises, Y and Colin, S and de Vargas, C and Gali, M and Simo, R and Not, F}
}
@article {Treusch2012,
	title = {Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids},
	journal = {The ISME journal},
	volume = {6},
	year = {2012},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {481{\textendash}492},
	keywords = {Bathycoccus, CHRYSOPHYCEAE, key?aper, Micromonas, Ostreococcus, pelagophyceae, Prasinophyceae, Prymnesiophyceae, QPCR, rcc, TRFLP},
	doi = {10.1038/ismej.2011.117},
	url = {http://dx.doi.org/10.1038/ismej.2011.117 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011117s1.html},
	author = {Treusch, Alexander H and Demir-Hilton, Elif and Vergin, Kevin L and Worden, Alexandra Z and Carlson, Craig A and Donatz, Michael G and Burton, Robert M and Giovannoni, Stephen J}
}
@article {Clerissi2012,
	title = {Prasinoviruses of the marine green alga Ostreococcus tauri are mainly species specific},
	journal = {Journal of Virology},
	volume = {86},
	number = {8},
	year = {2012},
	note = {tex.mendeley-tags: RCC1110,RCC1114,RCC1115,RCC1116,RCC1117,RCC1123,RCC1558,RCC1561,RCC745},
	pages = {4611{\textendash}4619},
	abstract = {Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. ({\textquotedblleft}Ostreococcus mediterraneus{\textquotedblright}) clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla. Thirty-four out of 40 viruses infected only O. tauri, 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants.},
	keywords = {rcc, RCC1110, RCC1114, RCC1115, RCC1116, RCC1117, RCC1123, RCC1558, RCC1561, RCC745},
	issn = {0022-538X},
	doi = {10.1128/jvi.07221-11},
	url = {http://jvi.asm.org/content/86/8/4611.abstract},
	author = {Clerissi, Camille and Desdevises, Yves and Grimsley, Nigel}
}
@article {Thompson2012,
	title = {Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga},
	journal = {Science},
	volume = {337},
	number = {6101},
	year = {2012},
	note = {tex.mendeley-tags: 2012,microb3,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1546{\textendash}1550},
	abstract = {Symbioses between nitrogen (N)2{\textendash}fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation.},
	keywords = {2012, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1126/science.1222700},
	url = {http://www.sciencemag.org/content/337/6101/1546.abstract},
	author = {Thompson, Anne W and Foster, Rachel A and Krupke, Andreas and Carter, Brandon J and Musat, Niculina and Vaulot, Daniel and Kuypers, Marcel M M and Zehr, Jonathan P}
}
@article {Demir-Hilton2011,
	title = {Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus},
	journal = {The ISME journal},
	volume = {5},
	year = {2011},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC745},
	pages = {1095{\textendash}1107},
	keywords = {rcc, RCC745},
	doi = {10.1038/ismej.2010.209},
	url = {http://dx.doi.org/10.1038/ismej.2010.209 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2010209s1.html http://www.nature.com/ismej/journal/v5/n7/full/ismej2010209a.html},
	author = {Demir-Hilton, Elif and Sudek, Sebastian and Cuvelier, Marie L and Gentemann, Chelle L and Zehr, Jonathan P and Worden, Alexandra Z}
}
@article {Bendif2011,
	title = {Integrative taxonomy of the pavlovophyceae (haptophyta) : a reassessment},
	journal = {Protist},
	volume = {162},
	year = {2011},
	note = {tex.mendeley-tags: 2011,RCC1526,RCC1527,RCC1528,RCC1529,RCC1530,RCC1531,RCC1532,RCC1533,RCC1534,RCC1535,RCC1536,RCC1537,RCC1538,RCC1539,RCC1540,RCC1541,RCC1542,RCC1543,RCC1544,RCC1545,RCC1546,RCC1548,RCC1549,RCC1551,RCC1552,RCC1553,RCC1554,RCC1557,rcc,rcc1523,rcc1524,rcc1525},
	pages = {738{\textendash}761},
	abstract = {The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species. Considering the importance of members of this class, we constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity and using type strains when available add on culture strains. Moreover, the morphology and ultrastructure of 12 of the described species was re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova andDiacronema. Unique combinations of morphological/ultrastructural characters were identified foreach of these clades. The ancestral pigment signature of the Pavlovophyceae consisted of a basic set of pigments plus MV chl cPAV, the latter being entirely absent in the Pavlova + Diacronema clade and supplemented by DV chl cPAV in part of the Exanthemachrysis clade. Based on this combination of characters, we propose a taxonomic revision of the class, with transfer of several Pavlova species to an emended Diacronema genus. The evolution of the class is discussed in the context of the phylogenetic reconstruction presented.},
	keywords = {2011, ASSEMBLE, rcc, RCC1523, rcc1524, rcc1525, RCC1526, RCC1527, RCC1528, RCC1529, RCC1530, RCC1531, RCC1532, RCC1533, RCC1534, RCC1535, RCC1536, RCC1537, RCC1538, RCC1539, RCC1540, RCC1541, RCC1542, RCC1543, RCC1544, RCC1545, RCC1546, RCC1548, RCC1549, RCC1551, RCC1552, RCC1553, RCC1554, RCC1557, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1016/j.protis.2011.05.001},
	author = {Bendif, E M and Probert, I and Herv{\'e}, A and Billard, C and Goux, D and Lelong, C and Cadoret, J P and V{\'e}ron, B}
}
@article {Blot2011,
	title = {Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress},
	journal = {Plant Physiology},
	volume = {156},
	year = {2011},
	note = {ISBN: 1532-2548 (Electronic) 0032-0889 (Linking) tex.mendeley-tags: 2011,rcc,sbr?hyto?app},
	pages = {1934{\textendash}1954},
	abstract = {Marine Synechococcus undergo a wide range of environmental stressors, especially high and variable irradiance, which may induce oxidative stress through the generation of reactive oxygen species (ROS). While light and ROS could act synergistically on the impairment of photosynthesis, inducing photodamage and inhibiting photosystem II repair, acclimation to high irradiance is also thought to confer resistance to other stressors. To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the photophysiological and transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H2O2) or methylviologen. While photosynthetic activity was much more affected in HL than in LL cells, only HL cells were able to recover growth and photosynthesis after addition of 25 microM H2O2. Depending upon light conditions and H2O2 concentration, the latter oxidizing agent induced photosystem II inactivation through both direct damages to the reaction centres and inhibition of its repair cycle. Although the global transcriptome response appeared similar in LL and HL cells, some processes were specifically induced in HL cells that seemingly helped them withstand oxidative stress, including enhancement of photoprotection and ROS detoxification, repair of ROS-driven damages and regulation of redox state. Detection of putative LexA binding sites allowed the identification of the putative LexA regulon, which was down-regulated in HL compared to LL cells, but up-regulated by oxidative stress under both growth irradiances.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21670225},
	author = {Blot, N and Mella-Flores, D and Six, C and Lecorguille, G and Boutte, C and Peyrat, A and Monnier, A and Ratin, M and Gourvil, P and Campbell, D A and Garczarek, L}
}
@article {Gobler2011,
	title = {Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {108},
	number = {11},
	year = {2011},
	note = {ISBN: 0027-8424 tex.mendeley-tags: RCC,rcc},
	pages = {4352{\textendash}4357},
	abstract = {Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.},
	keywords = {brown-tide blooms, comparative genomics, eutrophication, evolution, genome, genomics, long-island, marine-phytoplankton, multidrug, proteins, proteome, rcc, repeat, responses, san-francisco bay, signal-transduction, transporters},
	doi = {10.1073/pnas.1016106108},
