@article {wang_meta-analysis_2024,
	title = {Meta-analysis reveals responses of coccolithophores and diatoms to warming},
	journal = {Marine Environmental Research},
	volume = {193},
	year = {2024},
	pages = {106275},
	abstract = {A meta-analysis was conducted to explore the effects of warming on the physiological processes of coccolitho- phores and diatoms by synthesizing a large number of published literatures. A total of 154 studies consisting 301 experiments were synthesized in this study. Under a projected temperature increase of 3{\textendash}5 {\textopenbullet}C by IPCC AR6 at the end of this century, our results suggest that the growth and photosynthetic rate of coccolithophores were significantly enhanced by the rising temperature, while the calcification of coccolithophores was only slightly promoted. Warming also had significantly positive effects on the growth but not photosynthesis of diatoms. In comparison, the effect size of warming on the growth rate of coccolithophores was larger than that of diatoms. However, there was no significant effect of warming on either the ratio of particulate inorganic carbon to par- ticulate organic carbon (PIC:POC) of coccolithophores or the ratio of biogenic silica to carbon (BSi:C) of diatoms. Furthermore, the results reveal latitudinal and size-specific patterns of the effect sizes of warming. For diatoms, the effects of warming on growth were more prominent in high latitudes, specifically for the Southern Hemi- sphere species. In addition, the effect size of warming on the small-sized diatoms was larger than that of the large-sized diatoms. For coccolithophores, the growth of the Southern Hemisphere temperate strains was significantly promoted by warming. Overall, the results based on the meta-analysis indicate that the projected warming of the end of this century will be more favor to the growth of coccolithophores than that of diatoms, thus potentially affect the competitive advantages of coccolithophores over diatoms; while the mid-to high latitude species/strains of both coccolithophores and diatoms will benefit more than their counterparts in the lower latitudes. Therefore, this study offers novel insights into predicting both the inter- and intra-group competitive advantages of diatoms and coccolithophores under the future warming climate change scenario.},
	keywords = {rcc1238},
	issn = {01411136},
	doi = {10.1016/j.marenvres.2023.106275},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0141113623004038},
	author = {Wang, Jiawei and Zeng, Cong and Feng, Yuanyuan}
}
@article {bouquet_artificial_2023,
	title = {Artificial Substrates Coupled with qPCR (AS-qPCR) Assay for the Detection of the Toxic Benthopelagic Dinoflagellate Vulcanodinium rugosum},
	journal = {Toxins},
	volume = {15},
	number = {3},
	year = {2023},
	note = {Number: 3 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {mar},
	pages = {217},
	abstract = {Vulcanodinium rugosum is an emerging benthopelagic neuro-toxic dinoflagellate species responsible for seasonal Pinnatoxins and Portimines contaminations of shellfish and marine animals. This species is challenging to detect in the environment, as it is present in low abundance and difficult to be identified using light microscopy. In this work, we developed a method using artificial substrates coupled with qPCR (AS-qPCR) to detect V. rugosum in a marine environment. This sensitive, specific and easy-to-standardize alternative to current techniques does not require specialized expertise in taxonomy. After determining the limits and specificity of the qPCR, we searched for the presence of V. rugosum in four French Mediterranean lagoons using artificial substrates collected every two weeks for one year. The AS-qPCR method revealed its occurrences in summer 2021 in every studied lagoon and detected cells in more samples than light microscopy. As V. rugosum development induces shellfish contamination even at low microalga densities, the AS-qPCR method is accurate and relevant for monitoring V. rugosum in a marine environment.},
	keywords = {artificial substrate, benthopelagic, detection, PCR, RCC6328, RCC6338, RCC6344, RCC6548, RCC6550, toxins, \textitVulcanodinium rugosum},
	issn = {2072-6651},
	doi = {10.3390/toxins15030217},
	url = {https://www.mdpi.com/2072-6651/15/3/217},
	author = {Bouquet, Aur{\'e}lien and Felix, Christine and Masseret, Estelle and Reymond, Coralie and Abadie, Eric and Laabir, Mohamed and Rolland, Jean Luc}
}
@article {churakova_biogenic_2023,
	title = {Biogenic silica accumulation in picoeukaryotes: Novel players in the marine silica cycle},
	journal = {Environmental Microbiology Reports},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1758-2229.13144},
	abstract = {It is well known that the biological control of oceanic silica cycling is dominated by diatoms, with sponges and radiolarians playing additional roles. Recent studies have revealed that some smaller marine organisms (e.g. the picocyanobacterium Synechococcus) also take up silicic acid (dissolved silica, dSi) and accumulate silica, despite not exhibiting silicon dependent cellular structures. Here, we show biogenic silica (bSi) accumulation in five strains of picoeukaryotes (<2{\textendash}3 μm), including three novel isolates from the Baltic Sea, and two marine species (Ostreococcus tauri and Micromonas commoda), in cultures grown with added dSi (100 μM). Average bSi accumulation in these novel biosilicifiers was between 30 and 92 amol Si cell-1. Growth rate and cell size of the picoeukaryotes were not affected by dSi addition. Still, the purpose of bSi accumulation in these smaller eukaryotic organisms lacking silicon dependent structures remains unclear. In line with the increasing recognition of picoeukaryotes in biogeochemical cycling, our findings suggest that they can also play a significant role in silica cycling.},
	keywords = {RCC4221, RCC827},
	issn = {1758-2229},
	doi = {10.1111/1758-2229.13144},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1758-2229.13144},
	author = {Churakova, Yelena and Aguilera, Anabella and Charalampous, Evangelia and Conley, Daniel J. and Lundin, Daniel and Pinhassi, Jarone and Farnelid, Hanna}
}
@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}
}
@article {florenza_choice_2023,
	title = {Choice of methodology and surrogate prey are decisive for the quality of protistan bacterivory rate estimates},
	journal = {Aquatic Microbial Ecology},
	volume = {89},
	year = {2023},
	month = {mar},
	pages = {43{\textendash}53},
	abstract = {Microeukaryote predation on bacteria is a fundamental phenomenon to understand energy and nutrient dynamics at the base of the aquatic food web. To date, the most prevalent way to estimate grazing rates is by using epifluorescence microscopy to enumerate ingestion events of fluorescently labelled tracers (FLTs) after short-term incubation experiments. However, this approach can be sensitive to the type of FLT, requires skillful preparation of the samples and is limited to small sample sizes. We tested the susceptibility of rate estimates to the choice of prey and made a side-by-side comparison between microscopy and flow cytometry when recording ingestion by a bacterivorous flagellate. Short-term uptake experiments were established using 5 types of FLTs differing in quality (living, dead or inert) and size (large or small), with Ochromonas triangulata as a model flagellate. The experiments showed that (1) each of the different prey types yielded different clearing rates, ranging from 0.5 to 3.6 nl cell-1 h-1, with the largest differences (3fold or higher) between small prey (lower rates) and large prey (higher rates); (2) the cytometry estimate differed significantly from the microscopy estimate in 3 out of 4 experimental configurations; and (3) the precision of the cytometric analysis was greater, with > 3-fold higher uncertainty associated with microscopy counting. Our results validate that flow cytometry provides a more precise bacterivory estimate, and that the choice of FLT influences the grazing rate estimate to a high extent regardless of the analytical method used.},
	keywords = {RCC21},
	issn = {0948-3055, 1616-1564},
	doi = {10.3354/ame01996},
	url = {https://www.int-res.com/abstracts/ame/v89/p43-53/},
	author = {Florenza, J and Bertilsson, S}
}
@article {lopez-pacheco_growth_2023,
	title = {Growth Behavior, Biomass Composition and Fatty Acid Methyl Esters (FAMEs) Production Potential of Chlamydomonas reinhardtii, and Chlorella vulgaris Cultures},
	journal = {Marine Drugs},
	volume = {21},
	number = {8},
	year = {2023},
	month = {aug},
	pages = {450},
	abstract = {The production of biomolecules by microalgae has a wide range of applications in the development of various materials and products, such as biodiesel, food supplements, and cosmetics. Microalgae biomass can be produced using waste and in a smaller space than other types of crops (e.g., soja, corn), which shows microalgae{\textquoteright}s great potential as a source of biomass. Among the produced biomolecules of greatest interest are carbohydrates, proteins, lipids, and fatty acids. In this study, the production of these biomolecules was determined in two strains of microalgae (Chlamydomonas reinhardtii and Chlorella vulgaris) when exposed to different concentrations of nitrogen, phosphorus, and sulfur. Results show a significant microalgal growth (3.69 g L-1) and carbohydrates (163 mg g-1) increase in C. reinhardtii under low nitrogen concentration. Also, higher lipids content was produced under low sulfur concentration (246 mg g-1). It was observed that sulfur variation could affect in a negative way proteins production in C. reinhardtii culture. In the case of C. vulgaris, a higher biomass production was obtained in the standard culture medium (1.37 g L-1), and under a low-phosphorus condition, C. vulgaris produced a higher lipids concentration (248 mg g-1). It was observed that a low concentration of nitrogen had a better effect on the accumulation of fatty acid methyl esters (FAMEs) (C16-C18) in both microalgae. These results lead us to visualize the effects that the variation in macronutrients can have on the growth of microalgae and their possible utility for the production of microalgae-based subproducts.},
	keywords = {RCC2488},
	issn = {1660-3397},
	doi = {10.3390/md21080450},
	url = {https://www.mdpi.com/1660-3397/21/8/450},
	author = {L{\'o}pez-Pacheco, Itzel Y. and Ayala-Moreno, Victoria Guadalupe and Mejia-Melara, Catherinne Arlette and Rodr{\'\i}guez-Rodr{\'\i}guez, Jos{\'e} and Cuellar-Bermudez, Sara P. and Gonz{\'a}lez-Gonz{\'a}lez, Reyna Berenice and Coronado-Apodaca, Karina G. and Farfan-Cabrera, Leonardo I. and Gonz{\'a}lez-Meza, Georgia Mar{\'\i}a and Iqbal, Hafiz M. N. and Parra-Sald{\'\i}var, Roberto}
}
@article {concordio-reis_novel_2023,
	title = {Novel exopolysaccharide produced by the marine dinoflagellate Heterocapsa AC210: Production, characterization, and biological properties},
	journal = {Algal Research},
	volume = {70},
	year = {2023},
	pages = {103014},
	abstract = {Marine microalgae are promising sources of novel valuable biomolecules such as polysaccharides. In this study, the dinoflagellate Heterocapsa sp. AC210 was described as a new exopolysaccharide (EPS) producer. The cultivation and EPS production in bioreactor was evaluated for the first time in detail. The EPS was composed of seven different sugar monomers, including fucose and glucosamine, which are quite rare and have never been reported in dinoflagellates{\textquoteright} EPS. Moreover, the EPS had a high content of sulphate, which is often associated with biological properties. Cytotoxicity was accessed and the results showed that the EPS did not reduce cell viability for concentrations up to 1~g~L-1. Additionally, antioxidant and anti-inflammatory assays demonstrated that the EPS reduced by 18~\% the intracellular reactive oxygen species and decreased up to 79.3~\% and 46.2~\% of IL-8 and IL-6 secretion in keratinocytes, which supports its potential application in the cosmeceutical and biomedical fields.},
	keywords = {Anti-inflammatory, Cytotoxicity, Dinoflagellates, Exopolysaccharide production, Marine microalgae, RCC1514, sp. AC210},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2023.103014},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926423000474},
	author = {Conc{\'o}rdio-Reis, Patr{\'\i}cia and Cardeira, Martim and Macedo, Ana Catarina and Ferreira, S{\'o}nia S. and Serra, Ana Teresa and Coimbra, Manuel A. and Amorim, Ana and Reis, Maria A. M. and Freitas, Filomena}
}
@article {bendif_rapid_2023,
	title = {Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton},
	journal = {The ISME Journal},
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	pages = {1{\textendash}11},
	abstract = {Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (\textasciitilde140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.},
	keywords = {Microbial biooceanography, phylogenomics, population genetics, rcc1212, RCC1216, rcc1220, RCC1239, RCC1240, RCC1242, RCC1245, rcc1252, RCC1253, RCC1266, RCC1304, rcc1731, RCC1754, RCC1813, RCC1823, rcc1824, RCC1830, RCC1838, RCC1840, RCC1853, RCC1856, RCC3746, RCC4027, RCC4028, RCC4030, RCC5134, RCC5137, RCC5141, RCC6381, RCC6421, RCC6427, RCC6566, RCC6660, RCC6666, RCC911, RCC963},
	issn = {1751-7370},
	doi = {10.1038/s41396-023-01365-5},
	url = {https://www.nature.com/articles/s41396-023-01365-5},
	author = {Bendif, El Mahdi and Probert, Ian and Archontikis, Odysseas A. and Young, Jeremy R. and Beaufort, Luc and Rickaby, Rosalind E. and Filatov, Dmitry}
}
@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 {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 {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 {fernandes_effects_2022,
	title = {Effects of phosphorus-induced changes on the growth, nitrogen uptake, and biochemical composition of Pavlova pinguis and Hemiselmis cf. andersenii},
	journal = {Journal of Applied Phycology},
	year = {2022},
	abstract = {The understanding of the phosphorus-induced changes in the biochemical composition of microalgae is of great importance for achieving efficiency in high-value lipid production. To study the chemoplasticity of Pavlova pinguis (Haptophyceae) and Hemiselmis cf. andersenii (Cryptophyceae), their growth, carotenoid and chlorophyll a content, and their monosaccharide and lipid profiles were analyzed against several phosphorus (P) regimes: low (LP), medium (MP), and high (HP). For both microalgal cultures, increasing initial P concentrations showed a positive effect on biomass productivities. Carbon-rich pools presented significant differences (p< 0.05) for P. pinguis against P treatments, in contrast to H. cf. andersenii. Differential responses to P-induced changes in microalgae monosaccharide and lipid profile were observed. Hemiselmis cf. andersenii increased its proportion in galactose (up to 3 times) from LP to HP conditions, whereas P. pinguis decreased (up to 20\%) its glucose proportion from LP to HP conditions. For P. pinguis, the lowest amount (13.12 mg g-1 dw) of sterols was observed at LP conditions, in contrast to its carotenoid content (4.32 mg g-1 dw). P-replete conditions were the most effective in inducing high-value lipid accumulation. Non-targeted lipid analysis revealed which samples would need to be processed to fully exploit its high-value lipids, namely H. cf andersenii under MP and HP conditions. This study demonstrated that P played an important role in carbon allocation, nitrogen uptake, and lipid regulation on P. pinguis and H. cf. andersenii, and that P-replete conditions could be useful for optimizing high-value lipids with potential for nutraceutical and pharmaceutical fields.},
	keywords = {RCC1539},
	issn = {1573-5176},
