@article {stewart_altitudinal_2021,
	title = {Altitudinal Zonation of Green Algae Biodiversity in the French Alps},
	journal = {Frontiers in Plant Science},
	volume = {12},
	year = {2021},
	pages = {1066},
	abstract = {Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes.},
	keywords = {rcc, RCC1055, RCC130, RCC1563, RCC2501, RCC2960, RCC3402, RCC443, RCC4743, RCC537, RCC581, RCC6, RCC7, RCC891},
	issn = {1664-462X},
	doi = {10.3389/fpls.2021.679428},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.679428},
	author = {Stewart, Adeline and Rioux, Delphine and Boyer, Fr{\'e}deric and Gielly, Ludovic and Pompanon, Fran{\c c}ois and Saillard, Am{\'e}lie and Thuiller, Wilfried and Valay, Jean-Gabriel and Mar{\'e}chal, {\'E}ric and Coissac, Eric}
}
@article {phelps_carbon_2021,
	title = {Carbon Isotope Fractionation in Noelaerhabdaceae Algae in Culture and a Critical Evaluation of the Alkenone Paleobarometer},
	journal = {Geochemistry, Geophysics, Geosystems},
	volume = {22},
	number = {7},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2021GC009657},
	pages = {e2021GC009657},
	abstract = {The carbon isotope fractionation in algal organic matter ($\varepsilon$p), including the long-chain alkenones produced by the coccolithophorid family Noelaerhabdaceae, is used to reconstruct past atmospheric CO2 levels. The conventional proxy linearly relates $\varepsilon$p to changes in cellular carbon demand relative to diffusive CO2 supply, with larger $\varepsilon$p values occurring at lower carbon demand relative to supply (i.e., abundant CO2). However, the response of Gephyrocapsa oceanica, one of the dominant alkenone producers of the last few million years, has not been studied closely. Here, we subject G. oceanica to various CO2 levels by increasing pCO2 in the culture headspace, as opposed to increasing dissolved inorganic carbon (DIC) and alkalinity concentrations at constant pH. We note no substantial change in physiology, but observe an increase in $\varepsilon$p as carbon demand relative to supply decreases, consistent with DIC manipulations. We compile existing Noelaerhabdaceae $\varepsilon$p data and show that the diffusive model poorly describes the data. A meta-analysis of individual treatments (unique combinations of lab, strain, and light conditions) shows that the slope of the $\varepsilon$p response depends on the light conditions and range of carbon demand relative to CO2 supply in the treatment, which is incompatible with the diffusive model. We model $\varepsilon$p as a multilinear function of key physiological and environmental variables and find that both photoperiod duration and light intensity are critical parameters, in addition to CO2 and cell size. While alkenone carbon isotope ratios indeed record CO2 information, irradiance and other factors are also necessary to properly describe alkenone $\varepsilon$p.},
	keywords = {alkenone, carbon dioxide, carbon isotope, coccolithophore, irradiance, paleobarometry, rcc, RCC1303},
	issn = {1525-2027},
	doi = {10.1029/2021GC009657},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2021GC009657},
	author = {Phelps, Samuel R. and Hennon, Gwenn M. M. and Dyhrman, Sonya T. and Hern{\'a}ndez Lim{\'o}n, Mar{\'\i}a D. and Williamson, Olivia M. and Polissar, Pratigya J.}
}
@article {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 {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 {robla_determination_2021,
	title = {Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters},
	journal = {Environmental Science: Water Research \& Technology},
	volume = {7},
	number = {7},
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
	month = {jul},
	pages = {1230{\textendash}1239},
	abstract = {The most important question in sampling is {\textquotedblleft}Is the sample representative of the target population?{\textquotedblright} This question is necessary to understand how valid the sample taken is to the original population and if generalizations can be made from the sample. Samples taken for water quality measurement range from 1 mL for bacterial contamination to 100 mL or up to 1000 L for protozoan parasites. With larger samples taken, the confidence in detecting rare events increases dramatically. Here we illustrate that hollow fiber filters as routinely used for kidney dialysis can be adapted for environmental use. The filters retain all organisms down to viral particles and organic matter above 70 kDA, the molecular cutoff for urea, one of the waste products removed in kidney dialysis. With these filters, 50 liters of water can be filtered in about 90 minutes. Backflush of the filters recovers viable cells with minimal cell lysis that can be processed downstream for molecular analysis. Recovery rates were as high as 89\% and 75\% for phytoplankton and bacteria, respectively.},
	keywords = {rcc, RCC1507},
	issn = {2053-1419},
	doi = {10.1039/D0EW00927J},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/ew/d0ew00927j},
	author = {Robla, J. and Garc{\'\i}a-Hierrro, J. and Alguacil, F. J. and Dittami, S. M. and Marie, D. and Villa, E. and Deragon, E. and Guillebault, D. and Mengs, G. and Medlin, L. K.}
}
@article {long_dinophyceae_2021,
	title = {Dinophyceae can use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)},
	journal = {ISME Communications},
	volume = {1},
	number = {1},
	year = {2021},
	note = {Bandiera_abtest: a Cg_type: Nature Research Journals Number: 1 Primary_atype: Research Publisher: Nature Publishing Group Subject_term: Microbial ecology;Plant ecology;Water microbiology Subject_term_id: microbial-ecology;plant-ecology;water-microbiology},
	pages = {1{\textendash}10},
	abstract = {Parasites in the genus Amoebophrya sp. infest dinoflagellate hosts in marine ecosystems and can be determining factors in the demise of blooms, including toxic red tides. These parasitic protists, however, rarely cause the total collapse of Dinophyceae blooms. Experimental addition of parasite-resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or exudates into a well-established host-parasite coculture (Scrippsiella acuminata-Amoebophrya sp.) mitigated parasite success and increased the survival of the sensitive host. This effect was mediated by waterborne molecules without the need for a physical contact. The strength of the parasite defenses varied between dinoflagellate species, and strains of A. minutum and was enhanced with increasing resistant host cell concentrations. The addition of resistant strains or exudates never prevented the parasite transmission entirely. Survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. Parasite progeny drastically decreased with both species. Integrity of the dinospore membrane was altered by A. minutum, providing a first indication on the mode of action of anti-parasitic molecules. These results demonstrate that extracellular defenses can be an effective strategy against parasites that protects not only the resistant cells producing them, but also the surrounding community.},
	keywords = {microbial ecology, Plant ecology, rcc, RCC1627, RCC4383, RCC4714, RCC749, Water microbiology},
	issn = {2730-6151},
	doi = {10.1038/s43705-021-00035-x},
	url = {http://www.nature.com/articles/s43705-021-00035-x},
	author = {Long, Marc and Marie, Dominique and Szymczak, Jeremy and Toullec, Jordan and Bigeard, Estelle and Sourisseau, Marc and Le Gac, Micka{\"e}l and Guillou, Laure and Jauzein, C{\'e}cile}
}
@booklet {marc_dinophyceae_2021,
	title = {Dinophyceae use exudates as weapons against the parasite Amoebophrya sp. (Syndiniales)},
	year = {2021},
	note = {Company: Cold Spring Harbor Laboratory Distributor: Cold Spring Harbor Laboratory Label: Cold Spring Harbor Laboratory Section: New Results Type: article},
	month = {jan},
	pages = {2021.01.05.425281},
	abstract = {Parasites of the genus Amoebophrya sp. are important contributors to marine ecosystems and can be determining factors in the demise of blooms of Dinophyceae, including microalgae commonly responsible for toxic red tides. Yet they rarely lead to the total collapse of Dinophyceae blooms. The addition of resistant Dinophyceae (Alexandrium minutum or Scrippsiella donghaienis) or their exudate into a well-established host-parasite culture (Scrippsiella acuminata-Amoebophrya sp.) mitigated the success of the parasite and increased the survival of the sensitive host. Effect were mediated via water-borne molecules without the need of a physical contact. Severity of the anti-parasitic defenses fluctuated depending on the species, the strain and its concentration, but never totally prevented the parasite transmission. The survival time of Amoebophrya sp. free-living stages (dinospores) decreased in presence of A. minutum but not of S. donghaienis. The progeny drastically decreased with both species. Integrity of the membrane of dinospores was altered by A. minutum which provided a first indication on the mode of action of these anti-parasitic molecules. These results demonstrate that extracellular defenses are an effective strategy against parasites that does not only protect the resistant cells but also have the potential to affect the whole surrounding community.},
	keywords = {rcc, RCC1627, RCC4383, RCC4714, RCC749},
	doi = {10.1101/2021.01.05.425281},
	url = {https://www.biorxiv.org/content/10.1101/2021.01.05.425281v1},
	author = {Marc, Long and Dominique, Marie and Jeremy, Szymczak and Jordan, Toullec and Estelle, Bigeard and Marc, Sourisseau and Mickael, Le Gac and Laure, Guillou and C{\'e}cile, Jauzein}
}
@article {xie_disentangling_2021,
	title = {Disentangling the Effects of Ocean Carbonation and Acidification on Elemental Contents and Macromolecules of the Coccolithophore Emiliania huxleyi},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	pages = {3188},
	abstract = {Elemental contents change with shifts in macromolecular composition of marine phytoplankton. Recent studies focus on the responses of elemental contents of coccolithophores, a major calcifying phytoplankton group, to changing carbonate chemistry, caused by the dissolution of anthropogenically derived CO2 into the surface ocean. However, the effects of changing carbonate chemistry on biomacromolecules, such as protein and carbohydrate of coccolithophores, are less documented. Here, we disentangled the effects of elevated dissolved inorganic carbon (DIC) concentration (900 to 4,930μmolkg-1) and reduced pH value (8.04 to 7.70) on physiological rates, elemental contents, and macromolecules of the coccolithophore Emiliania huxleyi. Compared to present DIC concentration and pH value, combinations of high DIC concentration and low pH value (ocean acidification) significantly increased pigments content, particulate organic carbon (POC), and carbohydrate content and had less impact on growth rate, maximal relative electron transport rate (rETRmax), particulate organic nitrogen (PON), and protein content. In high pH treatments, elevated DIC concentration significantly increased growth rate, pigments content, rETRmax, POC, particulate inorganic carbon (PIC), protein, and carbohydrate contents. In low pH treatments, the extents of the increase in growth rate, pigments and carbohydrate content were reduced. Compared to high pH value, under low DIC concentration, low pH value significantly increased POC and PON contents and showed less impact on protein and carbohydrate contents; however, under high DIC concentration, low pH value significantly reduced POC, PON, protein, and carbohydrate contents. These results showed that reduced pH counteracted the positive effects of elevated DIC concentration on growth rate, rETRmax, POC, PON, carbohydrate, and protein contents. Elevated DIC concentration and reduced pH acted synergistically to increase the contribution of carbohydrate{\textendash}carbon to POC, and antagonistically to affect the contribution of protein{\textendash}nitrogen to PON, which further shifted the carbon/nitrogen ratio of E. huxleyi.},
	keywords = {rcc, RCC1266},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.737454},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2021.737454},
	author = {Xie, Emei and Xu, Kui and Li, Zhengke and Li, Wei and Yi, Xiangqi and Li, Hongzhou and Han, Yonghe and Zhang, Hong and Zhang, Yong}
}
@article {pan_effects_2021,
	title = {Effects of Epibiotic Diatoms on the Productivity of the Calanoid Copepod Acartia tonsa (Dana) in Intensive Aquaculture Systems},
	journal = {Frontiers in Marine Science},
	volume = {8},
	year = {2021},
	pages = {1386},
	abstract = {We evaluated here the effects of the epibiotic diatom Tabularia sp. on the productivity of the calanoid copepod Acartia tonsa (Dana) for assessing their risk on copepod intensive aquaculture industry for the provision of live feed. In the first experiment, uninfested and intensively infested females were cultivated individually for the assessment of egg production. Intensively infested females appeared to have a significantly lower egg production (5.0{\textendash}9.0 eggs/female/d) than uninfested females (22.0{\textendash}26.0 eggs/female/d) during 5 consecutive days. In the second experiment, effects of culture densities on diatom epibiosis were investigated in 9 L cultures at three different densities (200, 400, and 600 ind. L{\textendash}1). Another culture at higher volume (250 L) and lowest density (200 ind. L{\textendash}1) was also carried out to test the effect of culture volume on diatom epibiosis. The infestation rate (\%), infestation intensity (ratio of surface diatom coverage levels, classified as levels 0{\textendash}3) and daily egg harvest rate (number of harvested eggs per day per liter) were evaluated among the four culture populations. The copepods had higher infestation rate (53.69{\textendash}60.14\%) and intensity rate (high ratios at level 2 and 3) when the densities were increased from 200 ind./L to 400 and 600 ind./L. Although egg harvest increased with increasing culture density, it seemed that the diatom-infested A. tonsa population reach a saturated egg production when the density was higher than 400 ind./L. Nevertheless, the differences of culture volumes (250 and 9 L) appeared to be not to have any effect when the copepods were cultivated at the same density (200 ind./L). This study reveals for the first time that the epibiosis of the diatom Tabularia sp. reduces the individual egg production, and egg harvest rate in high-density culture of the copepod A. tonsa. Our findings implicate that diatom epibiosis should be avoid in copepod intensive culture systems.},
	keywords = {rcc, RCC350},
	issn = {2296-7745},
	doi = {10.3389/fmars.2021.728779},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.728779},
	author = {Pan, Yen-Ju and Wang, Wei-Lung and Hwang, Jiang-Shiou and Souissi, Sami}
}
@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 {zhang_isotope_2021,
	title = {An isotope label method for empirical detection of carbonic anhydrase in the calcification pathway of the coccolithophore Emiliania huxleyi},
	journal = {Geochimica et Cosmochimica Acta},
	volume = {292},
	year = {2021},
	pages = {78{\textendash}93},
	abstract = {Coccolithophores are a group of phytoplankton widely distributed in the ocean, which secrete extracellular calcite plates termed coccoliths. Coccoliths have been increasingly employed as an archive for geochemical, ecological and paleoclimate studies in recent years. A robust application of coccolith-based geochemical proxies relies on understanding the carbon acquisition strategies and the pathways of carbon supply for calcification. Carbonic anhydrase (CA) plays important roles in the carbon concentrating mechanism s of aquatic algae and potentially also in calcification. However, it is difficult to independently assess the role of CA in carbon supply for photosynthesis versus calcification. To fill this gap, we explored a new method to detect the CA activity inside coccolithophore. To achieve this, coccolithophores were cultured with oxygen and carbon isotope labeled dissolved inorganic carbon (DIC). By exploiting the different behavior of oxygen and carbon isotopes with (sea)water, this double label method can elucidate the significance of CA activity in the calcification pathway. Application of this method to Emiliania huxleyi shows that CA is present in the calcification pathway, and that there is no significant difference in the CA activity between a high and low CO2 treatment. However, under low CO2 treatment E. huxleyi enhanced the bicarbonate pumping rate on both cell and chloroplast membranes. This novel method could be performed on other species of coccolithophores in the future and have a potential to extend our knowledge on coccolith oxygen isotope vital effects.},
	keywords = {Carbonic anhjydrase, ccm, coccolithophore, Isotopic labelling, rcc, rcc1258},
	issn = {0016-7037},
	doi = {10.1016/j.gca.2020.09.008},
	url = {https://www.sciencedirect.com/science/article/pii/S0016703720305597},
	author = {Zhang, Hongrui and Blanco-Ameijeiras, Sonia and Hopkinson, Brian M. and Bernasconi, Stefano M. and Mejia, Luz Maria and Liu, Chuanlian and Stoll, Heather}
}
@article {schapira_les_2021,
	title = {Les Efflorescences de Lepidodinium chlorophorum au large de la Loire et de la Vilaine : D{\'e}terminisme et cons{\'e}quences sur la qualit{\'e} des masses d{\textquoteright}eau c{\^o}ti{\`e}res},
	year = {2021},
	abstract = {Ce projet, organis{\'e} en trois actions, avait pour objectif de mieux {\'e}valuer les risques d{\textquoteright}eaux color{\'e}es vertes se produisant sur le secteur c{\^o}tier situ{\'e} au large de la Loire et de la Vilaine, en termes (i) de fr{\'e}quence de ces {\'e}pisodes, (ii) d{\textquoteright}abondance et (iii) de localisation des zones {\`a} risque. Action 1 : Am{\'e}lioration du recensement des eaux vertes {\`a} L. chlorophorum Action 2 : Optimisation de l{\textquoteright}estimation des abondances de L. chlorophorum Action 3 : Identification des zones {\`a} risque au large de la Loire et de la Vilaine.},
	keywords = {? No DOI found, rcc, RCC1489},
	url = {https://archimer.ifremer.fr/doc/00724/83598/},
	author = {Schapira, Mathilde and Roux, Pauline and Andre, Coralie and Mertens, Kenneth and Bilien, Gwenael and Terre Terrillon, Aouregan and Le Gac-Abernot, Chantal and Siano, Raffaele and Qu{\'e}r{\'e}, Julien and Bizzozero, Lucie and Bonneau, Francoise and Bouget, Jean-Francois and Cochennec-Laureau, Nathalie and Collin, Karine and Fortune, Mireille and Gabellec, Raoul and Le Merrer, Yoann and Manach, Soazig and Pierre-Duplessix, Olivier and Retho, Michael and Schmitt, Anne and Souchu, Philippe and Stachowski-Haberkorn, Sabine}
}
@article {dayras_microalgal_2021,
	title = {Microalgal Diet Influences the Nutritive Quality and Reproductive Investment of the Cyclopoid Copepod Paracyclopina nana},
	journal = {Frontiers in Marine Science},
	volume = {8},
	year = {2021},
	pages = {1147},
	abstract = {Copepods represent an interesting alternative or a complement live food to brine shrimps and rotifers commonly used in aquaculture. They constitute the natural prey of many fish species and therefore do not require a potential nutritional enrichment. But an optimization of the microalgal diets used to feed copepods is essential to improve their mass culture. This study examined the effects of seven microalgal diets, namely single-species diets of Rhodomonas salina (R), Tisochrysis lutea (T), and Pavlova lutheri (=Diacronema lutheri) (P), two-species diets (R + T, T + P, and R + P), and a three-species diet (R + T + P), on the fatty acid and monosaccharide composition of the cyclopoid copepod Paracyclopina nana as well as its reproductive investment. Experiments were run during 15 days in 10-L beakers; starting with nauplii collected from a large 300-L batch culture. Copepods fatty acid contents were studied, particularly the relative amounts of docosahexaenoic acid (DHA) and eicosa-pentaenoic acid (EPA). The R + T, R, and T diets induced the highest total fatty acid amount in copepods. R + T and R also generated the lowest DHA/EPA ratios in copepods due to high EPA contents. The highest value of total monosaccharides was found in copepods fed with R + T + P. Diets R + T and R induced the greatest prosome volumes and clutch volumes in ovigerous females. Both prosome volume and clutch volume in P. nana ovigerous females were correlated to the individual EPA amount. The results demonstrated that all diets including R. salina enhanced the productivity of P. nana in mass culture, particularly when combined with T. lutea. R. salina, and T. lutea induced complementary fatty acid and monosaccharide profiles, confirming that R + T represents the best microalgae combination for productive culture of P. nana. Conversely, P. lutheri did not enhance the nutritional profile nor the fecundity of P. nana in the culture. This study is the first to demonstrate that R. salina is a suitable microalga for productive mass culture of P. nana for use as live food in aquaculture.},
	keywords = {rcc, RCC1349, RCC1537, RCC20},
	issn = {2296-7745},
	doi = {10.3389/fmars.2021.697561},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2021.697561},
	author = {Dayras, Paul and Bialais, Capucine and Sadovskaya, Irina and Lee, Min-Chul and Lee, Jae-Seong and Souissi, Sami}
}
@article {jimenez_no_2021,
	title = {No evidence of Phago-mixotropy in Micromonas polaris (Mamiellophyceae), the Dominant Picophytoplankton Species in the Arctic},
