@article {dedman_alterations_2024,
	title = {Alterations in metalloprotein abundance under ocean warming in the marine green alga Micromonas pusilla using the mebipred predictive tool},
	journal = {Algal Research},
	volume = {78},
	year = {2024},
	month = {mar},
	pages = {103412},
	abstract = {Metals are essential to life, required for the functioning of a substantial fraction of proteins. Marine phytoplankton drives the oceanic carbon cycle, influencing global biogeochemistry. These organisms rely on trace metal nutrients; however how trace nutrient demand will change under ocean warming is uncertain. The currently limited annotation of metalloproteins contributes to this lack of understanding. Herein, we utilise the recently published mebipred tool to predict the metalloproteome of the globally occurring green alga, Micromonas pusilla, revealing \~{}20~\% of its reference proteome to display ion-binding properties. Using the predicted metalloproteome, and existing Gene Ontology annotation, we present a comprehensive insight towards changes in metalloprotein abundance after exposure to ocean warming conditions (+6~{\textdegree}C), using a shotgun proteomic approach. We outline that predictions must be combined with existing annotation to fully capture the metalloprotein response. Approximately 50~\% of identified metalloproteins significantly altered in abundance under warming, largely related to changes in cellular function. Notably, warming appeared to shift Fe use from photosynthesis to storage in M. pusilla, indicated by a 2.36 log2 fold-increase in ferritin and decline in abundance of photosynthetic proteins. Ocean warming will inevitably alter cellular use and demand for metal cofactors in marine phytoplankton with possible implications for biogeochemical cycling. Bioinformatics tools such as mebipred greatly expand our ability to examine such changes.},
	keywords = {Biogeochemistry, marine phytoplankton, Ocean warming, proteomics, RCC1614, Trace metals},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2024.103412},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926424000249},
	author = {Dedman, Craig J. and Fournier, Marjorie and Rickaby, Rosalind E. M.}
}
@article {hachicha_combined_2024,
	title = {Combined biological treatments of olive mill wastewater using fungi and microalgae},
	journal = {Euro-Mediterranean Journal for Environmental Integration},
	year = {2024},
	month = {jan},
	abstract = {Olive mill wastewaters (OMWs), which are mainly composed of phenolic compounds, present an important environmental issue. This effluent was treated using fungal laccases from Tetraselmis sp. and Chlorella sp. and two green microalgae. In the first step in the removal of phenolic compounds, enzymatic pretreatment of diluted OMWs (30\% v/v) with the fungal laccases led to a 57.79 {\textpm} 2.21\% decrease in phenol concentration and a 54.79 {\textpm} 3.44\% decrease in the dark coloration of the diluted OMWs. This preatreated wastewater was suitable for microalgae culture under mixotrophy. The growth and biochemical composition of the two microalgae strains were determined and compared to those obtained from a control culture under autotrophy. Under mixotrophy, the growth of Chlorella sp. and Tetraselmis sp. reduced dramatically. Moroever, their photosynthetic pigment productivities (0.0071 {\textpm} 0.08 mg/104 cells/mL/day for Chlorella sp. and 0.011 {\textpm} 0.002 mg/104 cells/ mL/day for Tetraselmis sp.) were decreased when compared to those attained under autotrophy. In terms of starch and lipid production, the highest final contents of starch and lipids were obtained under autotrophy: 13.38 {\textpm} 2.17\% and 4.2 {\textpm} 0.35\% for Chlorella sp. and 15.66 {\textpm} 0.92\% and 5.22 {\textpm} 0.79\% for Tetraselmis sp., respectively. The mixotrophic cultivation mode of Chlorella sp. reinforces protein synthesis. These results highlight the opportunity to achieve high-value biomass production by the mixotrophic cultivation of microalgae using pretreated OMWs as a low-cost raw material.},
	keywords = {RCC288},
	issn = {2365-6433, 2365-7448},
	doi = {10.1007/s41207-023-00451-6},
	url = {https://link.springer.com/10.1007/s41207-023-00451-6},
	author = {Hachicha, Rihab and Dammak, Mouna and Hachicha, Ridha and Dubessay, Pascal and Abdelkafi, Slim and Michaud, Philippe and Fendri, Imen}
}
@article {varga_cytotoxicity_2024,
	title = {Cytotoxicity of Prymnesium parvum extracts and prymnesin analogs on epithelial fish gill cells RTgill-W1 and the human colon cell line HCEC-1CT},
	journal = {Archives of Toxicology},
	year = {2024},
	month = {jan},
	abstract = {Harmful algal blooms kill fish populations worldwide, as exemplified by the haptophyte microalga Prymnesium~parvum. The suspected causative agents are prymnesins, categorized as A-, B-, and C-types based on backbone carbon atoms. Impacts of P.~parvum extracts and purified prymnesins were tested on the epithelial rainbow trout fish gill cell line RTgill-W1 and on the human colon epithelial cells HCEC-1CT. Cytotoxic potencies ranked A > C > B-type with concentrations spanning from low (A- and C-type) to middle (B-type) nM ranges. Although RTgill-W1 cells were about twofold more sensitive than HCEC-1CT, the cytotoxicity of prymnesins is not limited to fish gills. Both cell lines responded rapidly to prymnesins; with EC50 values for B-types in RTgill-W1 cells of 110 {\textpm} 11~nM and 41.5 {\textpm} 0.6~nM after incubations times of 3 and 24~h. Results of fluorescence imaging and measured lytic effects suggest plasma membrane interactions. Postulating an osmotic imbalance as mechanisms of toxicity, incubations with prymnesins in media lacking either Cl-, Na+, or Ca2+ were performed. Cl- removal reduced morphometric rearrangements observed in RTgill-W1 and cytotoxicity in HCEC-1CT cells. Ca2+-free medium in RTgill-W1 cells exacerbated effects on the cell nuclei. Prymnesin composition of different P.~parvum strains showed that analog composition within one type scarcely influenced the cytotoxic potential, while analog type potentially dictate potency. Overall, A-type prymnesins were the most potent ones in both cell lines followed by the C-types, and lastly B-types. Disturbance of Ca2+ and Cl- ionoregulation may be integral to prymnesin toxicity.},
	keywords = {Fluorescence microscopy, Ichthyotoxin, Ionoregulation, Microalgae, MS, RCC1436, RCC191, UHPLC},
	issn = {1432-0738},
	doi = {10.1007/s00204-023-03663-5},
	url = {https://doi.org/10.1007/s00204-023-03663-5},
	author = {Varga, Elisabeth and Prause, H{\'e}l{\`e}ne-Christine and Riepl, Matthias and Hochmayr, Nadine and Berk, Deniz and Attakpah, Eva and Kiss, Endre and Medi{\'c}, Nikola and Del Favero, Giorgia and Larsen, Thomas Ostenfeld and Hansen, Per Juel and Marko, Doris}
}
@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}
}
@article {dulong_exopolysaccharide_2024,
	title = {Exopolysaccharide from marine microalgae belonging to the \textit{Glossomastix genus: fragile gel behavior and suspension stability},
	journal = {Bioengineered},
	volume = {15},
	number = {1},
	year = {2024},
	note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/21655979.2023.2296257},
	month = {dec},
	pages = {2296257},
	abstract = {With the aim to find new polysaccharides of rheological interest with innovated properties, rhamnofucans produced as exopolysaccharides (EPS) in a photobioreactor (PBR) and an airlift bioreactor (ABR) by the marine microalgae Glossomastix sp. RCC3707 and RCC3688 were fully studied. Chemical characterizations have been conducted (UHPLC {\textendash} MS HR). Analyses by size-exclusion chromatography (SEC) coupled online with a multiangle light scattering detector (MALS) and a differential refractive index detector showed the presence of large structures with molar masses higher than 106 g.mol-1. The rheological studies of these EPS solutions, conducted at different concentrations and salinities, have evidenced interesting and rare behavior characteristic of weak and fragile hydrogels i.e. gel behavior with very low elastic moduli (between 10-2 and 10 Pa) and yield stresses (between 10-2 and 2 Pa) according to the EPS source, concentration, and salinity. These results were confirmed by diffusing wave spectroscopy. Finally, as one of potential application, solutions of EPS from Glossomastix sp. have evidenced very good properties as anti-settling stabilizers, using microcrystalline cellulose particles as model, studied by multiple light scattering (MLS) with utilization in cosmetic or food industry. Compared to alginate solution with same viscosity for which sedimentation is observed over few hours, microalgae EPS leads to a stable suspension over few days.},
	keywords = {fragile gel, Glossomastix, Microalgae, Polysaccharide, RCC3688, RCC3707, stabilizer},
	issn = {2165-5979},
	doi = {10.1080/21655979.2023.2296257},
	url = {https://doi.org/10.1080/21655979.2023.2296257},
	author = {Dulong, Virginie and Rihouey, Christophe and Gaignard, Cl{\'e}ment and Bridiau, Nicolas and Gourvil, Priscilla and Laroche, C{\'e}line and Pierre, Guillaume and Varacavoudin, Tony and Probert, Ian and Maugard, Thierry and Michaud, Philippe and Picton, Luc and Le Cerf, Didier}
}
@booklet {krinos_intraspecific_2024,
	title = {Intraspecific diversity in thermal performance determines phytoplankton ecological niche},
	year = {2024},
	month = {feb},
	publisher = {Ecology},
	type = {preprint},
	abstract = {Abstract Temperature has a primary influence on phytoplankton physiology and affects biodiversity and ecology. To examine how intraspecific diversity and temperature shape plankton populations, we grew 12 strains of the ecologically-important coccolithophore Gephyrocapsa huxleyi isolated from regions of different temperature for \~{}45 generations (2 months), each at 6-8 temperatures, and characterized the acclimated thermal response curve of each strain. Even with virtually identical temperature optima and overlapping cell size, strain growth rates varied between 0.45 and 1 day -1 . While some thermal curves were effectively symmetrical, others had more slowly declining growth rates above the {\textquotedblleft}thermal optimum,{\textquotedblright} and thermal niche widths varied between 16.7 and 24.8 {\textdegree}C. This suggests that different strains use distinct thermal response mechanisms. We investigated the ecological implications of such intraspecific diversity on thermal response using an ocean ecosystem simulation resolving distinct phytoplankton thermal phenotypes. Resolving model analogs of thermal {\textquotedblleft}generalists{\textquotedblright} and {\textquotedblleft}specialists{\textquotedblright} (similar to those observed in G. huxleyi) resulted in a distinctive global biogeography of preferred thermal niche widths with a nonlinear latitudinal pattern. We leveraged the model output to predict the ranges of the 12 strains we studied in the laboratory and demonstrated how this approach could refine predictions of phytoplankton thermal geographic range in situ . Our combination of observed thermal traits and modeled biogeography highlights the capacity of diverse groups to persist through temperature shifts. Significance Statement Intraspecific diversity in the phytoplankton may underpin their distribution. We show that within a single coccolithophore species, thermal response curves have diverse trait parameters. For example, many strains had a variable range of temperatures at which they could survive (thermal niche width). Adding this thermal niche width diversity to an ecosystem model simulation impacted phytoplankton coexistence and overall biomass. These observations show that thermal niche width is a gap in phytoplankton representation in ecosystem models that impacts modeled phytoplankton biogeography and concomitant carbon cycle dynamics. Including thermal tolerance is crucial to predictive modeling as ocean temperature dynamics change.},
	keywords = {rcc1212, RCC3492, RCC3963, RCC4567, RCC6071, RCC874, RCC914},
	doi = {10.1101/2024.02.14.580366},
	url = {http://biorxiv.org/lookup/doi/10.1101/2024.02.14.580366},
	author = {Krinos, Arianna I. and Shapiro, Sara K. and Li, Weixuan and Haley, Sheean T. and Dyhrman, Sonya T. and Dutkiewicz, Stephanie and Follows, Michael J. and Alexander, Harriet}
}
@article {novak_vanclova_new_2024,
	title = {New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates},
	journal = {EMBO Reports},
	year = {2024},
	abstract = {Abstract Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a~model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera ( Karenia , Karlodinium , and Takayama ) and analyze their evolutionary patterns using automated tree building and sorting. We project a~relatively limited ( \textasciitilde 10\%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species ( Karlodinium armiger , Takayama helix ) possess plastids from different haptophyte orders than the rest.},
	keywords = {RCC1513, RCC3446, RCC6516},
	issn = {1469-3178},
	doi = {10.1038/s44319-024-00103-y},
	url = {https://www.embopress.org/doi/full/10.1038/s44319-024-00103-y},
	author = {Nov{\'a}k Vanclov{\'a}, Anna Mg and Nef, Charlotte and F{\"u}ssy, Zolt{\'a}n and Vancl, Ad{\'e}l and Liu, Fuhai and Bowler, Chris and Dorrell, Richard G}
}
@article {das_assessing_2023,
	title = {Assessing indicators of arsenic toxicity using variable fluorescence in a commercially valuable microalgae: physiological and toxicological aspects},
	journal = {Journal of Hazardous Materials},
	year = {2023},
	month = {mar},
	pages = {131215},
	abstract = {Indicators signaling Arsenic (As) stress through physiology of microalgae using non-destructive methods like variable fluorescence are rare but requisite. This study reports stress markers indicating arsenic (As) toxicity (in two concentrations 11.25{\textmu}g/L and 22.5{\textmu}g/L compared to a control) exposed to a microalga (Diacronema lutheri), using fast repetition rate fluorometry (FRRf). Growth and physiological parameters such as cell density, chl a and the maximum quantum yield Fv/Fm showed coherence and impeded after the exponential phase (day 9 - day 12) in As treatments compared to the control (p < 0.05). On contrary photo-physiological constants were elevated showing higher optical (aLHII) and functional [Sigma (σPSII)] absorption cross-section for the As treatments (p < 0.05) further implying the lack of biomass production yet an increase in light absorption. In addition, As exposure increased the energy dissipation by heat (NPQ-NSV) showing a strong relationship with the de-epoxidation ratio (DR) involving photoprotective pigments. Total As bioaccumulation by D. lutheri showed a strong affinity with Fe adsorption throughout the algal growth curve. This study suggests some prompt photo-physiological proxies signaling As contamination and endorsing its usefulness in risk assessments, given the high toxicity and ubiquitous presence of As in the ecosystem.},
	keywords = {Arsenic bioaccumulation, de-epoxidation ratio (DR), Optical absorption cross section, pigment concentrations, RCC1537},
	issn = {0304-3894},
	doi = {10.1016/j.jhazmat.2023.131215},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389423004971},
	author = {Das, Shagnika and Lizon, Fabrice and Gevaert, Fran{\c c}ois and Bialais, Capucine and Duong, Gwendoline and Ouddane, Baghdad and Souissi, Sami}
}
@booklet {dennu_biological_2023,
	title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: Insights into genetic diversity and major structural variations},
	year = {2023},
	note = {Pages: 2023.10.16.562038 Section: New Results},
	month = {oct},
	publisher = {bioRxiv},
	abstract = {Population-scale sequencing has become a standard practice to explore the natural genetic diversity underlying adaptation, notably in land plants. However, current sequencing initiatives for eukaryotic phytoplankton primarily concentrate on creating reference genomes for model organisms and characterizing natural communities through metagenomics approaches. Consequently, few species have been thoroughly sequenced and intraspecific genetic diversity remains virtually undescribed, limiting our understanding of diversity and adaptation mechanisms. Here we report a biological and genomic resource to explore the genetic diversity of the cosmopolitan and ecologically important Bathycoccus genus. To span broad geographical and temporal scales, we selected available strains but also isolated and genotyped strains from both the Banyuls bay (Mediterranean sea) and the Baffin bay (Arctic ocean). By combining ONT long reads and Illumina short reads technologies, we produced and annotated 28 Bathycoccus sp. de novo assembled genomes of high quality, including 24 genomes of Bathycoccus prasinos strains along a latitudinal gradient between 40{\textdegree} and 78{\textdegree} North, one reference genome of the Bathycoccus calidus species and 3 genomes of a yet undescribed Bathycoccus species named Bathycoccus catiminus. We assessed the genetic diversity of this genus through phylogenomic analyses and highlighted the central role of this genomic resource in providing new insights into the diversity of outlier chromosomal structures. The Bathycoccus biological and genomic resources offer a robust framework for investigating the diversity and adaptation mechanisms of eukaryotic phytoplankton in the Ocean. Significance statement Comparative and functional approaches for the study of eukaryotic phytoplankton and their adaptation to latitudes and seasons that rely on extensive biological and genomic resources are currently lacking. Here we report such resources and describe the natural diversity of the cosmopolitan phytoplankton Bathycoccus, providing insights into its species and intraspecific diversity and establishing it as a robust model for functional and ecological studies.},
	keywords = {RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685, RCC716},
	doi = {10.1101/2023.10.16.562038},
	url = {https://www.biorxiv.org/content/10.1101/2023.10.16.562038v1},
	author = {Dennu, Louis and Devic, Martine and Rigonato, Janaina and Falciatore, Angela and Lozano, Jean-Claude and Verg{\'e}, Val{\'e}rie and Mariac, C{\'e}dric and Jaillon, Olivier and Team, The Dark Edge genomics sampling and Sabot, Fran{\c c}ois and Bouget, Fran{\c c}ois-Yves}
}
@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 {de_vries_critical_2023,
	title = {A critical trade-off between nitrogen quota and growth allows Coccolithus braarudii life cycle phases{\textquoteright} to exploit varying environment},
	year = {2023},
	publisher = {Biodiversity and Ecosystem Function: Marine},
	type = {preprint},