	doi = {10.1007/s10811-021-02662-2},
	url = {https://doi.org/10.1007/s10811-021-02662-2},
	author = {Fernandes, Tom{\'a}sia and Cordeiro, Nereida}
}
@article {ebenezer_elemental_2022,
	title = {Elemental and macromolecular composition of the marine Chloropicophyceae, a major group of oceanic photosynthetic picoeukaryotes},
	journal = {Limnology and Oceanography},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.12013},
	abstract = {Chloropicophyceae (Prasinophyte Clade VII) are small nonmotile coccoid cells with cell diameters ranging from 1 to 3 μm. Molecular surveys indicate they are relatively high in abundance in moderately oligotrophic oceanic waters and may substantively contribute to biogeochemical cycling in the sea. Here, we quantify the elemental and macromolecular composition of three subtropical Chloropicophyceae strains: Chloropicon mariensis, Chloropicon maureeniae, and Chloropicon roscoffensis under nutrient-sufficient exponential growth and nitrate starvation. Under nutrient-sufficient conditions the Chloropicophyceae are high in C : N and quite low in C : P and N : P relative to the canonical Redfield ratio, reflecting their relatively high nucleic acid composition compared to many other phytoplankton taxa. Nitrate starvation causes increases in C : N and C : P and decreases in N : P, primarily due to increases in carbohydrate and lipid and decreases in protein and RNA. There is genetic evidence that unlike most other green algae, Chloropicophyceae are diploid. The high nucleic acid content in the Chloropicon is consistent with the hypothesis that the nucleus, as a nonscalable component, takes up a larger and substantial proportion of cell mass in diploid picoeukaryotes. The elemental and macromolecular composition of these Chloropicophyceae, and relatively homeostatic response to N-starvation compared to diatoms, provides some insight into their success in the moderately oligotrophic ocean.},
	keywords = {RCC138, RCC3374, RCC3375},
	issn = {1939-5590},
	doi = {10.1002/lno.12013},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1002/lno.12013},
	author = {Ebenezer, Vinitha and Hu, Yingyu and Carnicer, Olga and Irwin, Andrew J. and Follows, Michael J. and Finkel, Zoe V.}
}
@article {guerin_genomic_2022,
	title = {Genomic adaptation of the picoeukaryote Pelagomonas calceolata to iron-poor oceans revealed by a chromosome-scale genome sequence},
	journal = {Communications Biology},
	volume = {5},
	number = {1},
	year = {2022},
	note = {Number: 1 Publisher: Nature Publishing Group},
	pages = {1{\textendash}14},
	abstract = {The smallest phytoplankton species are key actors in oceans biogeochemical cycling and their abundance and distribution are affected with global environmental changes. Among them, algae of the Pelagophyceae class encompass coastal species causative of harmful algal blooms while others are cosmopolitan and abundant. The lack of genomic reference in this lineage is a main limitation to study its ecological importance. Here, we analysed Pelagomonas calceolata relative abundance, ecological niche and potential for the adaptation in all oceans using a complete chromosome-scale assembled genome sequence. Our results show that P. calceolata is one of the most abundant eukaryotic species in the oceans with a relative abundance favoured by high temperature, low-light and iron-poor conditions. Climate change projections based on its relative abundance suggest an extension of the P. calceolata habitat toward the poles at the end of this century. Finally, we observed a specific gene repertoire and expression level variations potentially explaining its ecological success in low-iron and low-nitrate environments. Collectively, these findings reveal the ecological importance of P. calceolata and lay the foundation for a global scale analysis of the adaptation and acclimation strategies of this small phytoplankton in a changing environment. Genomic inference reveals potential climate change-driven range expansion of the phytoplankton species Pelagomonas calceolata.},
	keywords = {Biogeography, comparative genomics, metagenomics, RCC100, Water microbiology},
	issn = {2399-3642},
	doi = {10.1038/s42003-022-03939-z},
	url = {https://www.nature.com/articles/s42003-022-03939-z},
	author = {Gu{\'e}rin, Nina and Ciccarella, Marta and Flamant, Elisa and Fr{\'e}mont, Paul and Mangenot, Sophie and Istace, Benjamin and Noel, Benjamin and Belser, Caroline and Bertrand, Laurie and Labadie, Karine and Cruaud, Corinne and Romac, Sarah and Bachy, Charles and Gachenot, Martin and Pelletier, Eric and Alberti, Adriana and Jaillon, Olivier and Wincker, Patrick and Aury, Jean-Marc and Carradec, Quentin}
}
@article {dore_global_2022,
	title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts},
	journal = {mSystems},
	year = {2022},
	note = {Publisher: American Society for Microbiology},
	pages = {e00656{\textendash}22},
	abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of {\textquotedblleft}who is where{\textquotedblright} by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.},
	keywords = {RCC1086, RCC1695, RCC2369, rcc2380, RCC2553, RCC2556, RCC2570, rcc791},
	doi = {10.1128/msystems.00656-22},
	url = {https://journals.asm.org/doi/full/10.1128/msystems.00656-22},
	author = {Dor{\'e}, Hugo and Leconte, Jade and Guyet, Ulysse and Breton, Sol{\`e}ne and Farrant, Gregory K. and Demory, David and Ratin, Morgane and Hoebeke, Mark and Corre, Erwan and Pitt, Frances D. and Ostrowski, Martin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Garczarek, Laurence}
}
@article {fernandes_high-value_2022,
	title = {High-value lipids accumulation by Pavlova pinguis as a response to nitrogen-induced changes},
	journal = {Biomass and Bioenergy},
	volume = {158},
	year = {2022},
	month = {mar},
	pages = {106341},
	abstract = {The challenges of exploring the potential of microalgal strains for biotechnological applications include the optimization of their cell growth and chemical composition. To overcome this, it is essential to understand the mechanisms that lead to the accumulation of desired products within microalgal cells. In this study, a gradient of nitrogen as nitrate (NO3{\textendash}N) concentrations was used for the preparation of P. pinguis growth medium. The algal growth dynamics, pigments, nutrient uptake, and detailed lipid composition across treatments were assessed. Increasing the NO3{\textendash}N level led to higher lipid content (21\%), a higher cell uptake rate (0.20 pg NO3{\textendash}N cell-1 d-1) and more accumulation of chlorophylls, carotenoids, and high-value lipids. Eicosapentaenoic acid, essential fatty acids, phytol and stigmasterol were the key high-value lipids that were positively influenced by higher NO3{\textendash}N levels. High NO3{\textendash}N conditions induced an increase of 54\% in total sterol content, while low NO3{\textendash}N conditions resulted in increased proportions of saturated fatty acids (66\% more) and decreased proportions of polyunsaturated fatty acids (14\% less). The low NO3{\textendash}N level also led to higher amounts of monoglyceride (1.60 mg g-1; 64\% more). The analysis of P. pinguis lipids before and after hydrolysis provided an insight into the composition of the esterified lipids across treatments. NO3{\textendash}N supplementation was revealed to be an effective strategy for enhancing P. pinguis lipid composition, for nutraceutical and pharmaceutical industries (high NO3{\textendash}N level). A greater understanding of the NO3{\textendash}N uptake and the use efficiency by P. pinguis was reached, showing its potential for further biotechnological applications.},
	keywords = {Biotechnological application, High-value lipids, RCC1359, supply},
	issn = {0961-9534},
	doi = {10.1016/j.biombioe.2022.106341},
	url = {https://www.sciencedirect.com/science/article/pii/S0961953422000022},
	author = {Fernandes, Tom{\'a}sia and Cordeiro, Nereida}
}
@article {falciatore_light-driven_2022,
	title = {Light-driven processes: key players of the functional biodiversity in microalgae},
	journal = {Comptes Rendus. Biologies},
	volume = {345},
	number = {2},
	year = {2022},
	pages = {1{\textendash}24},
	doi = {10.5802/crbiol.80},
	url = {https://comptes-rendus.academie-sciences.fr/biologies/articles/10.5802/crbiol.80/},
	author = {Falciatore, Angela and Bailleul, Benjamin and Boulouis, Alix and Bouly, Jean-Pierre and Bujaldon, Sandrine and Cheminant-Navarro, Soizic and Choquet, Yves and Vitry, Catherine de and Eberhard, Stephan and Jaubert, Marianne and Kuras, Richard and Lafontaine, Ingrid and Landier, Sophie and Selles, Julien and Vallon, Olivier and Wostrikoff, Katia}
}
@article {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 {fan_quantifying_2022,
	title = {Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter},
	journal = {Analytical Chemistry},
	year = {2022},
	month = {sep},
	pages = {acs.analchem.2c01971},
	abstract = {Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is nearuniversally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores�single cells encrusted with biogenic calcite�to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a singlespecies coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.},
	keywords = {RCC1198, RCC1216, RCC1314},
	issn = {0003-2700, 1520-6882},
	doi = {10.1021/acs.analchem.2c01971},
	url = {https://pubs.acs.org/doi/10.1021/acs.analchem.2c01971},
	author = {Fan, Xinmeng and Batchelor-McAuley, Christopher and Yang, Minjun and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {croteau_shifts_2022,
	title = {Shifts in growth light optima among diatom species support their succession during the spring bloom in the Arctic},
	journal = {Journal of Ecology},
	volume = {n/a},
	number = {n/a},
	year = {2022},
	note = {_eprint: https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/1365-2745.13874},
	abstract = {1. Diatoms of the Arctic Ocean annually experience extreme changes of light environment linked to photoperiodic cycles and seasonal variations of the snow and sea-ice cover extent and thickness which attenuate light penetration in the water column. Arctic diatom communities exploit this complex seasonal dynamic through a well-documented species succession during spring, beginning in sea-ice and culminating in massive phytoplankton blooms underneath sea-ice and in the marginal ice zone. The pattern of diatom taxa sequentially dominating this succession is relatively well conserved interannually, and taxonomic shifts seem to align with habitat transitions. 2. To understand whether differential photoadaptation strategies among diatom taxa explain these recurring succession sequences, we coupled lab experiments with field work in Baffin Bay at 67.5{\textdegree}N. Based on field data, we selected five diatom species typical of different ecological niches and measured their growth rates under light intensity ranges representative of their natural habitats. To characterize their photoacclimative responses, we sampled pigments and total particulate carbon, and conducted 14C-uptake photosynthesis response curves and variable fluorescence measurements. 3. We documented a gradient in species respective light intensity for maximal growth suggesting divergent light response plasticity, which for the most part align with species sequential dominance. Other photophysiological parameters supported this ecophysiological framing, although contrasts were always clear only between succession endmembers, Nitzschia frigida and Chaetoceros neogracilis. To validate that these photoacclimative responses are representative of in situ dynamics, we compared them to the chlorophyll a-specific light-limited slope (α*) and saturated rate of photosynthesis (P*M), monitored in Baffin Bay on sea-ice and planktonic communities. This complementary approach confirmed that unusual responses in α* and P*M as a function of light history intensity are similar between sentinel sympagic species N. frigida and natural ice-core communities. While no light-history-dependent trends were observed in planktonic communities, their α* and P*M values were in the range of measurements from our monospecific cultures. 4. Synthesis. Our results suggest that Arctic diatoms species photoadaptation strategy is tuned to the light environment of the habitats in which they dominate and indeed drives the seasonal taxonomic succession.},
	keywords = {Arctic Ocean, diatoms, Ecophysiology, photoacclimation, photoadaptation, primary production, RCC2046, RCC2278, seasonal species succession, spring bloom},
	issn = {1365-2745},
	doi = {10.1111/1365-2745.13874},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/1365-2745.13874},
	author = {Croteau, D. and Lacour, T. and Schiffrine, N. and Morin, P.-I. and Forget, M.-H. and Bruyant, F. and Ferland, J. and Lafond, A. and Campbell, D. A. and Tremblay, J.-E. and Babin, M. and Lavaud, J.}
}
@article {fernandes_comparative_2021,
	title = {Comparative lipidomic analysis of Chlorella stigmatophora and Hemiselmis cf. andersenii in response to nitrogen-induced changes},
	journal = {Algal Research},
	volume = {58},
	year = {2021},
	pages = {102417},
	abstract = {The current focus of algae biotechnology is the production of high-value lipids, and its improvement by employing abiotic perturbations such as nitrogen-induced changes. In the present study, the growth dynamics, nitrogen uptake, pigments, and lipid composition of Chlorellla stigmatophora and Hemiselmis cf. andersenii were studied, in response to low (LN), medium (MN) and high (HN) nitrogen supplementations. Both microalgae responded to increased nitrogen levels by increasing their nitrogen uptake rate and pigment content. However, for lipid accumulation, C. stigmatophora presented a different pattern (LN: 16.56\% > MN: 11.51\% > HN: 10.95\%) to that of H. cf. andersenii (MN: 15.37\% > HN: 13.06\% > LN: 6.71\%). Untargeted gas chromatography{\textendash}mass spectrometry analysis allowed the visualization of the biochemical diversity of C. stigmatophora and H. cf. andersenii, as well as differences in lipid regulation upon nitrogen-induced changes among species. For instance, glycosyl sterols were only detected for C. stigmatophora samples grown under MN and HN conditions. Moreover, lipid analysis of H. cf. andersenii, before and after alkaline hydrolysis, suggests that wax esters play a key role in the response of this microalga to high nitrogen levels. The cultivation of H. cf. andersenii at MN and HN was shown to be ideal for providing a rich source of ω3 and polyunsaturated fatty acids for nutraceutical purposes. The hierarchical cluster analysis showed the differential intra- and interspecific effects of nitrogen on lipid composition. The diverse ways by which both microalgae responded to nitrogen-induced changes highlighted the influence of phylogeny on the carbon flux through metabolic networks, and accumulation.},
	keywords = {cf., Lipidome analysis, Nitrogen supplementation, Nutraceutical lipids, rcc, RCC661},
	issn = {2211-9264},
	doi = {10.1016/j.algal.2021.102417},
	url = {https://www.sciencedirect.com/science/article/pii/S2211926421002368},
	author = {Fernandes, Tom{\'a}sia and Ferreira, Artur and Cordeiro, Nereida}
}
@article {croteau_contrasting_2021,
	title = {Contrasting nonphotochemical quenching patterns under high light and darkness aligns with light niche occupancy in Arctic diatoms},
	journal = {Limnology and Oceanography},
	volume = {66},
	number = {S1},
	year = {2021},
	note = {_eprint: https://aslopubs.onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11587},
	pages = {S231{\textendash}S245},