	author = {Gobler, C J and Berry, D L and Dyhrman, S T and Wilhelm, S W and Salamov, A and Lobanov, A V and Zhang, Y and Collier, J L and Wurch, L L and Kustka, A B and Dill, B D and Shah, M and VerBerkmoes, N C and Kuo, A and Terry, A and Pangilinan, J and Lindquist, E A and Lucas, S and Paulsen, I T and Hattenrath-Lehmann, T K and Talmage, S C and Walker, E A and Koch, F and Burson, A M and Marcoval, M A and Tang, Y Z and LeCleir, G R and Coyne, K J and Berg, G M and Bertrand, E M and Saito, M A and Gladyshev, V N and Grigoriev, I V}
}
@article {Beaufort2011,
	title = {Sensitivity of coccolithophores to carbonate chemistry and ocean acidification},
	journal = {Nature},
	volume = {476},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {80{\textendash}83},
	abstract = {Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from {\textquestiondown}700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH {\textexclamdown}8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1038/nature10295},
	author = {Beaufort, L and Probert, I and de Garidel-Thoron, T and Bendif, E M and Ruiz-Pino, D and Metzl, N and Goyet, C and Buchet, N and Coupel, P and Grelaud, M and Rost, B and Rickaby, R E M and de Vargas, C}
}
@article {Foresi2010,
	title = {Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent},
	journal = {The Plant Cell},
	volume = {22},
	number = {11},
	year = {2010},
	note = {Edition: 2010/12/02 ISBN: 1532-298X (Electronic) 1040-4651 (Linking) tex.mendeley-tags: RCC745},
	pages = {3816{\textendash}3830},
	abstract = {The search for a nitric oxide synthase (NOS) sequence in the plant kingdom yielded two sequences from the recently published genomes of two green algae species of the Ostreococcus genus, O. tauri and O. lucimarinus. In this study, we characterized the sequence, protein structure, phylogeny, biochemistry, and expression of NOS from O. tauri. The amino acid sequence of O. tauri NOS was found to be 45\% similar to that of human NOS. Folding assignment methods showed that O. tauri NOS can fold as the human endothelial NOS isoform. Phylogenetic analysis revealed that O. tauri NOS clusters together with putative NOS sequences of a Synechoccocus sp strain and Physarum polycephalum. This cluster appears as an outgroup of NOS representatives from metazoa. Purified recombinant O. tauri NOS has a K(m) for the substrate l-Arg of 12 +/- 5 muM. Escherichia coli cells expressing recombinant O. tauri NOS have increased levels of NO and cell viability. O. tauri cultures in the exponential growth phase produce 3-fold more NOS-dependent NO than do those in the stationary phase. In O. tauri, NO production increases in high intensity light irradiation and upon addition of l-Arg, suggesting a link between NOS activity and microalgal physiology.},
	keywords = {*Light, Amino Acid Sequence, Animals, Base Sequence, Chlorophyta/*enzymology/*growth \& development/phys, Humans, Isoenzymes/chemistry/genetics/metabolism, Models, Molecular, Molecular Sequence Data, Nitric Oxide Synthase/chemistry/genetics/*metaboli, Nitric Oxide/*biosynthesis, phylogeny, Plant Proteins/genetics/*metabolism, Protein Structure, rcc, RCC745, Sequence Alignment, Tertiary},
	doi = {10.1105/tpc.109.073510},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21119059},
	author = {Foresi, N and Correa-Aragunde, N and Parisi, G and Calo, G and Salerno, G and Lamattina, L}
}
@article {Frada2010,
	title = {A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy.},
	journal = {Journal of Nannoplankton Research},
	volume = {31},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {58{\textendash}112},
	keywords = {2010, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	author = {Frada, Miguel and Young, Jeremy and Cach{\~a}o, M{\'a}rio and Lino, S{\'\i}lvia and Martins, Ana and Narciso, {\'A}urea and Probert, Ian and de Vargas, Colomban}
}
@article {Moreau2010,
	title = {Marine Prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer},
	journal = {Journal of Virology},
	volume = {84},
	number = {24},
	year = {2010},
	note = {ISBN: 0022-538X tex.mendeley-tags: RCC1105,RCC745},
	pages = {12555{\textendash}12563},
	abstract = {Although marine picophytoplankton are at the base of the global food chain, accounting for half of the planetary primary production, they are outnumbered 10 to 1 and are largely controlled by hugely diverse populations of viruses. Eukaryotic microalgae form a ubiquitous and particularly dynamic fraction of such plankton, with environmental clone libraries from coastal regions sometimes being dominated by one or more of the three genera Bathycoccus, Micromonas, and Ostreococcus (class Prasinophyceae). The complete sequences of two double-stranded (dsDNA) Bathycoccus, one dsDNA Micromonas, and one new dsDNA Ostreococcus virus genomes are described. Genome comparison of these giant viruses revealed a high degree of conservation, both for orthologous genes and for synteny, except for one 36-kb inversion in the Ostreococcus lucimarinus virus and two very large predicted proteins in Bathycoccus prasinos viruses. These viruses encode a gene repertoire of certain amino acid biosynthesis pathways never previously observed in viruses that are likely to have been acquired from lateral gene transfer from their host or from bacteria. Pairwise comparisons of whole genomes using all coding sequences with homologous counterparts, either between viruses or between their corresponding hosts, revealed that the evolutionary divergences between viruses are lower than those between their hosts, suggesting either multiple recent host transfers or lower viral evolution rates.},
	keywords = {RCC1105, RCC745},
	doi = {10.1128/jvi.01123-10},
	author = {Moreau, Herv{\'e} and Piganeau, Gwenael and Desdevises, Yves and Cooke, Richard and Derelle, Evelyne and Grimsley, Nigel}
}
@article {Mohr2010,
	title = {A new chlorophyll d -containing cyanobacterium : evidence for niche adaptation in the genus Acaryochloris},
	journal = {The ISME journal},
	year = {2010},
	note = {tex.mendeley-tags: RCC,RCC1983,rcc},
	pages = {1456{\textendash}1469},
	abstract = {Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (231 260 31.200 S, 1511 540 50.400 E). The 16S ribosomal RNA is 2\% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371965nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms. The},
	keywords = {acaryochloris, chlorophyll d, coral reef, cyanobacteria, microbial diversity, overview, rcc, RCC1983},
	doi = {10.1038/ismej.2010.67},
	author = {Mohr, Remus and Schliep, Martin and Kurz, Thorsten and Maldener, Iris and Adams, David G and Larkum, Anthony D W and Chen, Min and Hess, Wolfgang R}
}
@article {Liu2009,
	title = {Extreme diversity in noncalcifying haptophytes explains a major pigment paradox in open oceans},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {106},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {12803{\textendash}12808},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.0905841106},
	author = {Liu, H and Probert, I and Uitz, J and Claustre, H and Aris-Brossou, S and Frada, M and Not, F and de Vargas, C}
}
@article {Worden2009,
	title = {Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas},
	journal = {Science},
	volume = {324},
	year = {2009},
	note = {tex.mendeley-tags: RCC299,RCC827},
	pages = {268{\textendash}272},
	abstract = {The photosynthetic picoeukaryote Micromonas thrives from tropical to polar marine ecosystems and belongs to an anciently diverged sister clade to land plants. We sequenced genomes from two Micromonas isolates (22 Mb, CCMP1545; 21 Mb, RCC299) and the results improve understanding of their ecology and green-lineage evolution. Despite high 18S rDNA sequence identity, only 90\% of their predicted genes were shared. Novel intronic repeat elements in CCMP1545, otherwise found only in metagenomic data, and unique riboswitch arrangements emphasized their independent evolutionary paths. Phylogenomic profiles revealed putative ancestral features, but also indicated selection/acquisition processes are actively shaping a {\textquoteleft}unique{\textquoteright} gene pool in each differently than {\textquoteleft}core{\textquoteright} genes. Current climate-change trajectories are predicted to produce conditions favoring picophytoplankton, making Micromonas potential indicators of biological change in ocean ecosystems.},