	abstract = {Coccolithophores have a distinct haplo-diplontic life cycle, which allows them to grow and divide in two different life cycle phases (haploid and diploid). These life cycle phases vary significantly in inorganic carbon content and morphology, and inhabit distinct niches, with haploids generally preferring low-nutrient and high-temperature and -light environments. This niche contrast indicates different physiology of the life cycle phases, which is considered here in the context of a trait trade-off 5 framework, in which a particular set of traits comes with both costs and benefits. However, coccolithophore{\textquoteright}s phase trade-offs are not fully identified, limiting our understanding of the functionality of the coccolithophore life cycle. Here, we investigate the response of the two life cycle phases of the coccolithophore Coccolithus braarudii to key environmental drivers: light, temperature and nutrients, using laboratory experiments. With this data, we identify the main trade-offs of each life cycle phase and use models to test the role of such trade-offs under different environmental conditions.},
	keywords = {RCC1200, RCC1203, RCC3777, RCC3779, RCC6535},
	doi = {10.5194/egusphere-2023-880},
	url = {https://egusphere.copernicus.org/preprints/2023/egusphere-2023-880/},
	author = {De Vries, Joost and Monteiro, Fanny and Langer, Gerald and Brownlee, Colin and Wheeler, Glen}
}
@article {ben-joseph_crystallization_2023,
	title = {Crystallization of Coccolith Calcite at Different Life-Cycle Phases Exhibits Distinct Degrees of Cellular Confinement},
	journal = {Small Structures},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/sstr.202200353},
	pages = {2200353},
	abstract = {Coccolithophores are a group of unicellular marine algae that shape global geochemical cycles via the production of calcium carbonate crystals. Interestingly, different life-cycle phases of the same coccolithophore species produce very different calcitic scales, called coccoliths. In the widely studied diploid phase, the crystals have anisotropic and complex morphologies, while haploid cells produce coccoliths consisting solely of calcite crystals with simple rhombohedral morphology. Understanding how these two life-cycle phases control crystallization is a highly sought-after goal, yet, haploid phase crystallization has rarely been studied, and the process by which they form is unknown. Herein, advanced electron microscopy is employed to elucidate the cellular architecture of the calcification process in haploid cells. The results show that in contrast to diploid-phase calcification, the coccolith-forming vesicle of haploid-phase cells is voluminous. In this solution-like environment, the crystals nucleate and grow asynchronously in a process that resembles calcite growth in bulk solution, leading to the simple morphologies of the crystals. The two distinct mineralization regimes of coccolithophore life-cycle phases suggest that cellular architecture, and specifically confinement of the crystallization process, is a pivotal determinant of biomineral morphology and assembly.},
	keywords = {biomineralization, calcites, Coccoliths, crystal growths, haploid{\textendash}diploid life cycles, RCC1181, RCC3777},
	issn = {2688-4062},
	doi = {10.1002/sstr.202200353},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/sstr.202200353},
	author = {Ben-Joseph, Oz and de Haan, Diede and Rechav, Katya and Shimoni, Eyal and Levin-Zaidman, Smadar and Langer, Gerald and Probert, Ian and Wheeler, Glen L. and Gal, Assaf}
}
@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 {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}
}
@booklet {devic_indel_2023,
	title = {An INDEL genomic approach to explore population diversity of phytoplankton : \textit{Bathycoccus , a case study},
	year = {2023},
	publisher = {Ecology},
	type = {preprint},
	abstract = {Abstract Although metabarcoding has generated large dataset on world-wide phytoplankton species diversity, little is known about the intraspecies diversity underlying adaptation to environmental niches. To gain insight into population diversity, a novel INDEL based method was developed on Bathycoccus prasinos . Oxford Nanopore Technology (ONT) sequencing was first used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in the bay of Banyuls-sur-Mer. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December and January. When tested directly on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation and between years. This INDEL-based genotyping constitutes a new methodological approach that may be used to assess the population structure and diversity of other species.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@article {moreno-cabezuelo_integrated_2023,
	title = {Integrated Proteomic and Metabolomic Analyses Show Differential Effects of Glucose Availability in Marine Synechococcus and Prochlorococcus},
	journal = {Microbiology Spectrum},
	year = {2023},
	month = {feb},
	pages = {e03275{\textendash}22},
	abstract = {<p>We compared changes induced by the addition of 100 nM and 5 mM glucose on the proteome and metabolome complements in Synechococcus sp. strains WH8102, WH7803, and BL107 and Prochlorococcus sp. strains MED4, SS120, and MIT9313, grown either under standard light conditions or in darkness. Our results suggested that glucose is metabolized by these cyanobacteria, using primarily the oxidative pentoses and Calvin pathways, while no proof was found for the involvement of the EntnerDoudoroff pathway in this process. We observed differences in the effects of glucose availability, both between genera and between Prochlorococcus MED4 and SS120 strains, which might be related to their specific adaptations to the environment. We found evidence for fermentation in Prochlorococcus sp. strain SS120 and Synechococcus sp. strain WH8102 after 5 mM glucose addition. Our results additionally suggested that marine cyanobacteria can detect nanomolar glucose concentrations in the environment and that glucose might be used to sustain metabolism under darkness. Furthermore, the KaiB and KaiC proteins were also affected in Synechococcus sp. WH8102, pointing to a direct link between glucose assimilation and circadian rhythms in marine cyanobacteria. In conclusion, our study provides a wide overview on the metabolic effects induced by glucose availability in representative strains of the diverse marine picocyanobacteria, providing further evidence for the importance of mixotrophy in marine picocyanobacteria.</p>
},
	keywords = {RCC156, RCC407, RCC515, rcc539, rcc752},
	issn = {2165-0497},
	doi = {10.1128/spectrum.03275-22},
	url = {https://journals.asm.org/doi/10.1128/spectrum.03275-22},
	author = {Moreno-Cabezuelo, Jos{\'e} {\'A}ngel and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel},
	editor = {Hom, Erik F. Y.}
}
@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}
}
@booklet {devic_population_2023,
	title = {Population dynamics of the cosmopolitan eukaryotic picophytoplankton Bathycoccus during seasonal blooms in the bay of Banyuls sur Mer (North Western Mediterranean sea)},
	year = {2023},
	publisher = {BioRxiv},
	type = {preprint},
	abstract = {Abstract Although Bathycoccus is one of the most abundant picophytoplankton, little is known about the genetic diversity underlying its adaptation to ecological niches. In this study, the diversity of Bathycoccus populations during their annual bloom in the Mediterranean bay of Banyuls France was assessed by an INDEL based approach. Oxford Nanopore Technology (ONT) was used to characterise structural variants (SV) among the genomes of Bathycoccus sampled from geographically distinct regions in the world ocean. Markers derived from INDEL were validated by PCR and sequencing in the world-wide strains. These markers were then used to genotype 55 Bathycoccus strains isolated during the winter bloom 2018-2019 in Banyuls. With five markers, eight Multi Loci Genotypes (MLG) were determined, two of which represented 53\% and 29\% of the isolates. Physiological studies confirmed that isolates are phenotypically different, cells isolated in February growing better at low temperature than those isolated in December. When tested on environmental samples, two diversity markers showed a similar allele frequency in sea water as in individual Bathycoccus strains isolated at the same period. We conclude that these markers constitute a resource to identify the most abundant variant alleles in a given bloom. A follow-up on three consecutive blooms revealed differences in allele abundance during the course of a bloom, particularly at initiation, and between years. In addition to Bathycoccus prasinos , two other species of Bathycoccus were identified including the recently described species B. calidus and a novel species B. catiminus , suggesting that species diversity of the genus Bathycoccus may be underestimated.},
	keywords = {RCC1613, RCC1615, RCC1868, RCC4222, RCC4752, RCC5417, RCC685},
	doi = {10.1101/2023.02.09.527951},
	url = {http://biorxiv.org/lookup/doi/10.1101/2023.02.09.527951},
	author = {Devic, Martine and Mariac, C{\'e}dric and Verg{\'e}, Val{\'e}rie and Schatt, Philipe and Dennu, Louis and Lozano, Jean-Claude and Bouget, Fran{\c c}ois-Yves and Sabot, Fran{\c c}ois}
}
@article {dedman_shotgun_2023,
	title = {Shotgun proteomics reveals temperature-dependent regulation of major nutrient metabolism in coastal Synechococcus sp. WH5701},
	journal = {Algal Research},
	year = {2023},
	month = {oct},
	pages = {103279},
	abstract = {Marine cyanobacteria are major contributors to the oceanic carbon sink and are predicted to increase in numbers in the future warmed ocean. As a result, the influence of marine cyanobacteria on marine biogeochemical cycling will likely be enhanced. Associated with elevations in temperature the ocean will undergo increased stratification, reducing supply of essential nutrients to upper phototrophic layers. It is therefore critical that we resolve the manners by which cyanobacteria respond to variations in temperature, and consequences for major nutrient metabolism which may ultimately direct global biogeochemistry and trophic transfer. In this study we use the coastal Synechococcus sp. WH5701 to examine proteomic alterations in major nutrient (C, N and P) metabolic pathways following exposure to varying temperature. In response to temperature treatments, Synechococcus displayed higher rates of growth and photosynthetic efficiency when temperatures were raised from 17 {\textdegree}C to 23 {\textdegree}C and 28 {\textdegree}C, associated with a significant \textasciitilde30{\textendash}40 \% alteration in the cellular proteome. As temperatures increased, proteomic investment towards photosynthetic machinery appeared up-regulated, whilst abundance of RuBisCO was reduced, associated with an apparent alteration in CCM composition and carbon metabolism. N demand appeared to increase in-line with temperature, associated with alterations in the GS-GOGAT pathway, likely due to increased demand for and efficiency of protein synthesis. In contrast, P demand at the highest temperature appeared reduced as investment in the ribosome declines due to improved translation efficiency, whilst luxury P-storage appeared a feature of growth at low temperature. It appears likely that as seawater temperatures rise under ocean warming, the biochemical composition of cyanobacteria will be altered, increasing cellular C- and N- to P ratios, ultimately impacting upon their contribution to oceanic biogeochemical cycling.},
	keywords = {climate change, Ocean warming, phytoplankton, Proteomics: Marine biogeochemistry, rcc1084},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103279},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423003120},
	author = {Dedman, Craig J. and Barton, Samuel and Fournier, Marjorie 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 {barbeyron_zobellia_2023,
	title = {\textit{Zobellia alginiliquefaciens sp. nov., a novel member of the flavobacteria isolated from the epibiota of the brown alga Ericaria zosteroides (C. Agardh) Molinari \& Guiry 2020},
	journal = {International Journal of Systematic and Evolutionary Microbiology},
	volume = {73},
	number = {6},
	year = {2023},
	note = {Publisher: Microbiology Society,},
	pages = {005924},
	abstract = {Strain LLG6346-3.1T, isolated from the thallus of the brown alga Ericaria zosteroides collected from the Mediterranean Sea near Bastia in Corsica, France, was characterised using a polyphasic method. Cells were Gram-stain-negative, strictly aerobic, non-flagellated, motile by gliding, rod-shaped and grew optimally at 30{\textendash}33 {\textdegree}C, at pH 8{\textendash}8.5 and with 4{\textendash}5 \% NaCl. LLG6346-3.1T used the seaweed polysaccharide alginic acid as a sole carbon source which was vigorously liquefied. The results of phylogenetic analyses indicated that the bacterium is affiliated to the genus Zobellia (family Flavobacteriaceae , class Flavobacteriia ). LLG6346-3.1T exhibited 16S rRNA gene sequence similarity values of 98.6 and 98.3 \% to the type strains of Zobellia russellii and Zobellia roscoffensis , respectively, and of 97.4{\textendash}98.5 \% to members of other species of the genus Zobellia . The DNA G+C content of LLG6346-3.1T was determined to be 38.3 mol\%. Digital DNA{\textendash}DNA hybridisation predictions by the average nucleotide identity (ANI) and genome to genome distance calculator (GGDC) methods between LLG6346-3.1T and other members of the genus Zobellia showed values of 76{\textendash}88 \% and below 37 \%, respectively. The results of phenotypic, phylogenetic and genomic analyses indicate that LLG6346-3.1T is distinct from species of the genus Zobellia with validly published names and that it represents a novel species of the genus Zobellia , for which the name Zobellia alginiliquefaciens sp. nov. is proposed. The type strain is LLG6346-3.1T (= RCC7657T = LMG 32918T).},
	keywords = {RCC7657},
	issn = {1466-5034},
	doi = {10.1099/ijsem.0.005924},
	url = {https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijsem.0.005924},
	author = {Barbeyron, Tristan and Le Duff, Nolwen and Duchaud, Eric and Thomas, Fran{\c c}ois}
}
@article {syhapanha_transcriptomicsguided_2023,
	title = {Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1},
	journal = {MicrobiologyOpen},
	volume = {12},
	number = {5},
	year = {2023},
	pages = {e1387},
	abstract = {In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., Algicidal bacteria shape the plankton communities of the oceans by lysing microalgae and consuming the released nutrients. Kordia algicida is an environmentally relevant marine bacterium whose algicidal activity is mediated by secreted proteases. In this study, we utilize a transcriptomics-guided approach to identify the secreted serine protease AlpA1 as a key factor in the algicidal process. This discovery offers new approaches for the real-time monitoring and manipulation of algicidal bacteria in algal blooms.},
	keywords = {RCC75},
	issn = {2045-8827},
	doi = {10.1002/mbo3.1387},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565126/},
	author = {Syhapanha, Kristy S. and Russo, David A. and Deng, Yun and Meyer, Nils and Poulin, Remington X. and Pohnert, Georg}
}
@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 {yee_v-type_2023,
	title = {The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis},
	journal = {Current Biology},
	year = {2023},
	month = {may},
	pages = {S0960982223006152},
	abstract = {Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6{\textendash}8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7\% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.},
	keywords = {RCC3387},
	issn = {09609822},
	doi = {10.1016/j.cub.2023.05.020},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982223006152},
	author = {Yee, Daniel P. and Samo, Ty J. and Abbriano, Raffaela M. and Shimasaki, Bethany and Vernet, Maria and Mayali, Xavier and Weber, Peter K. and Mitchell, B. Greg and Hildebrand, Mark and Decelle, Johan and Tresguerres, Martin}
}
@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 {grebert_diversity_2022,
	title = {Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria},
	journal = {Genome Biology and Evolution},
	year = {2022},
	pages = {evac035},
	abstract = {DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a {\textquoteleft}tycheposon{\textquoteright}-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events.},
	keywords = {RCC307, to add},
	issn = {1759-6653},
	doi = {10.1093/gbe/evac035},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267},
	author = {Gr{\'e}bert, Th{\'e}ophile and Garczarek, Laurence and Daubin, Vincent and Humily, Florian and Marie, Dominique and Ratin, Morgane and Devailly, Alban and Farrant, Gregory K. and Mary, Isabelle and Mella-Flores, Daniella and Tanguy, Gwenn and Labadie, Karine and Wincker, Patrick and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric},
	editor = {Angert, Esther}
}
@article {penot_genomic_2022,
	title = {Genomic and meta-genomic insights into the functions, diversity and global distribution of haptophyte algae},
	journal = {Applied Phycology},
	year = {2022},
	note = {Publisher: Taylor \& Francis _eprint: https://doi.org/10.1080/26388081.2022.2103732},
	pages = {1{\textendash}20},
	abstract = {Haptophytes are an environmentally important phylum of eukaryotic phytoplankton, forming the second most abundant algal group after diatoms in recent estimates of ocean biodiversity. Haptophytes are phylogenetically and functionally diverse, including globally distributed and bloom-forming calcifying species such as Emiliania and Coccolithus, and non-calcifying orders that may form important components of phytoplankton communities in polar (Phaeocystis, Chrysochromulina) through to sub-tropical latitudes (Pavlova). In this review, we synthesize available phylogenetic, genomic and environmental information concerning the diversity of haptophyte life, considering the origins and placement on the eukaryotic tree; the diversity of the five major orders (Pavlovophyceae, Phaeocystales, Prymnesiales, the CSZ clade, and Isochrysidales); and the contrasting biogeographical distributions of haptophyte groups across different Tara Oceans sampling stations and size fractions. We additionally consider outstanding questions within the fields of haptophyte diversity and biology, particularly in the context of newly discovered and largely uncultured major groups (DPL lineages and Rappemonads), and current gaps in our knowledge of genomic content and niche adaptation across the haptophyte tree.},
	keywords = {18S rDNA, coccolithophorid, dispersal, meta-genomics, niche adaptation, prymnesiophyte, RCC1129, RCC1187, RCC1387, RCC1480, RCC1532, RCC851, RCC914, systematics, to read},
	issn = {null},
	doi = {10.1080/26388081.2022.2103732},
	url = {https://doi.org/10.1080/26388081.2022.2103732},
	author = {Penot, Mathias and Dacks, Joel B. and Read, Betsy and Dorrell, Richard G.}
}
@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 {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 {dominguez-martin_marine_2022,
	title = {Marine \textit{Synechococcus sp. Strain WH7803 Shows Specific Adaptative Responses to Assimilate Nanomolar Concentrations of Nitrate},
	journal = {Microbiology Spectrum},
	volume = {10},
	number = {4},
	year = {2022},
	month = {aug},
	pages = {e00187{\textendash}22},