	abstract = {Over the seasons, Arctic diatom species occupy shifting habitats defined by contrasting light climates, constrained by snow and ice cover dynamics interacting with extreme photoperiod and solar angle variations. How Arctic diatom photoadaptation strategies differ across their heterogeneous light niches remains a poorly documented but crucial missing link to anticipate Arctic Ocean responses to shrinking sea-ice and increasing light. To address this question, we selected five Arctic diatom species with diverse life traits, representative of distinct light niches across the seasonal light environment continuum: from snow-covered dimly lit bottom ice to summer stratified waters. We studied their photoacclimation plasticity to two growth light levels and the subsequent responses of their nonphotochemical quenching (NPQ) and xanthophyll cycle to both dark incubations and light shifts. We deciphered NPQ and xanthophyll cycle tuning in darkness and their light-dependent induction kinetics, which aligned with species{\textquoteright} light niche occupancy. In ice-related species, NPQ was sustained in darkness and its induction was more reactive to moderate light shifts. Open-water species triggered strong NPQ induction in darkness and reached higher maximal NPQ under high light. Marginal ice zone species showed strong adaptation to light fluctuations with a dark response fine-tuned depending upon light history. We argue these traits are anchored in diverging photoadaption strategies fostering Arctic diatom success in their respective light niches.},
	keywords = {RCC2046, RCC2278, RCC5318},
	issn = {1939-5590},
	doi = {10.1002/lno.11587},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lno.11587},
	author = {Croteau, Dany and Gu{\'e}rin, S{\'e}bastien and Bruyant, Flavienne and Ferland, Joannie and Campbell, Douglas A. and Babin, Marcel and Lavaud, Johann}
}
@article {fenizia_cysteinolic_2021,
	title = {Cysteinolic Acid Is a Widely Distributed Compatible Solute of Marine Microalgae},
	journal = {Marine Drugs},
	volume = {19},
	number = {12},
	year = {2021},
	note = {Number: 12 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {dec},
	pages = {683},
	abstract = {Phytoplankton rely on bioactive zwitterionic and highly polar small metabolites with osmoregulatory properties to compensate changes in the salinity of the surrounding seawater. Dimethylsulfoniopropionate (DMSP) is a main representative of this class of metabolites. Salinity-dependent DMSP biosynthesis and turnover contribute significantly to the global sulfur cycle. Using advanced chromatographic and mass spectrometric techniques that enable the detection of highly polar metabolites, we identified cysteinolic acid as an additional widely distributed polar metabolite in phytoplankton. Cysteinolic acid belongs to the class of marine sulfonates, metabolites that are commonly produced by algae and consumed by bacteria. It was detected in all dinoflagellates, haptophytes, diatoms and prymnesiophytes that were surveyed. We quantified the metabolite in different phytoplankton taxa and revealed that the cellular content can reach even higher concentrations than the ubiquitous DMSP. The cysteinolic acid concentration in the cells of the diatom Thalassiosira weissflogii increases significantly when grown in a medium with elevated salinity. In contrast to the compatible solute ectoine, cysteinolic acid is also found in high concentrations in axenic algae, indicating biosynthesis by the algae and not the associated bacteria. Therefore, we add this metabolite to the family of highly polar metabolites with osmoregulatory characteristics produced by phytoplankton.},
	keywords = {cysteinolic acid, diatoms, DMSP, ectoine, LC/MS analysis, osmoadaptation, osmoregulation, phytoplankton, RCC76, salinity},
	doi = {10.3390/md19120683},
	url = {https://www.mdpi.com/1660-3397/19/12/683},
	author = {Fenizia, Simona and Weissflog, Jerrit and Pohnert, Georg}
}
@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 {zhang_growth-dependent_2021,
	title = {Growth-dependent changes in elemental stoichiometry and macromolecular allocation in the coccolithophore Emiliania huxleyi under different environmental conditions},
	journal = {Limnology and Oceanography},
	volume = {66},
	number = {8},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/lno.11854},
	pages = {2999{\textendash}3009},
	abstract = {The growth rate hypothesis (GRH) posits an increase in ribosomal ribonucleic acid (RNA) content, and therefore cellular phosphorus (P), with increasing growth rate. There is evidence that the GRH may not apply to phytoplankton under all conditions. Here, we experimentally controlled four conditions (light, temperature, pH, and CO2) to alter the growth rate of Emiliania huxleyi, a biogeochemically important coccolithophorid, and monitored changes in RNA, protein, and carbohydrate content. We show that an increase in growth rate caused by increasing light, pH, and CO2 resulted in increased RNA per unit of organic carbon (RNA : POC), but that increasing temperature, leading to increase of growth rate, resulted in a decrease in RNA : POC. Protein per unit of organic carbon (protein : POC) increased in our increased temperature, pH, and CO2 treatments that increased growth rate, but there was little change in protein : POC in our light treatment despite it inducing the same increase in growth rate. Carbohydrate per unit of organic carbon (Carbohydrate : POC) increased with growth rate under increased light and CO2 but did not vary significantly in the temperature or pH treatments. These results indicate that physiological acclimation to specific environmental conditions can lead to contrasting patterns in RNA, protein, and carbohydrate composition and therefore contrasting changes in carbon : nitrogen : phosphorus ratios with growth rate in E. huxleyi.},
	keywords = {rcc, RCC1266},
	issn = {1939-5590},
	doi = {10.1002/lno.11854},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/lno.11854},
	author = {Zhang, Yong and Li, Zhengke and Schulz, Kai G. and Hu, Yingyu and Irwin, Andrew J. and Finkel, Zoe V.}
}
@article {schapira_les_2021,
	title = {Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : D{\'e}terminisme et cons{\'e}quences sur la qualit{\'e} des masses d{\textquoteright}eau c{\^o}ti{\`e}res},
	year = {2021},
	abstract = {Ce projet, organis{\'e} en trois actions, avait pour objectif de mieux {\'e}valuer les risques d{\textquoteright}eaux color{\'e}es vertes se produisant sur le secteur c{\^o}tier situ{\'e} au large de la Loire et de la Vilaine, en termes (i) de fr{\'e}quence de ces {\'e}pisodes, (ii) d{\textquoteright}abondance et (iii) de localisation des zones {\`a} risque. Action 1 : Am{\'e}lioration du recensement des eaux vertes {\`a} L. chlorophorum Action 2 : Optimisation de l{\textquoteright}estimation des abondances de L. chlorophorum Action 3 : Identification des zones {\`a} risque au large de la Loire et de la Vilaine.},
	keywords = {? No DOI found, rcc, RCC1489},
	url = {https://archimer.ifremer.fr/doc/00724/83598/},
	author = {Schapira, Mathilde and Roux, Pauline and Andre, Coralie and Mertens, Kenneth and Bilien, Gwenael and Terre Terrillon, Aouregan and Le Gac-Abernot, Chantal and Siano, Raffaele and Qu{\'e}r{\'e}, Julien and Bizzozero, Lucie and Bonneau, Francoise and Bouget, Jean-Francois and Cochennec-Laureau, Nathalie and Collin, Karine and Fortune, Mireille and Gabellec, Raoul and Le Merrer, Yoann and Manach, Soazig and Pierre-Duplessix, Olivier and Retho, Michael and Schmitt, Anne and Souchu, Philippe and Stachowski-Haberkorn, Sabine}
}
@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 {filatov_mode_2021,
	title = {The mode of speciation during a recent radiation in open-ocean phytoplankton},
	journal = {Current Biology},
	year = {2021},
	month = {oct},
	abstract = {Despite the enormous ecological importance of marine phytoplankton, surprisingly little is known about how new phytoplankton species originate and evolve in the open ocean, in the absence of apparent geographic barriers that typically act as isolation mechanisms in speciation. To investigate the mechanism of open-ocean speciation, we combined fossil and climatic records from the late Quaternary with genome-wide evolutionary genetic analyses of speciation in the ubiquitous and abundant pelagic coccolithophore genus Gephyrocapsa (including G. huxleyi, formerly known as Emiliania huxleyi). Based on the analysis of 43 sequenced genomes, we report that the best-fitting scenario for all speciation events analyzed included an extended period of complete isolation followed by recent (Holocene) secondary contact, supporting the role of geographic or oceanographic barriers in population divergence and speciation. Consistent with this, fossil data reveal considerable diachroneity of species first occurrence. The timing of all speciation events coincided with glacial phases of glacial-interglacial cycles, suggesting that stronger isolation between the ocean basins and increased segregation of ecological niches during glaciations are important drivers of speciation in marine phytoplankton. The similarity across multiple speciation events implies the generality of this inferred speciation scenario for marine phytoplankton.},
	keywords = {phytoplankton, population genetic modeling, rcc1212, rcc1238, RCC1239, RCC1253, RCC1281, RCC1296, RCC1310, RCC1314, RCC1562, RCC1836, RCC3370, RCC3711, RCC3733, RCC3862, RCC3898, RCC4002, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, RCC5119, RCC5134, RCC5137, RCC5141, RCC6566, RCC6730, secondary contact, sequence polymorphism, speciation},
	issn = {0960-9822},
	doi = {10.1016/j.cub.2021.09.073},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982221013415},
	author = {Filatov, Dmitry A. and Bendif, El Mahdi and Archontikis, Odysseas A. and Hagino, Kyoko and Rickaby, Rosalind E. M.}
}
@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 {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 {castillo_seasonal_2021,
	title = {Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH},
	journal = {Environmental Microbiology},
	volume = {n/a},
	number = {n/a},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15504},
	abstract = {Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral{\textendash}host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21\% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. This article is protected by copyright. All rights reserved.},
	keywords = {RCC2590, RCC4221, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.15504},
	url = {http://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15504},
	author = {Castillo, Yaiza M. and Forn, Irene and Yau, Sheree and Mor{\'a}n, Xos{\'e} Anxelu G. and Alonso-S{\'a}ez, Laura and Arandia-Gorostidi, N{\'e}stor and Vaqu{\'e}, Dolors and Sebasti{\'a}n, Marta}
}
@article {decelle_subcellular_2021,
	title = {Subcellular architecture and metabolic connection in the planktonic photosymbiosis between Collodaria (radiolarians) and their microalgae},
	journal = {bioRxiv},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	pages = {2021.03.13.435225},
	abstract = {Photosymbiosis is widespread and ecologically important in the oceanic plankton but remains poorly studied. Here, we used multimodal subcellular imaging to investigate the photosymbiosis between colonial Collodaria and their microalga dinoflagellate (Brandtodinium) collected in surface seawaters. We showed that this symbiosis is a very dynamic system whereby symbionts interact with different host cells via extracellular vesicles within the {\textquotedblleft}greenhouse-like{\textquotedblright} colony. 3D electron microscopy revealed that the volume of the photosynthetic apparatus (plastid and pyrenoid) of the microalgae increased in symbiosis compared to free-living while the mitochondria volume was similar. Stable isotope probing coupled with NanoSIMS showed that carbon and nitrogen were assimilated and stored in the symbiotic microalga in starch granules and purine crystals, respectively. Nitrogen was also allocated to the algal nucleus (nucleolus). After 3 hours, low 13C and 15N transfer was detected in the host Golgi. Metal mapping revealed that intracellular iron concentration was similar in free-living and symbiotic microalgae (ca 40 ppm) and two-fold higher in the host, whereas copper concentration increased in symbiotic microalgae (up to 6900 ppm) and was detected in the host cell and extracellular vesicles. Sulfur mapping also pinpointed the importance of this nutrient for the algal metabolism. This study, which revealed subcellular changes of the morphology and nutrient homeostasis in symbiotic microalgae, improves our understanding on the metabolism of this widespread and abundant oceanic symbiosis and paves the way for more studies to investigate the metabolites exchanged.},
	doi = {10.1101/2021.03.13.435225},
	url = {https://www.biorxiv.org/content/10.1101/2021.03.13.435225v1},
	author = {Decelle, Johan and Veronesi, Giulia and LeKieffre, Charlotte and Gallet, Benoit and Chevalier, Fabien and Stryhanyuk, Hryhoriy and Marro, Sophie and Ravanel, St{\'e}phane and Tucoulou, R{\'e}mi and Schieber, Nicole and Finazzi, Giovanni and Schwab, Yannick and Musat, Niculina}
}
@article {Benner2019,
	title = {Capacity of the common Arctic picoeukaryote Micromonas to adapt to a warming ocean},
	journal = {Limnology and Oceanography Letters},
	volume = {5},
	number = {2},
	year = {2020},
	note = {tex.mendeley-tags: RCC807},
	month = {apr},
	pages = {221{\textendash}227},
	keywords = {RCC807},
	issn = {2378-2242},
	doi = {10.1002/lol2.10133},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10133},
	author = {Benner, Ina and Irwin, Andrew J and Finkel, Zoe V}
}
@article {Carrigee2020,
	title = {CpeY is a phycoerythrobilin lyase for cysteine 82 of the phycoerythrin I <span class="nocase">α</span>-subunit in marine Synechococcus},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	year = {2020},
	note = {Publisher: Elsevier B.V tex.mendeley-tags: RCC555},
	month = {apr},
	pages = {148215},
	keywords = {rcc555},
	issn = {00052728},
	doi = {10.1016/j.bbabio.2020.148215},
	url = {https://doi.org/10.1016/j.bbamem.2019.183135 https://linkinghub.elsevier.com/retrieve/pii/S0005272820300657},
	author = {Carrigee, Lyndsay A. and Mahmoud, Rania M. and Sanfilippo, Joseph E. and Frick, Jacob P. and Strnat, Johann A. and Karty, Jonathan A. and Chen, Bo and Kehoe, David M. and Schluchter, Wendy M.}
}
@article {Avrahami2020,
	title = {Detection of phagotrophy in the marine phytoplankton group of the coccolithophores (calcihaptophycidae, haptophyta) during Nutrient-replete and Phosphate-limited growth},
	journal = {Journal of Phycology},
	year = {2020},
	note = {tex.mendeley-tags: RCC1130,RCC1131,RCC1178,RCC1216,RCC1217,RCC3779},
	month = {apr},
	pages = {jpy.12997},
	abstract = {Mixotrophic algae that combine photoautotrophy with phagotrophy in a single cell are prevalent in marine ecosystems. Here, we assessed the ability of food ingestion in coccolithophores, an important group of calcifying haptophytes inhabiting the oceans. We tested four species from different coccolithophore lineages (Emiliania huxleyi, Calcidiscus leptoporus, Coccolithus braarudii, and Calyptrosphaera sphaeroidea). For both E. huxleyi and C. leptoporus we included different life phases (haploid and diploid). For C. braarudii we only tested diploid heterococcolithophore cells, while for C. sphaeroidea we only tested haploid holococcolithophore cells. Phagotrophy was assessed using fluorescently labeled bacteria (FLB) as model prey item, under nutrient-replete and phosphate-limited conditions. We detected by microscopy ingestion of FLB by all species, except the diploid C. braarudii strain. However, a previous study detected ingestion by haploid cells of C. braarudii. These overall results indicate that mixotrophy and the ability to ingest prey is widespread in coccolithophores. Yet, in all tested species the ingestion of FLB was low ({\textexclamdown}1\% of the population contained prey at all time points over 2 days), namely for E. huxleyi and the diploid cells from C. leptoporus where detection of ingestion was sporadic. Moreover, no clear differences were detected between life phases in E. huxleyi and C. leptoporus under equal circumstances, or between replete and limited growth conditions.},