	journal = {Journal of Phycology},
	volume = {57},
	number = {2},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jpy.13125},
	pages = {435{\textendash}446},
	abstract = {In the Arctic Ocean, the small green alga Micromonas polaris dominates picophytoplankton during the summer months but is also present in winter. It has been previously hypothesized to be phago-mixotrophic (capable of bacteria ingestion) based on laboratory and field experiments. Prey uptake was analyzed in several M. polaris strains isolated from different regions and depths of the Arctic Ocean and in Ochromonas triangulata, a known phago-mixotroph used as a control. Measuring ingestion of either fluorescent beads or fluorescently labeled bacteria by flow cytometry, we found no evidence of phago-mixotrophy in any M. polaris strain while O. triangulata was ingesting both beads and bacteria. In addition, in silico predictions revealed that members of the genus Micromonas lack a genetic signature of phagocytotic capacity.},
	keywords = {Arctic, Micromonas, phago-mixotrophy, phytoplankton, rcc, RCC21, RCC2288, RCC2306, RCC4298},
	issn = {1529-8817},
	doi = {10.1111/jpy.13125},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.13125},
	author = {Jimenez, Valeria and Burns, John A. and Le Gall, Florence and Not, Fabrice and Vaulot, Daniel}
}
@article {russo_production_2021,
	title = {Production of Omega-3 Oil by Aurantiochytrium mangrovei Using Spent Osmotic Solution from Candied Fruit Industry as Sole Organic Carbon Source},
	journal = {Processes},
	volume = {9},
	number = {10},
	year = {2021},
	note = {Number: 10 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {oct},
	pages = {1834},
	abstract = {Osmotic dehydration is an important phase in the production of dried products, including most fruits and vegetables, in the food industry. The drying process for candied fruit produces a liquid waste called {\textquotedblleft}spent osmotic solution{\textquotedblright}, which is characterized by a high content of organic compounds, mostly dissolved sugars. The sugar content of this food by-product could be valorized through the growth of biomass with a high added value. In this study, the spent osmotic solution from the candied fruit industry was used as an organic carbon source for the growth and production of docosahexaenoic acid (DHA) in the cultivation of Aurantiochytrium mangrovei RCC893. The carbon content of the standard media was completely replaced by the sugars present in this food by-product. After that, the growth condition of this strain was optimized through response surface methodologies using a central composite design (CCD), and the optimal combination of the spent osmotic solution and nitrogen was established. Moreover, a scale-up trial was performed using the optimal conditions obtained after CCD to evaluate the scalability of the process.},
	keywords = {DHA, food waste, Microalgae, PUFA, rcc, RCC893, sustainability},
	doi = {10.3390/pr9101834},
	url = {https://www.mdpi.com/2227-9717/9/10/1834},
	author = {Russo, Giovanni L. and Langellotti, Antonio L. and Blasco, Thierry and Oliviero, Maria and Sacchi, Raffaele and Masi, Paolo}
}
@article {royer_response_2021,
	title = {Response of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas to oxidative stress in three phytoplankton species},
	journal = {Journal of Plankton Research},
	volume = {43},
	number = {5},
	year = {2021},
	month = {sep},
	pages = {673{\textendash}690},
	abstract = {Several phytoplankton species produce the metabolites dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) but their intracellular roles need to be better understood. To improve the understanding of the DMSP antioxidant function suggested by Sunda et al. (2002), we exposed the diatom Skeletonema costatum, the Prymnesiophyceae Phaeocystis globosa and the dinoflagellate Heterocapsa triquetra to experimental treatments known to cause potential oxidative stress (high light intensities (HL); HL with 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU); menadione sodium bisulfite (MSB)). DMSP and DMSO concentrations decreased after 6 h in all treatments indicating an interaction with Reactive Oxygen Species (ROS) produced. DMSP and DMSO-to-cell ratios in control conditions were higher for H. triquetra, while being unable to grow under HL. DMSP and DMSO-to-cell carbon were the highest for P. globosa, while the other species had similar values. During long-term treatment, these ratios were not increased in high-light grown cells of P. globosa and S. costatum. Overall, this illustrates that (1) the DMSP- and DMSO-to-cell or carbon seems to be not indicative of the capability of the species to tolerate an oxidative stress, (2) these molecules could react with ROS and lower their cellular concentration, but no clues demonstrated that these molecules are part of the antioxidant response of the cell.},
	keywords = {rcc, RCC1719, RCC4800},
	issn = {0142-7873},
	doi = {10.1093/plankt/fbab052},
	url = {https://doi.org/10.1093/plankt/fbab052},
	author = {Royer, C and Gypens, N and Cardol, P and Borges, A V and Roberty, S}
}
@article {langer_role_2021,
	title = {Role of silicon in the development of complex crystal shapes in coccolithophores},
	journal = {New Phytologist},
	volume = {231},
	number = {5},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.17230},
	pages = {1845{\textendash}1857},
	abstract = {The development of calcification by the coccolithophores had a profound impact on ocean carbon cycling, but the evolutionary steps leading to the formation of these complex biomineralized structures are not clear. Heterococcoliths consisting of intricately shaped calcite crystals are formed intracellularly by the diploid life cycle phase. Holococcoliths consisting of simple rhombic crystals can be produced by the haploid life cycle stage but are thought to be formed extracellularly, representing an independent evolutionary origin of calcification. We use advanced microscopy techniques to determine the nature of coccolith formation and complex crystal formation in coccolithophore life cycle stages. We find that holococcoliths are formed in intracellular compartments in a similar manner to heterococcoliths. However, we show that silicon is not required for holococcolith formation and that the requirement for silicon in certain coccolithophore species relates specifically to the process of crystal morphogenesis in heterococcoliths. We therefore propose an evolutionary scheme in which the lower complexity holococcoliths represent an ancestral form of calcification in coccolithophores. The subsequent recruitment of a silicon-dependent mechanism for crystal morphogenesis in the diploid life cycle stage led to the emergence of the intricately shaped heterococcoliths, enabling the formation of the elaborate coccospheres that underpin the ecological success of coccolithophores.},
	keywords = {biomineralization, Calcification, coccolith, coccolithophore, evolution, rcc, RCC1178, RCC1181, RCC1456, RCC1460, RCC1461, RCC1477, RCC1800, RCC1801, RCC3777, RCC6506, silicon},
	issn = {1469-8137},
	doi = {10.1111/nph.17230},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17230},
	author = {Langer, Gerald and Taylor, Alison R. and Walker, Charlotte E. and Meyer, Erin M. and Ben Joseph, Oz and Gal, Assaf and Harper, Glenn M. and Probert, Ian and Brownlee, Colin and Wheeler, Glen L.}
}
@article {graeff_sterol_2021,
	title = {Sterol Composition of the Peridinioid Dinoflagellate Zooxanthella nutricula, A Symbiont of Polycystine Radiolarians},
	journal = {Protist},
	volume = {172},
	number = {3},
	year = {2021},
	month = {jul},
	pages = {125817},
	abstract = {Some dinoflagellates, such as Symbiodinium, are able to form symbiotic relationships with larger marine organisms. An important aspect of dinoflagellate symbiosis involves the exchange of lipids, namely sterols, from the symbiont to the host. Much research has explored the lipid biochemistry of the symbiotic relationship between cnidarians and Symbiodinium dinoflagellates. However, no research has addressed the sterol biochemistry of the symbiosis between radiolarians and dinoflagellates such as Zooxanthella nutricula. To this end, we have provided the first sterol characterization of Z. nutricula isolated from a spumellarian polycystine radiolarian. Fifteen sterols and one steroidal ketone were observed where the major sterol identified was C27 22-dehydrocholesterol, which does not tend to be a dominant sterol among dinoflagellates, including closely related peridinioid species in the genus Heterocapsa. However, C30 dinosterol and dinostanol were major sterols in both Z. nutricula and Heterocapsa spp., thus indicating common sterols between closely related taxa. Major sterols of the distantly related genus Symbiodinium, a symbiont of foraminifera and cnidarians, have included C27 cholesterol and C30 gorgosterol, whereas in Z. nutricula these sterols were minor and absent, respectively. Our results indicate potentially different sterol pools available to cnidarian and radiolarian symbiont hosts during their respective relationships with symbiotic dinoflagellates.},
	keywords = {Dinoflagellate, lipid, Peridiniales, Radiolaria, rcc, RCC3387, sterol},
	issn = {1434-4610},
	doi = {10.1016/j.protis.2021.125817},
	url = {https://www.sciencedirect.com/science/article/pii/S1434461021000262},
	author = {Graeff, Jori E. and Leblond, Jeffrey D.}
}
@article {muller_temperature_2021,
	title = {Temperature Induced Physiological Reaction Norms of the Coccolithophore Gephyrocapsa oceanica and Resulting Coccolith Sr/Ca and Mg/Ca Ratios},
	journal = {Frontiers in Earth Science},
	volume = {9},
	year = {2021},
	pages = {273},
	abstract = {Coccolithophores are one of the major contributors to the pelagic production of calcium carbonate and their fossilized remains are a key component of the biogeochemical cycles of calcium (Ca), magnesium (Mg), and other divalent cations present in the intracellular precipitated calcitic structures (coccoliths). The geochemical signature of coccoliths (e.g., Sr/Ca and Mg/Ca ratios) is used as paleoproxy to reconstruct past environmental conditions and to understand the underlying physiological precipitation kinetics. Here, we present the elemental fractionation of Sr and Mg in calcite of the coccolithophore Gephyrocapsa oceanica from controlled laboratory experiments applying an extended temperature gradient (12 to 27{\textdegree}C). The physiological reaction norm of G. oceanica, in terms of growth rate, exhibited optimum behavior while the partition coefficient of Sr (DSr) was linearly correlated with temperature and DMg indicated no specific trend. Our results indicate: (1) a presumably secondary physiological control of DSr, and (2) the importance of calibrating coccolithophore-based proxies using experiments that include the full physiological reaction norms (i.e., a possible non-linear response) to environmental drivers (e.g., temperature, salinity, and pH, etc.). The presented results contribute to an improved understanding of the underlying physiological kinetics involved in regulating coccolith elemental fractionation and give additional implications for designing future laboratory experiments to calibrate and apply coccolithophore based paleoproxies on the fossil sediment record.},
	keywords = {rcc, RCC1303},
	issn = {2296-6463},
	doi = {10.3389/feart.2021.582521},
	url = {https://www.frontiersin.org/article/10.3389/feart.2021.582521},
	author = {M{\"u}ller, Marius N. and Blanco-Ameijeiras, Sonia and Stoll, Heather M. and M{\'e}ndez-Vicente, Ana and Lebrato, Mario}
}
@article {labban_temperature_2021,
	title = {Temperature Responses of Heterotrophic Bacteria in Co-culture With a Red Sea Synechococcus Strain},
	journal = {Frontiers in Microbiology},
	volume = {12},
	year = {2021},
	pages = {612732},
	abstract = {Interactions between autotrophic and heterotrophic bacteria are fundamental for marine biogeochemical cycling. How global warming will affect the dynamics of these essential microbial players is not fully understood. The aims of this study were to identify the major groups of heterotrophic bacteria present in a Synechococcus culture originally isolated from the Red Sea and assess their joint responses to experimental warming within the metabolic ecology framework. A co-culture of Synechococcus sp. RS9907 and their associated heterotrophic bacteria, after determining their taxonomic affiliation by 16S rRNA gene sequencing, was acclimated and maintained in the lab at different temperatures (24{\textendash}34{\textdegree}C). The abundance and cellular properties of Synechococcus and the three dominant heterotrophic bacterial groups (pertaining to the genera Paracoccus, Marinobacter, and Muricauda) were monitored by flow cytometry. The activation energy of Synechococcus, which grew at 0.94{\textendash}1.38 d{\textendash}1, was very similar (0.34 {\textpm} 0.02 eV) to the value hypothesized by the metabolic theory of ecology (MTE) for autotrophs (0.32 eV), while the values of the three heterotrophic bacteria ranged from 0.16 to 1.15 eV and were negatively correlated with their corresponding specific growth rates (2.38{\textendash}24.4 d{\textendash}1). The corresponding carrying capacities did not always follow the inverse relationship with temperature predicted by MTE, nor did we observe a consistent response of bacterial cell size and temperature. Our results show that the responses to future ocean warming of autotrophic and heterotrophic bacteria in microbial consortia might not be well described by theoretical universal rules.},
	keywords = {rcc, RCC546},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2021.612732},
	url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8141594/},
	author = {Labban, Abbrar and Palacio, Antonio S. and Garc{\'\i}a, Francisca C. and Hadaidi, Ghaida and Ansari, Mohd I. and L{\'o}pez-Urrutia, {\'A}ngel and Alonso-S{\'a}ez, Laura and Hong, Pei-Ying and Mor{\'a}n, Xos{\'e} Anxelu G.}
}
@booklet {roquis_tropical_2021,
	title = {The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching},
	number = {6:195},
	year = {2021},
	note = {Type: article},
	month = {jul},
	publisher = {Wellcome Open Research},
	abstract = {<p>Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2\% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average \textasciitilde90\% of sequence similarities with mice and \textasciitilde96\% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta . The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.</p>
},
	keywords = {chromatin structure, Histone H3 clipping, invertebrate epigenetics, Pocillopora acuta, Pocillopora damicornis, rcc, RCC4017},
	doi = {10.12688/wellcomeopenres.17058.1},
	url = {https://wellcomeopenresearch.org/articles/6-195},
	author = {Roquis, David and Cosseau, C{\'e}line and Raffalli, Kelly Brener and Romans, Pascal and Masanet, Patrick and Mitta, Guillaume and Grunau, Christoph and Vidal-Dupiol, Jeremie}
}
@article {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 {Crenn2018,
	title = {Bacterial epibiotic communities of ubiquitous and abundant marine diatoms are distinct in short- and long-term associations},
	journal = {Frontiers in Microbiology},
	volume = {9},
	number = {December},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC2560,RCC2565,rcc},
	pages = {1{\textendash}12},
	abstract = {Interactions between phytoplankton and bacteria play a central role in mediatingbiogeochemical cycling and food web structure in the ocean. The cosmopolitan diatomsThalassiosiraandChaetocerosoften dominate phytoplankton communities in marinesystems. Past studies of diatom-bacterial associations have employed community-level methods and culture-based or natural diatom populations. Although bacterialassemblages attached to individual diatoms represents tight associations little is knownon their makeup or interactions. Here, we examined the epibiotic bacteria of 436Thalassiosiraand 329Chaetocerossingle cells isolated from natural samples andcollection cultures, regarded here as short- and long-term associations, respectively.Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning-sequencing of 16S rRNA genes obtained from whole-genome amplification products.The prevalence of epibiotic bacteria was higher in cultures and dependent of the hostspecies. Culture approaches demonstrated that both diatoms carry distinct bacterialcommunities in short- and long-term associations. Bacterial epibonts, commonlyassociated with phytoplankton, were repeatedly isolated from cells of diatom collectioncultures but were not recovered from environmental cells. Our results suggest thatin controlled laboratory culture conditions bacterial{\textendash}diatom and bacterial{\textendash}bacterialinteractions select for a simplified, but specific, epibiotic microbiota shaped and adaptedfor long-term associations.},
	keywords = {2018, Chaetoceros, diatoms, diversity, heterotrophic bacteria, interactions, microbiome, rcc, RCC2560, RCC2565, Thalassiosira, Western English Channel},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2018.02879},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2018.02879/full},
	author = {Crenn, Klervi and Duffieux, Delphine and Jeanthon, Christian}
}
@article {Guyon2018,
	title = {Comparative analysis of culture conditions for the optimization of carotenoid production in several strains of the picoeukaryote ostreococcus},
	journal = {Marine Drugs},
	volume = {16},
	number = {3},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC745,RCC802,RCC809,rcc},
	pages = {76},
	abstract = {Microalgae are promising sources for the sustainable production of compounds of interest for biotechnologies. Compared to higher plants, microalgae have a faster growth rate and can be grown in industrial photobioreactors. The microalgae biomass contains specific metabolites of high added value for biotechnology such as lipids, polysaccharides or carotenoid pigments. Studying carotenogenesis is important for deciphering the mechanisms of adaptation to stress tolerance as well as for biotechnological production. In recent years, the picoeukaryote Ostreococcus tauri has emerged as a model organism thanks to the development of powerful genetic tools. Several strains of Ostreococcus isolated from different environments have been characterized with respect to light response or iron requirement. We have compared the carotenoid contents and growth rates of strains of Ostreococcus (OTTH595, RCC802 and RCC809) under a wide range of light, salinity and temperature conditions. Carotenoid profiles and productivities varied in a strain-specific and stress-dependent manner. Our results also illustrate that phylogenetically related microalgal strains originating from different ecological niches present specific interests for the production of specific molecules under controlled culture conditions.},
	keywords = {2018, carotenoids, GROWTH RATE, Light, Ostreococcus, rcc, RCC745, RCC802, RCC809, salinity, temperature},
	issn = {1660-3397},
	doi = {10.3390/md16030076},
	url = {http://www.mdpi.com/1660-3397/16/3/76},
	author = {Guyon, Jean-baptiste and Schatt, Philippe and Lozano, Jean-Claude and Liennard, Marion and Bouget, Fran{\c c}ois-Yves}
}
@article {Dadaglio2018,
	title = {Differential responses of bacteria to diatom-derived dissolved organic matter in the Arctic Ocean},
	journal = {Aquatic Microbial Ecology},
	volume = {82},
	number = {1},
	year = {2018},
	note = {tex.mendeley-tags: 2018,rcc},
	pages = {59{\textendash}72},
	abstract = {ABSTRACT: The Arctic sea ice cover is undergoing an unprecedented decline due to climate change. This loss may result in the earlier start of ice algae blooms and more intense phytoplankton blooms, leading to higher concentrations of dissolved organic matter (DOM) derived from primary production. We investigated the response of early summer Arctic bacterial communities to the addition of Arctic diatom-derived DOM through biodegradation experiments in Baffin Bay. DOM produced by the planktonic diatom Chaetoceros neogracilis and the sea ice diatom Fragilariopsis cylindrus was added to seawater from 3 stations with different ice cover (2 ice zones and 1 open water zone) for 12 d. At the 3 stations, the addition of inorganic nutrients (PO4 and NO3) was not sufficient to stimulate bacterial growth compared to the controls, suggesting that bacteria were mainly limited by organic carbon. The addition of DOM from C. neogracilis stimulated bacterial abundance and production, with a more pronounced response in the ice zone compared to the open water zone. The enhanced bacterial metabolism was accompanied by changes in the bacterial community composition determined by 16S rRNA sequencing, driven by operational taxonomic units (OTUs) related to Pseudoalteromonas and Polaribacter that increased in relative abundance with DOM addition. Moreover, in the ice zone, DOM from C. neogracilis induced a priming effect on the bacterial utilization of ambient DOM. Our findings suggest that phytoplankton blooms, through the production of labile organic matter, will strongly affect bacterial heterotrophic activity, composition and dissolved organic carbon cycling in the Arctic Ocean.},
	keywords = {2018, rcc},
	doi = {10.3354/ame01883},
	url = {https://www.int-res.com/abstracts/ame/v82/n1/p59-72},
	author = {Dadaglio, L and Dinasquet, J and Obernosterer, I and Joux, F}
}
@article {Gu2017,