	abstract = {Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrient availability and temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to micromolar ammonium or nitrogen starvation. We found that Synechococcus has a specific response to a nanomolar nitrate concentration that differs from the response shown under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentrations of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural environment.},
	keywords = {rcc752},
	issn = {2165-0497},
	doi = {10.1128/spectrum.00187-22},
	url = {https://journals.asm.org/doi/10.1128/spectrum.00187-22},
	author = {Dom{\'\i}nguez-Mart{\'\i}n, Maria Agustina and L{\'o}pez-Lozano, Antonio and Melero-Rubio, Yesica and G{\'o}mez-Baena, Guadalupe and Jim{\'e}nez-Estrada, Juan Andr{\'e}s and Kukil, Kateryna and D{\'\i}ez, Jes{\'u}s and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel},
	editor = {Hom, Erik F. Y.}
}
@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 {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 {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 {das_trace_2022,
	title = {Trace metals exposure in three different coastal compartments show specific morphological and reproductive traits across generations in a sentinel copepod},
	journal = {Science of The Total Environment},
	year = {2022},
	month = {nov},
	pages = {160378},
	abstract = {The effect of exposure from several compartments of the environment at the level of individuals were rarely investigated. This study reports the effect of contaminants from varied compartments like sediment resuspension, elutriation from resuspended sediment (extract) and seawater spiked trace metal mixtures (TM) on morphological and reproductive traits of the pelagic bioindicator copepod Eurytemora affinis. At the population level of E. affinis, lowest survival was observed in dissolved exposures (TM and extract) in the first generation (G1), showing some adaptation in the second generation (G2). An opposite trend for resuspended sediment showed higher sensitivity in survival at G2. At the individual level, prosome length and volume proved to be sensitive parameters for resuspended sediments, whereas clutch size and egg diameter were more sensitive to TM and extract. Although the generation of decontamination (G3, no exposure), showed a significant recovery at the population level (survival \% along with clutch size) of E. affinis exposed to resuspended sediment, morphological characteristics like prosome length and volume showed no such recovery (lower than control, p <0.05). To the contrary, dissolved exposure showed no significant recovery from G1 to G3 on neither survival \%, clutch size, egg diameter, prosome volume, but an increase of prosome length (p <0.05). Such tradeoffs in combatting the stress from varied sources of toxicity was observed in all exposures, from G1 to G3. The number of lipid droplets inside the body cavity of E. affinis showed a significant positive correlation with trace metal bioaccumulation (p <0.01) along with a negative correlation (p <0.05) with survival and clutch size in each treatment. This confirms the inability of copepods to utilize lipids under stressful conditions. Our study tenders certain morphological and reproductive markers that show specificity to different compartments of exposure, promising an advantage in risk assessment and fish feed studies.},
	keywords = {RCC1537},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2022.160378},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969722074800},
	author = {Das, Shagnika and Souissi, Anissa and Ouddane, Baghdad and Hwang, Jiang-Shiou and Souissi, Sami}
}
@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 {phelps_carbon_2021,
	title = {Carbon Isotope Fractionation in Noelaerhabdaceae Algae in Culture and a Critical Evaluation of the Alkenone Paleobarometer},
	journal = {Geochemistry, Geophysics, Geosystems},
	volume = {22},
	number = {7},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021GC009657},
	pages = {e2021GC009657},
	abstract = {The carbon isotope fractionation in algal organic matter ($\varepsilon$p), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates $\varepsilon$p to changes in cellular carbon demand relative to diffusive CO2 supply, with larger $\varepsilon$p values occurring at lower carbon demand relative to supply (i.e., abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few million years, has not been studied closely. Here, we subject G. oceanica to various CO2 levels by increasing pCO2 in the culture headspace, as opposed to increasing dissolved inorganic carbon (DIC) and alkalinity concentrations at constant pH. We note no substantial change in physiology, but observe an increase in $\varepsilon$p as carbon demand relative to supply decreases, consistent with DIC manipulations. We compile existing Noelaerhabdaceae $\varepsilon$p data and show that the diffusive model poorly describes the data. A meta-analysis of individual treatments (unique combinations of lab, strain, and light conditions) shows that the slope of the $\varepsilon$p response depends on the light conditions and range of carbon demand relative to CO2 supply in the treatment, which is incompatible with the diffusive model. We model $\varepsilon$p as a multilinear function of key physiological and environmental variables and find that both photoperiod duration and light intensity are critical parameters, in addition to CO2 and cell size. While alkenone carbon isotope ratios indeed record CO2 information, irradiance and other factors are also necessary to properly describe alkenone $\varepsilon$p.},
	keywords = {alkenone, carbon dioxide, carbon isotope, coccolithophore, irradiance, paleobarometry, rcc, RCC1303},
	issn = {1525-2027},
	doi = {10.1029/2021GC009657},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021GC009657},
	author = {Phelps, Samuel R. and Hennon, Gwenn M. M. and Dyhrman, Sonya T. and Hern{\'a}ndez Lim{\'o}n, Mar{\'\i}a D. and Williamson, Olivia M. and Polissar, Pratigya J.}
}
@article {olusoji_cyanofilter_2021,
	title = {cyanoFilter: An R package to identify phytoplankton populations from flow cytometry data using cell pigmentation and granularity},
	journal = {Ecological Modelling},
	volume = {460},
	year = {2021},
	pages = {109743},
	abstract = {Flow cytometry is often employed in ecology to measure traits and population size of bacteria and phytoplankton. This technique allows measuring millions of particles in a relatively small amount of time. However, distinguishing between different populations is not a straightforward task. Gating is a process in the identification of particles measured in flow cytometry. Gates can either be created manually using known characteristics of these particles, or by using automated clustering techniques. Available automated techniques implemented in statistical packages for flow cytometry are primarily developed for medicinal applications, while only two exist for phytoplankton. cyanoFilter is an R package built to identify phytoplankton populations from flow cytometry data. The package also integrates gating functions from two other automated algorithms. It also provides a gating accuracy test function that can be used to determine the accuracy of a desired gating function if monoculture flowcytometry data is available. The central algorithm in the package exploits observed pigmentation and granularity of phytoplankton cells. We demonstrate how its performance depends on strain similarity, using a model system of six cyanobacteria strains. Using the same system, we compare the performance of the central gating function in the package to similar functions in other packages.},
	keywords = {Ecology, flow cytometry, Gating, phytoplankton, RCC2375, rcc2380, RCC2434, RCC2555, Software},
	issn = {0304-3800},
	doi = {10.1016/j.ecolmodel.2021.109743},
	url = {https://www.sciencedirect.com/science/article/pii/S030438002100291X},
	author = {Olusoji, Oluwafemi D. and Spaak, Jurg W. and Holmes, Mark and Neyens, Thomas and Aerts, Marc and De Laender, Frederik}
}
@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}
}
@article {morais_detection_2021,
	title = {Detection of Alexandrium minutum dinoflagellate in environ- mental samples using electrochemical genosensor},
	journal = {Chemistry Proceedings},
	year = {2021},
	pages = {7},
	abstract = {Dinoflagellates are aquatic microorganisms that inhabit both salt and fresh waters. These microorganisms are mostly harmless, however, under certain conditions, some species rapidly reproduce forming water blooms that not only discolor the waters but also compromise the health of every organism in the vicinity, as some dinoflagellates produce potent toxins deemed unsafe for human health (e.g. Alexandrium minutum). In this work, a disposable electrochemical genosensor for the detection of the toxic dinoflagellate Alexandrium minutum was developed. The analytical platform methodology consisted in a sandwich format heterogeneous hybridization of complementary DNA sequences assay. The 70 bp A. minutum-specific targeting probe, the 45 bp fluorescein isothiocyanate-labelled signaling DNA probe and the 25 bp thiolated-DNA-capture probe were designed, after analyzing public databases. To maximize the complementary DNA hybridization and to avoid the formation of strong secondary structures, a mixed mercaptohexanol (MCH) and self-assembled monolayer (SAM) A. minutum-specific DNA-capture probe was immobilized onto disposable screen-printed gold electrodes (SPGE). Using chronoamperometric measurements, the enzymatic amplification of the electrochemical signal was obtained with a concentration range from 0.12 to 1.0 nM, a LD of 24.78 pM with a RSD < 5.2 \%. This electrochemical genosensor was successfully applied to the selective analysis of the targeted A. minutum specific region of denatured genomic DNA, extracted from toxic dinoflagellates present in the Atlantic Ocean.},
	keywords = {? No DOI found, RCC3029},
	author = {Morais, Stephanie L and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C and Barroso, M F{\'a}tima}
}
@article {robla_determination_2021,
	title = {Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters},
	journal = {Environmental Science: Water Research \& Technology},
	volume = {7},
	number = {7},
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
	month = {jul},
	pages = {1230{\textendash}1239},
	abstract = {The most important question in sampling is {\textquotedblleft}Is the sample representative of the target population?{\textquotedblright} This question is necessary to understand how valid the sample taken is to the original population and if generalizations can be made from the sample. Samples taken for water quality measurement range from 1 mL for bacterial contamination to 100 mL or up to 1000 L for protozoan parasites. With larger samples taken, the confidence in detecting rare events increases dramatically. Here we illustrate that hollow fiber filters as routinely used for kidney dialysis can be adapted for environmental use. The filters retain all organisms down to viral particles and organic matter above 70 kDA, the molecular cutoff for urea, one of the waste products removed in kidney dialysis. With these filters, 50 liters of water can be filtered in about 90 minutes. Backflush of the filters recovers viable cells with minimal cell lysis that can be processed downstream for molecular analysis. Recovery rates were as high as 89\% and 75\% for phytoplankton and bacteria, respectively.},
	keywords = {rcc, RCC1507},
	issn = {2053-1419},
	doi = {10.1039/D0EW00927J},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/ew/d0ew00927j},
	author = {Robla, J. and Garc{\'\i}a-Hierrro, J. and Alguacil, F. J. and Dittami, S. M. and Marie, D. and Villa, E. and Deragon, E. and Guillebault, D. and Mengs, G. and Medlin, L. K.}
}
@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 {Magalhaes2018,
	title = {Hemiselmis aquamarina sp . nov . (Cryptomonadales , Cryptophyceae), a cryptomonad with a novel phycobiliprotein type (Cr-PC 564)},
	journal = {Protist},
	volume = {in press},
	year = {2021},
	keywords = {RCC4102, RCC5634, to add},
	doi = {10.1016/j.protis.2021.125832},
	url = {https://doi.org/10.1016/j.protis.2021.125832},
	author = {Magalh{\~a}es, Karoline and Lopes dos Santos, Adriana and Vaulot, Daniel and de Oliveira, Mariana Cabral}
}
@article {Henry2021,
	title = {The influences of phytoplankton species, mineral particles and concentrations of dispersed oil on the formation and fate of marine oil-related aggregates},
	journal = {Science of the Total Environment},
	volume = {752},
	year = {2021},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1698,RCC1719,RCC290},
	month = {jan},
	pages = {141786},
	abstract = {The formation and fallout of oil-related marine snow have been associated with interactions between dispersed oil and small marine particles, like phytoplankton and mineral particles. In these studies, the influences of phytoplankton species, mineral particle concentration, and oil concentration on the aggregation of oil in seawater (SW) were investigated. The experiments were performed in a low-turbidity carousel incubation system, using natural SW at 13 {\textdegree}C. Aggregation was measured by silhouette camera analyses, and oil compound group distribution and depletion by gas chromatography (GC-FID or GC{\textendash}MS). Aggregates with median sizes larger than 500 ??m in diameter were measured in the presence of dispersed oil and the phytoplankton species Thalassiosira rotula, Phaeocystis globosa, Skeletonema pseudocostatum, but not with the microalgae Micromonas pusilla. When mineral particles (diatomaceous earth) were incubated at different concentrations (5{\textendash}30 mg/L) with dispersed oil and S. pseudocostatum, the largest aggregates were measured at the lower mineral particle concentration (5 mg/L). Since dispersed oil rapidly dilutes in the marine water column, experiments were performed with oil concentrations of from 10 mg/L to 0.01 mg/L in the presence of S. pseudocostatum and diatomaceous earth. Aggregates larger than 500 ??m was measured only at the highest oil concentrations (10 mg/L). However, oil attachment to the marine particles were also measured at low oil concentrations (<=1 mg/L). Depletion of oil compound groups (n-alkanes, naphthalenes, PAHs, decalins) were measured at all oil concentrations, both in aggregate and water phases, with biodegradation as the expected main depletion process. These results showed that oil concentration may be important for oil-related marine snow formation, but that even oil droplets at low concentrations may attach to the particles and be transported by prevailing currents.},
	keywords = {Aggregation, Dispersed oil, Marine snow, Mineral particles, phytoplankton, RCC1698, RCC1719, RCC290},
	issn = {18791026},
	doi = {10.1016/j.scitotenv.2020.141786},
	author = {Henry, Ingrid A. and Netzer, Roman and Davies, Emlyn and Brakstad, Odd Gunnar}
}
@inbook {reddy_marine_2021,
	title = {Marine Biodiscovery in a Changing World},
	booktitle = {Progress in the Chemistry of Organic Natural Products 116},
	series = {Progress in the Chemistry of Organic Natural Products},
	year = {2021},
	pages = {1{\textendash}36},
	publisher = {Springer International Publishing},
	organization = {Springer International Publishing},
	address = {Cham},
	abstract = {The term {\textquotedblleft}marine biodiscovery{\textquotedblright} has been recently been adopted to describe the area of marine natural products dedicated to the search of new drugs. Several maritime countries such as Australia, New Zealand, South Korea, and Japan as well as some European countries have invested significantly in this area of research over the last 50 years. In the late 2000s, research in this field has received significant interest and support in Ireland for exploring new marine bioresources from the nutrient-rich waters of the Northeastern Atlantic Ocean. Despite undeniable success exemplified by the marketing of new drugs, especially in oncology, the integration of new technical but also environmental aspects should be considered. Indeed, global change, particularly in our oceans, such as climate change, biodiversity loss, and the emergence of microbial pathogens, not only affects the environment but ultimately contributes to social inequalities. In this contribution, new avenues and best practices are proposed, such as the development of biorepositories and shared data for the future of marine biodiscovery research. The extension of this type of scientific work will allow humanity to finally make the optimum use of marine bioresources.},
	keywords = {Bioprospecting, Biorepositories, Data management system, Marine biodiscovery, Marine natural products, Screenings, taxonomy},
	isbn = {978-3-030-80560-9},
	doi = {10.1007/978-3-030-80560-9_1},
	url = {https://doi.org/10.1007/978-3-030-80560-9_1},
	author = {Reddy, Maggie M. and Jennings, Laurence and Thomas, Olivier P.},
	editor = {Kinghorn, A. Douglas and Falk, Heinz and Gibbons, Simon and Asakawa, Yoshinori and Liu, Ji-Kai and Dirsch, Verena M.}
}
@article {dayras_microalgal_2021,
	title = {Microalgal Diet Influences the Nutritive Quality and Reproductive Investment of the Cyclopoid Copepod Paracyclopina nana},
	journal = {Frontiers in Marine Science},
	volume = {8},
	year = {2021},
	pages = {1147},
	abstract = {Copepods represent an interesting alternative or a complement live food to brine shrimps and rotifers commonly used in aquaculture. They constitute the natural prey of many fish species and therefore do not require a potential nutritional enrichment. But an optimization of the microalgal diets used to feed copepods is essential to improve their mass culture. This study examined the effects of seven microalgal diets, namely single-species diets of Rhodomonas salina (R), Tisochrysis lutea (T), and Pavlova lutheri (=Diacronema lutheri) (P), two-species diets (R + T, T + P, and R + P), and a three-species diet (R + T + P), on the fatty acid and monosaccharide composition of the cyclopoid copepod Paracyclopina nana as well as its reproductive investment. Experiments were run during 15 days in 10-L beakers; starting with nauplii collected from a large 300-L batch culture. Copepods fatty acid contents were studied, particularly the relative amounts of docosahexaenoic acid (DHA) and eicosa-pentaenoic acid (EPA). The R + T, R, and T diets induced the highest total fatty acid amount in copepods. R + T and R also generated the lowest DHA/EPA ratios in copepods due to high EPA contents. The highest value of total monosaccharides was found in copepods fed with R + T + P. Diets R + T and R induced the greatest prosome volumes and clutch volumes in ovigerous females. Both prosome volume and clutch volume in P. nana ovigerous females were correlated to the individual EPA amount. The results demonstrated that all diets including R. salina enhanced the productivity of P. nana in mass culture, particularly when combined with T. lutea. R. salina, and T. lutea induced complementary fatty acid and monosaccharide profiles, confirming that R + T represents the best microalgae combination for productive culture of P. nana. Conversely, P. lutheri did not enhance the nutritional profile nor the fecundity of P. nana in the culture. This study is the first to demonstrate that R. salina is a suitable microalga for productive mass culture of P. nana for use as live food in aquaculture.},