	keywords = {rcc, RCC299, RCC827, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1126/science.1167222},
	author = {Worden, A Z and Lee, J.- H and Mock, T and Rouz{\'e}, P and Simmons, M P and Aerts, A L and Allen, A E and Cuvelier, M L and Derelle, E and Everett, M V and Foulon, E and Grimwood, J and Gundlach, H and Henrissat, B and Napoli, C and McDonald, S M and Parker, M S and Rombauts, S and Salamov, A and Von Dassow, P and Badger, J H and Coutinho, P M and Demir, E and Dubchak, I and Gentemann, C and Eikrem, W and Gready, J E and John, U and Lanier, W and Lindquist, E A and Lucas, S and Mayer, K F X and Moreau, H and Not, F and Otillar, R and Panaud, O and Pangilinan, J and Paulsen, I and Piegu, B and Poliakov, A and Robbens, S and Schmutz, J and Toulza, E and Wyss, T and Zelensky, A and Zhou, K and Armbrust, E V and Bhattacharya, D and Goodenough, U W and Van de Peer, Y and Grigoriev, I V}
}
@article {Monier2009,
	title = {Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus},
	journal = {Genome Research},
	volume = {19},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {1441{\textendash}1449},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1101/gr.091686.109},
	author = {Monier, A and Pagarete, A and Allen, M J and Read, B A and de Vargas, C and Claverie, J M and Ogata, H}
}
@article {Six2009,
	title = {Photosystem II and pigment dynamics among ecotypes of the green alga Ostreococcus},
	journal = {Plant Physiology},
	volume = {151},
	year = {2009},
	note = {tex.mendeley-tags: RCC809},
	pages = {379{\textendash}390},
	abstract = {We investigated the photophysiological response of three ecotypes of the picophytoplankter Ostreococcus and a larger prasinophyte Pyramimonas obovata to a sudden increase in light irradiance. The deepwater Ostreococcus sp. RCC809 showed very high susceptibility to primary photoinactivation, likely a consequence of high oxidative stress, which may relate to the recently noted plastid terminal oxidase activity in this strain. The three Ostreococcus ecotypes were all able of deploying modulation of photosystem II repair cycle in order to cope with the light increase, but the effective clearance of photoinactivated D1 protein appeared to be slower in the deep water Ostreococcus sp. RCC809, suggesting that this step is rate-limiting in the photosystem II repair cycle in this strain. The deepwater Ostreococcus moreover accumulated lutein and showed substantial use of the xanthophyll cycle under light stress, demonstrating its high sensitivity to light fluctuations. The sustained component of the non-photochemical quenching of fluorescence correlated well with the xanthophyll de-epoxidation activity. Comparisons with the larger prasinophyte Pyramimonas obovata suggest that the photophysiology of Ostreococcus ecotypes requires high photosystem II repair rates to counter a high susceptibility to photoinactivation, consistent with low pigment package effects in their minute-sized cells.},
	keywords = {rcc, RCC809, SBR$_\textrmP$hyto$_\textrmP$PM},
	doi = {10.1104/pp.109.140566},
	author = {Six, C and Sherrard, R and Lionard, M and Roy, S and Campbell, D A}
}
@article {VonDassow2009,
	title = {Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell},
	journal = {Genome Biology},
	volume = {10},
	number = {10},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,rcc1216,rcc1217,sbr?hyto?ppo},
	pages = {R114},
	abstract = {BACKGROUND:Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38000 Expressed Sequence Tags (ESTs) from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism.RESULTS:The haploid and diploid transcriptomes showed a dramatic differentiation, with [almost equal to]20\% greater transcriptome richness in diploid cells than in haploid cells and only [less than or equal to]50\% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog.CONCLUSIONS:This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined.},
	keywords = {2009, rcc, RCC1216, rcc1217, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1186/gb-2009-10-10-r114},
	url = {http://genomebiology.com/2009/10/10/R114},
	author = {von Dassow, Peter and Ogata, Hiroyuki and Probert, Ian and Wincker, Patrick and Da Silva, Corinne and Audic, St{\'e}phane and Claverie, Jean-Michel and de Vargas, Colomban}
}
@article {Six2008,
	title = {Contrasting photoacclimation strategies in ecotypes of the eukayotic picoplankter {\textexclamdown}i{\textquestiondown}Ostreococcus{\textexclamdown}/i{\textquestiondown}},
	journal = {Limnology and Oceanography},
	volume = {53},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {255{\textendash}265},
	abstract = {Ostreococcus, the smallest known marine picoeukaryote, includes low- and high-light ecotypes. To determine the basis for niche partitioning between Ostreococcus sp. RCC809, isolated from the bottom of the tropical Atlantic euphotic zone, and the lagoon strain Ostreococcus tauri, we studied their photophysiologies under growth irradiances from 15 mmol photons m22 s21 to 800 mmol photons m22 s21 with a common nutrient replete regime. With increasing growth irradiance, both strains down-regulated cellular chlorophyll a and chlorophyll b (Chl a and Chl b) content, increased xanthophyll de-epoxidation correlated with nonphotochemical excitation quenching, and accumulated lutein. Ribulose-1,5-bisphosphate carboxylase/oxygenase content remained fairly stable. Under low-growth irradiances of 15{\textendash}80 mmol photons m22 s21, O. sp. RCC809 had equivalent or slightly higher growth rates, lower Chl a, a higher Chl b : Chl a ratio, and a larger photosystem II (PSII) antenna than O. tauri. O. tauri was more phenotypically plastic in response to growth irradiance, with a larger dynamic range in growth rate, Chl a, photosystem cell content, and cellular absorption cross-section of PSII. Estimating the amino acid and nitrogen costs for photoacclimation showed that the deep-sea oceanic O. sp. RCC809 relies largely on lower nitrogen cost changes in PSII antenna size to achieve a limited range of s-type light acclimation. O. sp. RCC809, however, suffers photoinhibition under higher light. This limited capacity for photoacclimation is compatible with the stable low-light and nutrient conditions at the base of the euphotic layer of the tropical Atlantic Ocean. In the more variable, high-nutrient, lagoon environment, O. tauri can afford to use a higher cost n-type acclimation of photosystem contents to exploit a wider range of light.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.4319/lo.2008.53.1.0255},
	author = {Six, C and Finkel, Z V and Rodriguez, F and Marie, D and Partensky, F and Campbell, D A}
}
@article {Foulon2008,
	title = {Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes},
	journal = {Environmental Microbiology},
	volume = {10},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {2433{\textendash}2443},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1111/j.1462-2920.2008.01673.x},
	author = {Foulon, E and Not, F and Jalabert, F and Cariou, T and Massana, R and Simon, N}
}
@article {Claquin2008,
	title = {Effects of temperature on photosynthetic parameters and TEP production in eight species of marine microalgae},
	journal = {Aquatic Microbial Ecology},
	volume = {51},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc},
	pages = {1{\textendash}11},
	keywords = {2008, rcc, SBR$_\textrmP$hyto},