	title = {Adenoides sinensis , a new sand-dwelling dinoflagellate species from China and reexamination of A. eludens from an Atlantic strain},
	journal = {Phycologia},
	volume = {57},
	number = {October},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC1982,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1{\textendash}13},
	abstract = {The sand-dwelling?1dinoflagellate generaAdenoidesandPseudadenoidesare morphologically very close butdistinct in their molecular phylogeny. We established three cultures by isolating single cells from sand samples collected inintertidal zones of Qingdao (Yellow Sea), Dongshan (South China Sea) and Brittany (English Channel, North Atlantic,France). Strain morphology was examined with light and scanning electron microscopy, and both large subunitribosomal DNA (LSU rDNA) and small subunit ribosomal DNA (SSU rDNA) sequences were amplified. Molecularphylogeny, corroborated by morphological examination showing the existence of a ventral pore, confirmed theidentification of the French strain (RCC1982) asAdenoides eludens. The Chinese strains differed fromAdenoides eludensin two additional posterior intercalary plates and differed fromPseudadenoidesin one additional apical plate having theplate formula of Po, Cp, X, 50,600, 4S, 5000, 5p, 10000or alternatively Po, Cp, X, 50,600, 5S, 5000, 3p, 20000. Maximumlikelihood and Bayesian inference carried out with concatenated LSU and SSU sequences demonstrated that the Chinesestrains were closely related but different fromA. eludensand, in corroboration with morphological evidence, supportedtheir classification as a distinct species,Adenoides sinensis sp. nov. Morphological and molecular results confirmed theclose relationship between the two generaAdenoidesandPseudadenoides.},
	keywords = {2017, rcc, RCC1982, sbr?hyto$_\textrmd$ipo},
	doi = {10.2216/17-76.1},
	author = {Gu, Haifeng and Li, Xintian and Chom{\'e}rat, Nicolas and Luo, Zhaohe and Sarno, Diana and Gourvil, Priscillia and Balzano, Sergio and Siano, Raffaele}
}
@article {Weynberg2017,
	title = {Marine prasinoviruses and their tiny plankton hosts : A review},
	journal = {Viruses},
	number = {March},
	year = {2017},
	note = {tex.mendeley-tags: 2017,RCC,rcc1105,rcc299,rcc809},
	pages = {1{\textendash}20},
	abstract = {Viruses play a crucial role in the marine environment, promoting nutrient recycling and biogeochemical cycling and driving evolutionary processes. Tiny marine phytoplankton called prasinophytes are ubiquitous and significant contributors to global primary production and biomass. A number of viruses (known as prasinoviruses) that infect these important primary producers have been isolated and characterised over the past decade. Here we review the current body of knowledge about prasinoviruses and their interactions with their algal hosts. Several genes, including those encoding for glycosyltransferases, methyltransferases and amino acid synthesis enzymes, which have never been identified in viruses of eukaryotes previously, have been detected in prasinovirus genomes. The host organisms are also intriguing; most recently, an immunity chromosome used by a prasinophyte in response to viral infection was discovered. In light of such recent, novel discoveries, we discuss why the cellular simplicity of prasinophytes makes for appealing model host organism{\textendash}virus systems to facilitate focused and detailed investigations into the dynamics of marine viruses and their intimate associations with host species. We encourage the adoption of the prasinophyte Ostreococcus and its associated viruses as a model host{\textendash}virus system for examination of cellular and molecular processes in the marine environment.},
	keywords = {2017, host interactions, marine virus ecology, rcc, RCC1105, RCC299, RCC809, virus, virus-driven evolution, virus{\textendash}host interactions},
	issn = {1999-4915},
	doi = {10.3390/v9030043},
	author = {Weynberg, Karen D and Allen, Michael J and Wilson, William H}
}
@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 {Simmons2016,
	title = {Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the eastern north pacific ocean},
	journal = {Applied and Environmental Microbiology},
	volume = {82},
	number = {6},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc},
	month = {mar},
	pages = {1693{\textendash}1705},
	abstract = {Eukaryotic algae within the picoplankton size class (<=2 ??m in diameter) are important marine primary producers, but their spatial and ecological distributions are not well characterized. Here, we studied three picoeukaryotic prasinophyte genera and their cyanobacterial counterparts, Prochlorococcus and Synechococcus , during two cruises along a North Pacific transect characterized by different ecological regimes. Picoeukaryotes and Synechococcus reached maximum abundances of 1.44 {\texttimes} 10 5 and 3.37 {\texttimes} 10 5 cells ? ml -1 , respectively, in mesotrophic waters, while Prochlorococcus reached 1.95 {\texttimes} 10 5 cells ? ml -1 in the oligotrophic ocean. Of the picoeukaryotes, Bathycoccus was present at all stations in both cruises, reaching 21,368 {\textpm} 327 18S rRNA gene copies ? ml -1 . Micromonas and Ostreococcus clade OI were detected only in mesotrophic and coastal waters and Ostreococcus clade OII only in the oligotrophic ocean. To resolve proposed Bathycoccus ecotypes, we established genetic distances for 1,104 marker genes using targeted metagenomes and the Bathycoccus prasinos genome. The analysis was anchored in comparative genome analysis of three Ostreococcus species for which physiological and environmental data are available to facilitate data interpretation. We established that two Bathycoccus ecotypes exist, named here BI (represented by coastal isolate Bathycoccus prasinos ) and BII. These share 82\% {\textpm} 6\% nucleotide identity across homologs, while the Ostreococcus spp. share 75\% {\textpm} 8\%. We developed and applied an analysis of ecomarkers to metatranscriptomes sequenced here and published -omics data from the same region. The results indicated that the Bathycoccus ecotypes cooccur more often than Ostreococcus clades OI and OII do. Exploratory analyses of relative transcript abundances suggest that Bathycoccus NRT2.1 and AMT2.2 are high-affinity NO 3 - and low-affinity NH 4 + transporters, respectively, with close homologs in multiple picoprasinophytes. Additionally, in the open ocean, where dissolved iron concentrations were low (0.08 nM), there appeared to be a shift to the use of nickel superoxide dismutases (SODs) from Mn/Fe/Cu SODs closer inshore. Our study documents the distribution of picophytoplankton along a North Pacific ecological gradient and offers new concepts and techniques for investigating their biogeography.},
	keywords = {2016, rcc},
	issn = {0099-2240},
	doi = {10.1128/AEM.02730-15},
	url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02730-15},
	author = {Simmons, Melinda P. and Sudek, Sebastian and Monier, Adam and Limardo, Alexander J. and Jimenez, Valeria and Perle, Christopher R. and Elrod, Virginia A. and Pennington, J. Timothy and Worden, Alexandra Z.},
	editor = {Schloss, P. D.}
}
@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 {Edvardsen2016,
	title = {Diversity and distribution of haptophytes revealed by environmental sequencing and metabarcoding {\textendash} a review},
	journal = {Perspectives in Phycology},
	volume = {3},
	number = {2},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo},
	month = {apr},
	pages = {77{\textendash}91},
	keywords = {2016, rcc, sbr?hyto$_\textrmd$ipo},
	issn = {2198-011X},
	doi = {10.1127/pip/2016/0052},
	url = {https://dx.doi.org/10.6084/m9.figshare.2759983.v1 http://www.schweizerbart.de/papers/pip/detail/3/85671/Diversity_and_distribution_of_haptophytes_revealed?af=crossref},
	author = {Edvardsen, Bente and Egge, Elianne Sirnaes and Vaulot, Daniel}
}
@article {Ichinomiya2016,
	title = {Diversity and oceanic distribution of Parmales (Bolidophyceae), a picoplankton group closely related to diatoms},
	journal = {The ISME Journal},
	volume = {in press},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	keywords = {2016, MACUMBA, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1038/ismej.2016.38},
	author = {Ichinomiya, Mutsuo and Lopes dos Santos, A and Gourvil, Priscillia and Yoshikawa, Shinya and Kamiya, Mitsunobu and Ohki, Kaori and Audic, S and de Vargas, Colomban and Vaulot, Daniel and Kuwata, Akira}
}
@article {Klouch2016,
	title = {Historical records from dated sediment cores reveal the multidecadal dynamic of the toxic dinoflagellate Alexandrium minutum in the Bay of Brest (France)},
	journal = {FEMS Microbiology Ecology},
	volume = {92},
	number = {7},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo},
	month = {jul},
	pages = {fiw101},
	abstract = {The multiannual dynamic of the cyst-forming and toxic marine dinoflagellate Alexandrium minutum was studied over a time scale of about 150 years by a paleoecological approach based on ancient DNA (aDNA) quantification and cyst revivification data obtained from two dated sediment cores of the Bay of Brest (Brittany, France). The first genetic traces of the species presence in the study area dated back to 1873 {\textpm} 6. Specific aDNA could be quantified by a newly-developed real-time PCR assay in the upper core layers, in which the germination of the species (in up to 17-19 year-old sediments) was also obtained. In both cores studied, our quantitative paleogenetic data showed a statistically significant increasing trend in the abundance of A. minutum ITS1 rDNA copies over time, corroborating three decades of local plankton data that have documented an increasing trend in the species cell abundance. By comparison, paleogenetic data of the dinoflagellate Scrippsiella donghaienis did not show a coherent trend between the cores studied, supporting the hypothesis of the existence of a species-specific dynamic of A. minutum in the study area. This work contributes to the development of paleoecological research, further showing its potential for biogeographical, ecological and evolutionary studies on marine microbes.},
	keywords = {2016, rcc, sbr?hyto$_\textrmd$ipo},
	issn = {1574-6941},
	doi = {10.1093/femsec/fiw101},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/27162179 https://academic.oup.com/femsec/article-lookup/doi/10.1093/femsec/fiw101},
	author = {Klouch, Khadidja Z and Schmidt, Sabine and Andrieux-Loyer, Fran{\c c}oise and Le Gac, Micka{\"e}l and Hervio-Heath, Dominique and Qui-Minet, Zujaila N and Qu{\'e}r{\'e}, Julien and Bigeard, Estelle and Guillou, Laure and Siano, Raffaele},
	editor = {Laanbroek, Riks}
}
@article {Waltman2016,
	title = {Identifying aspects of the post-transcriptional program governing the proteome of the green alga micromonas pusilla.},
	journal = {PloS one},
	volume = {11},
	number = {7},
	year = {2016},
	note = {ISBN: 10.1371/journal.pone.0155839 Publisher: Public Library of Science tex.mendeley-tags: 2016,RCC,rcc834},
	month = {jan},
	pages = {e0155839},
	abstract = {Micromonas is a unicellular motile alga within the Prasinophyceae, a green algal group that is related to land plants. This picoeukaryote ({\textexclamdown}2 ??m diameter) is widespread in the marine environment but is not well understood at the cellular level. Here, we examine shifts in mRNA and protein expression over the course of the day-night cycle using triplicated mid-exponential, nutrient replete cultures of Micromonas pusilla CCMP1545. Samples were collected at key transition points during the diel cycle for evaluation using high-throughput LC-MS proteomics. In conjunction, matched mRNA samples from the same time points were sequenced using pair-ended directional Illumina RNA-Seq to investigate the dynamics and relationship between the mRNA and protein expression programs of M. pusilla. Similar to a prior study of the marine cyanobacterium Prochlorococcus, we found significant divergence in the mRNA and proteomics expression dynamics in response to the light:dark cycle. Additionally, expressional responses of genes and the proteins they encoded could also be variable within the same metabolic pathway, such as we observed in the oxygenic photosynthesis pathway. A regression framework was used to predict protein levels from both mRNA expression and gene-specific sequence-based features. Several features in the genome sequence were found to influence protein abundance including codon usage as well as 3{\textquoteright} UTR length and structure. Collectively, our studies provide insights into the regulation of the proteome over a diel cycle as well as the relationships between transcriptional and translational programs in the widespread marine green alga Micromonas.},
	keywords = {2016, rcc, RCC834},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0155839},
	url = {http://dx.doi.org/10.1371/journal.pone.0155839},
	author = {Waltman, Peter H and Guo, Jian and Reistetter, Emily Nahas and Purvine, Samuel and Ansong, Charles K and van Baren, Marijke J and Wong, Chee-Hong and Wei, Chia-Lin and Smith, Richard D and Callister, Stephen J and Stuart, Joshua M and Worden, Alexandra Z}
}
@article {LopesdosSantos2016a,
	title = {Photosynthetic pigments of oceanic Chlorophyta belonging to prasinophytes clade VII},
	journal = {Journal of Phycology},
	volume = {52},
	number = {1},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,rcc1124,rcc15,rcc1871,rcc2337,rcc2339,rcc287,rcc3374,rcc3376,rcc3402,rcc719,rcc856,rcc857,rcc996,rcc998,sbr?hyto$_\textrmd$ipo},
	pages = {148{\textendash}155},
	abstract = {The ecological importance and diversity of pico/ nanoplanktonic algae remains poorly studied in marine waters, in part because many are tiny and without distinctive morphological features. Amongst green algae, Mamiellophyceae such as Micromonas or Bathycoccus are dominant in coastal waters while prasinophytes clade VII, yet not formerly described, appear to be major players in open oceanic waters. The pigment composition of 14 strains representative of different subclades of clade VII was analyzed using a method that improves the separation of loroxanthin and neoxanthin. All the prasinophytes clade VII analyzed here showed a pigment composition similar to that previously reported for RCC287 corresponding to pigment group prasino-2A. However, we detected in addition astaxanthin for which it is the first report in prasinophytes. Among the strains analyzed, the pigment signature is qualitatively similar within subclades A and B. By contrast, RCC3402 from subclade C (Picocystis) lacks loroxanthin, astaxanthin, and antheraxanthin but contains alloxanthin, diatoxanthin, and monadoxanthin that are usually found in diatoms or cryptophytes. For subclades A and B, loroxanthin was lowest at highest light irradiance suggesting a light-harvesting role of this pigment in clade VII as in Tetraselmis.},
	keywords = {2016, MACUMBA, rcc, RCC1124, RCC15, RCC1871, RCC2337, RCC2339, RCC287, RCC3374, RCC3376, RCC3402, RCC719, RCC856, RCC857, RCC996, RCC998, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1111/jpy.12376},
	author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Rodriguez-Hernandez, Francisco and Garrido, Jos{\'e} Luis and Vaulot, Daniel}
}
@article {Tragin2016,
	title = {Phylogenetic diversity and ecology of green micro algae in marine systems},
	journal = {Perspectives in Phycology},
	volume = {in press},
	year = {2016},
	note = {tex.mendeley-tags: 2016,rcc,sbr?hyto$_\textrmd$ipo},
	keywords = {2016, ? No DOI found, rcc, sbr?hyto$_\textrmd$ipo},
	author = {Tragin, M and Lopes dos Santos, Adriana and Christen, R. and Vaulot, D.}
}
@article {Bendif2016,
	title = {Recent reticulate evolution in the ecologically dominant lineage of coccolithophores},
	journal = {Frontiers in Microbiology},
	volume = {7},
	number = {May},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC4032,RCC4033,RCC4034,RCC4035,RCC4036,rcc,sbr?hyto},
	month = {may},
	keywords = {2016, coccolithophores, cyto-nuclear discordance, diversity, Emiliania, evolution, Gephyrocapsa, introgressive hybridization, rcc, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, Reticulofenestra, sbr?hyto},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2016.00784},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.00784 http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00784/abstract},
	author = {Bendif, El Mahdi and Probert, Ian and D{\'\i}az-Rosas, Francisco and Thomas, Daniela and van den Engh, Ger and Young, Jeremy R. and von Dassow, Peter}
}
@article {Coutinho2015,
	title = {Comparative genomics of Synechococcus and proposal of the new genus Parasynechococcus},
	journal = {PeerJ},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {e{\textendash}1522},
	keywords = {rcc},
	issn = {2167-8359},
	doi = {10.7717/peerj.1522},
	author = {Coutinho, Felipe and Tschoeke, Diogo Antonio and Thompson, Fabiano and Thomson, Cristiane}
}
@article {Varkey2015,
	title = {Effects of low temperature on tropical and temperate isolates of marine Synechococcus},
	journal = {The ISME Journal},
	year = {2015},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	pages = {1{\textendash}12},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2015.179},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2015.179},
	author = {Varkey, Deepa and Mazard, Sophie and Ostrowski, Martin and Tetu, Sasha G and Haynes, Paul and Paulsen, Ian T}
}
@article {Astorga-Elo2015,
	title = {Genomic potential for nitrogen assimilation in uncultivated members of Prochlorococcus from an anoxic marine zone},
	journal = {The ISME Journal},
	volume = {9},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {1264{\textendash}1267},
	abstract = {Cyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic marine organisms and key factors in the global carbon cycle. The understanding of their distribution and ecological importance in oligotrophic tropical and subtropical waters, and their differentiation into distinct ecotypes, is based on genetic and physiological information from several isolates. Currently, all available Prochlorococcus genomes show their incapacity for nitrate utilization. However, environmental sequence data suggest that some uncultivated lineages may have acquired this capacity. Here we report that uncultivated low-light-adapted Prochlorococcus from the nutrient-rich, low-light, anoxic marine zone (AMZ) of the eastern tropical South Pacific have the genetic potential for nitrate uptake and assimilation. All genes involved in this trait were found syntenic with those present in marine Synechococcus. Genomic and phylogenetic analyses also suggest that these genes have not been aquired recently, but perhaps were retained from a common ancestor, highlighting the basal characteristics of the AMZ lineages within Prochlorococcus.},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2015.21},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2015.21},
	author = {Astorga-El{\'o}, Marcia and Ram{\'\i}rez-Flandes, Salvador and DeLong, Edward F and Ulloa, Osvaldo}
}
@article {Schmidt2015,
	title = {Guanchochroma wildpretii gen. et spec. nov. (ochrophyta) provides new insights into the diversification and evolution of the algal class synchromophyceae.},
	journal = {PloS one},
	volume = {10},
	number = {7},
	year = {2015},
	note = {Publisher: Public Library of Science tex.mendeley-tags: rcc},
	month = {jan},
	pages = {e0131821},
	abstract = {A new relative of the chrysophyte genus Chrysopodocystis was found in Tenerife and termed Guanchochroma wildpretii. This unicellular alga was most noticeably discernible from Chrysopodocystis socialis (the only species of this genus) by the presence of a cyst-like stage with a multilayered lorica, which also functions as a dispersal unit and shows secondary wall growth. Secondary expansion of loricae (cell casings not involved in cell division, usually with a more or less pronounced opening) has never been observed previously and marks a unique feature of the new taxon. Plastids are non-randomly distributed within cells of G. wildpretii. 18S rRNA gene analyses identified the two species as sister lineages and placed them in a monophyletic group with the Synchromophyceae, a heterokont algal (Ochrophyta) class characterized by the presence of chloroplast complexes. Yet, neither Chrysopodocystis nor Guanchochroma showed this feature in ultrastructure analyses. Additionally, their 18S rRNA genes possessed distinct inserts, the highest GC-content known for Ochrophyta and exceptionally long branches on the Ochrophyta 18S rDNA phylogenetic tree, suggesting substantially increased substitution rates along their branch compared to Synchromophyceae. Plastid marker data (rbcL) recovered a monophyletic clade of Chrysopodocystis, Guanchochroma and Synchromophyceae as well, yet with lower supports for internal split order due to limited resolution of the marker. Evidence for the sequence of events leading to the formation of the plastid complex of Synchromophyceae still remains ambiguous because of the apparently short timeframe in which they occurred.},
	keywords = {rcc},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0131821},
	url = {http://dx.doi.org/10.1371/journal.pone.0131821},
	author = {Schmidt, Maria and Horn, Susanne and Ehlers, Katrin and Wilhelm, Christian and Schnetter, Reinhard}
}
@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 {Simmons2015,