	keywords = {rcc, RCC1349, RCC1537, RCC20},
	issn = {2296-7745},
	doi = {10.3389/fmars.2021.697561},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.697561},
	author = {Dayras, Paul and Bialais, Capucine and Sadovskaya, Irina and Lee, Min-Chul and Lee, Jae-Seong and Souissi, Sami}
}
@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 {decamp_new_2021,
	title = {A New, Quick, and Simple Protocol to Evaluate Microalgae Polysaccharide Composition},
	journal = {Marine Drugs},
	volume = {19},
	number = {2},
	year = {2021},
	pages = {101},
	abstract = {In this work, a new methodological approach, relying on the high specificity of enzymes in a complex mixture, was developed to estimate the composition of bioactive polysaccharides produced by microalgae, directly in algal cultures. The objective was to set up a protocol to target oligomers commonly known to be associated with exopolysaccharides{\textquoteright} (EPS) nutraceutical and pharmaceutical activities (i.e., rhamnose, fucose, acidic sugars, etc.) without the constraints classically associated with chromatographic methods, while maintaining a resolution sufficiently high to enable their monitoring in the culture system. Determination of the monosaccharide content required the application of acid hydrolysis (2 M trifluoroacetic acid) followed by NaOH (2 M) neutralization. Quantification was then carried out directly on the fresh hydrolysate using enzyme kits corresponding to the main monosaccharides in a pre-determined composition of the polysaccharides under analysis. Initial results showed that the enzymes were not sensitive to the presence of TFA and NaOH, so the methodology could be carried out on fresh hydrolysate. The limits of quantification of the method were estimated as being in the order of the log of nanograms of monosaccharides per well, thus positioning it among the chromatographic methods in terms of analytical performance. A comparative analysis of the results obtained by the enzymatic method with a reference method (high-performance anion-exchange chromatography) confirmed good recovery rates, thus validating the closeness of the protocol. Finally, analyses of raw culture media were carried out and compared to the results obtained in miliQ water; no differences were observed. The new approach is a quick, functional analysis method allowing routine monitoring of the quality of bioactive polysaccharides in algal cultures grown in photobioreactors.},
	keywords = {rcc2380, RCC3438},
	issn = {1660-3397},
	doi = {10.3390/md19020101},
	url = {https://www.mdpi.com/1660-3397/19/2/101},
	author = {Decamp, Antoine and Michelo, Orane and Rabbat, Christelle and Laroche, C{\'e}line and Grizeau, Dominique and Pruvost, J{\'e}r{\'e}my and Gon{\c c}alves, Olivier}
}
@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 {das_single_2021,
	title = {Single toxicity of arsenic and combined trace metal exposure to a microalga of ecological and commercial interest: Diacronema lutheri},
	journal = {Chemosphere},
	year = {2021},
	pages = {132949},
	abstract = {Eco-toxicological assays with species of economic interest such as Diacronema lutheri are essential for industries that produce aquaculture feed, natural food additives and also in drug developing industries. Our study involved the exposure of a single and combined toxicity of arsenic (As V) to D. lutheri for the entire algal growth phase and highlighted that a combined exposure of As V with other essential (Copper, Cu; Nickel, Ni) and non-essential (Cadmium, Cd; Lead, Pb) trace metals reduced significantly the cell number, chlorophyll a content, and also significantly increased the de-epoxidation ratio (DR) as a stress response when compared to the single toxicity of As V. Arsenic, as one of the ubiquitous trace metal and an active industrial effluent is reported to have an increased bio-concentration factor when in mixture with other trace metals in this study. In the combined exposure, the concentration of total As bio-accumulated by D. lutheri was higher than in the single exposure. Hence, polluted areas with the prevalence of multiple contaminants along with the highly toxic trace metals like As can impose a greater risk to the exposed organisms that may get further bio-magnified in the food chain. Our study highlights the consequences and the response of D. lutheri in terms of contamination from single and multiple trace metals in order to obtain a safer biomass production for the growing need of natural derivatives.},
	keywords = {Arsenic, bioaccumulation, Bioconcentration factor, Chlorophyll, de-epoxidation ratio, RCC1537, Trace metals mixture},
	issn = {0045-6535},
	doi = {10.1016/j.chemosphere.2021.132949},
	url = {https://www.sciencedirect.com/science/article/pii/S0045653521034214},
	author = {Das, Shagnika and Gevaert, Fran{\c c}ois and Ouddane, Baghdad and Duong, Gwendoline and Souissi, Sami}
}
@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}
}
@article {Pan2020,
	title = {Assessments of first feeding protocols on the larviculture of California grunion Leuresthes tenuis (Osteichthyes: Atherinopsidae)},
	journal = {Aquaculture Research},
	volume = {51},
	number = {7},
	year = {2020},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: RCC350},
	month = {jul},
	pages = {3054{\textendash}3058},
	keywords = {California grunion, Copepod, larval rearing, live feed, quiescent egg, RCC350},
	issn = {13652109},
	doi = {10.1111/are.14637},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/are.14637},
	author = {Pan, Yen Ju and D{\'e}pos{\'e}, Emilien and Souissi, Anissa and H{\'e}nard, St{\'e}phane and Schaadt, Mike and Mastro, Ed and Souissi, Sami}
}
@article {Androuin2020,
	title = {Better off alone? New insights in the symbiotic relationship between the flatworm Symsagittifera roscoffensis and the microalgae Tetraselmis convolutae},
	journal = {Symbiosis},
	number = {Keebles 1910},
	year = {2020},
	note = {tex.mendeley-tags: RCC1563},
	month = {jun},
	abstract = {The acoel flatworm Symsagittifera roscoffensis lives in obligatory symbiosis with the microalgal chlorophyte Tetraselmis convolutae. Although this interaction has been studied for more than a century, little is known on the potential reciprocal benefits of both partners, a subject that is still controversial. In order to provide new insights into this question, we have compared the photophysiology of the free-living microalgae to the symbiotic form in the flatworm, both acclimated at different light irradiances. Photosynthesis {\textendash} Irradiance curves showed that the free-living T. convolutae had greater photosynthetic performance (i.e., oxygen production rates, ability to harvest light) than their symbiotic form, regardless of the light acclimation. However, they were affected by photoinhibition under high irradiances, which did not happen for the symbiotic form. The resistance of symbiotic microalgae to photoinhibition were corroborated by pigment analyses, which evidenced the induction of photoprotective mechanisms such as xanthophyll cycle as well as lutein and β-carotene accumulation. These processes were induced even under low light acclimation and exacerbated upon high light acclimation, suggesting a global stress situation for the symbiotic microalgae. We hypothesize that the internal conditions in the sub-epidermal zone of the flatworm (e.g., osmotic and pH), as well as the phototaxis toward high light imposed by the worm in its environment, would be major reasons for this chronic stress situation. Overall, our study suggests that the relationship between S. roscoffensis and T. convolutae may be a farming strategy in favor of the flatworm rather than a symbiosis with mutual benefits.},
	keywords = {Animal-plant, Photobiology, RCC1563, symbiosis, Symsagittifera roscoffensis, Tetraselmis convolutae},
	issn = {0334-5114},
	doi = {10.1007/s13199-020-00691-y},
	url = {http://link.springer.com/10.1007/s13199-020-00691-y},
	author = {Androuin, Thibault and Six, Christophe and Bordeyne, Fran{\c c}ois and de Bettignies, Florian and Noisette, Fanny and Davoult, Dominique}
}
@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 {Morais2020,
	title = {Electrochemical genosensor for the detection of Alexandrium minutum dinoflagellates},
	journal = {Talanta},
	year = {2020},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC3029},
	pages = {121416},
	keywords = {RCC3029},
	issn = {00399140},
	doi = {10.1016/j.talanta.2020.121416},
	url = {https://doi.org/10.1016/j.talanta.2020.121416 https://linkinghub.elsevier.com/retrieve/pii/S0039914020307074},
	author = {Morais, Stephanie L. and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C. and F{\'a}tima Barroso, M.}
}
@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 {Henry2020,
	title = {Formation and fate of oil-related aggregates (ORAs) in seawater at different temperatures},
	journal = {Marine Pollution Bulletin},
	volume = {159},
	number = {July},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC4289},
	month = {oct},
	pages = {111483},
	abstract = {In this study, the formation and fate of oil-related aggregates (ORAs) from chemically dispersed oil in seawater (SW) were investigated at different temperatures (5 {\textdegree}C, 13 {\textdegree}C, 20 {\textdegree}C). Experiments in natural SW alone, and in SW amended with typical marine snow constituents (phytoplankton and mineral particles), showed that the presence of algae stimulated the formation of large ORAs, while high SW temperature resulted in faster aggregate formation. The ORAs formed at 5 {\textdegree}C and 13 {\textdegree}C required mineral particles for sinking, while the aggregates also sank in the absence of mineral particles at 20{\textdegree}. Early in the experimental periods, oil compound accumulation in ORAs was faster than biodegradation, particularly in aggregates with algae, followed by rapid biodegradation. High abundances of bacteria associated with hydrocarbon biodegradation were determined in the ORAs, together with algae-associated bacteria, while clustering analyses showed separation between bacterial communities in experiments with oil alone and oil with algae/mineral particles.},
	keywords = {Aggregation, biodegradation, Dispersed oil, Marine snow, Microbial communities, RCC4289, Sinking},
	issn = {0025326X},
	doi = {10.1016/j.marpolbul.2020.111483},
	url = {https://doi.org/10.1016/j.marpolbul.2020.111483 https://linkinghub.elsevier.com/retrieve/pii/S0025326X20306019},
	author = {Henry, Ingrid A. and Netzer, Roman and Davies, Emlyn J. and Brakstad, Odd Gunnar}
}
@article {Hackl2019,
	title = {Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis},
	journal = {Scientific Data},
	volume = {7},
	number = {1},
	year = {2020},
	note = {tex.mendeley-tags: RCC4623,RCC4624,RCC4625,RCC970},
	month = {dec},
	pages = {29},
	keywords = {RCC4623, RCC4624, RCC4625, RCC970},
	issn = {2052-4463},
	doi = {10.1038/s41597-020-0363-4},
	url = {http://www.nature.com/articles/s41597-020-0363-4},
	author = {Hackl, Thomas and Martin, Roman and Barenhoff, Karina and Duponchel, Sarah and Heider, Dominik and Fischer, Matthias G.}
}
@article {bottini_high_2020,
	title = {High resolution spatial analyses of trace elements in coccoliths reveal new insights into element incorporation in coccolithophore calcite},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {9825},
	abstract = {Coccolithophores are phytoplanktonic algae which produce an exoskeleton made of single platelets of calcite named coccoliths. They are widespread in all oceans and directly impact the short- and long-term C cycle. The study of coccolith size, morphology and elemental composition reveals important information regarding the ability of the cell to calcify and on the factors that influence this process. In this regard, very little is known about coccolith composition and its changes under altered environmental conditions. Here, we present high resolution (50 {\texttimes} 50 nm) elemental spatial distribution in pristine coccoliths of Coccolithus pelagicus and Gephyrocapsa oceanica reconstructed via X-ray fluorescence analyses at synchrotron. The studied specimens are from control culture and metal-enriched (V, Ni, Zn and Pb) experiments. The analysed specimens produced under stress conditions, display an irregular shape and are thinner, especially in the external rim, with ca. 1/3 lower Ca concentrations compared to specimens from the control. The same specimens also have higher Sr/Ca ratio with highest values in the coccolith external rim, suggesting that difficulty in calcification is additionally reflected in increased Sr/Ca ratios. Selenium is found in the coccolith as possible substitute of carbonate in the calcite. V and Pb apparently did not interact with the coccoliths while Zn and Ni were deposited on the coccolith surface.},
	keywords = {Environmental chemistry, Environmental impact, Marine chemistry, Pollution remediation, RCC1198, RCC1303},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-66503-x},
	url = {http://www.nature.com/articles/s41598-020-66503-x},
	author = {Bottini, Cinzia and Dapiaggi, Monica and Erba, Elisabetta and Faucher, Giulia and Rotiroti, Nicola}
}
@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 {Vigor2020,
	title = {Isoprostanoid profiling of marine microalgae},
	journal = {Biomolecules},
	volume = {10},
	number = {7},
	year = {2020},
	note = {Publisher: MDPI AG tex.mendeley-tags: RCC1349,RCC20,RCC69},
	month = {jul},
	pages = {1073},
	abstract = {{\textexclamdown}p{\textquestiondown}Algae result from a complex evolutionary history that shapes their metabolic network. For example, these organisms can synthesize different polyunsaturated fatty acids, such as those found in land plants and oily fish. Due to the presence of numerous double-bonds, such molecules can be oxidized nonenzymatically, and this results in the biosynthesis of high-value bioactive metabolites named isoprostanoids. So far, there have been only a few studies reporting isoprostanoid productions in algae. To fill this gap, the current investigation aimed at profiling isoprostanoids by liquid chromatography -mass spectrometry/mass spectrometry (LC-MS/MS) in four marine microalgae. A good correlation was observed between the most abundant polyunsaturated fatty acids (PUFAs) produced by the investigated microalgal species and their isoprostanoid profiles. No significant variations in the content of oxidized derivatives were observed for Rhodomonas salina and Chaetoceros gracilis under copper stress, whereas increases in the production of C18-, C20- and C22-derived isoprostanoids were monitored in Tisochrysis lutea and Phaeodactylum tricornutum. In the presence of hydrogen peroxide, no significant changes were observed for C. gracilis and for T. lutea, while variations were monitored for the other two algae. This study paves the way to further studying the physiological roles of isoprostanoids in marine microalgae and exploring these organisms as bioresources for isoprostanoid production.{\textexclamdown}/p{\textquestiondown}},
	keywords = {Isoprostanoids, Micro-LC-MS/MS, Microalgae, Oxidative stress, PUFAs, RCC1349, RCC20, RCC69},
	issn = {2218-273X},
	doi = {10.3390/biom10071073},
	url = {https://www.mdpi.com/2218-273X/10/7/1073},
	author = {Vigor, Claire and Oger, Camille and Reversat, Guillaume and Rocher, Amandine and Zhou, Bingqing and Linares-Maurizi, Amandyne and Guy, Alexandre and Bultel-Ponc{\'e}, Val{\'e}rie and Galano, Jean-Marie and Vercauteren, Joseph and Durand, Thierry and Potin, Philippe and Tonon, Thierry and Leblanc, Catherine}
}
@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 {Aveiro2020,
	title = {The polar lipidome of cultured emiliania huxleyi: A source of bioactive lipids with relevance for biotechnological applications},
	journal = {Biomolecules},
	volume = {10},
	number = {10},
	year = {2020},
	note = {tex.ids= Aveiro2020a tex.mendeley-tags: RCC1250 publisher: Multidisciplinary Digital Publishing Institute},
	pages = {1434},
	abstract = {Polar lipids from microalgae have aroused greater interest as a natural source of omega-3 (n-3) polyunsaturated fatty acids (PUFA), an alternative to fish, but also as bioactive compounds with multiple applications. The present study aims to characterize the polar lipid profile of cultured microalga Emiliania huxleyi using hydrophilic interaction liquid chromatography coupled with high-resolution mass spectrometry (HILIC{\textendash}MS) and fatty acids (FA) analysis by gas chromatography (GC{\textendash}MS). The lipidome of E. huxleyi revealed the presence of distinct n-3 PUFA (40\% of total FA), namely docosahexaenoic acid (22:6n-3) and stearidonic acid (18:4n-3), which give this microalga an increased commercial value as a source of n-3 PUFA present in the form of polar lipids. A total of 134 species of polar lipids were identified and some of these species, particularly glycolipids, have already been reported for their bioactive properties. Among betaine lipids, the diacylglyceryl carboxyhydroxymethylcholine (DGCC) class is the least reported in microalgae. For the first time, monomethylphosphatidylethanolamine (MMPE) has been found in the lipidome of E. huxleyi. Overall, this study highlights the potential of E. huxleyi as a sustainable source of high-value polar lipids that can be exploited for different applications, namely human and animal nutrition, cosmetics, and pharmaceuticals.},
	keywords = {Emiliania huxleyi, haptophyta, Lipidomics, Mass spectrometry, Microalgae, RCC1250},
	issn = {2218-273X},
	doi = {10.3390/biom10101434},
	url = {https://www.mdpi.com/2218-273X/10/10/1434},
	author = {Aveiro, Susana S. and Melo, T{\^a}nia and Figueiredo, Ana and Domingues, Pedro and Pereira, Hugo and Maia, In{\^e}s B. and Silva, Joana and Domingues, M. Ros{\'a}rio and Nunes, Cl{\'a}udia and Moreira, Ana S. P.}
}
@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 {Derilus2020,
	title = {Synergism between the Black Queen effect and the proteomic constraint on genome size reduction in the photosynthetic picoeukaryotes},
	journal = {Scientific Reports},
	volume = {10},
	number = {1},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC1110,RCC1116,RCC809},
	pages = {8918},
	keywords = {RCC1110, RCC1116, RCC809},
	issn = {2045-2322},
	doi = {10.1038/s41598-020-65476-1},
	url = {http://dx.doi.org/10.1038/s41598-020-65476-1 http://www.nature.com/articles/s41598-020-65476-1},
	author = {Derilus, D and Rahman, M Z and Pinero, F and Massey, S E}
}
@article {Demory2020,
	title = {A thermal trade-off between viral production and degradation drives phytoplankton-virus population dynamics},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC4229,RCC4265,RCC451,RCC4523,RCC829,RCC834},