	keywords = {bacterivory, coccolithophores, life cycle, mixotrophy, phytoplankton, RCC1130, RCC1131, RCC1178, RCC1216, rcc1217, RCC3779},
	issn = {0022-3646},
	doi = {10.1111/jpy.12997},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12997},
	author = {Avrahami, Yoav and Frada, Miguel J.},
	editor = {Mock, T.}
}
@article {Kayal2020,
	title = {Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {December},
	year = {2020},
	note = {tex.mendeley-tags: RCC1627,RCC4398},
	month = {dec},
	pages = {1{\textendash}11},
	abstract = {Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.},
	keywords = {amoebophrya, chloroplast, Dinoflagellate, frontiers in microbiology, frontiersin, kleptoplast, marine plankton, org, organelles, parasitism, RCC1627, RCC4398, www},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.600823},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full},
	author = {Kayal, Ehsan and Alves-de-Souza, Catharina and Farhat, Sarah and Velo-Suarez, Lourdes and Monjol, Joanne and Szymczak, Jeremy and Bigeard, Estelle and Marie, Dominique and Noel, Benjamin and Porcel, Betina M and Corre, Erwan and Six, Christophe and Guillou, Laure}
}
@article {Fitzsimons2020,
	title = {Dissolved organic phosphorus uptake by marine phytoplankton is enhanced by the presence of dissolved organic nitrogen},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {530-531},
	number = {July},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RC2563,RCC2565},
	month = {sep},
	pages = {151434},
	abstract = {Organic nutrients can constitute the major fractions (up to 70\%) of aquatic nitrogen (N) and phosphorus (P), but their cycling is poorly understood relative to the inorganic pools. Some phytoplankton species access P from the dissolved organic phosphorus (DOP) pool through expression of alkaline phosphatase (AP), which hydrolyses orthophosphate from organic molecules, and is thought to occur either at low concentrations of dissolved inorganic P (DIP), or elevated ratios of dissolved inorganic N (DIN) to DIP. Three algal strains native to the North-East Atlantic Ocean (coccolithophore, dinoflagellate and diatom species) were grown under representative, temperate conditions, and the dissolved N and P components amended to include dissolved organic N (DON) and DOP. The activity of AP was measured to determine the rate of DOP uptake by each algal species. The addition of DON and DOP enhanced the growth of the algal species, regardless of DIN and DIP concentrations. In cultures where the total concentrations and absolute N: P ratio was unchanged but the N pool included both DON and DIN, an increase in alkaline phosphatase activity (APA) was measured. This suggested that the presence of DON triggered the selective uptake of DOP. The uptake of organic P was confirmed by detection of adenosine in DOP-amended culture media, indicating that P had been cleaved from ADP and ATP added to the media as DOP, and cellular P concentration in these cultures exceeded the calculated concentration based on uptake of DIP only. Our data demonstrates that organic nutrients can enhance and sustain marine algal productivity. The findings have implications for marine ecosystem function and health, since climate change scenarios predict variable riverine inputs to coastal areas, altered N: P ratios, and changes in the inorganic to organic balance of the nutrient pools.},
	keywords = {Alkaline phosphatase, COASTAL WATERS, Dissolved organic nitrogen, Dissolved organic phosphorus, Marine algae, P-limitation, RCC2563, RCC2565},
	issn = {00220981},
	doi = {10.1016/j.jembe.2020.151434},
	url = {https://doi.org/10.1016/j.jembe.2020.151434 https://linkinghub.elsevier.com/retrieve/pii/S0022098119304666},
	author = {Fitzsimons, Mark F. and Probert, Ian and Gaillard, Fanny and Rees, Andrew P.}
}
@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 {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 {Fernandes2020,
	title = {Hemiselmis andersenii and chlorella stigmatophora as new sources of High-value compounds: A lipidomic approach},
	journal = {Journal of Phycology},
	year = {2020},
	note = {Publisher: Blackwell Publishing Inc. tex.mendeley-tags: RCC661},
	month = {aug},
	pages = {jpy.13042},
	abstract = {To unlock the potential of Chlorella stigmatophora (Trebouxiophyceae, Chlorophyta) and Hemiselmis andersenii (Cryptophyceae, Cryptophyta) as natural reactors for biotechnological exploitation, their lipophilic extracts were characterized using Fourier Transform Infrared spectroscopy with Attenuated Total Reflectance (FTIR-ATR) and Gas Chromatography-Mass Spectrometry (GC-MS) before and after alkaline hydrolysis. The GC-MS analysis enabled the identification of 62 metabolites{\textemdash}namely fatty acids (27), aliphatic alcohols (17), monoglycerides (7), sterols (4), and other compounds (7). After alkaline hydrolysis, monounsaturated fatty acids increased by as much as 87\%, suggesting that the esterified compounds were mainly neutral lipids. Hemiselmis andersenii yielded the highest Σω3/Σω6 ratio (7.26), indicating that it is a good source of ω3 fatty acids, in comparison to C. stigmatophora (Σω3/Σω6 = 1.24). Both microalgae presented significant amounts of aliphatic alcohols (6.81{\textendash}10.95 mg ? g dw-1), which are recognized by their cholesterol-lowering properties. The multivariate analysis allowed visualization of the chemical divergence among H. andersenii lipophilic extracts before and after alkaline hydrolysis, as well as species-specific differences. Chlorella stigmatophora showed to be a valuable source of essential fatty acids for nutraceuticals, whereas H. andersenii, due to its high chemical diversity, seems to be suitable for different fields of application.},
	keywords = {Chlorella stigmatophora, GC-MS, Hemiselmis andersenii, lipophilic fraction, Microalgae, RCC661},
	issn = {0022-3646},
	doi = {10.1111/jpy.13042},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13042},
	author = {Fernandes, Tom{\'a}sia and Cordeiro, Nereida},
	editor = {Li, Y.}
}
@article {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 {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 {Avilan2020,
	title = {ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2020},
	note = {Publisher: Cold Spring Harbor Laboratory tex.mendeley-tags: RCC2967},
	month = {mar},
	pages = {2020.03.05.978130},
	abstract = {{\textbullet} Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta-and tetraphosphate, or (p)ppGpp. In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. {\textbullet} Here, we studied the function of ppGpp in the diatom P. tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. {\textbullet} We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using non-targeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. {\textbullet} Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.},
	keywords = {chloroplast, diatoms, lipid droplets, Phaeodactylum tricornutum, Photosynthesis, ppGpp, proteome, RCC2967},
	doi = {10.1101/2020.03.05.978130},
	url = {https://doi.org/10.1101/2020.03.05.978130},
	author = {Avilan, Luisana and Lebrun, Regine and Puppo, Carine and Citerne, Sylvie and Cuin{\'e}, Stephane and Li-Beisson, Yonghua and Menand, Benoit and Field, Ben and Gontero, Brigitte}
}
@article {Bretherton2020,
	title = {Trait-dependent variability of the response of marine phytoplankton to oil and dispersant exposure},
	journal = {Marine Pollution Bulletin},
	volume = {153},
	number = {January},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC1614},
	pages = {110906},
	abstract = {The Deepwater Horizon oil spill released millions of barrels of crude oil into the Gulf of Mexico, and saw widespread use of the chemical dispersant Corexit. We assessed the role of traits, such as cell size, cell wall, motility, and mixotrophy on the growth and photosynthetic response of 15 phytoplankton taxa to oil and Corexit. We collected growth and photosynthetic data on five algal cultures. These responses could be separated into resistant (Tetraselmis astigmatica, Ochromonas sp., Heterocapsa pygmaea) and sensitive (Micromonas pusilla, Prorocentrum minimum). We combined this data with 10 species previously studied and found that cell size is most important in determining the biomass response to oil, whereas motility/mixotrophy is more important in the dispersed oil. Our analysis accounted for a third of the variance observed, so further work is needed to identify other factors that contribute to oil resistance.},
	keywords = {Chemical dispersants, Chlorophyll, crude oil, Photosynthesis, phytoplankton, RCC1614, Trait-based analysis},
	issn = {18793363},
	doi = {10.1016/j.marpolbul.2020.110906},
	url = {https://doi.org/10.1016/j.marpolbul.2020.110906},
	author = {Bretherton, Laura and Hillhouse, Jessica and Kamalanathan, Manoj and Finkel, Zoe V. and Irwin, Andrew J. and Quigg, Antonietta}
}
@article {Castillo2020,
	title = {Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC4221},
	month = {jul},
	pages = {1559},
	abstract = {One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.},
	keywords = {culture system, marine picoeukaryote, Ostreococcus tauri, Ostreococcus tauri virus 5, RCC4221, virus fluorescence in situ hybridization, virus-host interactions},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.01559},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01559/full},
	author = {Castillo, Yaiza M. and Sebasti{\'a}n, Marta and Forn, Irene and Grimsley, Nigel and Yau, Sheree and Moraru, Cristina and Vaqu{\'e}, Dolors}
}
@article {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 {Tsuboi2019,
	title = {Short-term changes in marine prokaryotic and eukaryotic microalgal communities exposed to the leachate of a seafloor hydrothermal sulfide},
	journal = {Water, Air, \& Soil Pollution},
	volume = {230},
	year = {2019},
	note = {tex.mendeley-tags: RCC,RCC1089,RCC262},
	pages = {175},
	abstract = {The effects of increased mining of seafloor massive sulfide deposits on marine ecosystems have not been characterized. In this study, the impact of leaching metals from a hydrothermal sulfide on photosynthetic protist and cyanobacterial communities in marine environments was investigated by amplicon analyses of small subunit rDNA (SSU rDNA) and rRNA (SSU rRNA). Seawater samples collected from the Iheya North region and Suruga Bay, Japan, were incubated with or without a leachate containing zinc, copper, cadmium, and manganese, of the actual seafloor hydrothermal sulfide from the Hakurei site in the Izena Hole region. The relative abundances of prasinophytes, diatom protists, and the cyanobacteria Synechococcus decreased substantially during incubation with leachate, indicating the vulnerability of these lineages to the leachate. Phylogenetic analysis based on the cyanobacterial phycocyanin cpcBA/rpcBA operon obtained from samples incubated with or without leachate indicated that the individual lineages of Synechococcus can determine sensitivity to heavy metals in different marine regions as well as particular clades and ecotypes.},
	keywords = {rcc, RCC1089, RCC262},
	doi = {10.1007/s11270-019-4224-8},
	author = {Tsuboi, Shun and Yamaguchi, Haruyo and Fuchida, Shigeshi and Koshikawa, Hiroshi and Kawachi, Masanobu}
}
@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 {Annunziata2018,
	title = {A bHLH-PAS protein regulates light-dependent rhythmic processes in the marine diatom Phaeodactylum tricornutum},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC2967},
	pages = {271445},
	abstract = {Periodic light dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diurnal rhythms in growth, cell cycle and gene expression, the molecular bases controlling these processes are still obscure. By exploring the regulatory landscape of diatom diurnal rhythms, we here unveil the key function of a Phaeodactylum tricornutum bHLH-PAS protein, named Pt bHLH1a, in the regulation of light-dependent rhythms. Peak expression of Pt bHLH1a mRNA occurs at the end of the light period and it is adjusted to photoperiod changes. Ectopic over-expression of Pt bHLH1a results in lines with altered cell division and gene expression and showing a phase shift in diurnal responses, compared to the wild-type cells. Reduced oscillations in gene expression are also observed in continuous darkness, showing that the regulation of rhythmicity by Pt bHLH1a is not directly dependent on light inputs and cell division. Pt bHLH1a orthologs are widespread in both pennate and centric diatom genomes, hinting at a common function in many species. This study adds new elements to understand diatom biology and ecology and offers new perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but still underinvestigated branch of the tree of life.},
	keywords = {RCC2967},
	doi = {10.1101/271445},
	url = {https://www.biorxiv.org/content/early/2018/02/25/271445},
	author = {Annunziata, Rossella and Ritter, Andr{\'e}s and Fortunato, Antonio Emidio and Cheminant-Navarro, Soizic and Agier, Nicolas and Huysman, Marie J. J. and Winge, Per and Bones, Atle and Bouget, Fran{\c c}ois-Yves and Lagomarsino, Marco Cosentino and Bouly, Jean Pierre and Falciatore, Angela}
}
@article {Fox2018,
	title = {Calcein staining as a tool to investigate coccolithophore calcification},
	journal = {Frontiers in Marine Science},
	volume = {5},
	number = {September},
	year = {2018},
	note = {tex.mendeley-tags: RCC 1461,RCC 3777,RCC1130,RCC1303,RCC1456},
	abstract = {This brief paper summarizes the literature on academic accommodations for students with psychiatric disabilities. A definition of psychiatric disability precedes a brief summary of the following specific psychiatric diagnoses: depression, bipolar affective disorder; borderline personality disorder; schizophrenia; and anxiety disorders. Also noted are behavior or personality disorders specifically excluded from coverage under the Americans with Disabilities Act. Functional limitations of this population that may affect academic performance are then listed and defined. Among these are medication side effects, sustaining concentration, maintaining stamina, interacting with others, responding to negative feedback, responding to change, and severe test anxiety. Examples of appropriate instructional strategies are followed by a discussion of reasonable accommodations to provide these students with equal access to the curriculum. Examples are then given of classroom accommodations, examination accommodations, and assignment accommodations. Characteristics of accommodations that are not reasonable are also listed. The paper concludes with a resource list including Web site and contact information for the DO-IT (Disabilities, Opportunities, Internetworking, and Technology) Project. (DB)},
	keywords = {bet hedging, calcein, Calcification, coccolith, coccolithophore, flow cytometry, haptophyte, RCC1130, RCC1303, RCC1456, RCC1461, RCC3777, secretion},
	issn = {2296-7745},
	doi = {10.3389/fmars.2018.00326},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00326/full},
	author = {Fox, Emily and Meyer, Erin and Panasiak, Natalie and Taylor, Alison R.}
}
@article {Farhat2018,
	title = {Comparative time-scale gene expression analysis highlights the infection processes of two amoebophrya strains},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {October},
	year = {2018},
	note = {tex.mendeley-tags: RCC1627,RCC3596,RCC4383,RCC4398},
	month = {oct},