	doi = {10.3354/ame01187},
	author = {Claquin, Pascal and Probert, Ian and Lefebvre, S{\'e}bastien and Veron, Benoit}
}
@article {Derelle2008,
	title = {Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga {\textexclamdown}i{\textquestiondown}Ostreococcus tauri{\textexclamdown}/i{\textquestiondown}},
	journal = {PLoS ONE},
	volume = {3},
	number = {5},
	year = {2008},
	note = {Publisher: Public Library of Science tex.mendeley-tags: RCC,rcc},
	pages = {e2250},
	abstract = {Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.},
	keywords = {rcc},
	doi = {10.1371/journal.pone.0002250},
	url = {http://dx.doi.org/10.1371/journal.pone.0002250},
	author = {Derelle, Evelyne and Ferraz, Conchita and Escande, Marie-Line and Eycheni{\'e}, Sophie and Cooke, Richard and Piganeau, Gwenael and Desdevises, Yves and Bellec, Laure and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Cardol2008,
	title = {An original adaptation of photosynthesis in the marine green alga Ostreococcus},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	number = {22},
	year = {2008},
	note = {tex.mendeley-tags: RCC745,RCC809},
	pages = {7881{\textendash}7886},
	abstract = {Adaptation of photosynthesis in marine environment has been examined in two strains of the green, picoeukaryote : OTH95, a surface/high-light strain, and RCC809, a deep-sea/low-light strain. Differences between the two strains include changes in the light-harvesting capacity, which is lower in OTH95, and in the photoprotection capacity, which is enhanced in OTH95. Furthermore, RCC809 has a reduced maximum rate of O evolution, which is limited by its decreased photosystem I (PSI) level, a possible adaptation to Fe limitation in the open oceans. This decrease is, however, accompanied by a substantial rerouting of the electron flow to establish an HO-to-HO cycle, involving PSII and a potential plastid plastoquinol terminal oxidase. This pathway bypasses electron transfer through the cytochrome complex and allows the pumping of {\^a}{\texteuro}{\oe}extra{\^a}{\texteuro} protons into the thylakoid lumen. By promoting the generation of a large {\^I}{\textquotedblright}pH, it facilitates ATP synthesis and nonphotochemical quenching when RCC809 cells are exposed to excess excitation energy. We propose that the diversion of electrons to oxygen downstream of PSII, but before PSI, reflects a common and compulsory strategy in marine phytoplankton to bypass the constraints imposed by light and/or nutrient limitation and allow successful colonization of the open-ocean marine environment.},
	keywords = {rcc, RCC745, RCC809},
	doi = {10.1073/pnas.0802762105},
	url = {http://www.pnas.org/content/105/22/7881.abstract},
	author = {Cardol, Pierre and Bailleul, Benjamin and Rappaport, Fabrice and Derelle, Evelyne and Baal, Daniel and Breyton, C{\'e}cile and Bailey, Shaun and Wollman, Francis Andr{\'e} and Grossman, Arthur and Moreau, Herv{\'e} and Finazzi, Giovanni}
}
@article {Fountain2008,
	title = {Permeation properties of a P2X receptor in the green algae Ostreococcus tauri},
	journal = {Journal of Biological Chemistry},
	volume = {283},
	number = {22},
	year = {2008},
	note = {ISBN: 0021-9258 tex.mendeley-tags: RCC,rcc},
	pages = {15122{\textendash}15126},
	abstract = {We have cloned a P2X receptor (OtP2X) from the green algae Ostreococcus tauri. The 42-kDa receptor shares similar to 28\% identity with human P2X receptors and 23\% with the Dictyostelium P2X receptor. ATP application evoked flickery single channel openings in outside-out membrane patches from human embryonic kidney 293 cells expressing OtP2X. Whole-cell recordings showed concentration-dependent cation currents reversing close to zero mV; ATP gave a half-maximal current at 250 mu m. alpha beta-Methylene-ATP evoked only small currents in comparison to ATP (EC50 {\textquestiondown} 5 mM). 2{\textquoteright},3{\textquoteright}-O-(4-Benzoylbenzoyl)-ATP, beta gamma-imido-ATP, ADP, and several other nucleotide triphosphates did not activate any current. The currents evoked by 300 mu m ATP were not inhibited by 100 mu m suramin, pyridoxal-phosphate-6-azophenyl-2{\textquoteright},4{\textquoteright}-disulfonic acid, 2{\textquoteright},3{\textquoteright}-O-(2,4,6-trinitrophenol)-ATP, or copper. Ion substitution experiments indicated permeabilities relative to sodium with the rank order calcium {\textquestiondown} choline {\textquestiondown} Tris {\textquestiondown} tetraethylammonium {\textquestiondown} N-methyl-D-glucosamine. However, OtP2X had a low relative calcium permeability (P-Ca/P-Na = 0.4) in comparison with other P2X receptors. This was due at least in part to the presence of an asparagine residue (Asn(353)) at a position in the second transmembrane domain in place of the aspartate that is completely conserved in all other P2X receptor subunits, because replacement of Asn(353) with aspartate increased calcium permeability by similar to 50\%. The results indicate that the ability of ATP to gate cation permeation across membranes exists in cells that diverged in evolutionary terms from animals about I billion years ago.},
	keywords = {CELLS, CHANNELS, EXTRACELLULAR ATP, FAMILY, FUNCTIONAL-CHARACTERIZATION, PERMEABILITY, PHARMACOLOGY, rcc},
	doi = {10.1074/jbc.M801512200},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2397467},
	author = {Fountain, S J and Cao, L S and Young, M T and North, R A}
}
@article {Bowler2008,
	title = {The Phaeodactylum genome reveals the evolutionary history of diatom genomes},
	journal = {Nature},
	volume = {456},
	number = {7219},
	year = {2008},
	note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo},
	pages = {239{\textendash}244},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPOdipo, sbr?hyto?ppo},
	doi = {10.1038/nature07410},
	url = {http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html},
	author = {Bowler, Chris and Allen, Andrew E and Badger, Jonathan H and Grimwood, Jane and Jabbari, Kamel and Kuo, Alan and Maheswari, Uma and Martens, Cindy and Maumus, Florian and Otillar, Robert P and Rayko, Edda and Salamov, Asaf and Vandepoele, Klaas and Beszteri, Bank and Gruber, Ansgar and Heijde, Marc and Katinka, Michael and Mock, Thomas and Valentin, Klaus and Verret, Frederic and Berges, John A and Brownlee, Colin and Cadoret, Jean-Paul and Chiovitti, Anthony and Choi, Chang Jae and Coesel, Sacha and De Martino, Alessandra and Detter, J Chris and Durkin, Colleen and Falciatore, Angela and Fournet, Jerome and Haruta, Miyoshi and Huysman, Marie J J and Jenkins, Bethany D and Jiroutova, Katerina and Jorgensen, Richard E and Joubert, Yolaine and Kaplan, Aaron and Kroger, Nils and Kroth, Peter G and La Roche, Julie and Lindquist, Erica and Lommer, Markus and Martin-Jezequel, Veronique and Lopez, Pascal J and Lucas, Susan and Mangogna, Manuela and McGinnis, Karen and Medlin, Linda K and Montsant, Anton and Secq, Marie-Pierre Oudot-Le and Napoli, Carolyn and Obornik, Miroslav and Parker, Micaela Schnitzler and Petit, Jean-Louis and Porcel, Betina M and Poulsen, Nicole and Robison, Matthew and Rychlewski, Leszek and Rynearson, Tatiana A and Schmutz, Jeremy and Shapiro, Harris and Siaut, Magali and Stanley, Michele and Sussman, Michael R and Taylor, Alison R and Vardi, Assaf and von Dassow, Peter and Vyverman, Wim and Willis, Anusuya and Wyrwicz, Lucjan S and Rokhsar, Daniel S and Weissenbach, Jean and Armbrust, E Virginia and Green, Beverley R and Van de Peer, Yves and Grigoriev, Igor V}
}
@article {Kettler2007,
	title = {Patterns and implications of gene gain and loss in the evolution of Prochlorococcus},
	journal = {PLoS genetics},
	volume = {3},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {e231},
	keywords = {rcc},
	doi = {10.1371/journal.pgen.0030231},