	month = {aug},
	pages = {2020.08.18.256156},
	abstract = {Marine viruses interact with their microbial hosts in dynamic environments shaped by variations in abiotic factors, including temperature. However, the impacts of temperature on viral infection of phytoplankton are not well understood. Here we coupled mathematical modeling with experimental datasets to explore the effect of temperature on three Micromonas-prasinovirus pairs. Our model shows the negative consequences of high temperatures on infection and suggests a temperature-dependent threshold between viral production and degradation. Modeling long-term dynamics in environments with different average temperatures revealed the potential for long-term host-virus coexistence, epidemic free, or habitat loss states. Hence, we generalized our model to global sea surface temperature of present and future seas and show that climate change may influence virus-host dynamics differently depending on the virus-host pair. Our study suggests that temperature-dependent changes in the infectivity of virus particles may lead to shifts in virus-host habitats in warmer oceans, analogous to projected changes in the habitats of macro-and microorganisms .},
	keywords = {RCC4229, RCC4265, RCC451, RCC4523, RCC829, RCC834},
	doi = {10.1101/2020.08.18.256156},
	url = {https://doi.org/10.1101/2020.08.18.256156},
	author = {Demory, David and Weitz, Joshua S and Baudoux, Anne-claire and Touzeau, Suzanne and Simon, Natalie and Rabouille, Sophie and Sciandra, Antoine and Bernard, Olivier}
}
@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 {Yau2020,
	title = {Virus-host coexistence in phytoplankton through the genomic lens},
	journal = {Science Advances},
	volume = {6},
	number = {14},
	year = {2020},
	note = {tex.mendeley-tags: RCC2590,RCC2596},
	month = {apr},
	pages = {eaay2587},
	abstract = {Virus-microbe interactions in the ocean are commonly described by {\textquotedblleft}boom and bust{\textquotedblright} dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this {\textquotedblleft}accordion{\textquotedblright} chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.},
	keywords = {RCC2590, RCC2596},
	issn = {2375-2548},
	doi = {10.1126/sciadv.aay2587},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587},
	author = {Yau, Sheree and Krasovec, Marc and Benites, L. Felipe and Rombauts, Stephane and Groussin, Mathieu and Vancaester, Emmelien and Aury, Jean-Marc and Derelle, Evelyne and Desdevises, Yves and Escande, Marie-Line and Grimsley, Nigel and Guy, Julie and Moreau, Herv{\'e} and Sanchez-Brosseau, Sophie and Van de Peer, Yves and Vandepoele, Klaas and Gourbi{\`e}re, S{\'e}bastien and Piganeau, Gwenael}
}
@article {Decelle2019,
	title = {Algal remodeling in a ubiquitous planktonic photosymbiosis},
	journal = {Current Biology},
	volume = {29},
	number = {6},
	year = {2019},
	note = {Publisher: Cell Press tex.mendeley-tags: RCC1719},
	month = {mar},
	pages = {968{\textendash}978.e4},
	abstract = {Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.},
	keywords = {RCC1719},
	issn = {0960-9822},
	doi = {10.1016/J.CUB.2019.01.073},
	url = {https://www.sciencedirect.com/science/article/abs/pii/S0960982219301320$\#$undfig1},
	author = {Decelle, Johan and Stryhanyuk, Hryhoriy and Gallet, Benoit and Veronesi, Giulia and Schmidt, Matthias and Balzano, Sergio and Marro, Sophie and Uwizeye, Clarisse and Jouneau, Pierre-Henri and Lupette, Josselin and Jouhet, Juliette and Mar{\'e}chal, {\'E}ric and Schwab, Yannick and Schieber, Nicole L. and Tucoulou, R{\'e}mi and Richnow, Hans and Finazzi, Giovanni and Musat, Niculina}
}
@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 {Weiss2019,
	title = {Hydrogen isotope fractionation response to salinity and alkalinity in a calcifying strain of Emiliania huxleyi},
	journal = {Organic Geochemistry},
	year = {2019},
	note = {Publisher: Elsevier Ltd tex.mendeley-tags: RCC2050},
	month = {jun},
	keywords = {RCC2050},
	issn = {01466380},
	doi = {10.1016/j.orggeochem.2019.06.001},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0146638019301020},
	author = {Weiss, Gabriella M. and Roepert, Anne and Middelburg, Jack J. and Schouten, Stefan and Sinninghe Damst{\'e}, Jaap S. and van der Meer, Marcel T.J.}
}
@article {Demory2019,
	title = {Picoeukaryotes of the Micromonas genus: sentinels of a warming ocean},
	journal = {The ISME Journal},
	volume = {13},
	number = {1},
	year = {2019},
	note = {tex.ids= Demory2018 tex.mendeley-tags: RCC114,RCC1697,RCC1862,RCC2257,RCC2306,RCC299,RCC451,RCC497,RCC746,RCC829,RCC834 publisher: Nature Publishing Group},
	month = {jan},
	pages = {132{\textendash}146},
	abstract = {Photosynthetic picoeukaryotesx in the genus Micromonas show among the widest latitudinal distributions on Earth, experiencing large thermal gradients from poles to tropics. Micromonas comprises at least four different species often found in sympatry. While such ubiquity might suggest a wide thermal niche, the temperature response of the different strains is still unexplored, leaving many questions as for their ecological success over such diverse ecosystems. Using combined experiments and theory, we characterize the thermal response of eleven Micromonas strains belonging to four species. We demonstrate that the variety of specific responses to temperature in the Micromonas genus makes this environmental factor an ideal marker to describe its global distribution and diversity. We then propose a diversity model for the genus Micromonas, which proves to be representative of the whole phytoplankton diversity. This prominent primary producer is therefore a sentinel organism of phytoplankton diversity at the global scale. We use the diversity within Micromonas to anticipate the potential impact of global warming on oceanic phytoplankton. We develop a dynamic, adaptive model and run forecast simulations, exploring a range of adaptation time scales, to probe the likely responses to climate change. Results stress how biodiversity erosion depends on the ability of organisms to adapt rapidly to temperature increase.},
	keywords = {Biogeography, change ecology, Climate, microbial ecology, RCC114, RCC1697, RCC1862, RCC2257, RCC2306, RCC299, RCC451, RCC497, RCC746, RCC829, RCC834},
	issn = {1751-7362},
	doi = {10.1038/s41396-018-0248-0},
	url = {http://www.nature.com/articles/s41396-018-0248-0},
	author = {Demory, David and Baudoux, Anne-claire and Monier, Adam and Simon, Nathalie and Six, Christophe and Ge, Pei and Rigaut-jalabert, Fabienne and Marie, Dominique and Sciandra, Antoine and Bernard, Olivier and Rabouille, Sophie}
}
@article {Gaignard2019,
	title = {Screening of marine microalgae: Investigation of new exopolysaccharide producers},
	journal = {Algal Research},
	volume = {44},
	year = {2019},
	note = {tex.ids= Gaignard2019a tex.mendeley-tags: RCC1084,RCC1196,RCC1504,RCC1714,RCC1774,RCC1786,RCC1863,RCC1978,RCC1983,RCC2035,RCC232,RCC2350,RCC2352,RCC2368,RCC2380,RCC2381,RCC2383,RCC2436,RCC2558,RCC2598,RCC2608,RCC2614,RCC2624,RCC2638,RCC269,RCC2696,RCC2703,RCC2932,RCC3069,RCC3072,RCC3092,RCC3093,RCC3436,RCC3649,RCC377,RCC4094,RCC4438,RCC4555,RCC4621,RCC4631,RCC4657,RCC76,RCC775,RCC821,RCC97 publisher: Elsevier},
	month = {dec},
	pages = {101711},
	abstract = {Biopolymers, such as exopolysaccharides are widely exploited by industry as hydrocolloids (gelling, thickening agents) and biological agents (anti-inflammatory, anti-parasitic, antioxidant, etc.). In this study, 166 marine microalgae and cyanobacteria species have been screened in order to identify strains producing original exopolysaccharides. This screening allowed the highlighting of 45 positive strains. In a second time, the monosaccharide compositions from 20 EPS of them were determined by GC/MS and HPAEC-PAD. The results led to a discovery of 8 new genera of microalgae producing EPS, including polymers with a very original composition like richness in GlcA. Finally, a phylogenic tree has been contructed in order to assess the link between the phylogeny of microalgae and the global composition of their exopolymers, based on data obtained in this study and from the literature.},
	keywords = {rcc1084, RCC1196, RCC1504, RCC1714, RCC1774, RCC1786, RCC1863, RCC1978, RCC1983, RCC2035, RCC232, RCC2350, RCC2352, RCC2368, rcc2380, RCC2381, RCC2383, RCC2436, RCC2558, RCC2598, RCC2608, RCC2614, RCC2624, RCC2638, RCC269, RCC2696, RCC2703, RCC2932, RCC3069, RCC3072, RCC3092, RCC3093, RCC3436, RCC3649, RCC377, RCC4094, RCC4438, RCC4555, RCC4621, RCC4631, RCC4657, RCC76, RCC775, RCC821, RCC97},
	issn = {22119264},
	doi = {10.1016/j.algal.2019.101711},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926419303261 https://linkinghub.elsevier.com/retrieve/pii/S2211926419303261},
	author = {Gaignard, C. and Laroche, C. and Pierre, G. and Dubessay, P. and Delattre, C. and Gardarin, C. and Gourvil, P. and Probert, I. and Dubuffet, A. and Michaud, P.}
}
@article {Breton2019,
	title = {Unveiling membrane thermoregulation strategies in marine picocyanobacteria},
	journal = {New Phytologist},
	number = {July},
	year = {2019},
	note = {ISBN: 0000000244022 tex.mendeley-tags: RCC2374,RCC2385,RCC515,RCC539},
	month = {oct},
	pages = {nph.16239},
	keywords = {RCC2374, RCC2385, RCC515, rcc539},
	issn = {0028-646X},
	doi = {10.1111/nph.16239},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.16239},
	author = {Breton, Sol{\`e}ne and Jouhet, Juliette and Guyet, Ulysse and Gros, Val{\'e}rie and Pittera, Justine and Demory, David and Partensky, Fr{\'e}d{\'e}ric and Dor{\'e}, Hugo and Ratin, Morgane and Mar{\'e}chal, {\'E}ric and Nguyen, Ngoc An and Garczarek, Laurence and Six, Christophe}
}
@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 {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 {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 {Kenworthy2018,
	title = {Compared stress tolerance to short-term exposure in native and invasive tunicates from the NE Atlantic: when the invader performs better},
	journal = {Marine Biology},
	volume = {165},
	number = {10},
	year = {2018},
	note = {tex.mendeley-tags: RCC179},
	pages = {164},
	abstract = {{The combined impact of invasive species and climate change threatens natural systems worldwide, often facilitating the expansion of harmful invasive species. It is imperative to understand the mechanisms behind why species become invasive and widespread. Traditionally, it is thought that invasive species have greater tolerances to a wider array of environmental conditions than natives. We, therefore, tested the hypothesis that invasive species are more tolerant to the effects of short-term exposure to temperature and salinity stress. Using unifactorial experiments, we compared the tolerances of two common fouling NE Atlantic ascidians, the native Ciona intestinalis and the invasive Styela clava, to increased temperature and decreased salinity. We measured lethal and behavioural responses affecting 50\% of populations to give an indication of the tolerance limits for temperature (LT50) and salinity (EC50), and respiration rate to give an indication of the change in metabolic response. The invasive S. clava was more tolerant to increased stress (LT50 = 29.5 {\textdegree}C},
	keywords = {RCC179},
	issn = {1432-1793},
	doi = {10.1007/s00227-018-3420-1},
	url = {https://doi.org/10.1007/s00227-018-3420-1},
	author = {Kenworthy, Joseph M and Davoult, Dominique and Lejeusne, Christophe}
}
@article {Dadaglio2018,
	title = {Differential responses of bacteria to diatom-derived dissolved organic matter in the Arctic Ocean},
	journal = {Aquatic Microbial Ecology},
	volume = {82},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: 2018,rcc},
	pages = {59{\textendash}72},
	abstract = {ABSTRACT: The Arctic sea ice cover is undergoing an unprecedented decline due to climate change. This loss may result in the earlier start of ice algae blooms and more intense phytoplankton blooms, leading to higher concentrations of dissolved organic matter (DOM) derived from primary production. We investigated the response of early summer Arctic bacterial communities to the addition of Arctic diatom-derived DOM through biodegradation experiments in Baffin Bay. DOM produced by the planktonic diatom Chaetoceros neogracilis and the sea ice diatom Fragilariopsis cylindrus was added to seawater from 3 stations with different ice cover (2 ice zones and 1 open water zone) for 12 d. At the 3 stations, the addition of inorganic nutrients (PO4 and NO3) was not sufficient to stimulate bacterial growth compared to the controls, suggesting that bacteria were mainly limited by organic carbon. The addition of DOM from C. neogracilis stimulated bacterial abundance and production, with a more pronounced response in the ice zone compared to the open water zone. The enhanced bacterial metabolism was accompanied by changes in the bacterial community composition determined by 16S rRNA sequencing, driven by operational taxonomic units (OTUs) related to Pseudoalteromonas and Polaribacter that increased in relative abundance with DOM addition. Moreover, in the ice zone, DOM from C. neogracilis induced a priming effect on the bacterial utilization of ambient DOM. Our findings suggest that phytoplankton blooms, through the production of labile organic matter, will strongly affect bacterial heterotrophic activity, composition and dissolved organic carbon cycling in the Arctic Ocean.},
	keywords = {2018, rcc},
	doi = {10.3354/ame01883},
	url = {https://www.int-res.com/abstracts/ame/v82/n1/p59-72},
	author = {Dadaglio, L and Dinasquet, J and Obernosterer, I and Joux, F}
}
@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 {Rastogi2017,
	title = {Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {ISBN: 4159801823106 Publisher: Springer US tex.mendeley-tags: RCC2967},
	month = {dec},
	pages = {4834},
	abstract = {2 3 Diatoms are one of the most successful and ecologically important groups of eukaryotic 4 phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better 5 understanding of their biological innovations, evolutionary origins, and ecological 6 underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions 7 combined with published expressed sequence tags and protein sequences from multiple taxa 8 to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 9 novel genes. The new annotation additionally permitted the discovery for the first time of 10 extensive alternative splicing (AS) in diatoms, including intron retention and exon skipping 11 which increases the diversity of transcripts to regulate gene expression in response to nutrient 12 limitations. In addition, we have used up-to-date reference sequence libraries to dissect the 13 taxonomic origins of diatom genomes. We show that the P. tricornutum genome is replete in 14 lineage-specific genes, with up to 47\% of the gene models present only possessing 15 orthologues in other stramenopile groups. Finally, we have performed a comprehensive de 16 novo annotation of repetitive elements showing novel classes of TEs such as SINE, MITE, LINE 17 and TRIM/LARD. This work provides a solid foundation for future studies of diatom gene 18 function, evolution and ecology.},
	keywords = {RCC2967},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-23106-x},
	url = {https://www.biorxiv.org/content/early/2017/08/14/176024\%0Ahttp://dx.doi.org/10.1101/176024 http://www.nature.com/articles/s41598-018-23106-x},
	author = {Rastogi, Achal and Maheswari, Uma and Dorrell, Richard G. and Vieira, Fabio Rocha Jimenez and Maumus, Florian and Kustka, Adam and McCarthy, James and Allen, Andy E. and Kersey, Paul and Bowler, Chris and Tirichine, Leila}
}
@article {Grebert2018,
	title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {in press},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC1016,RCC1017,RCC1018,RCC1020,RCC1023,RCC1027,RCC1030,RCC1031,RCC1084,RCC1085,RCC1086,RCC1087,RCC1096,RCC1097,RCC1649,RCC1661,RCC1688,RCC2032,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2370,RCC2372,RCC2373,RCC2374,RCC2375,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2384,RCC2385,RCC2415,RCC2432,RCC2433,RCC2434,RCC2435,RCC2436,RCC2437,RCC2438,RCC2457,RCC2525,RCC2526,RCC2527,RCC2528,RCC2529,RCC2530,RCC2532,RCC2533,RCC2534,RCC2536,RCC2553,RCC2554,RCC2555,RCC2556,RCC2567,RCC2568,RCC2569,RCC2570,RCC2571,RCC2673,RCC30,RCC3010,RCC3012,RCC3014,RCC307,RCC316,RCC318,RCC325,RCC326,RCC328,RCC37,RCC44,RCC46,RCC47,RCC515,RCC539,RCC542,RCC543,RCC550,RCC552,RCC553,RCC555,RCC556,RCC557,RCC558,RCC559,RCC62,RCC650,RCC66,RCC752,RCC753,RCC790,RCC791,RCC792,RCC793,RCC794,sbr?hyto?app},
	month = {feb},
	pages = {201717069},
	abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined so far due to the lack of a single-genetic marker resolving all pigment types (PT). Here, we developed a novel and robust method based on three distinct marker genes to estimate the relative abundance of all Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to unveil for the first time the global distribution of Synechococcus PTs and to decipher their realized environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified local populations in which CA4 might be inactive due to the lack of specific CA4 genes, notably in warm high nutrient low chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study brings unprecedented insights into the ecology of Synechococcus PTs and highlights the complex interactions between vertical phylogeny, pigmentation and environmental parameters that shape Synechococcus populations and evolution.},
	keywords = {2018, RCC1016, RCC1017, RCC1018, RCC1020, RCC1023, RCC1027, RCC1030, RCC1031, rcc1084, RCC1085, RCC1086, RCC1087, RCC1096, RCC1097, RCC1649, RCC1661, RCC1688, RCC2032, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2370, RCC2372, RCC2373, RCC2374, RCC2375, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2384, RCC2385, RCC2415, RCC2432, RCC2433, RCC2434, RCC2435, RCC2436, RCC2437, RCC2438, RCC2457, RCC2525, RCC2526, RCC2527, RCC2528, RCC2529, RCC2530, RCC2532, RCC2533, RCC2534, RCC2536, RCC2553, RCC2554, RCC2555, RCC2556, RCC2567, RCC2568, RCC2569, RCC2570, RCC2571, RCC2673, rcc30, RCC3010, RCC3012, RCC3014, RCC307, RCC316, RCC318, RCC325, RCC326, RCC328, RCC37, RCC44, RCC46, RCC47, RCC515, rcc539, RCC542, RCC543, RCC550, RCC552, RCC553, rcc555, RCC556, RCC557, RCC558, RCC559, RCC62, RCC650, RCC66, rcc752, RCC753, RCC790, rcc791, RCC792, RCC793, RCC794, sbr?hyto?app},
	issn = {0027-8424},
	doi = {10.1073/pnas.1717069115},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717069115},
	author = {Gr{\'e}bert, Th{\'e}ophile and Dor{\'e}, Hugo and Partensky, Fr{\'e}d{\'e}ric and Farrant, Gregory K. and Boss, Emmanuel S. and Picheral, Marc and Guidi, Lionel and Pesant, St{\'e}phane and Scanlan, David J. and Wincker, Patrick and Acinas, Silvia G. and Kehoe, David M. and Garczarek, Laurence}
}
@article {Delmont2018,
	title = {Linking pangenomes and metagenomes: the Prochlorococcus metapangenome},
	journal = {PeerJ},