	title = {Intron invasions trace algal speciation and reveal nearly identical Arctic and Antarctic Micromonas populations.},
	journal = {Molecular biology and evolution},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	month = {may},
	abstract = {Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, recently new families of spliceosomal introns that are repeated hundreds of times in individual genomes have been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements (ILEs) in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence-absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture (Micromonas Clade E2) isolated from a polar region where this alga is increasing in abundance due to climate change. The same two families were detected in metagenomic data from Antarctica - a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our work illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation and global distribution of this sentinel marine alga.},
	keywords = {rcc},
	issn = {1537-1719},
	doi = {10.1093/molbev/msv122},
	url = {http://mbe.oxfordjournals.org/cgi/content/long/msv122v1},
	author = {Simmons, Melinda P and Bachy, Charles and Sudek, Sebastian and van Baren, Marijke J and Sudek, Lisa and Ares, Manuel and Worden, Alexandra Z}
}
@article {Bendif2015,
	title = {Morphological and phylogenetic characterization of new gephyrocapsa isolates suggests introgressive hybridization in the Emiliania/Gephyrocapsa complex (haptophyta)},
	journal = {Protist},
	volume = {166},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: 2015,RCC1281,RCC1282,RCC1284,RCC1286,RCC1292,RCC1300,RCC1305,RCC1307,RCC1316,RCC1317,RCC1318,RCC1319,RCC1320,RCC1562,RCC1839,RCC3370,RCC3862,RCC3898,rcc},
	pages = {323{\textendash}336},
	abstract = {The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the No{\"e}laerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.},
	keywords = {2015, coccolithophores, Emiliania huxleyi, Gephyrocapsa muellerae, Gephyrocapsa oceanica, hybridization, phylogeny., rcc, RCC1281, RCC1282, RCC1284, RCC1286, RCC1292, RCC1300, RCC1305, RCC1307, RCC1316, RCC1317, RCC1318, RCC1319, RCC1320, RCC1562, RCC1839, RCC3370, RCC3862, RCC3898, species concept},
	issn = {14344610},
	doi = {10.1016/j.protis.2015.05.003},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461015000243},
	author = {Bendif, El Mahdi and Probert, Ian and Young, Jeremy R. and von Dassow, Peter}
}
@article {Potvin2015,
	title = {Morphology , molecular phylogeny , and pigment characterization of a novel phenotype of the dinoflagellate genus Pelagodinium from Korean waters},
	journal = {Algae},
	volume = {30},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {183{\textendash}195},
	abstract = {The dinoflagellate genus Pelagodinium is genetically classified in distinct sub-clades and subgroups. However, it is dif- ficult to determine whether this genetic diversity represents intra- or interspecific divergence within the genus since only the morphology of the type strain of the genus Pelagodinium, Pelagodinium bei, is available. An isolate associated with the genus Pelagodinium from Shiwha Bay, Korea, was recently cultured. This isolate formed a subgroup with 3 to 4 strains from the Atlantic Ocean, Mediterranean Sea, and Indian Ocean. This subgroup was distinct from the subgroup contain- ing P. bei. The morphology of the isolate was analyzed using optical and scanning electron microscopy and was almost identical to that of P. bei except that this isolate had two series of amphiesmal vesicles (AVs) in the cingulum, unlike P. bei that has one series. When the pigment compositions of the isolate and P. bei were analyzed using high-performance liquid chromatography, these two strains had peridinin as a major accessory pigment and their pigment compositions were almost identical. In addition, the swimming behaviors of these two strains were very similar. The re-examination of the type culture of P. bei revealed two series in the cingulum as for the isolate. The new findings on the number of series of AVs in the cingulum, the pigment composition, and the swimming behaviors suggest that P. bei and the isolate may be conspecific despite their association to genetically different subgroups. This study provides a basis to further understand the molecular classification within Pelagodinium combining genetic, morphological, pigment, and behavioral data.},
	keywords = {foraminifera, gymnodinium bei, pelagic symbiont, rcc, suessiaceae, suessiales},
	doi = {10.4490/algae.2015.30.3.183},
	author = {Potvin, {\'E}ric and Jeong, Hae Jin and Kang, Nam Seon and Noh, Jae Hoon and Yang, Eun Jin}
}
@article {Kamikawa2015,
	title = {Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)},
	journal = {Phycological Research},
	volume = {63},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {19{\textendash}28},
	abstract = {In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluores- cence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four- membrane-bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus-encoded large subunit rRNA genes showed eight distinct lineages for apochlo- rotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle. Key},
	keywords = {apochlorotic diatoms, genetic diversity, large subunit rrna, molecular phylogenetic analysis, nonphotosynthetic plastids, plastid 16s rrna, rcc},
	issn = {13220829},
	doi = {10.1111/pre.12072},
	url = {http://doi.wiley.com/10.1111/pre.12072},
	author = {Kamikawa, Ryoma and Yubuki, Naoji and Yoshida, Masaki and Taira, Misaka and Nakamura, Noriaki and Ishida, Ken-ichiro and Leander, Brian S. and Miyashita, Hideaki and Hashimoto, Tetsuo and Mayama, Shigeki and Inagaki, Yuji}
}
@article {MartinezMartinez2015,
	title = {New lipid envelope-containing dsDNA virus isolates infecting Micromonas pusilla reveal a separate phylogenetic group},
	journal = {Aquatic Microbial Ecology},
	volume = {74},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {17{\textendash}28},
	abstract = {Viral infection of phytoplankton has major implications for biochemical and energy cycles, community dynamics, and microbial evolution in the marine environment. The non-bloom forming picoplankter Micromonas pusilla, a significant component of the plankton community worldwide, is known to be susceptible to infection by both dsDNA and dsRNA viruses. Logically, comprehensive knowledge of the ecology of M. pusilla requires a better understanding of the div - ersity and infection mechanisms of their viruses. Here, we investigated 19 new M. pusilla-specific viruses (MpVs) isolated from different locations and years. We performed partial characterization of those MpVs including structural characteristics, genome size, phylogenetic analysis based on partial DNA polymerase gene sequences, host range, and stability at different temperatures and upon exposure to chloroform. Combined, these characteristics allowed classification of the MpVs into 2 groups. Exposure to chloroform led to loss of infectivity by all MpVs in one group, which sug- gests the presence of an outer lipid envelope. In addition, all except one of the members in that group formed a monophylogenetic clade that was distinct from all other MpV isolates. The distinc- tive characteristics of the 2 MpV groups suggest different infection strategies, which may have im- portant implications for the ecology of both host and virus populations in the environment. Knowl- edge gained from our study adds value to the MpV isolates as a scientific resource as it will aid in developing and testing in the laboratory new hypotheses about the ecological and biogeochemical implications of M. pusilla viral infection in the environment},
	keywords = {characterization, micromonas pusilla, ncldv, phycodnaviridae, rcc, RCC?o?dd, virus diversity},
	issn = {0948-3055},
	doi = {10.3354/ame01723},
	url = {http://www.int-res.com/abstracts/ame/v74/n1/p17-28/},
	author = {Mart{\'\i}nez Mart{\'\i}nez, J and Boere, A and Gilg, I and van Lent, Jwm and Witte, Hj and van Bleijswijk, Jdl and Brussaard, Cpd}
}
@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 {Andersen2015,
	title = {Phaeocystis rex sp. nov. (Phaeocystales, Prymnesiophyceae): a new solitary species that produces a multilayered scale cell covering},
	journal = {European Journal of Phycology},
	volume = {50},
	number = {2},
	year = {2015},
	note = {Publisher: Taylor \& Francis tex.mendeley-tags: 2015,RCC 4025,rcc},
	pages = {207{\textendash}222},
	abstract = {A morphologically distinct marine species, Phaeocystis rex sp. nov., was described on the basis of light microscopy, transmission electron microscopy and DNA sequence comparisons. Non-motile cells were solitary (non-colonial), 6{\textendash}10 {\textmu}m in diameter and 8{\textendash}15 {\textmu}m long, and possessed chloroplasts with distinctive finger-like lobes. TEM observations demonstrated the presence of two short flagella and a very short haptonema that arose from an invagination of the protoplast. Non-motile cells were surrounded by one to several dense layers composed of scales, presumably unmineralized, and an amorphous material. Phylogenetic analyses based upon combined partial nucleotide sequences for five nuclear-or plastid-encoded genes (18S rRNA, 28S rRNA, 16S rRNA, psbA and rbcL) from cultured strains and from uncharacterized acantharian symbionts confirmed that P. rex was a distinct species. These analyses implied that P. rex occupies an intermediate evolutionary position between solitary and colonial Phaeocystis species.},
	keywords = {2015, algae, organic scales, Phaeocystales, Phaeocystis rex, Prymnesiophyceae, rcc, RCC4025, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmE$PPO, systematics, ultrastructure},
	issn = {0967-0262},
	doi = {10.1080/09670262.2015.1024287},
	url = {http://www.tandfonline.com/doi/full/10.1080/09670262.2015.1024287},
	author = {Andersen, Robert A. and Bailey, J. Craig and Decelle, Johan and Probert, Ian}
}
@article {Decelle2015,
	title = {PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy},
	journal = {Molecular Ecology Resources},
	volume = {15},
	number = {6},
	year = {2015},
	note = {tex.mendeley-tags: 2015,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {1435{\textendash}1445},
	abstract = {Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongo- ing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF data- base that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classifica- tion were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.},
	keywords = {2015, MACUMBA, rcc, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$IPO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1755098X},
	doi = {10.1111/1755-0998.12401},
	url = {http://doi.wiley.com/10.1111/1755-0998.12401},
	author = {Decelle, Johan and Romac, Sarah and Stern, Rowena F. and Bendif, El Mahdi and Zingone, Adriana and Audic, St{\'e}phane and Guiry, Michael D. and Guillou, Laure and Tessier, D{\'e}sir{\'e} and Le Gall, Florence and Gourvil, Priscillia and dos Santos, Adriana Lopes and Probert, Ian and Vaulot, Daniel and de Vargas, Colomban and Christen, Richard}
}
@article {Abby2014,
	title = {Bacteria in Ostreococcus tauri cultures - friends, foes or hitchhikers?},
	journal = {Frontiers in microbiology},
	volume = {5},
	year = {2014},
	note = {Publisher: Frontiers tex.mendeley-tags: rcc},
	month = {jan},
	pages = {505},
	abstract = {Marine phytoplankton produce half of the oxygen we breathe and their astounding diversity is just starting to be unraveled. Many microbial phytoplankton are thought to be phototrophic, depending solely on inorganic sources of carbon and minerals for growth rather than preying on other planktonic cells. However, there is increasing evidence that symbiotic associations, to a large extent with bacteria, are required for vitamin or nutrient uptake for many eukaryotic microalgae. Here, we use in silico approaches to look for putative symbiotic interactions by analysing the gene content of microbial communities associated with 13 different Ostreococcus tauri (Chlorophyta, Mamilleophyceae) cultures sampled from the Mediterranean Sea. While we find evidence for bacteria in all cultures, there is no ubiquitous bacterial group, and the most prevalent group, Flavobacteria, is present in 10 out of 13 cultures. Among seven of the microbiomes, we detected genes predicted to encode type 3 secretion systems (T3SS, in 6/7 microbiomes) and/or putative type 6 secretion systems (T6SS, in 4/7 microbiomes). Phylogenetic analyses show that the corresponding genes are closely related to genes of systems identified in bacterial-plant interactions, suggesting that these T3SS might be involved in cell-to-cell interactions with O. tauri.},
	keywords = {bacterial diversity, Bacterial symbiosis, Illumina sequencing, microbiome, Ostreococcus, phycosphere, phytoplankton, picoeukaryote, rcc, RCC?o?dd, secretion system},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2014.00505},
	url = {http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00505/abstract},
	author = {Abby, Sophie S and Touchon, Marie and De Jode, Aurelien and Grimsley, Nigel and Piganeau, Gwenael}
}
@article {Probert2014a,
	title = {Brandtodinium gen. nov. and B. nutricula comb. Nov. (Dinophyceae), a dinoflagellate commonly found in symbiosis with polycystine radiolarians},
	journal = {Journal of Phycology},
	volume = {50},
	number = {2},
	year = {2014},
	note = {tex.mendeley-tags: RCC3378,RCC3379,RCC3380,RCC3381,RCC3382,RCC3383,RCC3384,RCC3385,RCC3386,RCC3387,RCC3388},
	pages = {388{\textendash}399},
	abstract = {Symbiotic interactions between pelagic hosts and microalgae have received little attention, although they are widespread in the photic layer of the world ocean, where they play a fundamental role in the ecology of the planktonic ecosystem. Polycystine radiolarians (including the orders Spumellaria, Collodaria and Nassellaria) are planktonic heterotrophic protists that are widely distributed and often abundant in the ocean. Many polycystines host symbiotic microalgae within their cytoplasm, mostly thought to be the dinoflagellate Scrippsiella nutricula, a species originally described by Karl Brandt in the late nineteenth century as Zooxanthella nutricula. The free-living stage of this dinoflagellate has never been characterized in terms of morphology and thecal plate tabulation. We examined morphological characters and sequenced conservative ribosomal markers of clonal cultures of the free-living stage of symbiotic dinoflagellates isolated from radiolarian hosts from the three polycystine orders. In addition, we sequenced symbiont genes directly from several polycystine-symbiont holobiont specimens from different oceanic regions. Thecal plate arrangement of the free-living stage does not match that of Scrippsiella or related genera, and LSU and SSU rDNA-based molecular phylogenies place these symbionts in a distinct clade within the Peridiniales. Both phylogenetic analyses and the comparison of morphological features of culture strains with those reported for other closely related species support the erection of a new genus that we name Brandtodinium gen. nov. and the recombination of S. nutricula as B. nutricula comb. nov.},
	keywords = {Dinoflagellate, MACUMBA, Peridiniales, polycystines, Radiolaria, rcc, RCC3378, RCC3379, RCC3380, RCC3381, RCC3382, RCC3383, RCC3384, RCC3385, RCC3386, RCC3387, RCC3388, SBR$_\textrmP$hyto$_\textrmD$PO, Scrippsiella, symbiosis, taxonomy, Zooxanthella},
	doi = {10.1111/jpy.12174},
	url = {http://dx.doi.org/10.1111/jpy.12174},
	author = {Probert, Ian and Siano, Raffaele and Poirier, Camille and Decelle, Johan and Biard, Tristan and Tuji, Akihiro and Suzuki, Noritoshi and Not, Fabrice}
}
@article {Bombar2014,
	title = {Comparative genomics reveals surprising divergence of two closely related strains of uncultivated UCYN-A cyanobacteria},
	journal = {The ISME Journal},
	volume = {8},
	number = {12},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	pages = {2530{\textendash}2542},
	keywords = {rcc},
	issn = {1751-7362},
	doi = {10.1038/ismej.2014.167},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2014.167},
	author = {Bombar, Deniz and Heller, Philip and Sanchez-Baracaldo, Patricia and Carter, Brandon J and Zehr, Jonathan P}
}
@article {Pittera2014,
	title = {Connecting thermal physiology and latitudinal niche partitioning in marine Synechococcus},
	journal = {The ISME journal},
	volume = {8},
	number = {6},
	year = {2014},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: 2014,macumba,microb3,rcc,sbr?hyto?app},
	pages = {1221{\textendash}1236},
	abstract = {Marine Synechococcus cyanobacteria constitute a monophyletic group that displays a wide latitudinal distribution, ranging from the equator to the polar fronts. Whether these organisms are all physiologically adapted to stand a large temperature gradient or stenotherms with narrow growth temperature ranges has so far remained unexplored. We submitted a panel of six strains, isolated along a gradient of latitude in the North Atlantic Ocean, to long- and short-term variations of temperature. Upon a downward shift of temperature, the strains showed strikingly distinct resistance, seemingly related to their latitude of isolation, with tropical strains collapsing while northern strains were capable of growing. This behaviour was associated to differential photosynthetic performances. In the tropical strains, the rapid photosystem II inactivation and the decrease of the antioxydant [beta]-carotene relative to chl a suggested a strong induction of oxidative stress. These different responses were related to the thermal preferenda of the strains. The northern strains could grow at 10[thinsp][deg]C while the other strains preferred higher temperatures. In addition, we pointed out a correspondence between strain isolation temperature and phylogeny. In particular, clades I and IV laboratory strains were all collected in the coldest waters of the distribution area of marine Synechococus. We, however, show that clade I Synechococcus exhibit different levels of adaptation, which apparently reflect their location on the latitudinal temperature gradient. This study reveals the existence of lineages of marine Synechococcus physiologically specialised in different thermal niches, therefore suggesting the existence of temperature ecotypes within the marine Synechococcus radiation.},
	keywords = {2014, adaptation, ecotype, MACUMBA, marine cyanobacteria, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app, Synechococcus, temperature},
	doi = {10.1038/ismej.2013.228},
	url = {http://dx.doi.org/10.1038/ismej.2013.228 10.1038/ismej.2013.228},
	author = {Pittera, Justine and Humily, Florian and Thorel, Maxine and Grulois, Daphne and Garczarek, Laurence and Six, Christophe}
}
@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 {Lepelletier2014a,
	title = {Dinomyces arenysensis gen. et sp. nov. (rhizophydiales, dinomycetaceae fam. nov.), a chytrid infecting marine dinoflagellates},
	journal = {Protist},
	volume = {165},
	number = {2},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {230{\textendash}244},
	abstract = {Environmental 18S rRNA gene surveys of microbial eukaryotes have recently revealed the diversity of major parasitic agents in pelagic freshwater systems, consisting primarily of chytrid fungi. To date, only a few studies have reported the presence of chydrids in the marine environment and a limited number of marine chytrids have been properly identified and characterized. Here, we report the isolation and cultivation of a marine chytrid from samples taken during a bloom of the toxic dinoflagellate Alexandrium minutum in the Arenys de Mar harbour (Mediterranean Sea, Spain). Cross-infections using cultures and natural phytoplankton communities revealed that this chytrid is only able to infect certain species of dinoflagellates, with a rather wide host range but with a relative preference for Alexandrium species. Phylogenetic analyses showed that it belongs to the order Rhizophydiales, but cannot be included in any of the existing families within this order. Several ultrastructural characters confirmed the placement of this taxon within the Rhizophydiales as well its novelty notably in terms of zoospore structure. This marine chytridial parasitoid is described as a new genus and species, Dinomyces arenysensis, within the Dinomycetaceae fam. nov.},
	keywords = {2014, chytrid, Dinoflagellates, Dinomyces arenysensis, Fungi, MACUMBA, microbial parasitoids, rcc, RCC?o?dd, Rhizophydiales., SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.1016/j.protis.2014.02.004},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461014000170},
	author = {Lepelletier, Fr{\'e}d{\'e}ric and Karpov, Sergey A and Alacid, Elisabet and Le Panse, Sophie and Bigeard, Estelle and Garc{\'e}s, Esther and Jeanthon, Christian and Guillou, Laure}
}
@article {Chambouvet2014,
	title = {Diverse molecular signatures for ribosomally {\textquoteright}active{\textquoteright} Perkinsea in marine sediments},
	journal = {BMC Microbiology},
	volume = {14},
	number = {1},
	year = {2014},
	note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?ppo},
	pages = {110},