	author = {Kettler, G and Martiny, A C and Huang, K and Zucker, J and Coleman, M L and Rodrigue, S and Chen, F and Lapidus, A and Ferriera, S and Johnson, J and Steglich, C and Church, G and Richardson, P and Chisholm, S W}
}
@article {Dimier2007,
	title = {Photophysiological properties of the marine picoeukaryote Picochlorum RCC 237 (Trebouxiophyceae, Chlorophyta)},
	journal = {Journal of Phycology},
	volume = {43},
	number = {2},
	year = {2007},
	note = {ISBN: 0022-3646 tex.mendeley-tags: RCC,rcc},
	pages = {275{\textendash}283},
	abstract = {The photophysiological properties of strain RCC 237 belonging to the marine picoplanktonic genus Picochlorum, first described by Henley et al., were investigated under different photon flux densities (PFD), ranging from 40 to 400 mu mol photons. m(-2).s(-1), mainly focusing on the development of the xanthophyll cycle and its relationship with the nonphotochemical quenching of fluorescence (NPQ). The functioning of the xanthophyll cycle and its photoprotective role was investigated by applying a progressive increase of PFD and using dithiotreitol and norflurazon to block specific enzymatic reactions in order to study in depth the relationship between xanthophyll cycle and NPQ. These two processes were significantly related only during the gradually increasing light periods and not during stable light periods, where NPQ and zeaxanthin were decoupled. This result reveals that NPQ is a photoprotective process developed by algae only when cells are experiencing increasing PFD or in response to stressful light variations, for instance after a sudden light shift. Results showed that the photobiological properties of Picochlorum strain RCC 237 seem to be well related to the surface water characteristics, as it is able to maintain its photosynthetic characteristics under different PFDs and to quickly activate the xanthophyll cycle under high light.},
	keywords = {A FLUORESCENCE, CHLAMYDOMONAS-REINHARDTII, DIATOM PHAEODACTYLUM-TRICORNUTUM, ENERGY-DISSIPATION, fluctuating light, fluorescence quantum yield, MANTONIELLA-SQUAMATA, nonphotochemical quenching of fluorescence, photoacclimation, PHOTOSYNTHETIC APPARATUS, picoplankton, POOL SIZE, rcc, VIOLAXANTHIN DE-EPOXIDASE, Xanthophyll cycle, XANTHOPHYLL-CYCLE, zeaxanthin},
	doi = {10.1111/j.1529-8817.2007.00327.x},
	author = {Dimier, C and Corato, F and Saviello, G and Brunet, C}
}
@article {Khan2007,
	title = {Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny},
	journal = {Molecular Biology and Evolution},
	volume = {24},
	number = {8},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1832{\textendash}1842},
	abstract = {Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other{\textquoteright}s closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.},
	keywords = {*DNA Replication, *Gene Transfer, *Genome, Bacteria/*genetics, Cryptophyta/*genetics, DNA, evolution, genes, Horizontal, Molecular, phylogeny, Plant, Plastids/*genetics, rcc, Sequence Analysis, symbiosis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17522086},
	author = {Khan, H and Parks, N and Kozera, C and Curtis, B A and Parsons, B J and Bowman, S and Archibald, J M}
}
@article {Countway2006,
	title = {Abundance and distribution of Ostreococcus sp in the San Pedro Channel, California, as revealed by quantitative PCR},
	journal = {Applied and Environmental Microbiology},
	volume = {72},
	number = {4},
	year = {2006},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {2496{\textendash}2506},
	abstract = {Ostreococcus is a genus of widely distributed marine phytoplankton which are picoplanktonic in size ({\textexclamdown} 2 mu m) and capable of rapid growth. Although Ostreococcus has been detected around the world, little quantitative information exists on its contribution to planktonic communities. We designed and implemented a genus-specific TaqMan-based quantitative PCR (qPCR) assay to investigate the dynamics and ecology of Ostreococcus at the USC Microbial Observatory (eastern North Pacific). Samples were collected from 5 m and the deep chlorophyll maximum (DCM) between September 2000 and August 2002. Ostreococcus abundance at 5 m was generally {\textexclamdown} 5.0 X 10(3) cells ml(-1), with a maximum of 8.2 X 10(4) cells ml(-1). Ostreococcus abundance was typically higher at the DCM, with a maximum of 3.2 X 10(5) cells ml(-1). The vertical distribution of Ostreococcus was examined in March 2005 and compared to the distribution of phototrophic picoeukaryotes (PPE) measured by flow cytometry. The largest contribution to PPE abundance by Ostreococcus was similar to 70\% and occurred at 30 m, near the DCM. Despite its relatively low abundance, the depth-integrated standing stock of Ostreococcus in March 2005 was similar to 30 mg C m(-2). Our work provides a new technique for quantifying the abundance of Ostreococcus and demonstrates the seasonal dynamics of this genus and its contribution to picoeukaryote biomass at our coastal sampling station.},
	keywords = {16s-ribosomal-rna, Biology-, english-channel, eukaryotic-picoplankton, in-situ-hybridization, marine-ecosystems, microbial-populations, microbiology-, Micromonas, pfiesteria-piscicida, rcc, Real-time-pcr, sp-nov, tauri-chlorophyta},
	doi = {10.1128/AEM.72.4.2496-2506.2006},
	author = {Countway, P D and Caron, D A}
}
@article {Fuller2006,
	title = {Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids},
	journal = {Aquatic Microbial Ecology},
	volume = {43},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {79{\textendash}93},
	keywords = {2006, PICOCEAN, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.3354/ame043079},
	author = {Fuller, Nicholas J and Campbell, Colin and Allen, David J and Pitt, Frances D and Le Gall, F and Vaulot, Daniel and Scanlan, David J}
}
@article {Derelle2006,
	title = {Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {31},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {11647{\textendash}11652},
	abstract = {The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world{\textquoteright}s smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1073/pnas.0604795103},
	url = {http://www.pnas.org/cgi/content/abstract/103/31/11647},
	author = {Derelle, Evelyne and Ferraz, Conchita and Rombauts, Stephane and Rouze, Pierre and Worden, Alexandra Z and Robbens, Steven and Partensky, Fr{\'e}d{\'e}ric and Degroeve, Sven and Echeynie, Sophie and Cooke, Richard and Saeys, Yvan and Wuyts, Jan and Jabbari, Kamel and Bowler, Chris and Panaud, Olivier and Piegu, Benoit and Ball, Steven G and Ral, Jean-Philippe and Bouget, Fran{\c c}ois-Yves and Piganeau, Gwenael and De Baets, Bernard and Picard, Andr{\'e} and Delseny, Michel and Demaille, Jacques and Van de Peer, Yves and Moreau, Herv{\'e}}
}
@article {Bruyant2005,
	title = {Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: combined effects of light and cell cycle},
	journal = {Limnology and Oceanography},
	volume = {50},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {850{\textendash}863},
	keywords = {2005, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.4319/lo.2005.50.3.0850},
	author = {Bruyant, F and Babin, M and Genty, B and Prasil, O and Behrenfeld, M J and Claustre, H and Bricaud, A and Holtzendorff, J and Koblizek, M and Garczareck, L and Partensky, F}
}
@article {Robbens2005,
	title = {Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {3},
	year = {2005},
	note = {tex.mendeley-tags: RCC745},
	pages = {589{\textendash}597},
	abstract = {The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms.},
	keywords = {Anaphase Promoting Complex, Arabidopsis Thaliana, Cdk Activity, cell division cycle, Chlorophyta, cyclin, cyclin dependant kinase, Green alga, Kinase, Ostreococcus tauri, Plant, Prasinophyceae, rcc, RCC745, Retinoblastoma Protein, Saccharomyces Cerevisiae, Yeast},
	doi = {10.1093/molbev/msi044},