	volume = {6},
	year = {2018},
	note = {ISBN: 2167-8359 tex.mendeley-tags: RCC156,RCC158,RCC162,RCC269,RCC278,RCC296,RCC3377,RCC407},
	pages = {e4320},
	abstract = {Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.},
	keywords = {RCC156, RCC158, rcc162, RCC269, RCC278, rcc296, RCC3377, RCC407},
	issn = {2167-8359},
	doi = {10.7717/peerj.4320},
	url = {https://peerj.com/articles/4320},
	author = {Delmont, Tom O. and Eren, A. Murat}
}
@article {Henriquez-Castillo2018,
	title = {Ostreococcus tauri luminescent reporter lines as biosensors for detecting pollution from copper-mine tailing effluents in coastal environments},
	journal = {Frontiers in Environmental Science},
	volume = {6},
	number = {May},
	year = {2018},
	note = {tex.mendeley-tags: RCC745},
	month = {may},
	pages = {1{\textendash}11},
	keywords = {biosensors, CDKA, copper pollution, ferritin, frontiers in environmental science, frontiersin, luciferase reporter, mine tailings, org, Ostreococcus, RCC745, www},
	issn = {2296-665X},
	doi = {10.3389/fenvs.2018.00022},
	url = {https://www.frontiersin.org/article/10.3389/fenvs.2018.00022/full},
	author = {Henr{\'\i}quez-Castillo, Carlos and Botebol, Hugo and Mouton, Adelaide and Ram{\'\i}rez-Flandes, Salvador and Lozano, Jean-Claude and Lelandais, Gaelle and Andrade, Santiago and Trefault, Nicole and de la Iglesia, Rodrigo and Bouget, Fran{\c c}ois-Yves}
}
@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 {Walker2018,
	title = {The requirement for calcification differs between ecologically important coccolithophore species},
	journal = {New Phytologist},
	volume = {in press},
	year = {2018},
	note = {tex.mendeley-tags: RCC1731},
	month = {jun},
	keywords = {Calcification, coccolithophore, Coccolithus braarudii, Emiliania huxleyi, phytoplankton, rcc1731},
	issn = {0028646X},
	doi = {10.1111/nph.15272},
	url = {http://doi.wiley.com/10.1111/nph.15272},
	author = {Walker, Charlotte E. and Taylor, Alison R. and Langer, Gerald and Durak, Gra{\.z}yna M. and Heath, Sarah and Probert, Ian and Tyrrell, Toby and Brownlee, Colin and Wheeler, Glen L.}
}
@article {Dorrell2017,
	title = {Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome},
	journal = {eLife},
	volume = {6},
	year = {2017},
	month = {may},
	pages = {1{\textendash}45},
	abstract = {Plastids are supported by a wide range of proteins encoded within the nucleus and imported from the cytoplasm. These plastid-targeted proteins may originate from the endosymbiont, the host, or other sources entirely. Here, we identify and characterise 770 plastid-targeted proteins that are conserved across the ochrophytes, a major group of algae including diatoms, pelagophytes and kelps, that possess plastids derived from red algae. We show that the ancestral ochrophyte plastid proteome was an evolutionary chimera, with 25\% of its phylogenetically tractable nucleus-encoded proteins deriving from green algae. We additionally show that functional mixing of host and plastid proteomes, such as through dual-targeting, is an ancestral feature of plastid evolution. Finally, we detect a clear phylogenetic signal from one ochrophyte subgroup, the lineage containing pelagophytes and dictyochophytes, in plastid-targeted proteins from another major algal lineage, the haptophytes. This may represent a possible serial endosymbiosis event deep in eukaryotic evolutionary history.},
	keywords = {2017, RCC1486, RCC1523, RCC1537, RCC1587, SBR$_\textrmP$hyto$_\textrmE$PPO},
	issn = {2050-084X},
	doi = {10.7554/eLife.23717},
	url = {http://elifesciences.org/lookup/doi/10.7554/eLife.23717},
	author = {Dorrell, Richard G and Gile, Gillian and McCallum, Giselle and M{\'e}heust, Rapha{\"e}l and Bapteste, Eric P and Klinger, Christen M and Brillet-Gu{\'e}guen, Loraine and Freeman, Katalina D and Richter, Daniel J and Bowler, Chris}
}
@article {Hennon2017,
	title = {Diverse CO2-Induced responses in physiology and gene expression among eukaryotic phytoplankton},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {December},
	year = {2017},
	note = {tex.mendeley-tags: RCC1303},
	month = {dec},
	pages = {1{\textendash}14},
	abstract = {With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (\~400 ppm) and elevated (\~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.},
	keywords = {algae, biophysical CCM, C4 CCM, carbon concentrating mechanism, carbon concentrating mechanism (CCM), ccm, photorespiration, RCC1303, transcriptomics},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.02547},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02547/full},
	author = {Hennon, Gwenn M. M. and Hern{\'a}ndez Lim{\'o}n, Mar{\'\i}a D. and Haley, Sheean T. and Juhl, Andrew R. and Dyhrman, Sonya T.}
}
@article {LopesdosSantos2016,
	title = {Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters},
	journal = {The ISME Journal},
	volume = {11},
	number = {2},
	year = {2017},
	note = {tex.mendeley-tags: 2016,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {feb},
	pages = {512{\textendash}528},
	keywords = {2016, MACUMBA, MicroB3, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.120},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.120},
	author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Tragin, Margot and No{\"e}l, Mary-H{\'e}l{\`e}ne and Decelle, Johan and Romac, Sarah and Vaulot, Daniel}
}
@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 {Kuhlisch2017,
	title = {A fast and direct liquid chromatography-mass spectrometry method to detect and quantify polyunsaturated aldehydes and polar oxylipins in diatoms},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {1},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd tex.mendeley-tags: RCC75,RCC776},
	month = {jan},
	pages = {70{\textendash}79},
	abstract = {Abstract Polyunsaturated aldehydes (PUAs) are a group of microalgal metabolites that have attracted a lot of attention due to their biological activity. Determination of PUAs has become an important routine procedure in plankton and biofilm investigations, especially those that deal with chemically mediated interactions. Here we introduce a fast and direct derivatization free method that allows quantifying PUAs in the nanomolar range, sufficient to undertake the analysis from cultures and field samples. The sample preparation requires one simple filtration step and the initiation of PUA formation by cell disruption. After centrifugation the samples are ready for measurement without any further handling. Within one chromatographic run this method additionally allows us to monitor the formation of the polar oxylipins arising from the cleavage of precursor fatty acids. The robust method is based on analyte separation and detection using ultra high performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (UHPLC-APCI MS) and enables high throughput investigations by employing an analysis time of only 5 min. Our protocol thus provides an alternative and extension to existing PUA determinations based on gas chromatography-mass spectrometry (GC-MS) with shorter run times and without any chemical derivatization. It also enables researchers with widely available LC-MS analytical platforms to monitor PUAs. Additionally, non-volatile oxylipins such as ?-oxo-acids and related compounds can be elucidated and monitored.},
	keywords = {RCC75, RCC776},
	issn = {1541-5856},
	doi = {10.1002/lom3.10143},
	url = {https://doi.org/10.1002/lom3.10143},
	author = {Kuhlisch, Constanze and Deicke, Michael and Ueberschaar, Nico and Wichard, Thomas and Pohnert, Georg}
}
@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 {Blanc-Mathieu2017,
	title = {Population genomics of picophytoplankton unveils novel chromosome hypervariability},
	journal = {Science Advances},
	volume = {3},
	number = {7},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC299,RCC4221,RCC809},
	month = {jul},
	pages = {e1700239},
	keywords = {RCC1105, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC299, RCC4221, RCC809},
	issn = {2375-2548},
	doi = {10.1126/sciadv.1700239},
	url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239},
	author = {Blanc-Mathieu, Romain and Krasovec, Marc and Hebrard, Maxime and Yau, Sheree and Desgranges, Elodie and Martin, Joel and Schackwitz, Wendy and Kuo, Alan and Salin, Gerald and Donnadieu, Cecile and Desdevises, Yves and Sanchez-Ferandin, Sophie and Moreau, Herv{\'e} and Rivals, Eric and Grigoriev, Igor V. and Grimsley, Nigel and Eyre-Walker, Adam and Piganeau, Gwenael}
}
@article {Derelle2017,
	title = {Prasinovirus attack of ostreococcus is furtive by day but savage by night},
	journal = {Journal of Virology},
	volume = {92},
	number = {4},
	year = {2017},
	note = {tex.mendeley-tags: RCC4221},
	month = {nov},
	pages = {JVI.01703{\textendash}17},
	abstract = {Prasinoviruses are large DNA viruses that infect diverse genera of green microalgae worldwide in aquatic ecosystems, but molecular knowledge of their life-cycles is lacking. Several complete genomes of both these viruses and their marine algal hosts are now available and have been used to show the pervasive presence of these species in microbial metagenomes. We have analysed the life-cycle of OtV5, a lytic virus, using RNA-Seq from 12 time points of healthy or infected Ostreococcus tauri cells over a day/night cycle in culture. In the day, viral gene transcription remained low while host nitrogen metabolism gene transcription was initially strongly repressed for two successive time points before being induced for 8 hours, but in the night viral transcription increased steeply while host nitrogen metabolism genes were repressed and many host functions that are normally reduced in the night appeared to be compensated either by genes expressed from the virus or by increased expression of a subset of 4.4 \% of the host{\textquoteright}s genes. Some host cells lysed progressively during the night, but a larger proportion lysed the following morning. Our data suggest that the life-cycles of algal viruses mirror the diurnal rhythms of their hosts.},
	keywords = {accepted 9, mamiellophyceae, ncldv, Ostreococcus, phycodnaviridae, prasinophytes, RCC4221, received 28 september 2017},
	issn = {0022-538X},
	doi = {10.1128/JVI.01703-17},
	url = {http://jvi.asm.org/lookup/doi/10.1128/JVI.01703-17},
	author = {Derelle, Evelyne and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel H.}
}
@article {Dominguez-Martin2017,
	title = {Quantitative proteomics shows extensive remodeling induced by nitrogen limitation in prochlorococcus marinus SS120},
	journal = {mSystems},
	volume = {2},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC156},
	month = {jun},
	pages = {e00008{\textendash}17},
	abstract = {Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57\% of the theoretical proteome, were identified{\textemdash}the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes ( P value of {\textexclamdown}0.05) were observed for 408 proteins, with the majority of proteins (92.4\%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins P II and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation.},
	keywords = {RCC156},
	issn = {2379-5077},
	doi = {10.1128/mSystems.00008-17},
	url = {http://msystems.asm.org/lookup/doi/10.1128/mSystems.00008-17},
	author = {Dom{\'\i}nguez-Mart{\'\i}n, Maria Agustina and G{\'o}mez-Baena, Guadalupe and D{\'\i}ez, Jes{\'u}s and L{\'o}pez-Grueso, Maria Jos{\'e} and Beynon, Robert J. and Garc{\'\i}a-Fern{\'a}ndez, Jos{\'e} Manuel},
	editor = {Huber, Julie A.}
}
@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 {Arias2017,
	title = {Removal and biodegradation of phenanthrene, fluoranthene and pyrene by the marine algae rhodomonas baltica enriched from north atlantic coasts},
	journal = {Bulletin of Environmental Contamination and Toxicology},
	volume = {98},
	number = {3},
	year = {2017},
	note = {tex.mendeley-tags: RCC350},
	pages = {392{\textendash}399},
	abstract = {This study is focused on the removal, accumulation and degradation of three environmental ubiquitous polycyclic aromatic hydrocarbons (PAHs), phenanthrene (PHE), fluoranthene (FLA) and pyrene (PYR), by the marine alga Rhodomonas baltica enriched from the English Channel. After separation, purification and culture in several phases, R. baltica was exposed to PAH concentrations that are frequently encountered in the field in several anthropized environments. The results showed that R. baltica can grow under PAH stress, efficiently remove up to 70\% of these compounds from the medium by 216 h of culture and selectively bioaccumulate PAHs by their hydrophobicity. Between PHE, FLA and PYR, phenanthrene was the compound with higher degradation rates throughout incubation. The equilibrium partitioning theoretical approach showed that physico-chemical partitioning, rather than active bioconcentration, was the major factor governing the bioaccumulation, outlying a potential application in decontamination processes for this species.},
	keywords = {RCC350},
	issn = {1432-0800},
	doi = {10.1007/s00128-016-1967-4},
	url = {https://doi.org/10.1007/s00128-016-1967-4},
	author = {Arias, Andr{\'e}s H and Souissi, Anissa and Glippa, Olivier and Roussin, Marion and Dumoulin, David and Net, Sopheak and Ouddane, Baghdad and Souissi, Sami}
}
@article {Simon2017,
	title = {Revision of the genus micromonas manton et parke (chlorophyta, mamiellophyceae), of the type species m. pusilla (butcher) manton \& parke and of the species m. commoda van baren, bachy and worden and description of two new species based on the genetic},
	journal = {Protist},
	volume = {168},
	number = {5},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1109,RCC114,RCC2306,RCC2308,RCC299,RCC372,RCC373,RCC418,RCC434,RCC447,RCC448,RCC449,RCC450,RCC451,RCC461,RCC465,RCC472,RCC497,RCC498,RCC570,RCC629,RCC647,RCC658,RCC676,RCC692,RCC746,RCC803,RCC804,RCC805,RCC806,RCC807,RCC808,RCC828,RCC829,RCC830,RCC831,RCC833,RCC834,RCC835,RCC836,sbr?hyto$_\textrmd$ipo},
	month = {nov},
	pages = {612{\textendash}635},
	keywords = {2017, ASSEMBLE, rcc, RCC1109, RCC114, RCC2306, RCC2308, RCC299, RCC372, RCC373, RCC418, RCC434, RCC447, RCC448, RCC449, RCC450, RCC451, RCC461, RCC465, RCC472, RCC497, RCC498, RCC570, RCC629, RCC647, RCC658, RCC676, RCC692, RCC746, RCC803, RCC804, RCC805, RCC806, RCC807, RCC808, RCC828, RCC829, RCC830, RCC831, RCC833, RCC834, RCC835, RCC836, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo},
	issn = {14344610},
	doi = {10.1016/j.protis.2017.09.002},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1434461017300780},
	author = {Simon, Nathalie and Foulon, Elodie and Grulois, Daphne and Six, Christophe and Desdevises, Yves and Latimier, Marie and Le Gall, Florence and Tragin, Margot and Houdan, Aude and Derelle, Evelyne and Jouenne, Fabien and Marie, Dominique and Le Panse, Sophie and Vaulot, Daniel and Marin, Birger}
}
@article {Demory2017,
	title = {Temperature is a key factor in Micromonas{\textendash}virus interactions},
	journal = {The ISME Journal},
	volume = {11},
	number = {3},
	year = {2017},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: 2017,RCC4229,RCC4253,RCC4265,RCC451,RCC829,RCC834,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	month = {mar},
	pages = {601{\textendash}612},
	abstract = {The genus Micromonas comprises phytoplankton that show among the widest latitudinal distributions on Earth, and members of this genus are recurrently infected by prasinoviruses in contrasted thermal ecosystems. In this study, we assessed how temperature influences the interplay between the main genetic clades of this prominent microalga and their viruses. The growth of three Micromonas strains (Mic-A, Mic-B, Mic-C) and the stability of their respective lytic viruses (MicV-A, MicV-B, MicV-C) were measured over a thermal range of 4{\textendash}32.5 {\textdegree}C. Similar growth temperature optima (Topt) were predicted for all three hosts but Mic-B exhibited a broader thermal tolerance than Mic-A and Mic-C, suggesting distinct thermoacclimation strategies. Similarly, the MicV-C virus displayed a remarkable thermal stability compared with MicV-A and MicV-B. Despite these divergences, infection dynamics showed that temperatures below Topt lengthened lytic cycle kinetics and reduced viral yield and, notably, that infection at temperatures above Topt did not usually result in cell lysis. Two mechanisms operated depending on the temperature and the biological system. Hosts either prevented the production of viral progeny or maintained their ability to produce virions with no apparent cell lysis, pointing to a possible switch in the viral life strategy. Hence, temperature changes critically affect the outcome of Micromonas infection and have implications for ocean biogeochemistry and evolution.},
	keywords = {2017, RCC4229, RCC4253, RCC4265, RCC451, RCC829, RCC834, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.160},
	url = {http://dx.doi.org/10.1038/ismej.2016.160 http://www.nature.com/doifinder/10.1038/ismej.2016.160},
	author = {Demory, David and Arsenieff, Laure and Simon, Nathalie and Six, Christophe and Rigaut-jalabert, Fabienne and Marie, Dominique and Ge, Pei and Bigeard, Estelle and Jacquet, St{\'e}phan and Sciandra, Antoine and Bernard, Olivier and Rabouille, Sophie and Baudoux, Anne-claire}
}
@article {Leliaert2016,
	title = {Chloroplast phylogenomic analyses reveal the deepest-branching lineage of the Chlorophyta, Palmophyllophyceae class. nov.},
	journal = {Scientific Reports},
	volume = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC15,RCC299},
	month = {may},
	pages = {25367},
	keywords = {2016, RCC15, RCC299},
	issn = {2045-2322},
	doi = {10.1038/srep25367},
	url = {http://www.nature.com/articles/srep25367},
	author = {Leliaert, Frederik and Tronholm, Ana and Lemieux, Claude and Turmel, Monique and DePriest, Michael S. and Bhattacharya, Debashish and Karol, Kenneth G. and Fredericq, Suzanne and Zechman, Frederick W. and Lopez-Bautista, Juan M.}
}
@article {Ichinomiya2016,
	title = {Diversity and oceanic distribution of Parmales (Bolidophyceae), a picoplankton group closely related to diatoms},
	journal = {The ISME Journal},
	volume = {in press},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	keywords = {2016, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1038/ismej.2016.38},
	author = {Ichinomiya, Mutsuo and Lopes dos Santos, A and Gourvil, Priscillia and Yoshikawa, Shinya and Kamiya, Mitsunobu and Ohki, Kaori and Audic, S and de Vargas, Colomban and Vaulot, Daniel and Kuwata, Akira}
}
@article {Bendif2016,
	title = {Recent reticulate evolution in the ecologically dominant lineage of coccolithophores},
	journal = {Frontiers in Microbiology},
	volume = {7},
	number = {May},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC4032,RCC4033,RCC4034,RCC4035,RCC4036,rcc,sbr?hyto},
	month = {may},
	keywords = {2016, coccolithophores, cyto-nuclear discordance, diversity, Emiliania, evolution, Gephyrocapsa, introgressive hybridization, rcc, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, Reticulofenestra, sbr?hyto},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2016.00784},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.00784 http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00784/abstract},