	abstract = {BACKGROUND:Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples. Only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity {\textquoteright}tag{\textquoteright} sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations.RESULTS:We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27\% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97\% sequence similarity as to suggest this diversity encompasses a range of biologically and ecologically distinct organisms.CONCLUSIONS:These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally {\textquoteright}active{\textquoteright} and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the {\textquoteright}seed bank{\textquoteright} microbial community.},
	keywords = {2014, Biomarks, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1186/1471-2180-14-110},
	url = {http://www.biomedcentral.com/1471-2180/14/110},
	author = {Chambouvet, Aurelie and Berney, Cedric and Romac, Sarah and Audic, St{\'e}phane and Maguire, Finlay and de Vargas, Colomban and Richards, Thomas}
}
@article {Bendif2014,
	title = {Genetic delineation between and within the widespread coccolithophore morpho-species Emiliania huxleyi and Gephyrocapsa oceanica (Haptophyta)},
	journal = {Journal of Phycology},
	volume = {50},
	year = {2014},
	note = {tex.mendeley-tags: 2014,cc3549,rcc,rcc1210,rcc1213,rcc1220,rcc1227,rcc1229,rcc1242,rcc1252,rcc1253,rcc1258,rcc1259,rcc1260,rcc1271,rcc1281,rcc1288,rcc1292,rcc1297,rcc1300,rcc1303,rcc1305,rcc1316,rcc1562,rcc174,rcc1839,rcc3545,rrcc1247,sbr?hyto?ppo},
	pages = {140{\textendash}148},
	keywords = {2014, cc3549, rcc, rcc1210, RCC1213, rcc1220, rcc1227, rcc1229, RCC1242, rcc1252, RCC1253, rcc1258, RCC1259, rcc1260, rcc1271, RCC1281, rcc1288, RCC1292, rcc1297, RCC1300, RCC1303, RCC1305, RCC1316, RCC1562, rcc174, RCC1839, rcc3545, rrcc1247, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/jpy.12147},
	author = {Bendif, El Mahdi and Probert, Ian and Carmichael, Margaux and Romac, Sarah and Hagino, Kyoko and de Vargas, Colomban}
}
@article {Nezan2014,
	title = {Genetic diversity of the harmful family Kareniaceae (Gymnodiniales, Dinophyceae) in France, with the description of {\textexclamdown}i{\textquestiondown}Karlodinium gentienii{\textexclamdown}/i{\textquestiondown} sp. nov.: A new potentially toxic dinoflagellate},
	journal = {Harmful Algae},
	volume = {40},
	year = {2014},
	note = {tex.mendeley-tags: 2014,rcc,sbr?hyto?app},
	pages = {75{\textendash}91},
	abstract = {A B S T R A C T The family Kareniaceae is mostly known in France for recurrent blooms of Karenia mikimotoi in the Atlantic, English Channel, and Mediterranean Sea and for the unusual green discoloration in the saltwater lagoon of Diana (Corsica) caused by Karlodinium corsicum in April 1994. In terms of diversity, this taxonomic group was long overlooked owing to the difficult identification of these small unarmored dinoflagellates. In this study, thanks to the molecular characterization performed on single cells from field samples and cultures, twelve taxonomic units were assigned to the known genera Karenia, Karlodinium and Takayama, whereas one could not be affiliated to any described genus. The molecular phylogeny inferred from the D1{\textendash}D2 region of the LSU rDNA showed that five of them formed a sister taxon of a known species, and could not be identified at species-level, on the basis of molecular analysis only. Among these latter taxa, one Karlodinium which was successfully cultured was investigated by studying the external morphological features (using two procedures for cells fixation), ultrastructure, pigment composition, and haemolytic activity. The results of our analyses corroborate the genetic results in favour of the erection of Karlodinium gentienii sp. nov., which possesses an internal complex system of trichocysts connected to external micro-processes particularly abundant in the epicone, and a peculiar pigment composition. In addition, preliminary assays showed a haemolytic activity.},
	keywords = {2014, rcc, sbr?hyto?app},
	issn = {15689883},
	doi = {10.1016/j.hal.2014.10.006},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S1568988314001863},
	author = {N{\'e}zan, Elisabeth and Siano, Raffaele and Boulben, Sylviane and Six, Christophe and Bilien, Gwenael and Ch{\`e}ze, Karine and Duval, Audrey and Le Panse, Sophie and Qu{\'e}r{\'e}, Julien and Chom{\'e}rat, Nicolas}
}
@article {Biller2014,
	title = {Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus},
	journal = {Scientific Data},
	volume = {1},
	year = {2014},
	note = {Publisher: Nature Publishing Group tex.mendeley-tags: rcc},
	month = {sep},
	pages = {1{\textendash}11},
	abstract = {The marine cyanobacterium Prochlorococcus is the numerically dominant photosynthetic organism in the oligotrophic oceans, and a model system in marine microbial ecology. Here we report 27 new whole genome sequences (2 complete and closed; 25 of draft quality) of cultured isolates, representing five major phylogenetic clades of Prochlorococcus. The sequenced strains were isolated from diverse regions of the oceans, facilitating studies of the drivers of microbial diversity{\textemdash}both in the lab and in the field. To improve the utility of these genomes for comparative genomics, we also define pre-computed clusters of orthologous groups of proteins (COGs), indicating how genes are distributed among these and other publicly available Prochlorococcus genomes. These data represent a significant expansion of Prochlorococcus reference genomes that are useful for numerous applications in microbial ecology, evolution and oceanography.},
	keywords = {Environmental microbiology, genomics, rcc, RCC?o?dd},
	issn = {2052-4463},
	doi = {10.1038/sdata.2014.34},
	url = {http://www.nature.com/articles/sdata201434},
	author = {Biller, Steven J. and Berube, Paul M. and Berta-Thompson, Jessie W. and Kelly, Libusha and Roggensack, Sara E. and Awad, Lana and Roache-Johnson, Kathryn H. and Ding, Huiming and Giovannoni, Stephen J. and Rocap, Gabrielle and Moore, Lisa R. and Chisholm, Sallie W. and H. and Ding, Huiming and Giovannoni, Stephen J. and Moore, Lisa R. and Chisholm, Sallie W.}
}
@article {Duanmu2014,
	title = {Marine algae and land plants share conserved phytochrome signaling systems},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {111},
	number = {44},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {15827{\textendash}15832},
	abstract = {Phytochrome photosensors control a vast gene network in streptophyte plants, acting as master regulators of diverse growth and developmental processes throughout the life cycle. In contrast with their absence in known chlorophyte algal genomes and most sequenced prasinophyte algal genomes, a phytochrome is found in Micromonas pusilla, a widely distributed marine picoprasinophyte ({\textexclamdown}2 {\textmu}m cell diameter). Together with phytochromes identified from other prasinophyte lineages, we establish that prasinophyte and streptophyte phytochromes share core light-input and signaling-output domain architectures except for the loss of C-terminal response regulator receiver domains in the streptophyte phytochrome lineage. Phylogenetic reconstructions robustly support the presence of phytochrome in the common progenitor of green algae and land plants. These analyses reveal a monophyletic clade containing streptophyte, prasinophyte, cryptophyte, and glaucophyte phytochromes implying an origin in the eukaryotic ancestor of the Archaeplastida. Transcriptomic measurements reveal diurnal regulation of phytochrome and bilin chromophore biosynthetic genes in Micromonas. Expression of these genes precedes both light-mediated phytochrome redistribution from the cytoplasm to the nucleus and increased expression of photosynthesis-associated genes. Prasinophyte phytochromes perceive wavelengths of light transmitted farther through seawater than the red/far-red light sensed by land plant phytochromes. Prasinophyte phytochromes also retain light-regulated histidine kinase activity lost in the streptophyte phytochrome lineage. Our studies demonstrate that light-mediated nuclear translocation of phytochrome predates the emergence of land plants and likely represents a widespread signaling mechanism in unicellular algae.},
	keywords = {Micromonas, rcc},
	doi = {10.1073/pnas.1416751111},
	url = {http://www.pnas.org/content/111/44/15827.abstract},
	author = {Duanmu, Deqiang and Bachy, Charles and Sudek, Sebastian and Wong, Chee-Hong and Jimenez, Valeria and Rockwell, Nathan C and Martin, Shelley S and Ngan, Chew Yee and Reistetter, Emily N and van Baren, Marijke J and Price, Dana C and Wei, Chia-Lin and Reyes-Prieto, Adrian and Lagarias, J Clark and Worden, Alexandra Z}
}
@article {Keeling2014,
	title = {The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing},
	journal = {PLoS biology},
	volume = {12},
	number = {6},
	year = {2014},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2014,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e1001889},
	abstract = {Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world{\textquoteright}s oceans},
	keywords = {2014, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pbio.1001889},
	url = {http://dx.doi.org/10.1371\%252Fjournal.pbio.1001889},
	author = {Keeling, Patrick J and Burki, Fabien and Wilcox, Heather M and Allam, Bassem and Allen, Eric E and Amaral-Zettler, Linda A and Armbrust, E Virginia and Archibald, John M and Bharti, Arvind K and Bell, Callum J and Beszteri, Bank and Bidle, Kay D and Cameron, Connor T and Campbell, Lisa and Caron, David A and Cattolico, Rose Ann and Collier, Jackie L and Coyne, Kathryn and Davy, Simon K and Deschamps, Phillipe and Dyhrman, Sonya T and Edvardsen, Bente and Gates, Ruth D and Gobler, Christopher J and Greenwood, Spencer J and Guida, Stephanie M and Jacobi, Jennifer L and Jakobsen, Kjetill S and James, Erick R and Jenkins, Bethany and John, Uwe and Johnson, Matthew D and Juhl, Andrew R and Kamp, Anja and Katz, Laura A and Kiene, Ronald and Kudryavtsev, Alexander and Leander, Brian S and Lin, Senjie and Lovejoy, Connie and Lynn, Denis and Marchetti, Adrian and McManus, George and Nedelcu, Aurora M and Menden-Deuer, Susanne and Miceli, Cristina and Mock, Thomas and Montresor, Marina and Moran, Mary Ann and Murray, Shauna and Nadathur, Govind and Nagai, Satoshi and Ngam, Peter B and Palenik, Brian and Pawlowski, Jan and Petroni, Giulio and Piganeau, Gwenael and Posewitz, Matthew C and Rengefors, Karin and Romano, Giovanna and Rumpho, Mary E and Rynearson, Tatiana and Schilling, Kelly B and Schroeder, Declan C and Simpson, Alastair G B and Slamovits, Claudio H and Smith, David R and Smith, G Jason and Smith, Sarah R and Sosik, Heidi M and Stief, Peter and Theriot, Edward and Twary, Scott N and Umale, Pooja E and Vaulot, Daniel and Wawrik, Boris and Wheeler, Glen L and Wilson, William H and Xu, Yan and Zingone, Adriana and Worden, Alexandra Z}
}
@article {Morrissey2014,
	title = {A novel protein, ubiquitous in marine phytoplankton, concentrates iron at the cell surface and facilitates uptake},
	journal = {Current Biology},
	volume = {25},
	number = {3},
	year = {2014},
	note = {tex.mendeley-tags: rcc},
	month = {dec},
	pages = {364{\textendash}371},
	abstract = {Numerous cellular functions including respiration require iron. Plants and phytoplankton must also maintain the iron-rich photosynthetic electron transport chain, which most likely evolved in the iron-replete reducing environments of the Proterozoic ocean [1]. Iron bioavailability has drastically decreased in the contemporary ocean [1], most likely selecting for the evolution of efficient iron acquisition mechanisms among modern phytoplankton. Mesoscale iron fertilization experiments often result in blooms dominated by diatoms [2], indicating that diatoms have adaptations that allow survival in iron-limited waters and rapid multiplication when iron becomes available. Yet the genetic and molecular bases are unclear, as very few iron uptake genes have been functionally characterized from marine eukaryotic phytoplankton, and large portions of diatom iron starvation transcriptomes are genes encoding unknown functions [3{\textendash}5]. Here we show that the marine diatom Phaeodactylum tricornutum utilizes ISIP2a to concentrate Fe(III) at the cell surface as part of a novel, copper-independent and thermodynamically controlled iron uptake system. ISIP2a is expressed in response to iron limitation several days prior to the induction of ferrireductase activity, and it facilitates significant Fe(III) uptake during the initial response to Fe limitation. ISIP2a is able to directly bind Fe(III) and increase iron uptake when heterologously expressed, whereas knockdown of ISIP2a in P. tricornutum decreases iron uptake, resulting in impaired growth and chlorosis during iron limitation. ISIP2a is expressed by diverse marine phytoplankton, indicating that it is an ecologically significant adaptation to the unique nutrient composition of marine environments.},
	keywords = {rcc},
	issn = {09609822},
	doi = {10.1016/j.cub.2014.12.004},
	url = {http://www.sciencedirect.com/science/article/pii/S0960982214015632},
	author = {Morrissey, Joe and Sutak, Robert and Paz-Yepes, Javier and Tanaka, Atsuko and Moustafa, Ahmed and Veluchamy, Alaguraj and Thomas, Yann and Botebol, Hugo and Bouget, Fran{\c c}ois-Yves and McQuaid, Jeffrey B. and Tirichine, Leila and Allen, Andrew E. and Lesuisse, Emmanuel and Bowler, Chris}
}
@article {DelCampo2014,
	title = {The others: our biased perspective of eukaryotic genomes},
	journal = {Trends in Ecology \& Evolution},
	volume = {29},
	number = {5},
	year = {2014},
	note = {Publisher: Elsevier tex.mendeley-tags: RCC,rcc},
	pages = {252{\textendash}259},
	abstract = {?There is an important bias in eukaryotic knowledge, affecting cultures and genomes.?Eukaryotic genomics are biased towards multicellular organisms and their parasites.?A phylogeny-driven initiative is needed to overcome the eukaryotic genomic bias.?We propose to sequence neglected cultures and increase culturing efforts.?Single-cell genomics should be embraced as a tool to explore eukaryotic diversity.},
	keywords = {rcc},
	doi = {10.1016/j.tree.2014.03.006},
	url = {http://www.cell.com/trends/ecology-evolution/abstract/S0169-5347(14)00064-0},
	author = {del Campo, Javier and Sieracki, Michael E and Molestina, Robert and Keeling, Patrick and Massana, Ramon and Ruiz-Trillo, I{\~n}aki}
}
@article {Lepelletier2014,
	title = {Parvilucifera rostrata sp. nov., a novel parasite in the phylum Perkinsozoa that infects the toxic dinoflagellate Alexandrium minutum (Dinophyceae)},
	journal = {Protist},
	volume = {165},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {31{\textendash}49},
	keywords = {2014, MACUMBA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.1016/j.protis.2013.09.005},
	author = {Lepelletier, F and Karpov, S A and Le Panse, S and Bigeard, E and Skovgaard, A and Jeanthon, C and Guillou, L}
}
@article {Dia2014,
	title = {Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum},
	journal = {Molecular Ecology},
	volume = {23},
	number = {3},
	year = {2014},
	note = {tex.mendeley-tags: 2014,macumba,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {549{\textendash}560},
	abstract = {Organisms with sexual and asexual reproductive systems benefit from both types of reproduction. Sexual recombination generates new combinations of alleles, whereas clonality favours the spread of the fittest genotype through the entire population. Therefore, the rate of sexual vs. clonal reproduction has a major influence on the demography and genetic structure of natural populations. We addressed the effect of reproductive system on populations of the dinoflagellate Alexandrium minutum. More specifically, we monitored the spatiotemporal genetic diversity during and between bloom events in two estuaries separated by 150 km for two consecutive years. An analysis of population genetic patterns using microsatellite markers revealed surprisingly high genotypic and genetic diversity. Moreover, there was significant spatial and temporal genetic differentiation during and between bloom events. Our results demonstrate that (i) interannual genetic differentiation can be very high, (ii) estuaries are partially isolated during bloom events and (iii) genetic diversity can change rapidly during a bloom event. This rapid genetic change may reflect selective effects that are nevertheless not strong enough to reduce allelic diversity. Thus, sexual reproduction and/or migration may regularly erase any genetic structure produced within estuaries during a bloom event.},
	keywords = {2014, bloom dynamics, clonality, linkage disequilibrium, MACUMBA, population genetics, rcc, RCC?o?dd, resting cyst, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sexual reproduction},
	doi = {10.1111/mec.12617},
	url = {http://dx.doi.org/10.1111/mec.12617},
	author = {Dia, A and Guillou, L and Mauger, S and Bigeard, E and Marie, D and Valero, M and Destombe, C}
}
@article {Clerissi2014,
	title = {Unveiling of the diversity of prasinoviruses (phycodnaviridae) in marine samples by using high-throughput sequencing analyses of PCR-Amplified DNA polymerase and major capsid protein genes},
	journal = {Applied and Environmental Microbiology},
	volume = {80},
	number = {10},
	year = {2014},
	note = {tex.mendeley-tags: Micromonas,rcc},
	pages = {3150{\textendash}3160},
	abstract = {Viruses strongly influence the ecology and evolution of their eukaryotic hosts in the marine environment, but little is known about their diversity and distribution. Prasinoviruses infect an abundant and widespread class of phytoplankton, the Mamiellophyceae, and thereby exert a specific and important role in microbial ecosystems. However, molecular tools to specifically identify this viral genus in environmental samples are still lacking. We developed two primer sets, designed for use with polymerase chain reactions and 454 pyrosequencing technologies, to target two conserved genes, encoding the DNA polymerase (PolB gene) and the major capsid protein (MCP gene). While only one copy of the PolB gene is present in Prasinovirus genomes, there are at least seven paralogs for MCP, the copy we named number 6 being shared with other eukaryotic alga-infecting viruses. Primer sets for PolB and MCP6 were thus designed and tested on 6 samples from the Tara Oceans project. The results suggest that the MCP6 amplicons show greater richness but that PolB gave a wider coverage of Prasinovirus diversity. As a consequence, we recommend use of the PolB primer set, which will certainly reveal exciting new insights about the diversity and distribution of prasinoviruses at the community scale.},
	keywords = {Micromonas, rcc, TARA-Oceans},
	doi = {10.1128/aem.00123-14},
	url = {http://aem.asm.org/content/80/10/3150.abstract},
	author = {Clerissi, Camille and Grimsley, Nigel and Ogata, Hiroyuki and Hingamp, Pascal and Poulain, Julie and Desdevises, Yves}
}
@article {Abida2013,
	title = {Bioprospecting marine plankton},
	journal = {Marine Drugs},
	volume = {11},
	number = {11},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {4594{\textendash}4611},
	keywords = {2013, MicroB3, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.3390/md11114594},
	url = {http://www.mdpi.com/1660-3397/11/11/4594},
	author = {Abida, Heni and Ruchaud, Sandrine and Rios, Laurent and Humeau, Anne and Probert, Ian and de Vargas, Colomban and Bach, St{\'e}phane and Bowler, Chris}
}
@article {Rousseau2013,
	title = {Characterization of {\textexclamdown}i{\textquestiondown}Phaeocystis globosa{\textexclamdown}/i{\textquestiondown} (haptophyceae), the blooming species in the southern north sea},
	journal = {Journal of Sea Research},
	volume = {76},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {105{\textendash}113},
	keywords = {2013, ASSEMBLE, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, Souchotheque},
	doi = {10.1016/j.seares.2012.07.011},
	author = {Rousseau, V and Lantoine, F and Rodriguez, F and Le Gall, F and Chr{\'e}tiennot-Dinet, M.-J. and Lancelot, C}
}
@article {Bendif2013,
	title = {On the description of Tisochrysis lutea gen . nov . sp . nov . and Isochrysis nuda sp. nov. in the Isochrysidales, and the transfer of Dicrateria to the Prymnesiales (Haptophyta)},
	journal = {Journal of Applied Phycology},
	volume = {25},
	year = {2013},
	note = {tex.mendeley-tags: 2013,RCC1195,RCC1207,RCC1281,RCC1286,RCC1344,RCC1346,RCC1347,RCC1348,RCC1349,RCC1350,RCC1353,RCC2477,RCC3681,RCC3684,RCC3686,RCC3687,RCC3690,RCC3691,RCC3692,RCC3693,RCC3694,RCC3695,RCC3696,RCC3699,RCC3701,RCC3707,rcc,sbr?hyto?ppo},
	pages = {1763{\textendash}1776},
	keywords = {2013, dicrateria, imantonia, isochrysidaceae, isochrysis galbana, phylogeny, rcc, RCC1195, RCC1207, RCC1281, RCC1286, RCC1344, RCC1346, RCC1347, RCC1348, RCC1349, RCC1350, RCC1353, RCC2477, RCC3681, RCC3684, RCC3686, RCC3687, RCC3690, RCC3691, RCC3692, RCC3693, RCC3694, RCC3695, RCC3696, RCC3699, RCC3701, RCC3707, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, taxonomy, ultrastructure},
	doi = {10.1007/s10811-013-0037-0},
	author = {Bendif, El Mahdi and Probert, Ian and Schroeder, Declan C and de Vargas, Colomban}
}
@article {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 {Subirana2013,
	title = {Morphology, genome plasticity, and phylogeny in the genus ostreococcus reveal a cryptic species, o. mediterraneus sp. nov. (mamiellales, mamiellophyceae)},
	journal = {Protist},
	volume = {164},
	number = {5},
	year = {2013},
	note = {tex.mendeley-tags: RCC1112,RCC1114,RCC1117,RCC143,RCC1620,RCC1621,RCC1623,RCC1624,RCC2572,RCC2573,RCC2574,RCC2575,RCC2577,RCC2578,RCC2579,RCC2582,RCC2583,RCC2584,RCC2585,RCC2587,RCC2590,RCC344,RCC356,RCC393,RCC501,RCC745,RCC809},