	pages = {1{\textendash}19},
	keywords = {amoebophrya, Dinoflagellates, Gene Expression, infection, oxidative stress response, parasite, plankton, RCC1627, RCC3596, RCC4383, RCC4398, syndiniales},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.02251},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02251/full},
	author = {Farhat, Sarah and Florent, Isabelle and Noel, Benjamin and Kayal, Ehsan and Da Silva, Corinne and Bigeard, Estelle and Alberti, Adriana and Labadie, Karine and Corre, Erwan and Aury, Jean-Marc and Rombauts, Stephane and Wincker, Patrick and Guillou, Laure and Porcel, Betina M.}
}
@article {Partensky2018,
	title = {Comparison of photosynthetic performances of marine picocyanobacteria with different configurations of the oxygen-evolving complex},
	journal = {Photosynthesis Research},
	volume = {138},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: RCC752},
	pages = {57{\textendash}71},
	abstract = {The extrinsic PsbU and PsbV proteins are known to play a critical role in stabilizing the Mn4CaO5 cluster of the PSII oxygen-evolving complex (OEC). However, most isolates of the marine cyanobacterium Prochlorococcus naturally miss these proteins, even though they have kept the main OEC protein, PsbO. A structural homology model of the PSII of such a natural deletion mutant strain (P. marinus MED4) did not reveal any obvious compensation mechanism for this lack. To assess the physiological consequences of this unusual OEC, we compared oxygen evolution between Prochlorococcus strains missing psbU and psbV (PCC 9511 and SS120) and two marine strains possessing these genes (Prochlorococcus sp. MIT9313 and Synechococcus sp. WH7803). While the low light-adapted strain SS120 exhibited the lowest maximal O2 evolution rates (Pmax per divinyl-chlorophyll a, per cell or per photosystem II) of all four strains, the high light-adapted strain PCC 9511 displayed even higher PChlmax and PPSIImax at high irradiance than Synechococcus sp. WH7803. Furthermore, thermoluminescence glow curves did not show any alteration in the B-band shape or peak position that could be related to the lack of these extrinsic proteins. This suggests an efficient functional adaptation of the OEC in these natural deletion mutants, in which PsbO alone is seemingly sufficient to ensure proper oxygen evolution. Our study also showed that Prochlorococcus strains exhibit negative net O2 evolution rates at the low irradiances encountered in minimum oxygen zones, possibly explaining the very low O2 concentrations measured in these environments, where Prochlorococcus is the dominant oxyphototroph.},
	keywords = {rcc752},
	issn = {1573-5079},
	doi = {10.1007/s11120-018-0539-3},
	url = {https://doi.org/10.1007/s11120-018-0539-3},
	author = {Partensky, Fr{\'e}d{\'e}ric and Mella-Flores, Daniella and Six, Christophe and Garczarek, Laurence and Czjzek, Mirjam and Marie, Dominique and Kotabov{\'a}, Eva and Felcmanov{\'a}, Kristina and Pr{\'a}{\v s}il, Ond{\v r}ej}
}
@article {Trainic,
	title = {Infection dynamics of a bloom-forming alga and its virus determine airborne coccolith emission from seawater},
	journal = {iScience},
	year = {2018},
	note = {tex.mendeley-tags: RCC1216},
	month = {aug},
	abstract = {Summary Sea spray aerosols (SSA), have a profound effect on the climate; however, the contribution of oceanic microbial activity to SSA is not fully established. We assessed aerosolization of the calcite units (coccoliths) that compose the exoskeleton of the cosmopolitan bloom-forming coccolithophore, Emiliania huxleyi. Airborne coccolith emission occurs in steady-state conditions and increases by an order of magnitude during E. huxleyi infection by E. huxleyi virus (EhV). Airborne to seawater coccolith ratio is 1:108, providing estimation of airborne concentrations from seawater concentrations. The coccoliths{\textquoteright} unique aerodynamic structure yields a characteristic settling velocity of \~0.01 cm s-1, \~25 times slower than average sea salt particles, resulting in coccolith fraction enrichment in the air. The calculated enrichment was established experimentally, indicating that coccoliths may be key contributors to coarse mode SSA surface area, comparable with sea salt aerosols. This study suggests a coupling between key oceanic microbial interactions and fundamental atmospheric processes like SSA formation.},
	keywords = {Atmospheric Science, Biogeoscience, Earth Sciences, Marine Organism, RCC1216},
	issn = {25890042},
	doi = {10.1016/j.isci.2018.07.017},
	url = {https://www.cell.com/iscience/fulltext/S2589-0042(18)30105-6 https://linkinghub.elsevier.com/retrieve/pii/S2589004218301056},
	author = {Trainic, Miri and Koren, Ilan and Sharoni, Shlomit and Frada, Miguel and Segev, Lior and Rudich, Yinon and Vardi, Assaf}
}
@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 {Liefer2018,
	title = {Nitrogen starvation induces distinct photosynthetic responses and recovery dynamics in diatoms and prasinophytes},
	journal = {PLOS ONE},
	volume = {13},
	number = {4},
	year = {2018},
	note = {ISBN: 1111111111 tex.mendeley-tags: RCC745},
	month = {apr},
	pages = {e0195705},
	abstract = {Nitrogen stress is an important control on the growth of phytoplankton and varying responses to this common condition among taxa may affect their relative success within phytoplankton communities.We analyzed photosynthetic responses to nitrogen (N) stress in two classes of phytoplankton that often dominate their respective size ranges, diatoms and prasinophytes, selecting species of distinct niches within each class. Changes in photosynthetic structures appeared similar within each class during N stress, but photophysiological and growth responses were more species -or niche-specific. In the coastal diatom Thalassiosira pseudonana and the oceanic diatom T. weissflogii, N starvation induced large declines in photosynthetic pigments and Photosystem II (PSII) quantity and activity as well as increases in the effective absorption cross-section of PSII photochemistry (σ{\textquoteright}PSII). These diatoms also increased photoprotection through energy-dependent non-photochemical quenching (NPQ) during N starvation. Resupply of N in diatoms caused rapid recovery of growth and relaxation of NPQ, while recovery of PSII photochemistry was slower. In contrast, the prasinophytes Micromonas sp., an Arctic Ocean species, and Ostreococcus tauri, a temperate coastal eutrophile, showed little change in photosynthetic pigments and structures and a decline or no change, respectively, inσ{\textquoteright}PSII with N starvation. Growth and PSII function recovered quickly in Micromonas sp. after resupply of N while O. tauri failed to recover N-replete levels of electron transfer from PSII and growth, possibly due to their distinct photoprotective strategies. O. tauri induced energy-dependent NPQ for photoprotection that may suit its variable and nutrient-rich habitat. Micromonas sp. relies upon both energy-dependent NPQ and a sustained, energy-independent NPQ mechanism. A strategy in Micromonas sp. that permits photoprotection with little change in photosynthetic structures is consistent with its Arctic niche, where low temperatures and thus low biosynthetic rates create higher opportunity costs to rebuild photosynthetic structures.},
	keywords = {RCC745},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0195705},
	url = {http://dx.plos.org/10.1371/journal.pone.0195705},
	author = {Liefer, Justin D and Garg, Aneri and Campbell, Douglas A and Irwin, Andrew J and Finkel, Zoe V},
	editor = {Ianora, Adrianna}
}
@article {Fiore2018,
	title = {A phosphate starvation response gene (psr1-like) is present and expressed in Micromonas pusilla and other marine algae},
	journal = {bioRxiv},
	year = {2018},
	note = {tex.mendeley-tags: RCC299,RCC834},
	keywords = {? No DOI found, RCC299, RCC834},
	url = {http://dx.doi.org/10.1101/484824},
	author = {Fiore, Cara L. and Alexander, Harriet and Soule, Melissa C. Kido and Kujawinski, Elizabeth B.}
}
@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 {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 {Fischer2017,
	title = {Identity of the limiting nutrient (N vs. P) affects the competitive success of mixotrophs},
	journal = {Marine Ecology Progress Series},
	volume = {563},
	year = {2017},
	note = {tex.mendeley-tags: RCC744},
	pages = {51{\textendash}63},
	abstract = {ABSTRACT: Empirical and theoretical evidence predicts that mixotrophic bacterivores dominate over specialized heterotrophic bacterivores and specialist photoautotrophs under conditions of high light and low loss rates. Here we extend this concept towards nutrient limitation and ask whether the identity of the limiting nutrient affects the competition of mixotrophs with their specialist competitors. Due to their photosynthetic machinery, mixotrophs should have higher cellular N contents than heterotrophs and, following this assumption, a higher demand for N. Conversely, heterotrophs, with their potential high growth rates compared to mixotrophs, may have a higher demand for P (?growth rate hypothesis?). Simplified, mixotrophs should be more prone to N-limitation, while heterotrophs should be more prone to P-limitation. We tested these predictions in artificial food webs studying the competitive success of mixotrophic bacterivores under a range of light intensities and loss rates and under either P- or N-limitation. Under low-light conditions, mixotrophs were more successful than heterotrophs under P-limitation, whereas the heterotrophs were more successful under N-limitation. At higher light intensity, mixotrophs had an advantage over photoautotrophs, due to the acquisition of nutrients ingested with prey. Overall, the effects of the limiting nutrient on the competitive success of mixotrophs were stronger under conditions already unfavorable for mixotrophs (low light). Further, our results suggest that communities dominated by mixotrophs might have low and relatively stable seston C:nutrient ratios. The results presented here supplement existing data well and help to define the ecological niche of mixotrophic protists.},
	keywords = {RCC744},
	doi = {10.3354/meps11968},
	url = {https://www.int-res.com/abstracts/meps/v563/p51-63},
	author = {Fischer, R and HA, Giebel and Ptacnik, R}
}
@article {faucher_impact_2017,
	title = {Impact of trace metal concentrations on coccolithophore growth and morphology: laboratory simulations of Cretaceous stress},
	journal = {Biogeosciences},
	volume = {14},
	number = {14},
	year = {2017},
	note = {Publisher: Copernicus GmbH},
	month = {jul},
	pages = {3603{\textendash}3613},
	abstract = {<p><strong class="journal-contentHeaderColor">Abstract.</strong> The Cretaceous ocean witnessed intervals of profound perturbations such as volcanic input of large amounts of CO$_\textrm2$, anoxia, eutrophication and introduction of biologically relevant metals. Some of these extreme events were characterized by size reduction and/or morphological changes of a few calcareous nannofossil species. The correspondence between intervals of high trace metal concentrations and coccolith dwarfism suggests a negative effect of these elements on nannoplankton biocalcification processes in past oceans. In order to test this hypothesis, we explored the potential effect of a mixture of trace metals on growth and morphology of four living coccolithophore species, namely \textitEmiliania huxleyi, Gephyrocapsa oceanica, Pleurochrysis carterae and \textitCoccolithus pelagicus. The phylogenetic history of coccolithophores shows that the selected living species are linked to Mesozoic species showing dwarfism under excess metal concentrations. The trace metals tested were chosen to simulate the environmental stress identified in the geological record and upon known trace metal interactions with living coccolithophore algae.<br><br>Our laboratory experiments demonstrated that elevated trace metal concentrations, similarly to the fossil record, affect coccolithophore algae size and/or weight. Smaller coccoliths were detected in \textitE. huxleyi and \textitC. pelagicus, while coccoliths of \textitG. oceanica showed a decrease in size only at the highest trace metal concentrations. \textitP. carterae coccolith size was unresponsive to changing trace metal concentrations. These differences among species allow discriminating the most- (\textitP. carterae), intermediate- (\textitE. huxleyi and \textitG. oceanica) and least-tolerant (\textitC. pelagicus) taxa. The fossil record and the experimental results converge on a selective response of coccolithophores to metal availability.<br><br>These species-specific differences must be considered before morphological features of coccoliths are used to reconstruct paleo-chemical conditions.</p>},
	keywords = {RCC1198, RCC1216, RCC1303},
	issn = {1726-4170},
	doi = {10.5194/bg-14-3603-2017},
	url = {https://bg.copernicus.org/articles/14/3603/2017/},
	author = {Faucher, Giulia and Hoffmann, Linn and Bach, Lennart T. and Bottini, Cinzia and Erba, Elisabetta and Riebesell, Ulf}
}
@article {Fischer2017a,
	title = {Importance of mixotrophic bacterivory can be predicted by light and loss rates},
	journal = {Oikos},
	volume = {126},
	number = {5},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC744},
	month = {may},
	pages = {713{\textendash}722},
	abstract = {Recent observational studies form oligotrophic waters provide ample evidence that mixotrophic flagellates often account for the bulk of bacterivory. However, we lack a general framework that allows a mechanistic understanding of success of mixotrophs in the competition with heterotrophic bacterivores. This is especially needed for integrating mixotrophy in models of the microbial loop. Based on general tradeoffs linked to the combined resource use in mixotrophs (generalist versus specialist), we propose a concept where mixotrophs are favored by conditions of high light ? low losses, corresponding to the situation found in the surface waters of oligotrophic oceans. Under such conditions, they can achieve positive net growth at very low resource levels, allowing simultaneous competition with specialized protists. Conversely, heterotrophic bacterivores and photoautotrophs should be especially favored in more productive and low-light conditions. We show experimentally that the combined effect of light and loss rates (dilution) predicts the success of mixotrophic bacterivorous flagellates. Moreover, our results suggest that total bacterivory, contrary as seen in the traditional microbial loop concept, has a more intricate coupling to light.},
	keywords = {RCC744},
	issn = {0030-1299},
	doi = {10.1111/oik.03539},
	url = {https://doi.org/10.1111/oik.03539},
	author = {Fischer, Robert and Giebel, Helge-Ansgar and Hillebrand, Helmut and Ptacnik, Robert}
}
@article {Steele2017,
	title = {Occurrence of chlorophyll allomers during virus-induced mortality and population decline in the ubiquitous picoeukaryote Ostreococcus tauri},
	journal = {Environmental Microbiology},
	volume = {in press},
	year = {2017},
	note = {ISBN: 3907122046 tex.mendeley-tags: RCC745},
	month = {nov},
	pages = {1{\textendash}41},