	author = {Bendif, El Mahdi and Probert, Ian and D{\'\i}az-Rosas, Francisco and Thomas, Daniela and van den Engh, Ger and Young, Jeremy R. and von Dassow, Peter}
}
@article {Durak2016,
	title = {A role for diatom-like silicon transporters in calcifying coccolithophores},
	journal = {Nature Communications},
	volume = {7},
	number = {February},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC1130,RCC1303,RCC1453,RCC1456,RCC3432},
	pages = {10543},
	abstract = {Biomineralisation by marine phytoplankton, such as the silicifying diatoms and calcifying coccolithophores, plays an important role in carbon and nutrient cycling in the oceans. Silicification and calcification are distinct cellular processes with no known common mechanisms. As a result, it is thought that coccolithophores are able to outcompete diatoms in Si-depleted waters, which can contribute to the formation of coccolithophore blooms. Here, we show that an expanded family of diatom-like silicon transporters (SITs) are present in both silicifying and calcifying haptophyte phytoplankton, including some coccolithophores of global ecological importance. We find an essential role for Si in calcification in these coccolithophores, indicating that Si uptake contributes to the very different forms of biomineralisation in diatoms and coccolithophores. However, SITs and the requirement for Si are significantly absent from the highly abundant bloom-forming coccolithophores, such as Emiliania huxleyi. These very different requirements for Si in coccolithophores are likely to have major influence on their competitive interactions with diatoms and other siliceous phytoplankton.},
	keywords = {(RCC1130, (RCC1456), 2016, biomineralisation, coccolithophores, Gephyrocapsa oceanica (RCC1303) and Scyphosphaera, haptophytes, RCC1130, RCC1303, RCC1453, RCC1456, RCC3432, silica, TMR5 (RCC3432{\textemdash}Sea of Japan) and PZ241 (RCC1453{\textemdash}Med},
	issn = {2041-1723},
	doi = {10.1038/ncomms10543},
	author = {Durak, Grazyna M and Taylor, Alison R and Probert, Ian and de Vargas, Colomban and Audic, St{\'e}phane and Schroeder, Declan C and Brownlee, Colin and Wheeler, Glen L}
}
@article {Vannier2016,
	title = {Survey of the green picoalga Bathycoccus genomes in the global ocean},
	journal = {Scientific Reports},
	volume = {6},
	number = {1},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC1105,RCC715,RCC716,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {dec},
	pages = {37900},
	keywords = {2016, RCC1105, RCC715, RCC716, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {2045-2322},
	doi = {10.1038/srep37900},
	url = {http://www.nature.com/articles/srep37900},
	author = {Vannier, Thomas and Leconte, Jade and Seeleuthner, Yoann and Mondy, Samuel and Pelletier, Eric and Aury, Jean-Marc and de Vargas, Colomban and Sieracki, Michael and Iudicone, Daniele and Vaulot, Daniel and Wincker, Patrick and Jaillon, Olivier}
}
@article {Yau2016,
	title = {A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri},
	journal = {PLOS Pathogens},
	volume = {12},
	number = {10},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC299,RCC4221,RCC809},
	month = {oct},
	pages = {e1005965},
	keywords = {2016, RCC299, RCC4221, RCC809},
	issn = {1553-7374},
	doi = {10.1371/journal.ppat.1005965},
	url = {http://dx.plos.org/10.1371/journal.ppat.1005965},
	author = {Yau, Sheree and Hemon, Claire and Derelle, Evelyne and Moreau, Herv{\'e} and Piganeau, Gwenael and Grimsley, Nigel},
	editor = {Ding, Shou-Wei}
}
@article {Astorga-Elo2015,
	title = {Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone},
	journal = {The ISME Journal},
	volume = {9},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {1264{\textendash}1267},
	abstract = {Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2015.21},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2015.21},
	author = {Astorga-El{\'o}, Marcia and Ram{\'\i}rez-Flandes, Salvador and DeLong, Edward F and Ulloa, Osvaldo}
}
@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 {Andersen2015,
	title = {Phaeocystis rex sp. nov. (Phaeocystales, Prymnesiophyceae): a new solitary species that produces a multilayered scale cell covering},
	journal = {European Journal of Phycology},
	volume = {50},
	number = {2},
	year = {2015},
	note = {Publisher: Taylor \& Francis tex.mendeley-tags: 2015,RCC 4025,rcc},
	pages = {207{\textendash}222},
	abstract = {A morphologically distinct marine species, Phaeocystis rex sp. nov., was described on the basis of light microscopy, transmission electron microscopy and DNA sequence comparisons. Non-motile cells were solitary (non-colonial), 6{\textendash}10 {\textmu}m in diameter and 8{\textendash}15 {\textmu}m long, and possessed chloroplasts with distinctive finger-like lobes. TEM observations demonstrated the presence of two short flagella and a very short haptonema that arose from an invagination of the protoplast. Non-motile cells were surrounded by one to several dense layers composed of scales, presumably unmineralized, and an amorphous material. Phylogenetic analyses based upon combined partial nucleotide sequences for five nuclear-or plastid-encoded genes (18S rRNA, 28S rRNA, 16S rRNA, psbA and rbcL) from cultured strains and from uncharacterized acantharian symbionts confirmed that P. rex was a distinct species. These analyses implied that P. rex occupies an intermediate evolutionary position between solitary and colonial Phaeocystis species.},
	keywords = {2015, algae, organic scales, Phaeocystales, Phaeocystis rex, Prymnesiophyceae, rcc, RCC4025, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmE$PPO, systematics, ultrastructure},
	issn = {0967-0262},
	doi = {10.1080/09670262.2015.1024287},
	url = {http://www.tandfonline.com/doi/full/10.1080/09670262.2015.1024287},
	author = {Andersen, Robert A. and Bailey, J. Craig and Decelle, Johan and Probert, Ian}
}
@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 {Abby2014,
	title = {Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?},
	journal = {Frontiers in microbiology},
	volume = {5},
	year = {2014},
	note = {Publisher: Frontiers tex.mendeley-tags: rcc},
	month = {jan},
	pages = {505},
	abstract = {Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri.},
	keywords = {bacterial diversity, Bacterial symbiosis, Illumina sequencing, microbiome, Ostreococcus, phycosphere, phytoplankton, picoeukaryote, rcc, RCC?o?dd, secretion system},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2014.00505},
	url = {http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00505/abstract},
	author = {Abby, Sophie S and Touchon, Marie and De Jode, Aurelien and Grimsley, Nigel and Piganeau, Gwenael}
}
@article {Probert2014a,
	title = {Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians},
	journal = {Journal of Phycology},
	volume = {50},
	number = {2},
	year = {2014},
	note = {tex.mendeley-tags: RCC3378,RCC3379,RCC3380,RCC3381,RCC3382,RCC3383,RCC3384,RCC3385,RCC3386,RCC3387,RCC3388},
	pages = {388{\textendash}399},
	abstract = {Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.},
	keywords = {Dinoflagellate, MACUMBA, Peridiniales, polycystines, Radiolaria, rcc, RCC3378, RCC3379, RCC3380, RCC3381, RCC3382, RCC3383, RCC3384, RCC3385, RCC3386, RCC3387, RCC3388, SBR$_\textrmP$hyto$_\textrmD$PO, Scrippsiella, symbiosis, taxonomy, Zooxanthella},
	doi = {10.1111/jpy.12174},
	url = {http://dx.doi.org/10.1111/jpy.12174},
	author = {Probert, Ian and Siano, Raffaele and Poirier, Camille and Decelle, Johan and Biard, Tristan and Tuji, Akihiro and Suzuki, Noritoshi and Not, Fabrice}
}
@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 {Duanmu2014,
	title = {Marine algae and land plants share conserved phytochrome signaling systems},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {111},
	number = {44},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {15827{\textendash}15832},
	abstract = {Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte ({\textexclamdown}2 {\textmu}m cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.},
	keywords = {Micromonas, rcc},
	doi = {10.1073/pnas.1416751111},
	url = {http://www.pnas.org/content/111/44/15827.abstract},
	author = {Duanmu, Deqiang and Bachy, Charles and Sudek, Sebastian and Wong, Chee-Hong and Jimenez, Valeria and Rockwell, Nathan C and Martin, Shelley S and Ngan, Chew Yee and Reistetter, Emily N and van Baren, Marijke J and Price, Dana C and Wei, Chia-Lin and Reyes-Prieto, Adrian and Lagarias, J Clark and Worden, Alexandra Z}
}
@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 {DelCampo2014,
	title = {The others: our biased perspective of eukaryotic genomes},
	journal = {Trends in Ecology \& Evolution},
	volume = {29},
	number = {5},
	year = {2014},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC,rcc},
	pages = {252{\textendash}259},
	abstract = {?There is an important bias in eukaryotic knowledge, affecting cultures and genomes.?Eukaryotic genomics are biased towards multicellular organisms and their parasites.?A phylogeny-driven initiative is needed to overcome the eukaryotic genomic bias.?We propose to sequence neglected cultures and increase culturing efforts.?Single-cell genomics should be embraced as a tool to explore eukaryotic diversity.},
	keywords = {rcc},
	doi = {10.1016/j.tree.2014.03.006},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00064-0},
	author = {del Campo, Javier and Sieracki, Michael E and Molestina, Robert and Keeling, Patrick and Massana, Ramon and Ruiz-Trillo, I{\~n}aki}
}
@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 {Dia2014,
	title = {Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum},
	journal = {Molecular Ecology},
	volume = {23},
	number = {3},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {549{\textendash}560},
	abstract = {Organisms with sexual and asexual reproductive systems benefit from both types of reproduction. Sexual recombination generates new combinations of alleles, whereas clonality favours the spread of the fittest genotype through the entire population. Therefore, the rate of sexual vs. clonal reproduction has a major influence on the demography and genetic structure of natural populations. We addressed the effect of reproductive system on populations of the dinoflagellate Alexandrium minutum. More specifically, we monitored the spatiotemporal genetic diversity during and between bloom events in two estuaries separated by 150 km for two consecutive years. An analysis of population genetic patterns using microsatellite markers revealed surprisingly high genotypic and genetic diversity. Moreover, there was significant spatial and temporal genetic differentiation during and between bloom events. Our results demonstrate that (i) interannual genetic differentiation can be very high, (ii) estuaries are partially isolated during bloom events and (iii) genetic diversity can change rapidly during a bloom event. This rapid genetic change may reflect selective effects that are nevertheless not strong enough to reduce allelic diversity. Thus, sexual reproduction and/or migration may regularly erase any genetic structure produced within estuaries during a bloom event.},
	keywords = {2014, bloom dynamics, clonality, linkage disequilibrium, MACUMBA, population genetics, rcc, RCC?o?dd, resting cyst, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sexual reproduction},
	doi = {10.1111/mec.12617},
	url = {http://dx.doi.org/10.1111/mec.12617},
	author = {Dia, A and Guillou, L and Mauger, S and Bigeard, E and Marie, D and Valero, M and Destombe, C}
}
@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 {Abida2013,
	title = {Bioprospecting marine plankton},
	journal = {Marine Drugs},
	volume = {11},
	number = {11},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {4594{\textendash}4611},
	keywords = {2013, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.3390/md11114594},
	url = {http://www.mdpi.com/1660-3397/11/11/4594},
	author = {Abida, Heni and Ruchaud, Sandrine and Rios, Laurent and Humeau, Anne and Probert, Ian and de Vargas, Colomban and Bach, St{\'e}phane and Bowler, Chris}
}
@article {Bendif2013,
	title = {On the description of Tisochrysis lutea gen . nov . sp . nov . and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta)},
	journal = {Journal of Applied Phycology},
	volume = {25},
	year = {2013},
	note = {tex.mendeley-tags: 2013,RCC1195,RCC1207,RCC1281,RCC1286,RCC1344,RCC1346,RCC1347,RCC1348,RCC1349,RCC1350,RCC1353,RCC2477,RCC3681,RCC3684,RCC3686,RCC3687,RCC3690,RCC3691,RCC3692,RCC3693,RCC3694,RCC3695,RCC3696,RCC3699,RCC3701,RCC3707,rcc,sbr?hyto?ppo},
	pages = {1763{\textendash}1776},
	keywords = {2013, dicrateria, imantonia, isochrysidaceae, isochrysis galbana, phylogeny, rcc, RCC1195, RCC1207, RCC1281, RCC1286, RCC1344, RCC1346, RCC1347, RCC1348, RCC1349, RCC1350, RCC1353, RCC2477, RCC3681, RCC3684, RCC3686, RCC3687, RCC3690, RCC3691, RCC3692, RCC3693, RCC3694, RCC3695, RCC3696, RCC3699, RCC3701, RCC3707, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, taxonomy, ultrastructure},
	doi = {10.1007/s10811-013-0037-0},
	author = {Bendif, El Mahdi and Probert, Ian and Schroeder, Declan C and de Vargas, Colomban}
}
@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 {Subirana2013,
	title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae)},
	journal = {Protist},
	volume = {164},
	number = {5},
	year = {2013},
	note = {tex.mendeley-tags: RCC1112,RCC1114,RCC1117,RCC143,RCC1620,RCC1621,RCC1623,RCC1624,RCC2572,RCC2573,RCC2574,RCC2575,RCC2577,RCC2578,RCC2579,RCC2582,RCC2583,RCC2584,RCC2585,RCC2587,RCC2590,RCC344,RCC356,RCC393,RCC501,RCC745,RCC809},
	pages = {643{\textendash}659},
	abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species{\textquoteright} descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species{\textquoteright} divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified {\textquestiondown}30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.},
	keywords = {barcode, Chromosome, culture, ITS2, karyotype, picoeukaryote, rcc, RCC1112, RCC1114, RCC1117, RCC143, RCC1620, RCC1621, RCC1623, RCC1624, RCC2572, RCC2573, RCC2574, RCC2575, RCC2577, RCC2578, RCC2579, RCC2582, RCC2583, RCC2584, RCC2585, RCC2587, RCC2590, RCC344, RCC356, RCC393, rcc501, RCC745, RCC809, ribosomal gene},
	doi = {10.1016/j.protis.2013.06.002},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461013000497},
	author = {Subirana, Lucie and P{\'e}quin, B{\'e}rang{\`e}re and Michely, St{\'e}phanie and Escande, Marie-Line and Meilland, Julie and Derelle, Evelyne and Marin, Birger and Piganeau, Gwenael and Desdevises, Yves and Moreau, Herv{\'e} and Grimsley, Nigel H}
}
@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 {Drescher2012,
	title = {Coccolithogenesis in scyphosphaera apsteinii (prymnesiophyceae)},
	journal = {Journal of Phycology},
	volume = {48},
	number = {6},
	year = {2012},
	note = {tex.mendeley-tags: RCC1456},
	pages = {1343{\textendash}1361},
	abstract = {Coccolithophores are the most significant producers of marine biogenic calcite, although the intracellular calcification process is poorly understood. In the case of Scyphosphaera apsteinii Lohmann 1902, flat ovoid muroliths and bulky, vase-shaped lopadoliths with a range of intermediate morphologies may be produced by a single cell. This polymorphic species is within the Zygodiscales, a group that remains understudied with respect to ultrastructure and coccolith ontogeny. We therefore undertook an analysis of cell ultrastructure, morphology, and coccolithogenesis. The cell ultrastructure showed many typical haptophyte features, with calcification following a similar pattern to that described for other heterococcolith bearing species including Emiliania huxleyi. Of particular significance was the reticular body role in governing fine-scale morphology, specifically the central pore formation of the coccolith. Our observations also highlighted the essential role of the inter- and intracrystalline organic matrix in growth and arrangement of the coccolith calcite. S. apsteinii secreted mature coccoliths that attached to the plasma membrane via fibrillar material. Time-lapse light microscopy demonstrated secretion of lopadoliths occurred base first before being actively repositioned at the cell surface. Significantly, growth irradiance influenced the coccosphere composition with fewer lopadoliths being formed relative to muroliths at higher light intensities. Overall, our observations support dynamic metabolic (i.e., in response to growth irradiance), sensory and cytoskeletal control over the morphology and secretion of polymorphic heterococcoliths. With a basic understanding of calcification established, S. apsteinii could be a valuable model to further study coccolithophore calcification and cell physiological responses to ocean acidification.},
	keywords = {Calcification, coccolithogenesis, coccolithophore, organic matrix, rcc, RCC1456, reticular body, secretion, ultrastructure, Zygodiscales},
	doi = {10.1111/j.1529-8817.2012.01227.x},
	url = {http://dx.doi.org/10.1111/j.1529-8817.2012.01227.x},
	author = {Drescher, Brandon and Dillaman, Richard M and Taylor, Alison R}
}
@article {Frada2012,
	title = {In situ survey of life cycle phases of the coccolithophore Emiliania huxleyi (Haptophyta)},
	journal = {Environmental Microbiology},
	volume = {14},
	number = {6},
	year = {2012},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo},
	pages = {1558{\textendash}1569},
	abstract = {The cosmopolitan coccolithophore Emiliania huxleyi is characterized by a strongly differentiated haplodiplontic life cycle consisting of a diploid phase, generally bearing coccoliths (calcified) but that can be also non-calcified, and a non-calcified biflagellated haploid phase. Given most studies have focused on the bloom-producing calcified phase, there is little-to-no information about non-calcified cells in nature. Using field mesocoms as experimental platforms, we quantitatively surveyed calcified and non-calcified cells using the combined calcareous detection fluorescent in situ hybridization (COD-FISH) method and qualitatively screened for haploid specific transcripts using reverse transcription-PCR during E. huxleyi bloom successions. Diploid, calcified cells formed dense blooms that were followed by the massive proliferation of E. huxleyi viruses (EhVs), which caused bloom demise. Non-calcified cells were also detected throughout the experiment, accounting for a minor fraction of the population but becoming progressively more abundant during mid-late bloom periods concomitant with EhV burst. Non-calcified cell growth also paralleled a distinct window of haploid-specific transcripts and the appearance of autotrophic flagellates morphologically similar to haploid cells, both of which are suggestive of meiosis and sexual life cycling during natural blooms of this prominent marine phytoplankton species.},
	keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1462-2920.2012.02745.x},