	pages = {643{\textendash}659},
	abstract = {Coastal marine waters in many regions worldwide support abundant populations of extremely small (1-3 ??m diameter) unicellular eukaryotic green algae, dominant taxa including several species in the class Mamiellophyceae. Their diminutive size conceals surprising levels of genetic diversity and defies classical species{\textquoteright} descriptions. We present a detailed analysis within the genus Ostreococcus and show that morphological characteristics cannot be used to describe diversity within this group. Karyotypic analyses of the best-characterized species O. tauri show it to carry two chromosomes that vary in size between individual clonal lines, probably an evolutionarily ancient feature that emerged before species{\textquoteright} divergences within the Mamiellales. By using a culturing technique specifically adapted to members of the genus Ostreococcus, we purified {\textquestiondown}30 clonal lines of a new species, Ostreococcus mediterraneus sp. nov., previously known as Ostreococcus clade D, that has been overlooked in several studies based on PCR-amplification of genetic markers from environment-extracted DNA. Phylogenetic analyses of the S-adenosylmethionine synthetase gene, and of the complete small subunit ribosomal RNA gene, including detailed comparisons of predicted ITS2 (internal transcribed spacer 2) secondary structures, clearly support that this is a separate species. In addition, karyotypic analyses reveal that the chromosomal location of its ribosomal RNA gene cluster differs from other Ostreococcus clades.},
	keywords = {barcode, Chromosome, culture, ITS2, karyotype, picoeukaryote, rcc, RCC1112, RCC1114, RCC1117, RCC143, RCC1620, RCC1621, RCC1623, RCC1624, RCC2572, RCC2573, RCC2574, RCC2575, RCC2577, RCC2578, RCC2579, RCC2582, RCC2583, RCC2584, RCC2585, RCC2587, RCC2590, RCC344, RCC356, RCC393, rcc501, RCC745, RCC809, ribosomal gene},
	doi = {10.1016/j.protis.2013.06.002},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461013000497},
	author = {Subirana, Lucie and P{\'e}quin, B{\'e}rang{\`e}re and Michely, St{\'e}phanie and Escande, Marie-Line and Meilland, Julie and Derelle, Evelyne and Marin, Birger and Piganeau, Gwenael and Desdevises, Yves and Moreau, Herv{\'e} and Grimsley, Nigel H}
}
@article {Blanc-Mathieu2013,
	title = {Organellar inheritance in the green lineage: Insights from ostreococcus tauri},
	journal = {Genome Biology and Evolution},
	volume = {5},
	number = {8},
	year = {2013},
	note = {tex.mendeley-tags: RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC745},
	pages = {1503{\textendash}1511},
	abstract = {Along the green lineage (Chlorophyta and Streptophyta), mitochondria and chloroplast are mainly uniparentally transmitted and their evolution is thus clonal. The mode of organellar inheritance in their ancestor is less certain. The inability to make clear phylogenetic inference is partly due to a lack of information for deep branching organisms in this lineage. Here, we investigate organellar evolution in the early branching green alga Ostreococcus tauri using population genomics data from the complete mitochondrial and chloroplast genomes. The haplotype structure is consistent with clonal evolution in mitochondria, while we find evidence for recombination in the chloroplast genome. The number of recombination events in the genealogy of the chloroplast suggests that recombination, and thus biparental inheritance, is not rare. Consistent with the evidence of recombination, we find that the ratio of the number of nonsynonymous to the synonymous polymorphisms per site is lower in chloroplast than in the mitochondria genome. We also find evidence for the segregation of two selfish genetic elements in the chloroplast. These results shed light on the role of recombination and the evolutionary history of organellar inheritance in the green lineage.},
	keywords = {rcc, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC745},
	doi = {10.1093/gbe/evt106},
	url = {http://gbe.oxfordjournals.org/content/5/8/1503.abstract},
	author = {Blanc-Mathieu, Romain and Sanchez-Ferandin, Sophie and Eyre-Walker, Adam and Piganeau, Gwenael}
}
@article {Shukla2013,
	title = {Phycoerythrin-specific bilin lyase{\textendash}isomerase controls blue-green chromatic acclimation in marine Synechococcus},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto?app},
	pages = {20136{\textendash}20141},
	keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1073/pnas.1211777109},
	author = {Shukla, A and Biswas, A and Blot, N and Partensky, F and Karty, J A and Hammad, L A and Garczarek, L and Gutu, A and Schluchter, W M and Kehoe, D M}
}
@article {Vandepoele2013,
	title = {pico-PLAZA, a genome database of microbial photosynthetic eukaryotes},
	journal = {Environmental Microbiology},
	volume = {15},
	number = {8},
	year = {2013},
	note = {tex.mendeley-tags: Micromonas,rcc},
	pages = {2147{\textendash}2153},
	abstract = {With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/1462-2920.12174},
	url = {http://dx.doi.org/10.1111/1462-2920.12174},
	author = {Vandepoele, Klaas and Van Bel, Michiel and Richard, Guilhem and Van Landeghem, Sofie and Verhelst, Bram and Moreau, Herv{\'e} and Van de Peer, Yves and Grimsley, Nigel and Piganeau, Gwenael}
}
@article {Guillou2013,
	title = {The protist ribosomal reference database (PR2): a catalog of unicellular eukaryote small SubUnit rRNA sequences with curated taxonomy},
	journal = {Nucleic Acids Research},
	volume = {41},
	year = {2013},
	note = {tex.mendeley-tags: 2013,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {D597{\textendash}D604},
	keywords = {2013, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1093/nar/gks1160},
	author = {Guillou, Laure and Bachar, Dipankar and Audic, St{\'e}phane and Bass, David and Berney, Cedric and Bittner, Lucie and Boutte, Christophe and Burgaud, Gaetan and de Vargas, Colomban and Decelle, Johan and del Campo, Javier and Dolan, John and Dunthorn, Micah and Bente, Edvardsen and Holzmann, Maria and Kooistra, Wiebe H C F and Lara, Enrique and Lebescot, Noan and Logares, Ramiro and Mah{\'e}, Fr{\'e}d{\'e}ric and Massana, Ramon and Montresor, Marina and Morard, Raphael and Not, Fabrice and Pawlowski, Jan and Probert, Ian and Sauvadet, Anne-Laure and Siano, Raffaele and Stoeck, Thorsten and Vaulot, Daniel and Zimmermann, Pascal and Christen, Richard}
}
@article {Drescher2012,
	title = {Coccolithogenesis in scyphosphaera apsteinii (prymnesiophyceae)},
	journal = {Journal of Phycology},
	volume = {48},
	number = {6},
	year = {2012},
	note = {tex.mendeley-tags: RCC1456},
	pages = {1343{\textendash}1361},
	abstract = {Coccolithophores are the most significant producers of marine biogenic calcite, although the intracellular calcification process is poorly understood. In the case of Scyphosphaera apsteinii Lohmann 1902, flat ovoid muroliths and bulky, vase-shaped lopadoliths with a range of intermediate morphologies may be produced by a single cell. This polymorphic species is within the Zygodiscales, a group that remains understudied with respect to ultrastructure and coccolith ontogeny. We therefore undertook an analysis of cell ultrastructure, morphology, and coccolithogenesis. The cell ultrastructure showed many typical haptophyte features, with calcification following a similar pattern to that described for other heterococcolith bearing species including Emiliania huxleyi. Of particular significance was the reticular body role in governing fine-scale morphology, specifically the central pore formation of the coccolith. Our observations also highlighted the essential role of the inter- and intracrystalline organic matrix in growth and arrangement of the coccolith calcite. S. apsteinii secreted mature coccoliths that attached to the plasma membrane via fibrillar material. Time-lapse light microscopy demonstrated secretion of lopadoliths occurred base first before being actively repositioned at the cell surface. Significantly, growth irradiance influenced the coccosphere composition with fewer lopadoliths being formed relative to muroliths at higher light intensities. Overall, our observations support dynamic metabolic (i.e., in response to growth irradiance), sensory and cytoskeletal control over the morphology and secretion of polymorphic heterococcoliths. With a basic understanding of calcification established, S. apsteinii could be a valuable model to further study coccolithophore calcification and cell physiological responses to ocean acidification.},
	keywords = {Calcification, coccolithogenesis, coccolithophore, organic matrix, rcc, RCC1456, reticular body, secretion, ultrastructure, Zygodiscales},
	doi = {10.1111/j.1529-8817.2012.01227.x},
	url = {http://dx.doi.org/10.1111/j.1529-8817.2012.01227.x},
	author = {Drescher, Brandon and Dillaman, Richard M and Taylor, Alison R}
}
@article {Balzano2012,
	title = {Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples},
	journal = {The ISME journal},
	volume = {6},
	number = {8},
	year = {2012},
	note = {ISBN: 1751-7362 tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {1480{\textendash}1498},
	abstract = {The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture.},
	keywords = {2012, ASSEMBLE, Chaetoceros, MALINA, Pyramimonas, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, Souchotheque},
	issn = {1751-7362},
	doi = {10.1038/ismej.2011.213},
	author = {Balzano, Sergio and Marie, Dominique and Gourvil, Priscillia and Vaulot, Daniel}
}
@article {Balzano2012a,
	title = {Diversity of cultured photosynthetic flagellates in the North East Pacific and Arctic Oceans in summer},
	journal = {Biogeosciences},
	volume = {9},
	year = {2012},
	note = {tex.mendeley-tags: 2012,macumba,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {4553{\textendash}4571},
	keywords = {2012, ASSEMBLE, MACUMBA, MALINA, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.5194/bg-9-4553-2012},
	author = {Balzano, Sergio and Gourvil, Priscillia and Siano, Raffaele and Chanoine, M{\'e}lanie and Marie, Dominique and Lessard, Sylvie and Sarno, Diana and Vaulot, Daniel}
}
@article {Stern2012,
	title = {Evaluating the ribosomal internal transcribed spacer (ITS) as a candidate dinoflagellate barcode marker},
	journal = {PLoS ONE},
	volume = {7},
	year = {2012},
	note = {tex.mendeley-tags: 2012,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e42780},
	keywords = {2012, ASSEMBLE, Barcoding, ITS, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pone.0042780},
	url = {http://www.plosone.org/article/info\%253Adoi\%252F10.1371\%252Fjournal.pone.0042780},
	author = {Stern, Rowena F and Andersen, Robert A and Jameson, Ian and K{\"u}pper, Frithjof C and Coffroth, Mary-Alice and Vaulot, Daniel and Gall, Florence Le and Veron, Benoit and Brand, Jerry J and Skelton, Hayley and Kasai, Fumai and Lilly, Emily L and Keeling, Patrick J}
}
@article {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 {Zeng2012,
	title = {Marine viruses exploit their host{\textquoteright}s two-component regulatory system in response to resource limitation},
	journal = {Current Biology},
	year = {2012},
	note = {Publisher: Cell Press tex.mendeley-tags: rcc},
	abstract = {Phosphorus (P) availability, which often limits productivity in marine ecosystems, shapes the P-acquisition gene content of the marine cyanobacteria Prochlorococcus [1 4] and its viruses (cyanophages) [5, 6]. As in other bacteria, in Prochlorococcus these genes are regulated by the PhoR/PhoB two-component regulatory system that is used to sense and respond to P availability and is typical of signal transduction systems found in diverse organisms [7]. Replication of cyanophage genomes requires a significant amount of P, and therefore these phages could gain a fitness advantage by influencing host P acquisition in P-limited environments. Here we show that the transcription of a phage-encoded high-affinity phosphate-binding protein gene (pstS) and alkaline phosphatase gene (phoA) both of which have host orthologs is elevated when the phages are infecting host cells that are P starved, relative to P-replete control cells. We further show that the phage versions of these genes are regulated by the host{\textquoteright}s PhoR/PhoB system. This not only extends this fundamental signaling mechanism to viruses but is also the first example of regulation of lytic phage genes by nutrient limitation in the host. As such, it reveals an important new dimension of the intimate coevolution of phage, host, and environment in the world{\textquoteright}s oceans. {\textordmasculine} Phage production, but not lytic cycle, is reduced in P-starved host cells {\textordmasculine} Transcription of phage P acquisition genes is upregulated in P-starved hosts {\textordmasculine} Phage P-acquisition genes are regulated by the host PhoR/PhoB two-component system {\textordmasculine} This is the first incidence of regulation of virus genes by a two-component system},
	keywords = {NATL2A, rcc, RCC?o?dd},
	doi = {10.1016/j.cub.2011.11.055},
	url = {http://linkinghub.elsevier.com/retrieve/pii/S0960982211013704},
	author = {Zeng, Qinglu and Chisholm, Sallie W}
}
@article {Decelle2012,
	title = {An original mode of symbiosis in open ocean plankton},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {109},
	year = {2012},
	note = {tex.mendeley-tags: 2012,rcc,sbr?hyto?ppo},
	pages = {18000{\textendash}18005},
	keywords = {2012, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.1212303109},
	author = {Decelle, J and Probert, I and Bittner, L and Desdevises, Y and Colin, S and de Vargas, C and Gali, M and Simo, R and Not, F}
}
@article {Monier2012,
	title = {Phosphate transporters in marine phytoplankton and their viruses: cross-domain commonalities in viral-host gene exchanges},
	journal = {Environmental Microbiology},
	volume = {14},
	number = {1},
	year = {2012},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {162{\textendash}176},
	abstract = {Phosphate (PO4) is an important limiting nutrient in marine environments. Marine cyanobacteria scavenge PO4 using the high-affinity periplasmic phosphate binding protein PstS. The pstS gene has recently been identified in genomes of cyanobacterial viruses as well. Here, we analyse genes encoding transporters in genomes from viruses that infect eukaryotic phytoplankton. We identified inorganic PO4 transporter-encoding genes from the PHO4 superfamily in several virus genomes, along with other transporter-encoding genes. Homologues of the viral pho4 genes were also identified in genome sequences from the genera that these viruses infect. Genome sequences were available from host genera of all the phytoplankton viruses analysed except the host genus Bathycoccus. Pho4 was recovered from Bathycoccus by sequencing a targeted metagenome from an uncultured Atlantic Ocean population. Phylogenetic reconstruction showed that pho4 genes from pelagophytes, haptophytes and infecting viruses were more closely related to homologues in prasinophytes than to those in what, at the species level, are considered to be closer relatives (e.g. diatoms). We also identified PHO4 superfamily members in ocean metagenomes, including new metagenomes from the Pacific Ocean. The environmental sequences grouped with pelagophytes, haptophytes, prasinophytes and viruses as well as bacteria. The analyses suggest that multiple independent pho4 gene transfer events have occurred between marine viruses and both eukaryotic and bacterial hosts. Additionally, pho4 genes were identified in available genomes from viruses that infect marine eukaryotes but not those that infect terrestrial hosts. Commonalities in marine host-virus gene exchanges indicate that manipulation of host-PO4 uptake is an important adaptation for viral proliferation in marine systems. Our findings suggest that PO4-availability may not serve as a simple bottom-up control of marine phytoplankton.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/j.1462-2920.2011.02576.x},
	url = {http://dx.doi.org/10.1111/j.1462-2920.2011.02576.x},
	author = {Monier, Adam and Welsh, Rory M and Gentemann, Chelle and Weinstock, George and Sodergren, Erica and Armbrust, E Virginia and Eisen, Jonathan A and Worden, Alexandra Z}
}
@article {Treusch2012,
	title = {Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids},
	journal = {The ISME journal},
	volume = {6},
	year = {2012},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {481{\textendash}492},
	keywords = {Bathycoccus, CHRYSOPHYCEAE, key?aper, Micromonas, Ostreococcus, pelagophyceae, Prasinophyceae, Prymnesiophyceae, QPCR, rcc, TRFLP},
	doi = {10.1038/ismej.2011.117},
	url = {http://dx.doi.org/10.1038/ismej.2011.117 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2011117s1.html},
	author = {Treusch, Alexander H and Demir-Hilton, Elif and Vergin, Kevin L and Worden, Alexandra Z and Carlson, Craig A and Donatz, Michael G and Burton, Robert M and Giovannoni, Stephen J}
}
@article {Clerissi2012,
	title = {Prasinoviruses of the marine green alga Ostreococcus tauri are mainly species specific},
	journal = {Journal of Virology},
	volume = {86},
	number = {8},
	year = {2012},
	note = {tex.mendeley-tags: RCC1110,RCC1114,RCC1115,RCC1116,RCC1117,RCC1123,RCC1558,RCC1561,RCC745},
	pages = {4611{\textendash}4619},
	abstract = {Prasinoviruses infecting unicellular green algae in the order Mamiellales (class Mamiellophyceae) are commonly found in coastal marine waters where their host species frequently abound. We tested 40 Ostreococcus tauri viruses on 13 independently isolated wild-type O. tauri strains, 4 wild-type O. lucimarinus strains, 1 Ostreococcus sp. ({\textquotedblleft}Ostreococcus mediterraneus{\textquotedblright}) clade D strain, and 1 representative species of each of two other related species of Mamiellales, Bathycoccus prasinos and Micromonas pusilla. Thirty-four out of 40 viruses infected only O. tauri, 5 could infect one other species of the Ostreococcus genus, and 1 infected two other Ostreococcus spp., but none of them infected the other genera. We observed that the overall susceptibility pattern of Ostreococcus strains to viruses was related to the size of two host chromosomes known to show intraspecific size variations, that genetically related viruses tended to infect the same host strains, and that viruses carrying inteins were strictly strain specific. Comparison of two complete O. tauri virus proteomes revealed at least three predicted proteins to be candidate viral specificity determinants.},
	keywords = {rcc, RCC1110, RCC1114, RCC1115, RCC1116, RCC1117, RCC1123, RCC1558, RCC1561, RCC745},
	issn = {0022-538X},
	doi = {10.1128/jvi.07221-11},
	url = {http://jvi.asm.org/content/86/8/4611.abstract},
	author = {Clerissi, Camille and Desdevises, Yves and Grimsley, Nigel}
}
@article {Kulk2012,
	title = {Temperature-dependent growth and photophysiology of prokaryotic and eukaryotic oceanic picophytoplankton},
	journal = {Marine Ecology Progress Series},
	volume = {466},
	year = {2012},
	note = {tex.mendeley-tags: RCC407,RCC410,RCC879},
	pages = {43{\textendash}55},
	abstract = {ABSTRACT: It is expected that climate change will expand the open oligotrophic oceans by enhanced thermal stratification. Because temperature defines the geographic distribution of picophytoplankton in open-ocean ecosystems and regulates photophysiological responses, it is important to understand how temperature affects picophytoplankton growth and photophysiology. Two prokaryotic and 2 eukaryotic picophytoplankton strains were acclimated to 3 different temperatures, ranging from 16 to 24{\textdegree}C. Temperature-dependent growth and photophysiology were assessed by measurements of specific growth rates, cell size, pigment composition, absorption and electron transport rates. Growth of Prochlorococcus marinus (eMED4), Prochlorococcus sp. (eMIT9313), Ostreococcus sp. (clade B) and Pelagomonas calceolata was positively related to temperature, especially in the prokaryotic strains. Changes in photophysiology included increased light harvesting, increased electron transport and reduced photoinhibition at elevated temperatures. However, the changes related to light harvesting and electron transport could not fully explain the observed difference in growth. This suggests that other processes, such as Calvin cycle activity, are likely to limit growth at sub-optimal temperatures in these picophytoplankton strains. The overall changes in photophysiology during temperature acclimation will possibly allow photosynthesis at higher irradiance intensities, but the genetically defined low temperature tolerances and photosynthetic characteristics of the different ecotypes will likely be more important in determining picophytoplankton (depth) distribution and community composition.},
	keywords = {Absorption, Electron transport rate, Eukaryotic picophytoplankton, Growth, Pigment, Prochlorococcus, rcc, RCC407, rcc410, RCC879, temperature},
	issn = {01718630},
	doi = {10.3354/meps09898},
	url = {http://www.int-res.com/abstracts/meps/v466/p43-55/},
	author = {Kulk, Gemma and De Vries, Pablo and Van De Poll, Willem H. and Visser, Ronald J W and Buma, Anita G J}
}
@article {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 {Kirkham2011,
	title = {Basin-scale distribution patterns of photosynthetic picoeukaryotes along an Atlantic Meridional Transect},
	journal = {Environmental Microbiology},