	abstract = {Phytoplankton have been shown to harbour a diversity of hydrocarbonoclastic bacteria (HCB), yet it is not understood how these phytoplankton-associated HCB would respond in the event of an oil spill at sea. Here, we assess the diversity and dynamics of the bacterial community associated with a natural population of marine phytoplankton under oil spill-simulated conditions, and compare it to that of the free-living (non phytoplankton-associated) bacterial community. Whilst the crude oil severely impacted the phytoplankton population and was likely conducive to marine oil snow (MOS) formation, analysis of the MiSeq-derived 16S rRNA data revealed dramatic and differential shifts in the oil-amended communities that included blooms of recognised HCB (e.g. Thalassospira, Cycloclasticus), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential (Olleya, Winogradskyella, and members of the inconspicuous BD7-3 phylum). Notably, the oil biodegradation potential of the phytoplankton-associated community exceeded that of the free-living community, and it showed a preference to degrade substituted and non-substituted polycyclic aromatic hydrocarbons. Our study provides evidence of compartmentalisation of hydrocarbon-degrading capacity in the marine water column, wherein HCB associated with phytoplankton are better tuned to degrading crude oil hydrocarbons than that by the community of planktonic free-living bacteria.},
	keywords = {biodegradation, crude oil, eukaryotic phytoplankton, hydrocarbon-degrading bacteria (HCB), marine environment, micro- algae, RCC745},
	issn = {14622912},
	doi = {10.1111/1462-2920.13980},
	url = {http://doi.wiley.com/10.1111/1462-2920.13980},
	author = {Steele, Deborah J. and Kimmance, Susan A. and Franklin, Daniel J. and Airs, Ruth L.}
}
@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 {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 {Bolton2016,
	title = {Decrease in coccolithophore calcification and CO2 since the middle Miocene},
	journal = {Nature Communications},
	volume = {7},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	pages = {10284},
	abstract = {Marine algae are instrumental in carbon cycling and atmospheric carbon dioxide (CO2) regulation. One group, coccolithophores, uses carbon to photosynthesize and to calcify, covering their cells with chalk platelets (coccoliths). How ocean acidification influences coccolithophore calcification is strongly debated, and the effects of carbonate chemistry changes in the geological past are poorly understood. This paper relates degree of coccolith calcification to cellular calcification, and presents the first records of size-normalized coccolith thickness spanning the last 14 Myr from tropical oceans. Degree of calcification was highest in the low-pH, high-CO2 Miocene ocean, but decreased significantly between 6 and 4 Myr ago. Based on this and concurrent trends in a new alkenone ep record, we propose that decreasing CO2 partly drove the observed trend via reduced cellular bicarbonate allocation to calcification. This trend reversed in the late Pleistocene despite low CO2, suggesting an additional regulator of calcification such as alkalinity. 1},
	keywords = {2016, rcc},
	issn = {2041-1723},
	doi = {10.1038/ncomms10284},
	url = {http://www.nature.com/doifinder/10.1038/ncomms10284},
	author = {Bolton, Clara T. and Hern{\'a}ndez-S{\'a}nchez, Mar{\'\i}a T. and Fuertes, Miguel-{\'A}ngel and Gonz{\'a}lez-Lemos, Sa{\'u}l and Abrevaya, Lorena and M{\'e}ndez-Vicente, Ana and Flores, Jos{\'e}-Abel and Probert, Ian and Giosan, Liviu and Johnson, Joel and Stoll, Heather M.}
}
@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 {Stuken2015,
	title = {Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains},
	journal = {Frontiers in Microbiology},
	volume = {6},
	number = {May},
	year = {2015},
	note = {tex.mendeley-tags: 2015,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1{\textendash}10},
	abstract = {Dinoflagellates are microscopic aquatic eukaryotes with huge genomes and an unusual cell regulation. For example, most genes are present in numerous copies and all copies seem to be obligatorily transcribed. The consequence of the gene copy number (CPN) for final protein synthesis is, however, not clear. One such gene is sxtA, the starting gene of paralytic shellfish toxin (PST) synthesis. PSTs are small neurotoxic compounds that can accumulate in the food chain and cause serious poisoning incidences when ingested. They are produced by dinoflagellates of the genera Alexandrium, Gymnodium, and Pyrodinium. Here we investigated if the genomic CPN of sxtA4 is related to PST content in Alexandrium minutum cells. SxtA4 is the 4th domain of the sxtA gene and its presence is essential for PST synthesis in dinoflagellates. We used PST and genome size measurements as well as quantitative PCR to analyze sxtA4 CPN and toxin content in 15 A. minutum strains. Our results show a strong positive correlation between the sxtA4 CPN and the total amount of PST produced in actively growing A. minutum cells. This correlation was independent of the toxin profile produced, as long as the strain contained the genomic domains sxtA1 and sxtA4.},
	keywords = {2015, Alexandrium, copy, copy number variation, Dinoflagellate, gene dosage, genome size, number variation, paralytic shellfish toxin, paralytic shellfish toxin (PST), pst, rcc, RCC?o?dd, saxitoxin, saxitoxin (STX), sbr?hyto$_\textrmd$ipo, stx, sxtA},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2015.00404},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2015.00404},
	author = {St{\"u}ken, Anke and Riob{\'o}, Pilar and Franco, Jos{\'e} and Jakobsen, Kjetill S. and Guillou, Laure and Figueroa, Rosa I.}
}
@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 {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 {Monier2013,
	title = {Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity},
	journal = {The ISME journal},
	volume = {7},
	year = {2013},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {1764{\textendash}1774},
	keywords = {horizontal transfer, inteins, invasive elements, metagenomics, Micromonas, polymorphic introns, rcc, viridiplantae},
	doi = {10.1038/ismej.2013.70},
	url = {http://dx.doi.org/10.1038/ismej.2013.70 10.1038/ismej.2013.70},
	author = {Monier, Adam and Sudek, Sebastian and Fast, Naomi M and Worden, Alexandra Z}
}
@article {Humily2013,
	title = {A gene island with two possible configurations is involved in chromatic acclimation in marine synechococcus},
	journal = {PLoS ONE},
	volume = {8},
	number = {12},
	year = {2013},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2013,macumba,rcc,sbr?hyto?app},
	pages = {e84459},
	abstract = {{\textexclamdown}p{\textquestiondown}{\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown}, the second most abundant oxygenic phototroph in the marine environment, harbors the largest pigment diversity known within a single genus of cyanobacteria, allowing it to exploit a wide range of light niches. Some strains are capable of Type IV chromatic acclimation (CA4), a process by which cells can match the phycobilin content of their phycobilisomes to the ambient light quality. Here, we performed extensive genomic comparisons to explore the diversity of this process within the marine {\textexclamdown}italic{\textquestiondown}Synechococcus{\textexclamdown}/italic{\textquestiondown} radiation. A specific gene island was identified in all CA4-performing strains, containing two genes ({\textexclamdown}italic{\textquestiondown}fciA{\textexclamdown}/italic{\textquestiondown}/b) coding for possible transcriptional regulators and one gene coding for a phycobilin lyase. However, two distinct configurations of this cluster were observed, depending on the lineage. CA4-A islands contain the {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} gene, encoding a recently characterized phycoerythrobilin lyase-isomerase, and a third, small, possible regulator called {\textexclamdown}italic{\textquestiondown}fciC{\textexclamdown}/italic{\textquestiondown}. In CA4-B islands, the lyase gene encodes an uncharacterized relative of MpeZ, called MpeW. While {\textexclamdown}italic{\textquestiondown}mpeZ{\textexclamdown}/italic{\textquestiondown} is expressed more in blue light than green light, this is the reverse for {\textexclamdown}italic{\textquestiondown}mpeW{\textexclamdown}/italic{\textquestiondown}, although only small phenotypic differences were found among chromatic acclimaters possessing either CA4 island type. This study provides novel insights into understanding both diversity and evolution of the CA4 process.{\textexclamdown}/p{\textquestiondown}},
	keywords = {2013, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1371/journal.pone.0084459},
	url = {http://dx.doi.org/10.1371/journal.pone.0084459},
	author = {Humily, Florian and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Farrant, Gregory K and Ratin, Morgane and Marie, Dominique and Garczarek, Laurence}
}
@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 {Thompson2012,
	title = {Unicellular cyanobacterium symbiotic with a single-celled eukaryotic alga},
	journal = {Science},
	volume = {337},
	number = {6101},
	year = {2012},
	note = {tex.mendeley-tags: 2012,microb3,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1546{\textendash}1550},
	abstract = {Symbioses between nitrogen (N)2{\textendash}fixing prokaryotes and photosynthetic eukaryotes are important for nitrogen acquisition in N-limited environments. Recently, a widely distributed planktonic uncultured nitrogen-fixing cyanobacterium (UCYN-A) was found to have unprecedented genome reduction, including the lack of oxygen-evolving photosystem II and the tricarboxylic acid cycle, which suggested partnership in a symbiosis. We showed that UCYN-A has a symbiotic association with a unicellular prymnesiophyte, closely related to calcifying taxa present in the fossil record. The partnership is mutualistic, because the prymnesiophyte receives fixed N in exchange for transferring fixed carbon to UCYN-A. This unusual partnership between a cyanobacterium and a unicellular alga is a model for symbiosis and is analogous to plastid and organismal evolution, and if calcifying, may have important implications for past and present oceanic N2 fixation.},
	keywords = {2012, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1126/science.1222700},
	url = {http://www.sciencemag.org/content/337/6101/1546.abstract},
	author = {Thompson, Anne W and Foster, Rachel A and Krupke, Andreas and Carter, Brandon J and Musat, Niculina and Vaulot, Daniel and Kuypers, Marcel M M and Zehr, Jonathan P}
}
@article {Foresi2010,
	title = {Characterization of a nitric oxide synthase from the plant kingdom: NO generation from the green alga Ostreococcus tauri is light irradiance and growth phase dependent},
	journal = {The Plant Cell},
	volume = {22},
	number = {11},
	year = {2010},
	note = {Edition: 2010/12/02 ISBN: 1532-298X (Electronic) 1040-4651 (Linking) tex.mendeley-tags: RCC745},
	pages = {3816{\textendash}3830},
	abstract = {The search for a nitric oxide synthase (NOS) sequence in the plant kingdom yielded two sequences from the recently published genomes of two green algae species of the Ostreococcus genus, O. tauri and O. lucimarinus. In this study, we characterized the sequence, protein structure, phylogeny, biochemistry, and expression of NOS from O. tauri. The amino acid sequence of O. tauri NOS was found to be 45\% similar to that of human NOS. Folding assignment methods showed that O. tauri NOS can fold as the human endothelial NOS isoform. Phylogenetic analysis revealed that O. tauri NOS clusters together with putative NOS sequences of a Synechoccocus sp strain and Physarum polycephalum. This cluster appears as an outgroup of NOS representatives from metazoa. Purified recombinant O. tauri NOS has a K(m) for the substrate l-Arg of 12 +/- 5 muM. Escherichia coli cells expressing recombinant O. tauri NOS have increased levels of NO and cell viability. O. tauri cultures in the exponential growth phase produce 3-fold more NOS-dependent NO than do those in the stationary phase. In O. tauri, NO production increases in high intensity light irradiation and upon addition of l-Arg, suggesting a link between NOS activity and microalgal physiology.},
	keywords = {*Light, Amino Acid Sequence, Animals, Base Sequence, Chlorophyta/*enzymology/*growth \& development/phys, Humans, Isoenzymes/chemistry/genetics/metabolism, Models, Molecular, Molecular Sequence Data, Nitric Oxide Synthase/chemistry/genetics/*metaboli, Nitric Oxide/*biosynthesis, phylogeny, Plant Proteins/genetics/*metabolism, Protein Structure, rcc, RCC745, Sequence Alignment, Tertiary},
	doi = {10.1105/tpc.109.073510},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21119059},
	author = {Foresi, N and Correa-Aragunde, N and Parisi, G and Calo, G and Salerno, G and Lamattina, L}
}
@article {Franklin2010,
	title = {Dimethylsulphoniopropionate (DMSP), DMSP-lyase activity (DLA) and dimethylsulphide (DMS) in 10 species of coccolithophore},
	journal = {Marine Ecology-Progress Series},
	volume = {410},
	year = {2010},
	note = {ISBN: 0171-8630 tex.mendeley-tags: 2010,rcc},
	pages = {13{\textendash}23},
	abstract = {We investigated dimethylsulphoniopropionate (DMSP) quota (pg DMSP cell(-1)), intracellular DMSP concentration (mM), in vitro and in vivo DMSP-lyase activity (DLA) and dimethylsulphide (DMS) concentration in batch cultures of 10 species of coccolithophore. Species were chosen to span the phylogenetic and size range that exists within the coccolithophores. Our overall objective was to examine if Emiliania huxleyi, considered a {\textquoteright}model{\textquoteright} coccolithophore species, is representative in terms of DMSP, DLA and DMS, because other coccolithophores contribute substantially to phyto-plankton biomass and carbon fluxes in temperate and tropical waters. DMSP was found in all species, and DMSP quotas correlated significantly with cell volume, reflecting the fundamental physiological role of DMSP as a compatible solute in this group. This DMSP quota-cell volume relationship can be used to calculate the relative contribution of different species to total DMSP. Lowered nutrient availability (batch growth at a 10-fold lower nutrient concentration) did not significantly affect DMSP quota. In contrast to DMSP, DLA and DMS concentration were variable between the subset of species investigated. Coccolithophore DLA is known only in E. huxleyi and Gephyrocapsa oceanica, and we found DLA to be restricted to these closely related species. If DLA is restricted to a subset of coccolithophores, then those species are more likely to emit DMS directly in the sea. Our results indicate that in ecosystems where coccolithophores form stable populations, species other than E. huxleyi can make significant contributions to the particulate DMSP pool and hence to the amount of DMSP potentially available to the microbial loop.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.3354/meps08596},
	author = {Franklin, D J and Steinke, M and Young, J and Probert, I and Malin, G}
}
@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}
}
@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 {Gadler2009,
	title = {Enantiocomplementary inverting sec-alkylsulfatase activity in cyano- and thio-bacteria Synechococcus and Paracoccus spp.: selectivity enhancement by medium engineering},
	journal = {Tetrahedron: Asymmetry},
	volume = {20},
	year = {2009},
	note = {tex.mendeley-tags: rcc},
	pages = {115{\textendash}118},
	keywords = {rcc},
	doi = {10.1016/j.tetasy.2009.01.007},
	author = {Gadler, Petra and Reiter, Tamara C and Hoelsch, Kathrin and Weuster-Botz, Dirk and Fabe, Kurt}
}
@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 {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 {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 {Six2008,
	title = {Contrasting photoacclimation strategies in ecotypes of the eukayotic picoplankter {\textexclamdown}i{\textquestiondown}Ostreococcus{\textexclamdown}/i{\textquestiondown}},
	journal = {Limnology and Oceanography},
	volume = {53},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {255{\textendash}265},