	author = {Robbens, S and Khadaroo, B and Camasses, A and Derelle, E and Ferraz, C and Inze, D and Van, de Peer Y and Moreau, H}
}
@article {Guillou2004,
	title = {Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems},
	journal = {Protist},
	volume = {155},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {193{\textendash}214},
	keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SOMLIT},
	doi = {10.1078/143446104774199592},
	author = {Guillou, Laure and Eikrem, W and Chr{\'e}tiennot-Dinet, M.-J. and Le Gall, F and Massana, R and Romari, K and Pedr{\'o}s-Ali{\'o}, C and Vaulot, D}
}
@article {Ral2004,
	title = {Starch division and partitioning. A mechanism for granule propagation and maintenance in the picophytoplanktonic green alga Ostreococcus tauri},
	journal = {Plant Physiology},
	volume = {136},
	number = {2},
	year = {2004},
	note = {tex.mendeley-tags: RCC745},
	pages = {3333{\textendash}3340},
	abstract = {Whereas Glc is stored in small-sized hydrosoluble glycogen particles in archaea, eubacteria, fungi, and animal cells, photosynthetic eukaryotes have resorted to building starch, which is composed of several distinct polysaccharide fractions packed into a highly organized semicrystalline granule. In plants, both the initiation of polysaccharide synthesis and the nucleation mechanism leading to formation of new starch granules are currently not understood. Ostreococcus tauri, a unicellular green alga of the Prasinophyceae family, defines the tiniest eukaryote with one of the smallest genomes. We show that it accumulates a single starch granule at the chloroplast center by using the same pathway as higher plants. At the time of plastid division, we observe elongation of the starch and division into two daughter structures that are partitioned in each newly formed chloroplast. These observations suggest that in this system the information required to initiate crystalline polysaccharide growth of a new granule is contained within the preexisting polysaccharide structure and the design of the plastid division machinery.},
	keywords = {Adp Glucose Pyrophosphorylase, Amylopectin, Arabidopsis, Bacterial Glycogen, Biogenesis, Biosynthesis, Chlamydomonas Reinhardtii, Enzyme, Prasinophyceae, rcc, RCC745, Synthase},
	doi = {10.1104/pp.104.044131},
	author = {Ral, J P and Derelle, E and Ferraz, C and Wattebled, F and Farinas, B and Corellou, F and Buleon, A and Slomianny, M C and Delvalle, D and D, Hulst C and Rombauts, S and Moreau, H and Ball, S}
}
@article {Palenik2003,
	title = {The genome of a motile marine Synechococcus},
	journal = {Nature},
	volume = {424},
	number = {6952},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {1037{\textendash}1042},
	abstract = {Marine unicellular cyanobacteria are responsible for an estimated 20-40\% of chlorophyll biomass and carbon fixation in the oceans(1). Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria(2).},
	keywords = {2003, Cyanobacterium Synechococcus, Degradation, Ecology, Gene, IDENTIFICATION, Polypeptide, Prochlorococcus, rcc, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, Sp Pcc7942, Strains},
	doi = {10.1038/nature01943},
	author = {Palenik, B and Brahamsha, B and Larimer, F W and Land, M and Hauser, L and Chain, P and Lamerdin, J and Regala, W and Allen, E E and McCarren, J and Paulsen, I and Dufresne, A and Partensky, F and Webb, E A and Waterbury, J}
}
@article {Derelle2002,
	title = {DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): The smallest free-living eukaryotic cell},
	journal = {Journal of Phycology},
	volume = {38},
	number = {6},
	year = {2002},
	note = {tex.mendeley-tags: RCC745},
	pages = {1150{\textendash}1156},
	abstract = {Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free-living eukaryotic cells, and we showed by pulsed-field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18-fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12\% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome.},
	keywords = {Pico$_\textrmR$eview, rcc, RCC745},
	doi = {10.1046/j.1529-8817.2002.02021.x},
	url = {c:\%5CDV\%5CPapers reprints\%5CPhytoplankton Physiology\%5CDerelle Ostreococcus DNA libraries JPhycol 02.pdf},
	author = {Derelle, E and Ferraz, C and Lagoda, P and Eychenie, S and Cooke, R and Regad, F and Sabau, X and Courties, C and Delseny, M and Demaille, J and Picard, A and Moreau, H}
}
@article {Rocap2002,
	title = {Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences},
	journal = {Applied and Environmental Microbiology},
	volume = {68},
	number = {3},
	year = {2002},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1180{\textendash}1191},
	abstract = {Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96\% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world{\textquoteright}s oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.},
	keywords = {Divinyl Chlorophyll a, genetic diversity, Marine Cyanobacterium Synechococcus, Multiple Evolutionary Origins, North Atlantic, Nucleotide Sequence, rcc, Region, Rna Operon, sargasso sea, Water Column},
	doi = {10.1128/AEM.68.3.1180-1191.2002},
	author = {Rocap, G and Distel, D L and Waterbury, J B and Chisholm, S W}
}
@article {Jacquet2001,
	title = {Cell cycle regulation by light in Prochlorococcus strains},
	journal = {Applied and Environmental Microbiology},
	volume = {67},
	number = {2},
	year = {2001},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {782{\textendash}790},
	abstract = {<p>The effect of light on the synchronization of cell cycling was investigated in several strains of the oceanic photosynthetic prokaryote Prochlorococcus using flow cytometry. When exposed to a light-dark (L-D) cycle with an irradiance of 25 mu mol of quanta m(-2) s(-1), the low-light-adapted strain SS 120 appeared to be better synchronized than the high-light-adapted strain PCC 9511. Submitting LD-entrained populations to shifts (advances or delays) in the timing of the "light on" signal translated to corresponding shifts in the initiation of the S phase, suggesting that this signal is a key parameter for the synchronization of population cell cycles. Cultures that were shifted from an L-D cycle to continuous irradiance showed persistent diel oscillations of flow-cytometric signals (light scatter and chlorophyll fluorescence) but with significantly reduced amplitudes and a phase shift. Complete darkness arrested most of the cells in the G(1), phase of the cell cycle, indicating that light is required to trigger the initiation of DNA replication and cell division. However, some cells also arrested in the S phase, suggesting that cell cycle controls in Prochlorococcus spp. are not as strict as in marine Synechococcus spp. Shifting Prochlorococcus cells from low to high irradiance translated quasi-instantaneously into an increase of cells in both the S and G(2) phases of the cell cycle and then into faster growth, whereas the inverse shift induced rapid slowing of the population growth rate. These data suggest a close coupling between irradiance levels and cell cycling in Prochloroeoccus spp.</p>
},
	keywords = {cyanobacteria, Equatorial Pacific, Gene Expression, Growth, Mediterranean Sea, North Atlantic, Photosynthetic Prokaryote, picoplankton, Populations, rcc, Synechococcus},
	doi = {10.1128/AEM.67.2.782-790.2001},
	author = {Jacquet, S and Partensky, F and Marie, D and Casotti, R and Vaulot, D}
}
@article {Guillou2001,
	title = {Grazing impact of two small heterotrophic flagellates on Prochlorococcus and Synechococcus},
	journal = {Aquatic Microbial Ecology},
	volume = {26},
	number = {2},
	year = {2001},
	note = {tex.mendeley-tags: 2001,rcc,sbr?hyto},
	pages = {201{\textendash}207},