	volume = {13},
	number = {4},
	year = {2011},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {975{\textendash}990},
	abstract = {Summary Photosynthetic picoeukaryotes (PPEs) of a size {\textexclamdown} 3 {\textmu}m play a crucial role in oceanic primary production. However, little is known of the structure of the PPE community over large spatial scales. Here, we investigated the distribution of various PPE classes along an Atlantic Meridional Transect sampled in boreal autumn 2004 that encompasses a range of ocean provinces (gyres, upwelling, temperate regions), using dot blot hybridization technology targeting plastid 16S rRNA gene amplicons. Two algal classes, Prymnesiophyceae and Chrysophyceae, dominated the PPE community throughout the Atlantic Ocean, over a range of water masses presenting different trophic profiles. However, these classes showed strongly complementary distributions with Chrysophyceae dominating northern temperate waters, the southern gyre and equatorial regions, while prymnesiophytes dominated the northern gyre. Phylogenetic analyses using both plastid and nuclear rRNA genes revealed a high diversity among members of both classes, including sequences contained in lineages with no close cultured counterpart. Other PPE classes were less prevalent along the transect, with members of the Cryptophyceae, Pelagophyceae and Eustigmatophyceae essentially restricted to specific regions. Multivariate statistical analyses revealed strong relationships between the distribution patterns of some of these latter PPE classes and temperature, light intensity and nutrient concentrations. Cryptophyceae, for example, were mostly found in the upwelling region and associated with higher nutrient concentrations. However, the key classes of Prymnesiophyceae and Chrysophyceae were not strongly influenced by the variables measured. Although there appeared to be a positive relationship between Chrysophyceae distribution and light intensity, the complementary distributions of these classes could not be explained by the variables recorded and this requires further explanation.},
	keywords = {Micromonas, rcc},
	doi = {10.1111/j.1462-2920.2010.02403.x},
	url = {http://dx.doi.org/10.1111/j.1462-2920.2010.02403.x},
	author = {Kirkham, Amy R and Jardillier, Ludwig E and Tiganescu, Ana and Pearman, John and Zubkov, Mikhail V and Scanlan, David J}
}
@article {Guillou2011,
	title = {Characterization of the Parmales: much more than the resolution of a taxonomic enigma},
	journal = {Journal of Phycology},
	volume = {47},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {2{\textendash}4},
	keywords = {2011, rcc, SBR$_\textrmP$hyto, sbr?hyto$_\textrmd$ipo},
	doi = {10.1111/j.1529-8817.2010.00951.x},
	author = {Guillou, L}
}
@article {Langer2011a,
	title = {CO2 mediation of adverse effects of seawater acidification in Calcidiscus leptoporus},
	journal = {Geochemistry Geophysics Geosystems},
	volume = {12},
	number = {5},
	year = {2011},
	note = {ISBN: 1525-2027 tex.mendeley-tags: 2011,RCC1135,rcc},
	pages = {1{\textendash}8},
	abstract = {The coccolithophore Calcidiscus leptoporus (strain RCC1135) was grown in dilute batch culture at CO2 levels ranging from \~200 to \~1600 matm. Increasing CO2 concentration led to an increased percentage of malformed coccoliths and eventually (at \~1500 matm CO2) to aggregation of cells. Carbonate chemistry of natural seawater was manipulated in three ways: first, addition of acid; second, addition of a HCO3 -/CO3 2- solution; and third, addition of both acid and HCO3 -/CO32- solution. The data set allowed the disentangling of putative effects of the different parameters of the carbonate system. It is concluded that CO2 is the parameter of the carbonate system which causes both aberrant coccolithogenesis and aggregation of cells.},
	keywords = {2011, Calcification, coccolithophores, morphology, ocean acidification., rcc, RCC1135},
	issn = {1525-2027},
	doi = {10.1029/2010GC003393},
	url = {http://www.agu.org/pubs/crossref/2011/2010GC003393.shtml},
	author = {Langer, Gerald and Bode, Maya}
}
@article {Reid2011,
	title = {Coccolithophores: Functional biodiversity, enzymes and bioprospecting},
	journal = {Marine Drugs},
	volume = {9},
	number = {4},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc},
	pages = {586{\textendash}602},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.3390/md9040586},
	url = {http://www.mdpi.com/1660-3397/9/4/586/},
	author = {Reid, Emma L and Worthy, Charlotte A and Probert, Ian and Ali, Sohail T and Love, John and Napier, Johnathan and Littlechild, Jenny A and Somerfield, Paul J and Allen, Michael J}
}
@article {Jeanthon2011,
	title = {Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea},
	journal = {Biogeosciences},
	volume = {8},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {1955{\textendash}1970},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.5194/bg-8-1955-2011},
	author = {Jeanthon, Christian and Boeuf, Dominique and Dahan, Oc{\'e}ane and Le Gall, F and Garczarek, Laurence and Bendif, El Mahdi and Lehours, Anne-Catherine}
}
@article {Demir-Hilton2011,
	title = {Global distribution patterns of distinct clades of the photosynthetic picoeukaryote Ostreococcus},
	journal = {The ISME journal},
	volume = {5},
	year = {2011},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: RCC745},
	pages = {1095{\textendash}1107},
	keywords = {rcc, RCC745},
	doi = {10.1038/ismej.2010.209},
	url = {http://dx.doi.org/10.1038/ismej.2010.209 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej2010209s1.html http://www.nature.com/ismej/journal/v5/n7/full/ismej2010209a.html},
	author = {Demir-Hilton, Elif and Sudek, Sebastian and Cuvelier, Marie L and Gentemann, Chelle L and Zehr, Jonathan P and Worden, Alexandra Z}
}
@article {Ota2011,
	title = {Gymnochlora dimorpha sp. nov., a chlorarachniophyte with unique daughter cell behaviour.},
	journal = {Phycologia},
	volume = {50},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {317{\textendash}326},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.2216/09-102.1},
	author = {Ota, S and Kudo, A and Ishida, K}
}
@article {Bendif2011,
	title = {Integrative taxonomy of the pavlovophyceae (haptophyta) : a reassessment},
	journal = {Protist},
	volume = {162},
	year = {2011},
	note = {tex.mendeley-tags: 2011,RCC1526,RCC1527,RCC1528,RCC1529,RCC1530,RCC1531,RCC1532,RCC1533,RCC1534,RCC1535,RCC1536,RCC1537,RCC1538,RCC1539,RCC1540,RCC1541,RCC1542,RCC1543,RCC1544,RCC1545,RCC1546,RCC1548,RCC1549,RCC1551,RCC1552,RCC1553,RCC1554,RCC1557,rcc,rcc1523,rcc1524,rcc1525},
	pages = {738{\textendash}761},
	abstract = {The Pavlovophyceae (Haptophyta) contains four genera (Pavlova, Diacronema, Exanthemachrysis and Rebecca) and only thirteen characterised species. Considering the importance of members of this class, we constructed molecular phylogenies inferred from sequencing of ribosomal gene markers with comprehensive coverage of the described diversity and using type strains when available add on culture strains. Moreover, the morphology and ultrastructure of 12 of the described species was re-examined and the pigment signatures of many culture strains were determined. The molecular analysis revealed that sequences of all described species differed, although those of Pavlova gyrans and P. pinguis were nearly identical, these potentially forming a single cryptic species complex. Four well-delineated genetic clades were identified, one of which included species of both Pavlova andDiacronema. Unique combinations of morphological/ultrastructural characters were identified foreach of these clades. The ancestral pigment signature of the Pavlovophyceae consisted of a basic set of pigments plus MV chl cPAV, the latter being entirely absent in the Pavlova + Diacronema clade and supplemented by DV chl cPAV in part of the Exanthemachrysis clade. Based on this combination of characters, we propose a taxonomic revision of the class, with transfer of several Pavlova species to an emended Diacronema genus. The evolution of the class is discussed in the context of the phylogenetic reconstruction presented.},
	keywords = {2011, ASSEMBLE, rcc, RCC1523, rcc1524, rcc1525, RCC1526, RCC1527, RCC1528, RCC1529, RCC1530, RCC1531, RCC1532, RCC1533, RCC1534, RCC1535, RCC1536, RCC1537, RCC1538, RCC1539, RCC1540, RCC1541, RCC1542, RCC1543, RCC1544, RCC1545, RCC1546, RCC1548, RCC1549, RCC1551, RCC1552, RCC1553, RCC1554, RCC1557, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1016/j.protis.2011.05.001},
	author = {Bendif, E M and Probert, I and Herv{\'e}, A and Billard, C and Goux, D and Lelong, C and Cadoret, J P and V{\'e}ron, B}
}
@article {Blot2011,
	title = {Light history influences the response of the marine cyanobacterium Synechococcus sp. WH7803 to oxidative stress},
	journal = {Plant Physiology},
	volume = {156},
	year = {2011},
	note = {ISBN: 1532-2548 (Electronic) 0032-0889 (Linking) tex.mendeley-tags: 2011,rcc,sbr?hyto?app},
	pages = {1934{\textendash}1954},
	abstract = {Marine Synechococcus undergo a wide range of environmental stressors, especially high and variable irradiance, which may induce oxidative stress through the generation of reactive oxygen species (ROS). While light and ROS could act synergistically on the impairment of photosynthesis, inducing photodamage and inhibiting photosystem II repair, acclimation to high irradiance is also thought to confer resistance to other stressors. To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the photophysiological and transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H2O2) or methylviologen. While photosynthetic activity was much more affected in HL than in LL cells, only HL cells were able to recover growth and photosynthesis after addition of 25 microM H2O2. Depending upon light conditions and H2O2 concentration, the latter oxidizing agent induced photosystem II inactivation through both direct damages to the reaction centres and inhibition of its repair cycle. Although the global transcriptome response appeared similar in LL and HL cells, some processes were specifically induced in HL cells that seemingly helped them withstand oxidative stress, including enhancement of photoprotection and ROS detoxification, repair of ROS-driven damages and regulation of redox state. Detection of putative LexA binding sites allowed the identification of the putative LexA regulon, which was down-regulated in HL compared to LL cells, but up-regulated by oxidative stress under both growth irradiances.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=21670225},
	author = {Blot, N and Mella-Flores, D and Six, C and Lecorguille, G and Boutte, C and Peyrat, A and Monnier, A and Ratin, M and Gourvil, P and Campbell, D A and Garczarek, L}
}
@article {Hagino2011,
	title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes},
	journal = {Journal of Phycology},
	volume = {47},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {1164{\textendash}1176},
	abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1529-8817.2011.01053.x},
	author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H}
}
@article {Gobler2011,
	title = {Niche of harmful alga Aureococcus anophagefferens revealed through ecogenomics},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {108},
	number = {11},
	year = {2011},
	note = {ISBN: 0027-8424 tex.mendeley-tags: RCC,rcc},
	pages = {4352{\textendash}4357},
	abstract = {Harmful algal blooms (HABs) cause significant economic and ecological damage worldwide. Despite considerable efforts, a comprehensive understanding of the factors that promote these blooms has been lacking, because the biochemical pathways that facilitate their dominance relative to other phytoplankton within specific environments have not been identified. Here, biogeochemical measurements showed that the harmful alga Aureococcus anophagefferens outcompeted co-occurring phytoplankton in estuaries with elevated levels of dissolved organic matter and turbidity and low levels of dissolved inorganic nitrogen. We subsequently sequenced the genome of A. anophagefferens and compared its gene complement with those of six competing phytoplankton species identified through metaproteomics. Using an ecogenomic approach, we specifically focused on gene sets that may facilitate dominance within the environmental conditions present during blooms. A. anophagefferens possesses a larger genome (56 Mbp) and has more genes involved in light harvesting, organic carbon and nitrogen use, and encoding selenium-and metal-requiring enzymes than competing phytoplankton. Genes for the synthesis of microbial deterrents likely permit the proliferation of this species, with reduced mortality losses during blooms. Collectively, these findings suggest that anthropogenic activities resulting in elevated levels of turbidity, organic matter, and metals have opened a niche within coastal ecosystems that ideally suits the unique genetic capacity of A. anophagefferens and thus, has facilitated the proliferation of this and potentially other HABs.},
	keywords = {brown-tide blooms, comparative genomics, eutrophication, evolution, genome, genomics, long-island, marine-phytoplankton, multidrug, proteins, proteome, rcc, repeat, responses, san-francisco bay, signal-transduction, transporters},
	doi = {10.1073/pnas.1016106108},
	author = {Gobler, C J and Berry, D L and Dyhrman, S T and Wilhelm, S W and Salamov, A and Lobanov, A V and Zhang, Y and Collier, J L and Wurch, L L and Kustka, A B and Dill, B D and Shah, M and VerBerkmoes, N C and Kuo, A and Terry, A and Pangilinan, J and Lindquist, E A and Lucas, S and Paulsen, I T and Hattenrath-Lehmann, T K and Talmage, S C and Walker, E A and Koch, F and Burson, A M and Marcoval, M A and Tang, Y Z and LeCleir, G R and Coyne, K J and Berg, G M and Bertrand, E M and Saito, M A and Gladyshev, V N and Grigoriev, I V}
}
@article {Ishida2011,
	title = {Partenskyella glossopodia (Chlorarachniophyceae) possesses a nucleomorph genome of approximately 1 Mbp},
	journal = {Phycological Research},
	volume = {59},
	number = {2},
	year = {2011},
	note = {Publisher: Blackwell Publishing Asia tex.mendeley-tags: RCC,rcc},
	pages = {120{\textendash}122},
	abstract = {SUMMARY The nucleomorph genome size of the recently described chlorarachniophyte Partenskyella glossopodia, which forms an independent lineage in the phylogeny of chlorarachniophytes, was analyzed by pulse-field gel electrophoresis and Southern hybridization. These analyses showed that the nucleomorph genome of P. glossopodia is composed of three linear chromosomes that are about 445 kbp, 313 kbp, and 275 kbp in size. Thus, the total genome size is approximately 1033 kbp, which is significantly larger than the known size of chlorarachniophyte nucleomorph genomes, i.e. 330{\textendash}610 kbp. This is the first study to report a nucleomorph genome that reaches approximately 1 Mbp in size.},
	keywords = {Chlorarachniophytes, genome reduction, genome size, nucleomorph, Partenskyella glossopodia, rcc},
	doi = {10.1111/j.1440-1835.2011.00608.x},
	url = {http://dx.doi.org/10.1111/j.1440-1835.2011.00608.x},
	author = {Ishida, Ken-ichiro and Endo, Hiroko and Koike, Sayaka}
}
@article {Laviale2011,
	title = {Relationships between pigment ratios and growth irradiance in 11 marine phytoplankton species},
	journal = {Marine Ecology Progress Series},
	volume = {425},
	year = {2011},
	note = {tex.mendeley-tags: rcc},
	month = {mar},
	pages = {63{\textendash}77},
	keywords = {cultures, hplc, irradiance, of the publisher, permitted without written consent, phytoplankton, pigment ratios, rcc, RCC?o?dd, regression analysis},
	issn = {0171-8630},
	doi = {10.3354/meps09013},
	url = {http://www.int-res.com/abstracts/meps/v425/p63-77/},
	author = {Laviale, M and Neveux, J}
}
@article {Edvardsen2011,
	title = {Ribosomal DNA phylogenies and a morphological revision privide the basis for a new taxonomy of Prymnesiales (Haptophyta)},
	journal = {European Journal of Phycology},
	volume = {46},
	year = {2011},
	note = {tex.mendeley-tags: 2011,RCC1185,RCC1187,RCC1189,RCC1385,RCC1387,RCC1388,RCC1390,RCC1432,RCC1438,RCC1440,RCC1441,RCC1448,RCC1453,RCC2056,RCC2057,RCC2059,RCC2060,RCC2061,RCC2063,RCC2064,RCC305,RCC339,RCC3417,RCC3421,RCC3422,RCC3424,RCC3425,RCC3429,RCC406,rcc},
	pages = {202{\textendash}228},
	keywords = {2011, ASSEMBLE, rcc, RCC1185, RCC1187, RCC1189, RCC1385, RCC1387, RCC1388, RCC1390, RCC1432, RCC1438, RCC1440, RCC1441, RCC1448, RCC1453, RCC2056, RCC2057, RCC2059, RCC2060, RCC2061, RCC2063, RCC2064, RCC305, RCC339, RCC3417, RCC3421, RCC3422, RCC3424, RCC3425, RCC3429, RCC406, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1080/09670262.2011.594095},
	author = {Edvardsen, B and Eikrem, W and Throndsen, J and A., Saez and Probert, I and Medlin, L}
}
@article {Beaufort2011,
	title = {Sensitivity of coccolithophores to carbonate chemistry and ocean acidification},
	journal = {Nature},
	volume = {476},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {80{\textendash}83},
	abstract = {Coccolithophores produce the major fraction of pelagic carbonate, a key component of the carbon cycle. The effect of elevated CO2 on their calcification is poorly understood. Culture experiments have yielded varied calcification responses to increased pCO2 between and within coccolithophore taxa. We used a novel automated method for pattern recognition and morphometric analysis to quantify the calcite mass of coccolithophores from {\textquestiondown}700 samples from present past (last 40-Kyr) oceans. Comparison of morphological data with ocean carbonate chemistry reconstructed in both space and time indicate decreasing calcification with increasing pCO2, and decreasing CO32. At pH {\textexclamdown}8.0, delicate Emiliania huxleyi are strongly affected by decalcification. However, highly calcified E. huxleyi morphotypes predominate in waters with lowest pH. This suggests that coccolithophore strains pre-adapted to future, more acidic oceans already populate regions of contemporary oceans. The future carbon feedback from coccolithophore calcification will depend on the genetic diversity and adaptability of coccolithophore populations.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1038/nature10295},
	author = {Beaufort, L and Probert, I and de Garidel-Thoron, T and Bendif, E M and Ruiz-Pino, D and Metzl, N and Goyet, C and Buchet, N and Coupel, P and Grelaud, M and Rost, B and Rickaby, R E M and de Vargas, C}
}
@article {Rokitta2011,
	title = {Transcriptome analyses reveal differential gene expression patterns between the life-cycle stages of Emiliania huxleyi (Haptophyta) and reflect specialization to different ecological niches},
	journal = {Journal of Phycology},
	volume = {47},
	number = {4},
	year = {2011},
	note = {Publisher: Blackwell Publishing Ltd tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {829{\textendash}838},
	abstract = {Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 ??m diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit.},
	keywords = {2011, endocytosis, Life-cycle stages, microarray, quantitative RT-PCR, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo, transcriptome profiling},
	doi = {10.1111/j.1529-8817.2011.01014.x},
	url = {http://dx.doi.org/10.1111/j.1529-8817.2011.01014.x},
	author = {Rokitta, Sebastian D and de Nooijer, Lennart J and Trimborn, Scarlett and de Vargas, Colomban and Rost, Bj{\"o}rn and John, Uwe}
}
@article {Lepere2011,
	title = {Whole Genome Amplification (WGA) of marine photosynthetic eukaryote populations},
	journal = {FEMS Microbiology Ecology},
	volume = {76},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	pages = {516{\textendash}523},
	keywords = {2011, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	doi = {10.1111/j.1574-6941.2011.01072.x},
	author = {Lepere, Cecile and Demura, M and Kawachi, M and Romac, S and Probert, I and Vaulot, D}
}
@article {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}
}
@article {McDonald2010,
	title = {The mixed lineage nature of nitrogen transport and assimilation in marine eukaryotic phytoplankton: a case study of Micromonas},
	journal = {Molecular Biology and Evolution},
	volume = {27},
	number = {10},
	year = {2010},
	note = {tex.mendeley-tags: RCC299},
	pages = {2268{\textendash}2283},
	abstract = {The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (<=2 ??m diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer{\textendash}probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of {\textquotedblleft}mixed lineage gene affiliations{\textquotedblright} among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton.},
	keywords = {rcc, RCC299},
	doi = {10.1093/molbev/msq113},
	url = {http://mbe.oxfordjournals.org/content/27/10/2268.abstract},
	author = {McDonald, Sarah M and Plant, Joshua N and Worden, Alexandra Z}
}
@article {Marin2010,
	title = {Molecular phylogeny and classification of the Mamiellophyceae class. nov. (Chlorophyta) based on sequence comparisons of the nuclear- and plastid-encoded rRNA operons},
	journal = {Protist},
	volume = {161},
	number = {2},
	year = {2010},
	note = {ISBN: 1618-0941 tex.mendeley-tags: Micromonas,rcc},
	pages = {304{\textendash}336},