	abstract = {Ostreococcus, the smallest known marine picoeukaryote, includes low- and high-light ecotypes. To determine the basis for niche partitioning between Ostreococcus sp. RCC809, isolated from the bottom of the tropical Atlantic euphotic zone, and the lagoon strain Ostreococcus tauri, we studied their photophysiologies under growth irradiances from 15 mmol photons m22 s21 to 800 mmol photons m22 s21 with a common nutrient replete regime. With increasing growth irradiance, both strains down-regulated cellular chlorophyll a and chlorophyll b (Chl a and Chl b) content, increased xanthophyll de-epoxidation correlated with nonphotochemical excitation quenching, and accumulated lutein. Ribulose-1,5-bisphosphate carboxylase/oxygenase content remained fairly stable. Under low-growth irradiances of 15{\textendash}80 mmol photons m22 s21, O. sp. RCC809 had equivalent or slightly higher growth rates, lower Chl a, a higher Chl b : Chl a ratio, and a larger photosystem II (PSII) antenna than O. tauri. O. tauri was more phenotypically plastic in response to growth irradiance, with a larger dynamic range in growth rate, Chl a, photosystem cell content, and cellular absorption cross-section of PSII. Estimating the amino acid and nitrogen costs for photoacclimation showed that the deep-sea oceanic O. sp. RCC809 relies largely on lower nitrogen cost changes in PSII antenna size to achieve a limited range of s-type light acclimation. O. sp. RCC809, however, suffers photoinhibition under higher light. This limited capacity for photoacclimation is compatible with the stable low-light and nutrient conditions at the base of the euphotic layer of the tropical Atlantic Ocean. In the more variable, high-nutrient, lagoon environment, O. tauri can afford to use a higher cost n-type acclimation of photosystem contents to exploit a wider range of light.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.4319/lo.2008.53.1.0255},
	author = {Six, C and Finkel, Z V and Rodriguez, F and Marie, D and Partensky, F and Campbell, D A}
}
@article {Foulon2008,
	title = {Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes},
	journal = {Environmental Microbiology},
	volume = {10},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {2433{\textendash}2443},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1111/j.1462-2920.2008.01673.x},
	author = {Foulon, E and Not, F and Jalabert, F and Cariou, T and Massana, R and Simon, N}
}
@article {Misumi2008,
	title = {Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana},
	journal = {Journal of Plant Research},
	volume = {121},
	number = {1},
	year = {2008},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {3{\textendash}17},
	abstract = {Algae play a more important role than land plants in the maintenance of the global environment and productivity. Progress in genome analyses of these organisms means that we can now obtain information on algal genomes, global annotation and gene expression. The full genome information for several algae has already been analyzed. Whole genomes of the red alga Cyanidioshyzon merolae, the green algae Ostreococcus tauri and Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana have been sequenced. Genome composition and the features of cells among the four algae were compared. Each alga maintains basic genes as photosynthetic eukaryotes and possesses additional gene groups to represent their particular characteristics. This review discusses and introduces the latest research that makes the best use of the particular features of each organism and the significance of genome analysis to study biological phenomena. In particular, examples of post-genome studies of organelle multiplication in C. merolae based on analyzed genome information are presented.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18074102},
	author = {Misumi, O and Yoshida, Y and Nishida, K and Fujiwara, T and Sakajiri, T and Hirooka, S and Nishimura, Y and Kuroiwa, T}
}
@article {Derelle2008,
	title = {Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga {\textexclamdown}i{\textquestiondown}Ostreococcus tauri{\textexclamdown}/i{\textquestiondown}},
	journal = {PLoS ONE},
	volume = {3},
	number = {5},
	year = {2008},
	note = {Publisher: Public Library of Science tex.mendeley-tags: RCC,rcc},
	pages = {e2250},
	abstract = {Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.},
	keywords = {rcc},
	doi = {10.1371/journal.pone.0002250},
	url = {http://dx.doi.org/10.1371/journal.pone.0002250},
	author = {Derelle, Evelyne and Ferraz, Conchita and Escande, Marie-Line and Eycheni{\'e}, Sophie and Cooke, Richard and Piganeau, Gwenael and Desdevises, Yves and Bellec, Laure and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Cardol2008,
	title = {An original adaptation of photosynthesis in the marine green alga Ostreococcus},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	number = {22},
	year = {2008},
	note = {tex.mendeley-tags: RCC745,RCC809},
	pages = {7881{\textendash}7886},
	abstract = {Adaptation of photosynthesis in marine environment has been examined in two strains of the green, picoeukaryote : OTH95, a surface/high-light strain, and RCC809, a deep-sea/low-light strain. Differences between the two strains include changes in the light-harvesting capacity, which is lower in OTH95, and in the photoprotection capacity, which is enhanced in OTH95. Furthermore, RCC809 has a reduced maximum rate of O evolution, which is limited by its decreased photosystem I (PSI) level, a possible adaptation to Fe limitation in the open oceans. This decrease is, however, accompanied by a substantial rerouting of the electron flow to establish an HO-to-HO cycle, involving PSII and a potential plastid plastoquinol terminal oxidase. This pathway bypasses electron transfer through the cytochrome complex and allows the pumping of {\^a}{\texteuro}{\oe}extra{\^a}{\texteuro} protons into the thylakoid lumen. By promoting the generation of a large {\^I}{\textquotedblright}pH, it facilitates ATP synthesis and nonphotochemical quenching when RCC809 cells are exposed to excess excitation energy. We propose that the diversion of electrons to oxygen downstream of PSII, but before PSI, reflects a common and compulsory strategy in marine phytoplankton to bypass the constraints imposed by light and/or nutrient limitation and allow successful colonization of the open-ocean marine environment.},
	keywords = {rcc, RCC745, RCC809},
	doi = {10.1073/pnas.0802762105},
	url = {http://www.pnas.org/content/105/22/7881.abstract},
	author = {Cardol, Pierre and Bailleul, Benjamin and Rappaport, Fabrice and Derelle, Evelyne and Baal, Daniel and Breyton, C{\'e}cile and Bailey, Shaun and Wollman, Francis Andr{\'e} and Grossman, Arthur and Moreau, Herv{\'e} and Finazzi, Giovanni}
}
@article {Fountain2008,
	title = {Permeation properties of a P2X receptor in the green algae Ostreococcus tauri},
	journal = {Journal of Biological Chemistry},
	volume = {283},
	number = {22},
	year = {2008},
	note = {ISBN: 0021-9258 tex.mendeley-tags: RCC,rcc},
	pages = {15122{\textendash}15126},
	abstract = {We have cloned a P2X receptor (OtP2X) from the green algae Ostreococcus tauri. The 42-kDa receptor shares similar to 28\% identity with human P2X receptors and 23\% with the Dictyostelium P2X receptor. ATP application evoked flickery single channel openings in outside-out membrane patches from human embryonic kidney 293 cells expressing OtP2X. Whole-cell recordings showed concentration-dependent cation currents reversing close to zero mV; ATP gave a half-maximal current at 250 mu m. alpha beta-Methylene-ATP evoked only small currents in comparison to ATP (EC50 {\textquestiondown} 5 mM). 2{\textquoteright},3{\textquoteright}-O-(4-Benzoylbenzoyl)-ATP, beta gamma-imido-ATP, ADP, and several other nucleotide triphosphates did not activate any current. The currents evoked by 300 mu m ATP were not inhibited by 100 mu m suramin, pyridoxal-phosphate-6-azophenyl-2{\textquoteright},4{\textquoteright}-disulfonic acid, 2{\textquoteright},3{\textquoteright}-O-(2,4,6-trinitrophenol)-ATP, or copper. Ion substitution experiments indicated permeabilities relative to sodium with the rank order calcium {\textquestiondown} choline {\textquestiondown} Tris {\textquestiondown} tetraethylammonium {\textquestiondown} N-methyl-D-glucosamine. However, OtP2X had a low relative calcium permeability (P-Ca/P-Na = 0.4) in comparison with other P2X receptors. This was due at least in part to the presence of an asparagine residue (Asn(353)) at a position in the second transmembrane domain in place of the aspartate that is completely conserved in all other P2X receptor subunits, because replacement of Asn(353) with aspartate increased calcium permeability by similar to 50\%. The results indicate that the ability of ATP to gate cation permeation across membranes exists in cells that diverged in evolutionary terms from animals about I billion years ago.},
	keywords = {CELLS, CHANNELS, EXTRACELLULAR ATP, FAMILY, FUNCTIONAL-CHARACTERIZATION, PERMEABILITY, PHARMACOLOGY, rcc},
	doi = {10.1074/jbc.M801512200},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2397467},
	author = {Fountain, S J and Cao, L S and Young, M T and North, R A}
}
@article {Bowler2008,
	title = {The Phaeodactylum genome reveals the evolutionary history of diatom genomes},
	journal = {Nature},
	volume = {456},
	number = {7219},
	year = {2008},
	note = {Publisher: Macmillan Publishers Limited. All rights reserved tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo},
	pages = {239{\textendash}244},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPOdipo, sbr?hyto?ppo},
	doi = {10.1038/nature07410},
	url = {http://dx.doi.org/10.1038/nature07410 http://www.nature.com/nature/journal/v456/n7219/suppinfo/nature07410_S1.html},
	author = {Bowler, Chris and Allen, Andrew E and Badger, Jonathan H and Grimwood, Jane and Jabbari, Kamel and Kuo, Alan and Maheswari, Uma and Martens, Cindy and Maumus, Florian and Otillar, Robert P and Rayko, Edda and Salamov, Asaf and Vandepoele, Klaas and Beszteri, Bank and Gruber, Ansgar and Heijde, Marc and Katinka, Michael and Mock, Thomas and Valentin, Klaus and Verret, Frederic and Berges, John A and Brownlee, Colin and Cadoret, Jean-Paul and Chiovitti, Anthony and Choi, Chang Jae and Coesel, Sacha and De Martino, Alessandra and Detter, J Chris and Durkin, Colleen and Falciatore, Angela and Fournet, Jerome and Haruta, Miyoshi and Huysman, Marie J J and Jenkins, Bethany D and Jiroutova, Katerina and Jorgensen, Richard E and Joubert, Yolaine and Kaplan, Aaron and Kroger, Nils and Kroth, Peter G and La Roche, Julie and Lindquist, Erica and Lommer, Markus and Martin-Jezequel, Veronique and Lopez, Pascal J and Lucas, Susan and Mangogna, Manuela and McGinnis, Karen and Medlin, Linda K and Montsant, Anton and Secq, Marie-Pierre Oudot-Le and Napoli, Carolyn and Obornik, Miroslav and Parker, Micaela Schnitzler and Petit, Jean-Louis and Porcel, Betina M and Poulsen, Nicole and Robison, Matthew and Rychlewski, Leszek and Rynearson, Tatiana A and Schmutz, Jeremy and Shapiro, Harris and Siaut, Magali and Stanley, Michele and Sussman, Michael R and Taylor, Alison R and Vardi, Assaf and von Dassow, Peter and Vyverman, Wim and Willis, Anusuya and Wyrwicz, Lucjan S and Rokhsar, Daniel S and Weissenbach, Jean and Armbrust, E Virginia and Green, Beverley R and Van de Peer, Yves and Grigoriev, Igor V}
}
@article {Rodriguez2008,
	title = {Phylogenetic and morphological characterization of the green algae infesting blue mussel Mytilus edulis in the North and South Atlantic},
	journal = {Diseases of Aquatic Organisms},
	volume = {81},
	year = {2008},
	note = {tex.mendeley-tags: RCC894},
	pages = {231{\textendash}240},
	keywords = {rcc, RCC894, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.3354/dao01956},
	author = {Rodriguez, F and Feist, S W and Guillou, L and Harkestad, L S and Bateman, K and Renault, T and Mortensen, S}
}
@article {Viprey2008,
	title = {Wide genetic diversity of picoplanktonic green algae (Chloroplastida) in the Mediterranean Sea uncovered by a phylum-biased PCR approach},
	journal = {Environmental Microbiology},
	volume = {10},
	number = {7},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1804{\textendash}1822},
	abstract = {The genetic diversity of picoplanktonic (i.e. cells that can pass through a 3 mum pore-size filter) green algae was investigated in the Mediterranean Sea in late summer by a culture-independent approach. Genetic libraries of the 18S rRNA gene were constructed using two different primer sets. The first set is commonly used to amplify the majority of eukaryotic lineages, while the second was composed of a general eukaryotic forward primer and a reverse primer biased towards the phylum Chloroplastida. A total of 3980 partial environmental sequences were obtained: 1668 using the general eukaryotic primer set and 2312 using the Chloroplastida-biased primer set. Of these sequences, 65 (4\%) and 594 (26\%) belonged to the Chloroplastida respectively. A 99.5\% sequence similarity cut-off value allowed classification of these 659 Chloroplastida sequences into 74 different operational taxonomic units. A majority of the Chloroplastida sequences (99\%) belonged to the prasinophytes. In addition to the seven independent prasinophyte lineages previously described, we discovered two new clades (clades VIII and IX), as well as a significant genetic diversity at the species and subspecies levels, notably among the genera Crustomastix, Dolichomastix and Mamiella (Mamiellales), but also within Pyramimonas and Halosphaera (Pyramimonadales). Such diversity within prasinophytes has not previously been observed by cloning approaches, illustrating the power of using targeted primers for clone library construction. Prasinophyte assemblages differed especially in relation to nutrient levels. Micromonas and Ostreococcus were mainly recovered from mesotrophic areas, whereas Mamiella, Crustomastix and Dolichomastix were mostly detected in oligotrophic surface waters. Within genera such as Ostreococcus or Crustomastix for which several clades were observed, depth seemed to be the main factor controlling differential distribution of genotypes.},
	keywords = {2008, rcc, sbr?hyto$_\textrmd$ipo},
	author = {Viprey, Manon and Guillou, Laure and Ferr{\'e}ol, Martial and Vaulot, Daniel}
}
@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 {Lobanov2007,
	title = {Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life},
	journal = {Genome Biology},
	volume = {8},
	number = {9},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {R198},
	abstract = {BACKGROUND: Selenocysteine (Sec) is a selenium-containing amino acid that is co-translationally inserted into nascent polypeptides by recoding UGA codons. Selenoproteins occur in both eukaryotes and prokaryotes, but the selenoprotein content of organisms (selenoproteome) is highly variable and some organisms do not utilize Sec at all. RESULTS: We analyzed the selenoproteomes of several model eukaryotes and detected 26 and 29 selenoprotein genes in the green algae Ostreococcus tauri and Ostreococcus lucimarinus, respectively, five in the social amoebae Dictyostelium discoideum, three in the fly Drosophila pseudoobscura, and 16 in the diatom Thalassiosira pseudonana, including several new selenoproteins. Distinct selenoprotein patterns were verified by metabolic labeling of O. tauri and D. discoideum with 75Se. More than half of the selenoprotein families were shared by unicellular eukaryotes and mammals, consistent with their ancient origin. Further analyses identified massive, independent selenoprotein losses in land plants, fungi, nematodes, insects and some protists. Comparative analyses of selenoprotein-rich and -deficient organisms revealed that aquatic organisms generally have large selenoproteomes, whereas several groups of terrestrial organisms reduced their selenoproteomes through loss of selenoprotein genes and replacement of Sec with cysteine. CONCLUSION: Our data suggest many selenoproteins originated at the base of the eukaryotic domain and show that the environment plays an important role in selenoproteome evolution. In particular, aquatic organisms apparently retained and sometimes expanded their selenoproteomes, whereas the selenoproteomes of some terrestrial organisms were reduced or completely lost. These findings suggest a hypothesis that, with the exception of vertebrates, aquatic life supports selenium utilization, whereas terrestrial habitats lead to reduced use of this trace element due to an unknown environmental factor.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17880704},