	abstract = {In open oceanic waters, phytoplankton biomass is dominated by organisms below 2 to 3 mum in size (pico- and small nanophytoplankton). The cell concentration of these populations is very stable in time and space as a consequence of nutrient limitation and strong grazing pressure, Although the identity of the organisms that directly graze on picoplankton is largely unknown, they are thought to be very small, i.e. {\textexclamdown}3 to 5 {\textexclamdown}mu{\textquestiondown}m, Here, we analyze the grazing impact of 2 small flagellates, Symbiomonas scintillans and Picophagus flagellatus, upon 2 oceanic cyanobacteria, Prochlorococcus and Synechococcus. S. scintillans does not feed on the 2 cyanobacteria. In contrast, P. flagellatus appears as an active predator capable of drastically reducing prey concentrations. The flagellate displays a substantial division rate of the order of 2 doublings d(-1) when fed on Prochlorococcus cells, but no significant growth is recorded when Synechococcus is used as prey. As the majority ({\textquestiondown} 80\%) of P. flagellatus cells can pass throughout a 2 mum filter, the impact of such tiny predators should be taken into consideration during field experiments that rely on size fractionation to separate grazers from prey.},
	keywords = {2001, Algal Class, Equatorial Pacific, Growth Rates, Laboratory Cultures, Marine, Nanoplankton, PICODIV, picoplankton, Prey, rcc, SBR$_\textrmP$hyto, sbr?hyto, Size, Sp Nov},
	doi = {10.3354/ame026201},
	author = {Guillou, L and Jacquet, S and Chr{\'e}tiennot-Dinet, M.-J. and Vaulot, D}
}
@article {Dupuy2000,
	title = {Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the Mediterranean Thau Lagoon},
	journal = {Marine Ecology - Progress Series},
	volume = {205},
	year = {2000},
	note = {ISBN: 0171-8630 Publisher: Inter-Research tex.address: Nordbunte 23, D-21385 Oldendorf Luhe, Germany tex.mendeley-tags: RCC,rcc},
	pages = {171{\textendash}184},
	abstract = {The Mediterranean Thau Lagoon is an important oyster farming area in Europe. Oyster growth rates are among the highest in France, although chlorophyll a concentration is low. Previous studies have demonstrated that picophytoplankton, nano-microphytoplankton, dinoflagellates and loricate ciliates such as tintinnids are abundant. However, heterotrophic flagellates and aloricate ciliates have not been investigated. The aim of this study was to assess picophytoplankton, protist and zooplankton abundances in the Lagoon and to investigate the particular structure of the microbial food web, which may explain such paradoxical oyster growth. In oligotrophic waters in the Thau Lagoon, the picoeukaryote Ostreococcus tauri is the dominant autotrophic picoplankter, with an abundance maximum in summer. On 17 August 1998, following a rainfall event, pico- and nanophytoplankton abundances were not as high as expected and we observed a high abundance of large diatoms. At this time, the available carbon resources were produced by microphytoplankton (84.5\%), and picoplank-tonic cells represented only 1.27 \% in terms of carbon. Heterotrophic cells were low in abundance and constituted {\textexclamdown}14\% of carbon resources. In order to evaluate the importance of the {\textquoteright}protozoan trophic link{\textquoteright} for energy transfer from the microbial food web to large benthic suspension feeders, the oyster Crassostrea gigas was offered a planktonic community as potential prey. In the grazing experiment, all {\textquestiondown}5 mum flagellates, microphytoplankton, dinoflagellates, ciliates and large zooplankton were retained by the oyster gills. Only flagellates {\textexclamdown}5 pm and O. Tauri were not very well retained (45 and 2\% respectively). The high clearance rates of C. Gigas found in this experiment can be explained by a low concentration of suspended particulate matter (0.65 mg l(-1)). The oysters adapted their retention mechanism when they Lived in oligotrophic waters. These results indicate that, under the given experimental conditions, picophytoplankton did not represent a valuable trophic resource for farmed oysters because (1) C. Gigas cannot retain picoparticles and (2) the picoplankton represented a poor carbon resource capable of being transferred via a weak heterotrophic protist community. In the oyster pens of the Thau Lagoon during this study, microphytoplanktonic primary producers, in particular diatoms, were the main food sources for bivalve suspension feeders.},
	keywords = {ABUNDANCE, bivalve, carbon, COASTAL WATERS, EPIFLUORESCENCE MICROSCOPY, FILTRATION-RATE, food source, FOOD-CHAINS, GEUKENSIA-DEMISSA, heterotrophic protist, microbial food web, MYTILUS-EDULIS, oyster, PARTICLE SELECTION, picophytoplankton, rcc, RETENTION, Thau Lagoon, trophic link},
	doi = {10.3354/meps205171},
	author = {Dupuy, C and Vaquer, A and LamHoai, T and Rougier, C and Mazouni, N and Lautier, J and Collos, Y and LeGall, S}
}
@article {Guillou1999,
	title = {Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta)},
	journal = {Journal of Phycology},
	volume = {35},
	year = {1999},
	note = {tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {368{\textendash}381},
	abstract = {A new algal class, the Bolidophyceae (Heterokonta), is described from one genus, Bolidomonas, gen, nov., and two species, Bolidomonas pacifica, sp, nov and Bolidomonas mediterranea, sp, nov., isolated from the equatorial Pacific Ocean and the Mediterranean Sea, respectively. Both species are approximately 1.2 mu m in diameter and have two unequal flagella; the longer flagellum bears tubular hairs, whereas the shorter is smooth. The flagellar basal apparatus is restricted to two basal bodies, and there is no transitional helix. Cells are naked, devoid of walls or siliceous structures. The internal cellular organization is simple with a single plastid containing a ring genophore and a girdle lamella, one mitochondrion with tubular cristae, and one Golgi apparatus close to the basal bodies. The Mediterranean and the Pacific species differ in the insertion angle between their flagella and their pattern of swimming, these differences possibly being linked to each other. Analyses of the SSU rDNA gene place the two strains as a sister group to the diatoms, Moreover, pigment analyses confirm this position, as fucoxanthin is found as the major carotenoid in both lineages. These data strongly suggest that the ancestral heterokont that gave rise to the diatom lineage was probably a biflagellated unicell.},
	keywords = {10$_\textrmb$est, 1999, Bolidophyceae, CELL-CYCLE, CHRYSOPHYCEAE, diatoms, DIVINYL-CHLOROPHYLL, FINE-STRUCTURE, FLAGELLAR APPARATUS, Heterokonta, Marine, marine picoeukaryotes, oligotrophic ocean, rcc, RNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, sp-nov, stramenopiles, ultrastructure},
	doi = {10.1046/j.1529-8817.1999.3520368.x},
	author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Medlin, L K and Claustre, H and Loiseaux-de Go{\"e}r, S and Vaulot, D}
}
@article {Guillou1999a,
	title = {Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions},
	journal = {Applied and Environmental Microbiology},
	volume = {65},
	number = {10},
	year = {1999},
	note = {ISBN: 0099-2240 Publisher: Amer Soc Microbiology tex.address: 1325 Massachusetts Avenue, NW, Washington, DC 20005-4171, USA tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {4528{\textendash}4536},