	url = {http://dx.doi.org/10.1111/j.1462-2920.2012.02745.x},
	author = {Frada, Miguel J and Bidle, Kay D and Probert, Ian and de Vargas, Colomban}
}
@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 {Kulk2012,
	title = {Temperature-dependent growth and photophysiology of prokaryotic and eukaryotic oceanic picophytoplankton},
	journal = {Marine Ecology Progress Series},
	volume = {466},
	year = {2012},
	note = {tex.mendeley-tags: RCC407,RCC410,RCC879},
	pages = {43{\textendash}55},
	abstract = {ABSTRACT: It is expected that climate change will expand the open oligotrophic oceans by enhanced thermal stratification. Because temperature defines the geographic distribution of picophytoplankton in open-ocean ecosystems and regulates photophysiological responses, it is important to understand how temperature affects picophytoplankton growth and photophysiology. Two prokaryotic and 2 eukaryotic picophytoplankton strains were acclimated to 3 different temperatures, ranging from 16 to 24{\textdegree}C. Temperature-dependent growth and photophysiology were assessed by measurements of specific growth rates, cell size, pigment composition, absorption and electron transport rates. Growth of Prochlorococcus marinus (eMED4), Prochlorococcus sp. (eMIT9313), Ostreococcus sp. (clade B) and Pelagomonas calceolata was positively related to temperature, especially in the prokaryotic strains. Changes in photophysiology included increased light harvesting, increased electron transport and reduced photoinhibition at elevated temperatures. However, the changes related to light harvesting and electron transport could not fully explain the observed difference in growth. This suggests that other processes, such as Calvin cycle activity, are likely to limit growth at sub-optimal temperatures in these picophytoplankton strains. The overall changes in photophysiology during temperature acclimation will possibly allow photosynthesis at higher irradiance intensities, but the genetically defined low temperature tolerances and photosynthetic characteristics of the different ecotypes will likely be more important in determining picophytoplankton (depth) distribution and community composition.},
	keywords = {Absorption, Electron transport rate, Eukaryotic picophytoplankton, Growth, Pigment, Prochlorococcus, rcc, RCC407, rcc410, RCC879, temperature},
	issn = {01718630},
	doi = {10.3354/meps09898},
	url = {http://www.int-res.com/abstracts/meps/v466/p43-55/},
	author = {Kulk, Gemma and De Vries, Pablo and Van De Poll, Willem H. and Visser, Ronald J W and Buma, Anita G J}
}
@article {Jeanthon2011,
	title = {Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea},
	journal = {Biogeosciences},
	volume = {8},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {1955{\textendash}1970},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.5194/bg-8-1955-2011},
	author = {Jeanthon, Christian and Boeuf, Dominique and Dahan, Oc{\'e}ane and Le Gall, F and Garczarek, Laurence and Bendif, El Mahdi and Lehours, Anne-Catherine}
}
@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 {Hagino2011,
	title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes},
	journal = {Journal of Phycology},
	volume = {47},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {1164{\textendash}1176},
	abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1529-8817.2011.01053.x},
	author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H}
}
@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 {Rokitta2011,
	title = {Transcriptome analyses reveal differential gene expression patterns between the life-cycle stages of Emiliania huxleyi (Haptophyta) and reflect specialization to different ecological niches},
	journal = {Journal of Phycology},
	volume = {47},
	number = {4},
	year = {2011},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {829{\textendash}838},
	abstract = {Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 ??m diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit.},
	keywords = {2011, endocytosis, Life-cycle stages, microarray, quantitative RT-PCR, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, transcriptome profiling},
	doi = {10.1111/j.1529-8817.2011.01014.x},
	url = {http://dx.doi.org/10.1111/j.1529-8817.2011.01014.x},
	author = {Rokitta, Sebastian D and de Nooijer, Lennart J and Trimborn, Scarlett and de Vargas, Colomban and Rost, Bj{\"o}rn and John, Uwe}
}
@article {Lepere2011,
	title = {Whole Genome Amplification (WGA) of marine photosynthetic eukaryote populations},
	journal = {FEMS Microbiology Ecology},
	volume = {76},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {516{\textendash}523},
	keywords = {2011, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1111/j.1574-6941.2011.01072.x},
	author = {Lepere, Cecile and Demura, M and Kawachi, M and Romac, S and Probert, I and Vaulot, D}
}
@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 {Siano2010,
	title = {Pelagodinium gen. nov. and P. beii comb. nov., a dinoflagellate symbiont of planktonic foraminifera},
	journal = {Protist},
	volume = {161},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,rcc1491,sbr?hyto?ppo},
	pages = {385{\textendash}399},
	abstract = {The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium b{\'e}ii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium b{\'e}ii is reclassified as Pelagodinium b{\'e}ii.},
	keywords = {2010, ASSEMBLE, rcc, rcc1491, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1016/j.protis.2010.01.002},
	author = {Siano, R and Montresor, M and Probert, I and Not, F and de Vargas, C}
}
@article {Liu2010,
	title = {A timeline of the environmental genetics of the haptophytes},
	journal = {Molecular Biology and Evolution},
	volume = {27},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {171{\textendash}176},
	abstract = {The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying four to six "supergroups". Yet our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the timeline of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to (i) data partitioning, (ii) the origin of the genes (host vs. endosymbiont), (iii) across-site rate variation and (iv) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 MYA (95\% highest probability density 1031-637 MYA). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329-291 MYA, in the Carboniferous period, and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal / neritic waters to the pelagic realm (291-243 MYA, around the P/Tr boundary event), the emergence of calcification, full autotrophy and oceanic lifestyle seem mutually independent.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1093/molbev/msp222},
	url = {http://mbe.oxfordjournals.org/cgi/content/abstract/msp222v1},
	author = {Liu, Hui and Aris-Brosou, Stephane and Probert, Ian and de Vargas, Colomban}
}
@conference {Meusnier2009,
	title = {DNA barcoding of protists in culture collections},
	booktitle = {Third international barcode of life conference},
	year = {2009},
	note = {tex.mendeley-tags: RCC,rcc},
	address = {Mexico City},
	keywords = {? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO},
	author = {Meusnier, Isabelle and Andersen, Robert A and Stern, Rowena and Bertrand, C and Kuepper, Frithjof and Brand, Jerry and Friedl, Thomas and Blackburn, Susan and Dinh, Donna and Acreman, Judy and Sedl{\'a}{\v c}ek, Ivo and P{\v r}ibyl, Pavel and Jutson, Maria and Phang, Siew Moi and Melkonian, M and Karpov, S and Hajibabaei, Mehrdad}
}
@article {Scanlan2009,
	title = {Ecological genomics of marine picocyanobacteria},
	journal = {Microbiology and Molecular Biology Reviews},
	volume = {73},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?app},
	pages = {249{\textendash}299},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1128/MMBR.00035-08},
	author = {Scanlan, D J and Ostrowski, M and Mazard, S and Dufresne, A and Garczarek, L and Hess, W R and Post, A F and Hagemann, M and Paulsen, I and Partensky, F}
}
@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 {Richier2009,
	title = {Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi},
	journal = {Applied and Environmental Microbiology},
	volume = {75},
	year = {2009},
	note = {Edition: 2009/03/24 ISBN: 1098-5336 (Electronic) tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {3366{\textendash}3369},
	abstract = {The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1128/aem.02737-08},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19304825},
	author = {Richier, S and Kerros, M E and de Vargas, C and Haramaty, L and Falkowski, P G and Gattuso, J P}
}
@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 {Frada2008,
	title = {The {\textquotedblleft}Cheshire Cat{\textquotedblright} escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo},
	pages = {15944{\textendash}15949},
	abstract = {The coccolithophore is one of the most successful eukaryotes in modern oceans. The two phases in its haplodiploid life cycle exhibit radically different phenotypes. The diploid calcified phase forms extensive blooms, which profoundly impact global biogeochemical equilibria. By contrast, the ecological role of the noncalcified haploid phase has been completely overlooked. Giant phycodnaviruses ( viruses, EhVs) have been shown to infect and lyse diploid-phase cells and to be heavily implicated in the regulation of populations and the termination of blooms. Here, we demonstrate that the haploid phase of is unrecognizable and therefore resistant to EhVs that kill the diploid phase. We further show that exposure of diploid to EhVs induces transition to the haploid phase. Thus we have clearly demonstrated a drastic difference in viral susceptibility between life cycle stages with different ploidy levels in a unicellular eukaryote. Resistance of the haploid phase of provides an escape mechanism that involves separation of meiosis from sexual fusion in time, thus ensuring that genes of dominant diploid clones are passed on to the next generation in a virus-free environment. These {\^a}{\texteuro}{\oe}Cheshire Cat{\^a}{\texteuro} ecological dynamics release host evolution from pathogen pressure and thus can be seen as an opposite force to a classic {\^a}{\texteuro}{\oe}Red Queen{\^a}{\texteuro} coevolutionary arms race. In , this phenomenon can account for the fact that the selective balance is tilted toward the boom-and-bust scenario of optimization of both growth rates of calcifying cells and infectivity of EhVs.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.0807707105},
	author = {Frada, Miguel and Probert, Ian and Allen, Michael J and Wilson, William H and de Vargas, Colomban}
}
@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 {Descles2008,
	title = {New tools for labeling silica in living diatoms},
	journal = {New Phytologist},
	volume = {177},
	number = {3},
	year = {2008},
	note = {ISBN: 0028-646X tex.mendeley-tags: rcc},
	pages = {822{\textendash}829},
	abstract = {Silicon biomineralization is a widespread mechanism found in several kingdoms that concerns both unicellular and multicellular organisms. As a result of genomic and molecular tools, diatoms have emerged as a good model for biomineralization studies and have provided most of the current knowledge on this process. However, the number of techniques available to study its dynamics at the cellular level is still rather limited. Here, new probes were developed specifically to label the pre-existing or the newly synthesized silica frustule of several diatoms species. It is shown that the LysoTracker Yellow HCK-123, which can be used to visualize silica frustules with common filter sets, presents an enhanced signal-to-noise ratio and allows details of the frustules to be imaged without of the use of ionophores. It is also demonstrated that methoxysilane derivatives can be coupled to fluorescein-5-isothiocyanate (FITC) to preferentially label the silica components of living cells. The coupling of labeling procedures might help to address the challenging question of the process of frustule exocytosis.},
	keywords = {3D-imaging, BACILLARIOPHYCEAE, BIOLOGY, biomineralization, DEPOSITION, diatoms, exocytosis, FLUORESCENT, nanopattern, pH, phaeodactylum-tricornutum, PLANTS, rcc, THALASSIOSIRA-PSEUDONANA, ultrastructure, VESICLE},
	doi = {10.1111/j.1469-8137.2007.02303.x},
	author = {Descles, J and Vartanian, M and El Harrak, A and Quinet, M and Bremond, N and Sapriel, G and Bibette, J and Lopez, P J}
}
@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 {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 {Robbens2007,
	title = {The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction},
	journal = {Molecular Biology and Evolution},
	volume = {24},
	number = {4},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {956{\textendash}968},
	abstract = {The complete nucleotide sequence of the mt (mitochondrial) and cp (chloroplast) genomes of the unicellular green alga Ostreococcus tauri has been determined. The mt genome assembles as a circle of 44,237 bp and contains 65 genes. With an overall average length of only 42 bp for the intergenic regions, this is the most gene-dense mt genome of all Chlorophyta. Furthermore, it is characterized by a unique segmental duplication, encompassing 22 genes and covering 44\% of the genome. Such a duplication has not been observed before in green algae, although it is also present in the mt genomes of higher plants. The quadripartite cp genome forms a circle of 71,666 bp, containing 86 genes divided over a larger and a smaller single-copy region, separated by 2 inverted repeat sequences. Based on genome size and number of genes, the Ostreococcus cp genome is the smallest known among the green algae. Phylogenetic analyses based on a concatenated alignment of cp, mt, and nuclear genes confirm the position of O. tauri within the Prasinophyceae, an early branch of the Chlorophyta.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17251180},
	author = {Robbens, S and Derelle, E and Ferraz, C and Wuyts, J and Moreau, H and Van de Peer, Y}
}
@article {Six2007,
	title = {Diversity and evolution of phycobilisomes in marine Synechococcus spp. - a comparative genomics study},
	journal = {Genome Biology},
	volume = {8},
	year = {2007},
	note = {tex.mendeley-tags: 2007,rcc,sbr?hyto?app},
	pages = {R259},
	keywords = {2007, rcc, SBR$_\textrmP$hyto, sbr?hyto?app},
	doi = {10.1186/gb-2007-8-12-r259},
	author = {Six, C and Thomas, J.-C. and Garczarek, L and Ostrowski, M and Dufresne, A and Blot, N and Scanlan, D J and Partensky, F}
}
@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 {Palenik2007,
	title = {The tiny eukaryote \textit{Ostreococcus provides genomic insights into the paradox of plankton speciation},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {104},
	number = {18},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {7705{\textendash}7710},
	abstract = {The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17460045},
	author = {Palenik, B and Grimwood, J and Aerts, A and Rouz{\'e}, P and Salamov, A and Putnam, N and Dupont, C and Jorgensen, R and Derelle, E and Rombauts, S and Zhou, K and Otillar, R and Merchant, S S and Podell, S and Gaasterland, T and Napoli, C and Gendler, K and Manuell, A and Tai, V and Vallon, O and Piganeau, G and Jancek, S and Heijde, M and Jabbari, K and Bowler, C and Lohr, M and Robbens, S and Werner, G and Dubchak, I and Pazour, G J and Ren, Q and Paulsen, I and Delwiche, C and Schmutz, J and Rokhsar, D and Van de Peer, Y and Moreau, H and Grigoriev, I V}
}
@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 {Palenik2006,
	title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {36},
	year = {2006},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {13555{\textendash}13559},
	abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.},
	keywords = {rcc},
	doi = {10.1073/pnas.0602963103},
	url = {http://www.pnas.org/cgi/content/abstract/103/36/13555},
	author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L and Myers, Garry S and Heidelberg, John F and Badger, Jonathan H and Madupu, Ramana and Nelson, William C and Brinkac, Lauren M and Dodson, Robert J and Durkin, A Scott and Daugherty, Sean C and Sullivan, Stephen A and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T}
}
@article {palenik_genome_2006,
	title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {103},
	number = {36},
	year = {2006},
	note = {Publisher: National Academy of Sciences Section: Biological Sciences},
	pages = {13555{\textendash}13559},
	abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.},
	keywords = {cyanobacteria, genomics, Marine, RCC1086},
	issn = {0027-8424, 1091-6490},
	doi = {10.1073/pnas.0602963103},
	url = {https://www.pnas.org/content/103/36/13555},
	author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L. and Myers, Garry S. and Heidelberg, John F. and Badger, Jonathan H. and Madupu, Ramana and Nelson, William C. and Brinkac, Lauren M. and Dodson, Robert J. and Durkin, A. Scott and Daugherty, Sean C. and Sullivan, Stephen A. and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T.}
}
@article {Rodriguez2005h,
	title = {Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae).},
	journal = {Environmental Microbiology},
	volume = {7},
	year = {2005},
	note = {tex.mendeley-tags: RCC113,RCC143,RCC343,RCC356,RCC371,RCC393,RCC410,RCC420,RCC434,RCC501,RCC658,RCC745,Rcc141},
	pages = {853{\textendash}859},
	keywords = {rcc, RCC113, Rcc141, RCC143, RCC343, RCC356, RCC371, RCC393, rcc410, RCC420, RCC434, rcc501, RCC658, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1111/j.1462-2920.2005.00758.x},
	author = {Rodriguez, F and Derelle, E and Guillou, L and Le Gall, F and Vaulot, D and Moreau, H}
}
@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 {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 {Laloui2002,
	title = {Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-{\textquoteright}Synechococcus{\textquoteright} clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon},
	journal = {Microbiology},
	volume = {148},
	number = {2},
	year = {2002},
	note = {tex.mendeley-tags: 2002,rcc,sbr?hyto},
	pages = {453{\textendash}465},
	abstract = {PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of {\textquoteright}Synechococcus{\textquoteright} (wH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 165 rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-{\textquoteright}Synechococcus{\textquoteright} strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted Glade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems.},
	keywords = {2002, Blue Green Alga, Chlorophyll B, community structure, cyanobacteria, Escherichia Coli, Marine Prokaryote, Multiple Evolutionary Origins, North Atlantic Ocean, Pacific Ocean, rcc, Rna Operon, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1099/00221287-148-2-453},
	author = {Laloui, W and Palinska, K A and Rippka, R and Partensky, F and de Marsac, N T and Herdman, M and Iteman, I}
}
@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 {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}
}