	author = {Lobanov, A V and Fomenko, D E and Zhang, Y and Sengupta, A and Hatfield, D L and Gladyshev, V N}
}
@article {Probert2007a,
	title = {Light and electron microscope observations of Algirosphaera robusta (Prymnesiophyceae)},
	journal = {Journal of Phycology},
	volume = {43},
	year = {2007},
	note = {tex.mendeley-tags: 2007,rcc},
	pages = {319{\textendash}332},
	keywords = {2007, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1111/j.1529-8817.2007.00324.x},
	author = {Probert, I and Fresnel, J and Billard, C and Geisen, Markus and Young, J R}
}
@article {Kettler2007,
	title = {Patterns and implications of gene gain and loss in the evolution of Prochlorococcus},
	journal = {PLoS genetics},
	volume = {3},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {e231},
	keywords = {rcc},
	doi = {10.1371/journal.pgen.0030231},
	author = {Kettler, G and Martiny, A C and Huang, K and Zucker, J and Coleman, M L and Rodrigue, S and Chen, F and Lapidus, A and Ferriera, S and Johnson, J and Steglich, C and Church, G and Richardson, P and Chisholm, S W}
}
@article {Fuller2006,
	title = {Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids},
	journal = {Aquatic Microbial Ecology},
	volume = {43},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {79{\textendash}93},
	keywords = {2006, PICOCEAN, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.3354/ame043079},
	author = {Fuller, Nicholas J and Campbell, Colin and Allen, David J and Pitt, Frances D and Le Gall, F and Vaulot, Daniel and Scanlan, David J}
}
@article {Derelle2006,
	title = {Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {31},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {11647{\textendash}11652},
	abstract = {The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world{\textquoteright}s smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1073/pnas.0604795103},
	url = {http://www.pnas.org/cgi/content/abstract/103/31/11647},
	author = {Derelle, Evelyne and Ferraz, Conchita and Rombauts, Stephane and Rouze, Pierre and Worden, Alexandra Z and Robbens, Steven and Partensky, Fr{\'e}d{\'e}ric and Degroeve, Sven and Echeynie, Sophie and Cooke, Richard and Saeys, Yvan and Wuyts, Jan and Jabbari, Kamel and Bowler, Chris and Panaud, Olivier and Piegu, Benoit and Ball, Steven G and Ral, Jean-Philippe and Bouget, Fran{\c c}ois-Yves and Piganeau, Gwenael and De Baets, Bernard and Picard, Andr{\'e} and Delseny, Michel and Demaille, Jacques and Van de Peer, Yves and Moreau, Herv{\'e}}
}
@article {Farinas2006,
	title = {Natural synchronisation for the study of cell division in the green unicellular alga Ostreococcus tauri},
	journal = {Plant Molecular Biology},
	volume = {60},
	number = {2},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {277{\textendash}292},
	abstract = {Ostreococcus tauri (Prasinophyceae) is a marine unicellular green alga which diverged early in the green lineage. The interest of O. tauri as a potential model to study plant cell division is based on its key phylogenetic position, its simple binary division, a very simple cellular organisation and now the availability of the full genome sequence. In addition O. tauri has a minimal yet complete set of cell cycle control genes. Here we show that division can be naturally synchronised by light/dark cycles and that organelles divide before the nucleus. This natural synchronisation, although being only partial, enables the study of the expression of CDKs throughout the cell cycle. The expression patterns of OtCDKA and OtCDKB were determined both at the mRNA and protein levels. The single OtCDKA gene is constantly expressed throughout the cell cycle, whereas OtCDKB is highly regulated and expressed only in S/G2/M phases. More surprisingly, OtCDKA is not phosphorylated at the tyrosine residue, in contrast to OtCDKB which is strongly phosphorylated during cell division. OtCDKA kinase activity appears before the S phase, indicating a possible role of this protein in the G1/S transition. OtCDKB kinase activity occurs later than OtCDKA, and its tyrosine phosphorylation is correlated to G2/M, suggesting a possible control of the mitotic activity. To our knowledge this is the first organism in the green lineage which showed CDKB tyrosine phosphorylation during cell cycle progression.},
	keywords = {Cyclin-dependent kinases, Green alga, Histone H1 kinase activity, Ostreococcus tauri, Phosphorylation, RCC745, Synchronisation of the cell division},
	issn = {01674412},
	doi = {10.1007/s11103-005-4066-1},
	author = {Farinas, Beno{\^\i}t and Mary, Camille and De O Manes, Carmem Lara and Bhaud, Yvonne and Peaucellier, G{\'e}rard and Moreau, Herv{\'e}}
}
@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 {Henley2004,
	title = {Phylogenetic analysis of the Nannochloris-like{\textquoteright} algae and diagnoses of Picochlorum oklahomensis gen. et sp nov (Trebouxiophyceae, Chlorophyta)},
	journal = {Phycologia},
	volume = {43},
	number = {6},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {641{\textendash}652},
	abstract = {A broadly halotolerant new isolate of a small asexual coccoid chlorophyte and six new, related freshwater isolates provided the impetus for a phylogenetic analysis of the so-called {\textquoteright}Nannochloris-like{\textquoteright} algae within the Trebouxiophyceae. Previous taxonomic disagreements concerning this group had not been rigorously tested with molecular phylogenetic analyses. We show with 18S ribosomal DNA (rDNA) sequence phylogeny that 19 of 22 isolates previously assigned to either Nannochloris or Nanochlorum fall within a diverse sister clade to a clade including the four {\textquoteright}true{\textquoteright} Chlorella species sensu loto. In addition, Marvania geminata, Gloeotila contorta, Chlorella sp. Yanaqocha RA1, Koliella spiculiformis, {\textquoteright}Chlorella minutissima{\textquoteright} C-1.1.9. and new Koliella, Gloeotila and Marvania isolates were included in the Nannochloris-like clade. Distinct freshwater and marine or saline lineages comprise at least three major subclades, generally corresponding to cell division pattern. Seven of 14 marine or saline isolates are known (and the others presumed) to divide by autosporulation. Eight freshwater isolates divide by binary fission, including two Koliella, two Gloeotila, N. bacillaris, Chlorella sp. Yanaqocha RA1, and two new unassigned isolates. Four freshwater isolates divide by budding or autosporulation (three Marvania, including CCAP 251/1b. previously assigned to N. coccoides). The autosporic taxa N. eucaryotum UTEX 2502 (marine) and C. minutissima C-1.1.9 (freshwater), which have nearly identical 18S rDNA sequences, are deeper-branching than the freshwater and marine or saline lineages. We propose including the 13 marine or saline, autosporic taxa (excluding N. eucaryotum UTEX 2502) in the new genus Picochlorum until distinctive morphological or biochemical characters are identified that would indicate multiple genera corresponding to subclades. Such characters exist in the freshwater lineages, supporting retention of Koliella, Gloeotila, Marvania and Nannochloris as distinct genera, although each is currently represented by few isolates. Nannochloris at this time may be restricted to N. bacillaris and Chlorella sp. Yanaqocha RA1. We also describe halotolerant P. oklahomensis Hironaka sp. nov. Based on 18S rDNA sequence and lack of chlorophyll b, Nannochloris sp. UTEX 2379 should be reassigned to the Eustigmatophyceae.},
	keywords = {18s-, 2004, Aquatic-sciences, cell-wall, chlorella-, green-alga, life-cycle, marvania-geminata, morphology-, Nanochlorum-eucaryotum, position-, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SEQUENCES},
	doi = {10.2216/i0031-8884-43-6-641.1},
	author = {Henley, W J and Hironaka, J L and Guillou, L and Buchheim, M A and Buchheim, J A and Fawley, M W and Fawley, K P}
}
@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 {Fuller2003,
	title = {Clade-specific 16S ribosomal DNA oligonucleotides reveal the predominance of a single marine Synechococcus clade throughout a stratified water column in the Red Sea},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {2430{\textendash}2443},
	abstract = {Phylogenetic relationships among members of the marine Synechococcus genus were determined following sequencing of the 16S ribosomal DNA (rDNA) from 31 novel cultured isolates from the Red Sea and several other oceanic environments. This revealed a large genetic diversity within the marine Synechococcus cluster consistent with earlier work but also identified three novel clades not previously recognized. Phylogenetic analyses showed one clade, containing halotolerant isolates lacking phycoerythrin (PE) and including strains capable, or not, of utilizing nitrate as the sole N source, which clustered within the MC-A (Synechococcus subcluster 5.1) lineage. Two copies of the 16S rRNA gene are present in marine Synechococcus genomes, and cloning and sequencing of these copies from Synechococcus sp. strain WH 7803 and genomic information from Synechococcus sp. strain WH 8102 reveal these to be identical. Based on the 16S rDNA sequence information, clade-specific oligonucleotides for the marine Synechococcus genus were designed and their specificity was optimized. Using dot blot hybridization technology, these probes were used to determine the in situ community structure of marine Synechococcus populations in the Red Sea at the time of a Synechococcus maximum during April 1999. A predominance of genotypes representative of a single clade was found, and these genotypes were common among strains isolated into culture. Conversely, strains lacking PE, which were also relatively easily isolated into culture, represented only a minor component of the Synechococcus population. Genotypes corresponding to well-studied laboratory strains also appeared to be poorly represented in this stratified water column in the Red Sea.},
	keywords = {2003, PICODIV, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	issn = {0099-2240},
	doi = {10.1128/AEM.69.5.2430-2443.2003},
	url = {http://aem.asm.org/cgi/content/abstract/69/5/2430},
	author = {Fuller, Nicholas J and Marie, Dominique and Partensky, Fr{\'e}d{\'e}ric and Vaulot, Daniel and Post, Anton F and Scanlan, David 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 {West2001,
	title = {Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides},
	journal = {Microbiology - UK},
	volume = {147},
	number = {7},
	year = {2001},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1731{\textendash}1744},
	abstract = {An in situ hybridization method was applied to the identification of marine cyanobacteria assignable to the genus Procholorococcus using harseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA). With this method very bright signals were obtained, in contrast to hybridizations with oligonucleotides monolabelled with fluorochromes, which failed to give positive signals. Genotype-specific oligonucleotides for high light (HL)- and low light (LL)adapted members of this genus were identified by 16S rRNA sequence analyses and their specificities confirmed in whole-cell hybridizations with cultured strains of Prochlorococcus marinus Chisholm et al., 1992, Prochlorococcus sp. and Synechococcus sp. In situ hybridization of these genotype-specific probes to field samples from stratified water bodies collected in the North Atlantic Ocean and the Red Sea allowed a rapid assessment of the abundance and spatial distribution of HL- and LL-adapted Prochlorococcus. In both oceanic regions the LL-adapted Prochlorococcus populations were localized in deeper water whereas the HL-adapted Prochlorococcus populations were not only distinct in each region but also exhibited strikingly different depth distributions, HLI being confined to shallow wafer in the North Atlantic, in contrast to HLII, which was present throughout the water column in the Red Sea.},
	keywords = {Escherichia Coli, IDENTIFICATION, Marine Cyanobacterium, Nucleic Acid Probes, Photosynthetic Prokaryote, PICODIV, Populations, rcc, Ribosomal Rna, SEQUENCES, Tyramide Signal Amplification, Whole Cell Hybridization},
	doi = {10.1099/00221287-147-7-1731},
	author = {West, N J and Schonhuber, W A and Fuller, N J and Amann, R I and Rippka, R and Post, A F and Scanlan, D J}
}
@article {Fawley2000,
	title = {Phylogenetic analyses of 18S rDNA sequences reveal a new coccoid lineage of the Prasinophyceae (Chlorophyta)},
	journal = {Journal of Phycology},
	volume = {36},
	number = {2},
	year = {2000},
	note = {ISBN: 0022-3646 Publisher: Phycological Soc Amer Inc tex.address: 810 East 10Th St, Lawrence, KS 66044, USA tex.mendeley-tags: RCC,rcc},
	pages = {387{\textendash}393},
	abstract = {Phylogenetic analyses of 18S rDNA sequences from 25 prasinophytes, including 10 coccoid isolates, reveals that coccoid organisms are-found in at least three prasinophyte lineages, The coccoid Ostreococcus tauri is included in the Mamiellales lineage and Pycnococcus provasolii is allied with the f dfellate Pseudoscourfieldia marina. A previously undescribed prasinophyte lineage is comprised of the coccoid Prasinococcus cf. Capsulatus (CCMP 1407) and other isolates tentatively identified as Prasinococcussp. (CCMP 1202, CCMP 1614, and CCMP 1194), as well as three unnamed coccoids (CCMP 1193, CCMP 1413, and CCMP 1220). No flagellate organisms are known from this lineage. Organisms of this new lineage share some characteristics of both the Pycnococcaceae and the Mamiellales, although relationships among these separate lineages were not supported by bootstrap analyses. An additional unnamed coccoid isolate (CCMP 1205) is separate from all major prasinophyte lineages. The analyses did not resolve the relationships among the major prasinophyte lineages, although they support previous conclusions that the Prasinophyceae are not monophyletic.},
	keywords = {ALGAL CAROTENOIDS, coccoid algae, EVOLUTIONARY TREES, Gen, GREEN-ALGAE, LIGHT-HARVESTING COMPLEX, MICROMONADOPHYCEAE CHLOROPHYTA, Prasinophyceae, PRASINOXANTHIN, PSEUDOSCOURFIELDIA-MARINA, rcc, RDNA, RIBOSOMAL-RNA SEQUENCES, Sequence Analysis, sp-nov},
	doi = {10.1046/j.1529-8817.2000.99105.x},
	author = {Fawley, M W and Yun, Y and Qin, M}
}
@article {Chisholm1992,
	title = {\textit{Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b},
	journal = {Archives of Microbiology},
	volume = {157},
	year = {1992},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {297{\textendash}300},
	keywords = {rcc, systematics, \#PROCHLOROPHYTE},
	doi = {10.1007/BF00245165},
	author = {Chisholm, S W and Frankel, S L and Goericke, R and Olson, R J and Palenik, B and Waterbury, J B and West-Johnsrud, L and Zettler, E R}
}
@inbook {Waterbury1986,
	title = {Biological and ecological characterization of the marine unicellular cyanobacterium Synechococcus},
	booktitle = {Photosynthetic picoplankton},
	volume = {214},
	year = {1986},
	note = {tex.mendeley-tags: Canad. Bull. Fish. Aquatic Sci.,RCC,rcc},
	pages = {71{\textendash}120},
	keywords = {Canad. Bull. Fish. Aquatic Sci., phytoplankton, rcc, Synechococcus},
	author = {Waterbury, J B and Watson, S W and Valois, F W and Franks, D G},
	editor = {Platt, T and Li, W K W}
}