	abstract = {The diversity and abundance of the Bolidophyceae (Heterokonta), a newly described picoplanktonic algal class which is a sister group to the diatoms, was assessed in the equatorial Pacific Ocean and in the Mediterranean Sea by culture isolation, molecular biology techniques, and pigment analyses. Eight strains of Bolidophyceae were isolated in culture from different mesotrophic and oligotrophic areas. The corresponding small subunit (SSU) rRNA gene sequences allowed us to design two probes specific for the Bolidophyceae. These probes have been used in natural samples (i) to selectively amplify and detect Bolidophyceae sequences and (ii) to quantify the relative abundance of Bolidophyceae within the picoeukaryote community. Sequences available to date indicate that the class Bolidophyceae comprises at least three different clades, two corresponding to the previously described species Bolidomonas pacifica and Bolidomonas mediterranea and the third one corresponding to a subspecies of B. Pacifica. Amplification of the SSU rRNA gene from natural samples with universal primers and hybridization using a Bolidomonas-specific probe followed by a eukaryote-specific probe allowed us to estimate the contribution of the Bolidophyceae to the eukaryotic DNA in both Pacific and Mediterranean waters to be lower than 1\%. Similarly, high-performance liquid chromatography analyses of fucoxanthin, the major carotenoid present in Bolidophyceae, indicated that less than 4\% of the total chlorophyll a in the picoplanktonic fraction in the equatorial Pacific was due to Bolidophyceae. Consequently, although strains of Bolidophyceae have been isolated from samples collected at several stations, this new class seems to have been a minor component of the natural picoeukaryotic populations in the ecosystems investigated, at least during the periods sampled.},
	keywords = {1999, ATLANTIC, BACTERIOPLANKTON, community structure, flow-cytometry, MOLECULAR PHYLOGENY, PACIFIC, phytoplankton, PIGMENT SIGNATURES, rcc, RNA GENE SEQUENCE, SBR$_\textrmP$hyto, sbr?hyto, ULTRAPHYTOPLANKTON},
	doi = {10.1128/AEM.65.10.4528-4536.1999},
	author = {Guillou, L and Moon-van der Staay, S Y and Claustre, H and Partensky, F and Vaulot, D}
}
@article {Guillou1999b,
	title = {Symbiomonas scintillans gen. et sp nov and Picophagus flagellatus gen. et sp nov (Heterokonta): Two new heterotrophic flagellates of picoplanktonic size},
	journal = {Protist},
	volume = {150},
	number = {4},
	year = {1999},
	note = {ISBN: 1434-4610 Publisher: Urban \& Fischer Verlag tex.address: Branch Office Jena, P O Box No.100 537, D-07705 Jena, Germany tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {383{\textendash}398},
	abstract = {Two new oceanic free-living heterotrophic Heterokonta species with picoplanktonic size ({\textexclamdown} 2 mu m) are described, Symbiomonas scintillans Guillou et Chretiennot-Dinet gen. Ef sp. Nov, was isolated from samples collected both in the equatorial Pacific Ocean and the Mediterranean Sea. This new species possesses ultrastructural features of the bicosoecids, such as the absence of a helix in the flagellar transitional region (found in Cafeteria roenbergensis and in a few bicosoecids), and a flagellar root system very similar to that of C. Roenbergensis, Acronema sippewissettensis, and Bicosoeca maris. This new species is characterized by a single flagellum with mastigonemes, the presence of endosymbiotic bacteria located close to the nucleus, the absence of a lorica and a R3 root composed of a 6+3+x microtubular structure. Phylogenetical analyses of nuclear-encoded SSU rDNA gene sequences indicate that this species is close to the bicosoecids C. Roenbergensis and Siluania monomastiga. Picophagus flagellatus Guillou et Chretiennot-Dinet gen. Et sp. Nov. Was collected in the equatorial Pacific Ocean, Cells are naked and possess two flagella, This species is characterized by the lack of a transitional helix and lateral filaments on the flagellar tubular hairs, the absence of siliceous scales, two unequal flagella, R1 + R3 roots, and the absence of a rhizoplast. SSU rDNA analyses place this strain at the base of the Chrysophyceae/Synurophyceae lineages.},
	keywords = {1999, APPARATUS, DEVELOPAYELLA-ELEGANS, EMPHASIS, MOLECULAR PHYLOGENY, picophytoplankton, PLASTIDS, rcc, RDNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCES},
	doi = {10.1016/S1434-4610(99)70040-4},
	author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Boulben, S and Moon-van der Staay, S Y and Vaulot, D}
}
@article {Courties1998,
	title = {Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta, Prasinophyceae)},
	journal = {Journal of Phycology},
	volume = {34},
	number = {5},
	year = {1998},
	note = {tex.mendeley-tags: RCC745},
	pages = {844{\textendash}849},
	abstract = {Ostreococcus tauri Courties et Chretiennot-Dinet is the smallest described autotrophic eukaryote dominating the phytoplanktonic assemblage of the marine Mediterranean Thau lagoon (France). Its taxonomic position was partly elucidated from ultrastructure and high-pressure liquid chromatography (HLPC) pigment analysis. The sequence analysis of the 18S rDNA gene of O. Tauri measured here is available in EMBL Nucleotide Sequence Database (accession number: Y15814) and allowed to clarify its phylogenetic position. O. Tauri belongs to the Prasinophyceae and appears very close to Mantoniella, a typical scaly Prasinophyceae, morphologically very different from the naked and coccoid Ostreococcus. An electrophoretic analysis of O. Tauri shows that the nucleus contains 10.20 mbp. This small genome fragmented into 14 chromosomes ranging in size from 300 to 1500 kbp, confirms the minimalist characteristics of Ostreococcus tauri.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1046/j.1529-8817.1998.340844.x},
	author = {Courties, C and Perasso, R and Chr{\'e}tiennot-Dinet, M.-J. and Gouy, M and Guillou, L and Troussellier, M}
}
@article {Moore1995,
	title = {Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties},
	journal = {Marine Ecology - Progress Series},
	volume = {116},
	year = {1995},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {259{\textendash}275},
	keywords = {GROWTH RATE, Light, MARINE OPTICS, rcc, Synechococcus, temperature, \#PROCHLOROPHYTE},
	doi = {10.3354/meps116259},
	author = {Moore, L R and Goericke, R and Chisholm, S W}
}
@article {Chretiennot-Dinet1995,
	title = {A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae)},
	journal = {Phycologia},
	volume = {34},
	number = {4},
	year = {1995},
	note = {tex.mendeley-tags: RCC745},
	pages = {285{\textendash}292},
	keywords = {FRESH-WATER ECOSYSTEMS, morphology, picoplankton, pigments, PROCHLOROCOCCUS-MARINUS, Prokaryote, rcc, RCC745, Size},
	doi = {10.2216/i0031-8884-34-4-285.1},
	author = {Chr{\'e}tiennot-Dinet, M.-J. and Courties, C and Vaquer, A and Neveux, J and Claustre, H and Lautier, J and Machado, M C}
}
@article {Vaulot1994,
	title = {Phaeocystis spp.: morphology, ploidy, pigment composition and genome size of cultured strains},
	journal = {Journal of Phycology},
	volume = {30},
	year = {1994},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1022{\textendash}1035},
	keywords = {rcc, RCC SBR$_\textrmP$hyto},
	doi = {10.1111/j.0022-3646.1994.01022.x},
	author = {Vaulot, D and Birrien, J.-L. and Marie, D and Casotti, R and Veldhuis, M J W and Kraay, G W and Chr{\'e}tiennot-Dinet, M.-J.}
}
@article {Morel1993,
	title = {Prochlorococcus and Synechococcus: a comparative study of their size, pigmentation and related optical properties},
	journal = {Journal of Marine Research},
	volume = {51},
	year = {1993},
	note = {tex.mendeley-tags: 1993,rcc,sbr?hyto},
	pages = {617{\textendash}649},
	keywords = {1993, hplc, OPTICS, Pigment, rcc, SBR$_\textrmP$hyto, sbr?hyto, Synechococcus, \#PROCHLOROPHYTE},
	doi = {10.1357/0022240933223963},
	author = {Morel, A and Ahn, Y.-W. and Partensky, F and Vaulot, Daniel and Claustre, H}
}
@article {Chisholm1992,
	title = {\textit{Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b},
	journal = {Archives of Microbiology},
	volume = {157},
	year = {1992},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {297{\textendash}300},
	keywords = {rcc, systematics, \#PROCHLOROPHYTE},
	doi = {10.1007/BF00245165},
	author = {Chisholm, S W and Frankel, S L and Goericke, R and Olson, R J and Palenik, B and Waterbury, J B and West-Johnsrud, L and Zettler, E R}
}