	abstract = {Molecular phylogenetic analyses of the Mamiellophyceae classis nova, a ubiquitous group of largely picoplanktonic green algae comprising scaly and non-scaly prasinophyte unicells, were performed using single and concatenated gene sequence comparisons of the nuclear- and plastid-encoded rRNA operons. The study resolved all major clades within the class, identified molecular signature sequences for most clades through an exhaustive search for non-homoplasious synapomorphies [Marin et al. (2003): Protist 154: 99-145] and incorporated these signatures into the diagnoses of two novel orders, Monomastigales ord nov., Dolichomastigales ord. nov., and four novel families, Monomastigaceae fam. nov., Dolichomastigaceae fam. nov., Crustomastigaceae fam. nov., and Bathycoccaceae fam. nov., within a revised classification of the class. A database search for the presence of environmental rDNA sequences in the Monomastigales and Dolichomastigales identified an unexpectedly large genetic diversity of Monomastigales confined to freshwater, a novel clade (Dolicho$_\textrmB$) in the Dolichomastigaceae from deep sea sediments and a novel freshwater clade in the Crustomastigaceae. The Mamiellophyceae represent one of the ecologically most successful groups of eukaryotic, photosynthetic picoplankters in marine and likely also freshwater environments. Copyright 2009 Elsevier GmbH. All rights reserved.},
	keywords = {Index Medicus, Micromonas, rcc},
	doi = {10.1016/j.protis.2009.10.002},
	author = {Marin, Birger and Melkonian, Michael}
}
@article {Mohr2010,
	title = {A new chlorophyll d -containing cyanobacterium : evidence for niche adaptation in the genus Acaryochloris},
	journal = {The ISME journal},
	year = {2010},
	note = {tex.mendeley-tags: RCC,RCC1983,rcc},
	pages = {1456{\textendash}1469},
	abstract = {Chlorophyll d is a photosynthetic pigment that, based on chemical analyses, has only recently been recognized to be widespread in oceanic and lacustrine environments. However, the diversity of organisms harbouring this pigment is not known. Until now, the unicellular cyanobacterium Acaryochloris marina is the only characterized organism that uses chlorophyll d as a major photopigment. In this study we describe a new cyanobacterium possessing a high amount of chlorophyll d, which was isolated from waters around Heron Island, Great Barrier Reef (231 260 31.200 S, 1511 540 50.400 E). The 16S ribosomal RNA is 2\% divergent from the two previously described isolates of A. marina, which were isolated from waters around the Palau islands (Pacific Ocean) and the Salton Sea lake (California), suggesting that it belongs to a different clade within the genus Acaryochloris. An overview sequence analysis of its genome based on Illumina technology yielded 871 contigs with an accumulated length of 8 371965nt. Their analysis revealed typical features associated with Acaryochloris, such as an extended gene family for chlorophyll-binding proteins. However, compared with A. marina MBIC11017, distinct genetic, morphological and physiological differences were observed. Light saturation is reached at lower light intensities, Chl d/a ratios are less variable with light intensity and the phycobiliprotein phycocyanin is lacking, suggesting that cyanobacteria of the genus Acaryochloris occur in distinct ecotypes. These data characterize Acaryochloris as a niche-adapted cyanobacterium and show that more rigorous attempts are worthwhile to isolate, cultivate and analyse chlorophyll d-containing cyanobacteria for understanding the ecophysiology of these organisms. The},
	keywords = {acaryochloris, chlorophyll d, coral reef, cyanobacteria, microbial diversity, overview, rcc, RCC1983},
	doi = {10.1038/ismej.2010.67},
	author = {Mohr, Remus and Schliep, Martin and Kurz, Thorsten and Maldener, Iris and Adams, David G and Larkum, Anthony D W and Chen, Min and Hess, Wolfgang R}
}
@article {Siano2010,
	title = {Pelagodinium gen. nov. and P. beii comb. nov., a dinoflagellate symbiont of planktonic foraminifera},
	journal = {Protist},
	volume = {161},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,rcc1491,sbr?hyto?ppo},
	pages = {385{\textendash}399},
	abstract = {The taxonomic status of the free-living stage of the dinoflagellate Gymnodinium b{\'e}ii, symbiont of the foraminifer Orbulina universa, was reassessed on the basis of detailed morpho-genetic analyses. Electron microscopy observations revealed previously undescribed morphological features of the cell that are important for species recognition. The presence of a single elongated apical vesicle (EAV) ornamented with a row of small knobs, absent in species of the genus Gymnodinium, calls into question the current taxonomic position of the symbiont. The presence of a type E extraplastidial eyespot, the arrangement of the amphiesmal vesicles in series and the absence of trichocysts confirm the affiliation with other symbiotic dinoflagellates and certain genetically related non-symbiotic genera, all belonging to the order Suessiales. The arrangement of the series of vesicles of the analyzed strain is unique within the Suessiales, and the ultrastructure of the pyrenoid is different from other symbiotic dinoflagellates. A large subunit (LSU) rDNA phylogenetic analysis confirmed that the analyzed pelagic symbiont clusters in an independent, well-supported clade within the Suessiales with other sequences of symbiotic dinoflagellates extracted from planktonic foraminifera. Hence a novel genus, Pelagodinium gen. nov., is erected for this pelagic, symbiotic dinoflagellate, and Gymnodinium b{\'e}ii is reclassified as Pelagodinium b{\'e}ii.},
	keywords = {2010, ASSEMBLE, rcc, rcc1491, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1016/j.protis.2010.01.002},
	author = {Siano, R and Montresor, M and Probert, I and Not, F and de Vargas, C}
}
@article {Minge2010,
	title = {A phylogenetic mosaic plastid proteome and unusual plastid-targeting signals in the green-colored dinoflagellate Lepidodinium chlorophorum},
	journal = {BMC Evolutionary Biology},
	volume = {10},
	year = {2010},
	note = {ISBN: 1471-2148 tex.mendeley-tags: 2010,rcc},
	pages = {191},
	abstract = {Background: Plastid replacements through secondary endosymbioses include massive transfer of genes from the endosymbiont to the host nucleus and require a new targeting system to enable transport of the plastid-targeted proteins across 3-4 plastid membranes. The dinoflagellates are the only eukaryotic lineage that has been shown to have undergone several plastid replacement events, and this group is thus highly relevant for studying the processes involved in plastid evolution. In this study, we analyzed the phylogenetic origin and N-terminal extensions of plastid-targeted proteins from Lepidodinium chlorophorum, a member of the only dinoflagellate genus that harbors a green secondary plastid rather than the red algal-derived, peridinin-containing plastid usually found in photosynthetic dinoflagellates. Results: We sequenced 4,746 randomly picked clones from a L. chlorophorum cDNA library. 22 of the assembled genes were identified as genes encoding proteins functioning in plastids. Some of these were of green algal origin. This confirms that genes have been transferred from the plastid to the host nucleus of L. chlorophorum and indicates that the plastid is fully integrated as an organelle in the host. Other nuclear-encoded plastid-targeted protein genes, however, are clearly not of green algal origin, but have been derived from a number of different algal groups, including dinoflagellates, streptophytes, heterokonts, and red algae. The characteristics of N-terminal plastid-targeting peptides of all of these genes are substantially different from those found in peridinin-containing dinoflagellates and green algae. Conclusions: L. chlorophorum expresses plastid-targeted proteins with a range of different origins, which probably arose through endosymbiotic gene transfer (EGT) and horizontal gene transfer (HGT). The N-terminal extension of the genes is different from the extensions found in green alga and other dinoflagellates (peridinin- and haptophyte plastids). These modifications have likely enabled the mosaic proteome of L. chlorophorum.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1186/1471-2148-10-191},
	author = {Minge, M A and Shalchian-Tabrizi, K and Torresen, O K and Takishita, K and Probert, I and Inagaki, Y and Klaveness, D and Jakobsen, K S}
}
@article {Jardillier2010,
	title = {Significant CO2 fixation by small prymnesiophytes in the subtropical and tropical northeast Atlantic Ocean},
	journal = {The ISME Journal},
	volume = {4},
	year = {2010},
	note = {Publisher: International Society for Microbial Ecology tex.mendeley-tags: Micromonas,rcc},
	pages = {1180{\textendash}1192},
	keywords = {Micromonas, rcc},
	doi = {10.1038/ismej.2010.36},
	url = {http://dx.doi.org/10.1038/ismej.2010.36 http://www.nature.com/ismej/journal/vaop/ncurrent/suppinfo/ismej201036s1.html},
	author = {Jardillier, Ludwig and Zubkov, Mikhail V and Pearman, John and Scanlan, David J}
}
@article {Liu2010,
	title = {A timeline of the environmental genetics of the haptophytes},
	journal = {Molecular Biology and Evolution},
	volume = {27},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {171{\textendash}176},
	abstract = {The use of genomic data and the rise of phylogenomics have radically changed our view of the eukaryotic tree of life at a high taxonomic level by identifying four to six "supergroups". Yet our understanding of the evolution of key innovations within each of these supergroups is limited because of poor species sampling relative to the massive diversity encompassed by each supergroup. Here we apply a multigene approach that incorporates a wide taxonomic diversity to infer the timeline of the emergence of strategic evolutionary transitions in the haptophytes, a group of ecologically and biogeochemically significant marine protists that belong to the Chromalveolata supergroup. Four genes (SSU, LSU, tufA and rbcL) were extensively analyzed under several Bayesian models to assess the robustness of the phylogeny, particularly with respect to (i) data partitioning, (ii) the origin of the genes (host vs. endosymbiont), (iii) across-site rate variation and (iv) across-lineage rate variation. We show with a relaxed clock analysis that the origin of haptophytes dates back to 824 MYA (95\% highest probability density 1031-637 MYA). Our dating results show that the ability to calcify evolved earlier than previously thought, between 329-291 MYA, in the Carboniferous period, and that the transition from mixotrophy to autotrophy occurred during the same time period. Although these two transitions precede a habitat change of major diversities from coastal / neritic waters to the pelagic realm (291-243 MYA, around the P/Tr boundary event), the emergence of calcification, full autotrophy and oceanic lifestyle seem mutually independent.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1093/molbev/msp222},
	url = {http://mbe.oxfordjournals.org/cgi/content/abstract/msp222v1},
	author = {Liu, Hui and Aris-Brosou, Stephane and Probert, Ian and de Vargas, Colomban}
}
@conference {Meusnier2009,
	title = {DNA barcoding of protists in culture collections},
	booktitle = {Third international barcode of life conference},
	year = {2009},
	note = {tex.mendeley-tags: RCC,rcc},
	address = {Mexico City},
	keywords = {? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO},
	author = {Meusnier, Isabelle and Andersen, Robert A and Stern, Rowena and Bertrand, C and Kuepper, Frithjof and Brand, Jerry and Friedl, Thomas and Blackburn, Susan and Dinh, Donna and Acreman, Judy and Sedl{\'a}{\v c}ek, Ivo and P{\v r}ibyl, Pavel and Jutson, Maria and Phang, Siew Moi and Melkonian, M and Karpov, S and Hajibabaei, Mehrdad}
}
@article {Scanlan2009,
	title = {Ecological genomics of marine picocyanobacteria},
	journal = {Microbiology and Molecular Biology Reviews},
	volume = {73},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?app},
	pages = {249{\textendash}299},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmP$PM, sbr?hyto?app},
	doi = {10.1128/MMBR.00035-08},
	author = {Scanlan, D J and Ostrowski, M and Mazard, S and Dufresne, A and Garczarek, L and Hess, W R and Post, A F and Hagemann, M and Paulsen, I and Partensky, F}
}
@article {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 {Wolhowe2009,
	title = {Growth phase dependent hydrogen isotopic fractionation in alkenone-producing haptophytes},
	journal = {Biogeosciences},
	volume = {6},
	number = {8},
	year = {2009},
	note = {ISBN: 1726-4170 tex.mendeley-tags: 2009,rcc},
	pages = {1681{\textendash}1694},
	abstract = {Recent works have investigated use of the hydrogen isotopic composition Of C-37 alkenones (delta D-K37s), lipid biomarkers of certain haptophyte microalgae, as an independent paleosalinity proxy. We discuss herein the factors impeding the success of such an application and identify the potential alternative use of delta D-K37s measurements as a proxy for non-thermal, physiological stress impacts on the U-37(K{\textquoteright}) paleotemperature index. Batch-culture experiments with the haptophyte Emiliania huxleyi (CCMP 1742) were conducted to determine the magnitude and variability of the isotopic contrasts between individual C-37 alkenones. Further experiments were conducted with Emiliania huxleyi (CCMP 1742) and Gephyrocapsa oceanica (PZ3-1) to determine whether, and to what extent, delta D-K37s varies between the physiological extremes of nutrient-replete exponential growth and nutrient-depleted senescence. Emiliania huxleyi was observed to exhibit an isotopic contrast between di- and tri-unsaturated C-37 alkenones (alpha(K37:3-K37:2)approximate to 0.97) that is nearly identical to that reported recently by others for environmental samples. Furthermore, this contrast appears to be constant with growth stage. The consistency of the offset across different growth stages suggests that a single, well-defined value for alpha(K37:3-K37:2) may exist and that its use in an isotope mass-balance will allow accurate determination of delta D values for individual alkenones without having to rely on time- and labor-intensive chemical separations. The isotopic fractionation between growth medium and C-37 alkenones was observed to increase dramatically upon the onset of nutrient-depletion-induced senescence, suggesting that delta D-K37s, may serve as an objective tool for recognizing and potentially correcting, at least semi-quantitatively, for the effects of nutrient stress on U-37(K{\textquoteright}) temperature records.},
	keywords = {2009, rcc, RCC1300, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.5194/bg-6-1681-2009},
	author = {Wolhowe, M D and Prahl, F G and Probert, I and Maldonado, M}
}
@article {Monier2009,
	title = {Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus},
	journal = {Genome Research},
	volume = {19},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {1441{\textendash}1449},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1101/gr.091686.109},
	author = {Monier, A and Pagarete, A and Allen, M J and Read, B A and de Vargas, C and Claverie, J M and Ogata, H}
}
@article {Richier2009,
	title = {Light-dependent transcriptional regulation of genes of biogeochemical interest in the diploid and haploid life cycle stages of Emiliania huxleyi},
	journal = {Applied and Environmental Microbiology},
	volume = {75},
	year = {2009},
	note = {Edition: 2009/03/24 ISBN: 1098-5336 (Electronic) tex.mendeley-tags: 2009,rcc,sbr?hyto?ppo},
	pages = {3366{\textendash}3369},
	abstract = {The expression of genes of biogeochemical interest in calcifying and noncalcifying life stages of the coccolithophore Emiliania huxleyi was investigated. Transcripts potentially involved in calcification were tested through a light-dark cycle. These transcripts were more abundant in calcifying cells and were upregulated in the light. Their application as potential candidates for in situ biogeochemical proxies is also suggested.},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1128/aem.02737-08},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19304825},
	author = {Richier, S and Kerros, M E and de Vargas, C and Haramaty, L and Falkowski, P G and Gattuso, J P}
}
@article {Ota2009,
	title = {Partenskyella glossopodia gen. et sp. nov., the first report of chlorarachniophyte that lacks pyrenoid},
	journal = {Protist},
	volume = {160},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {137{\textendash}150},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1016/j.protis.2008.09.003},
	author = {Ota, S and Vaulot, D and Le Gall, F and Yabuki, A and Ishida, K}
}
@article {Six2009,
	title = {Photosystem II and pigment dynamics among ecotypes of the green alga Ostreococcus},
	journal = {Plant Physiology},
	volume = {151},
	year = {2009},
	note = {tex.mendeley-tags: RCC809},
	pages = {379{\textendash}390},
	abstract = {We investigated the photophysiological response of three ecotypes of the picophytoplankter Ostreococcus and a larger prasinophyte Pyramimonas obovata to a sudden increase in light irradiance. The deepwater Ostreococcus sp. RCC809 showed very high susceptibility to primary photoinactivation, likely a consequence of high oxidative stress, which may relate to the recently noted plastid terminal oxidase activity in this strain. The three Ostreococcus ecotypes were all able of deploying modulation of photosystem II repair cycle in order to cope with the light increase, but the effective clearance of photoinactivated D1 protein appeared to be slower in the deep water Ostreococcus sp. RCC809, suggesting that this step is rate-limiting in the photosystem II repair cycle in this strain. The deepwater Ostreococcus moreover accumulated lutein and showed substantial use of the xanthophyll cycle under light stress, demonstrating its high sensitivity to light fluctuations. The sustained component of the non-photochemical quenching of fluorescence correlated well with the xanthophyll de-epoxidation activity. Comparisons with the larger prasinophyte Pyramimonas obovata suggest that the photophysiology of Ostreococcus ecotypes requires high photosystem II repair rates to counter a high susceptibility to photoinactivation, consistent with low pigment package effects in their minute-sized cells.},
	keywords = {rcc, RCC809, SBR$_\textrmP$hyto$_\textrmP$PM},
	doi = {10.1104/pp.109.140566},
	author = {Six, C and Sherrard, R and Lionard, M and Roy, S and Campbell, D A}
}
@article {Langer2009,
	title = {Strain-specific responses of Emiliania huxleyi to changing seawater carbonate chemistry},
	journal = {Biogeosciences},
	volume = {6},
	number = {11},
	year = {2009},
	note = {ISBN: 1726-4170 tex.mendeley-tags: 2009,rcc},
	pages = {2637{\textendash}2646},
	abstract = {Four strains of the coccolithophore E. huxleyi (RCC1212, RCC1216, RCC1238, RCC1256) were grown in dilute batch culture at four CO2 levels ranging from similar to 200 mu atm to similar to 1200 mu atm. Growth rate, particulate organic carbon content, and particulate inorganic carbon content were measured, and organic and inorganic carbon production calculated. The four strains did not show a uniform response to carbonate chemistry changes in any of the analysed parameters and none of the four strains displayed a response pattern previously described for this species. We conclude that the sensitivity of different strains of E. huxleyi to acidification differs substantially and that this likely has a genetic basis. We propose that this can explain apparently contradictory results reported in the literature.},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.5194/bg-6-2637-2009},
	author = {Langer, G and Nehrke, G and Probert, I and Ly, J and Ziveri, P}
}
@article {VonDassow2009,
	title = {Transcriptome analysis of functional differentiation between haploid and diploid cells of Emiliania huxleyi, a globally significant photosynthetic calcifying cell},
	journal = {Genome Biology},
	volume = {10},
	number = {10},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,rcc1216,rcc1217,sbr?hyto?ppo},
	pages = {R114},
	abstract = {BACKGROUND:Eukaryotes are classified as either haplontic, diplontic, or haplo-diplontic, depending on which ploidy levels undergo mitotic cell division in the life cycle. Emiliania huxleyi is one of the most abundant phytoplankton species in the ocean, playing an important role in global carbon fluxes, and represents haptophytes, an enigmatic group of unicellular organisms that diverged early in eukaryotic evolution. This species is haplo-diplontic. Little is known about the haploid cells, but they have been hypothesized to allow persistence of the species between the yearly blooms of diploid cells. We sequenced over 38000 Expressed Sequence Tags (ESTs) from haploid and diploid E. huxleyi normalized cDNA libraries to identify genes involved in important processes specific to each life phase (2N calcification or 1N motility), and to better understand the haploid phase of this prominent haplo-diplontic organism.RESULTS:The haploid and diploid transcriptomes showed a dramatic differentiation, with [almost equal to]20\% greater transcriptome richness in diploid cells than in haploid cells and only [less than or equal to]50\% of transcripts estimated to be common between the two phases. The major functional category of transcripts differentiating haploids included signal transduction and motility genes. Diploid-specific transcripts included Ca2+, H+, and HCO3- pumps. Potential factors differentiating the transcriptomes included haploid-specific Myb transcription factor homologs and an unusual diploid-specific histone H4 homolog.CONCLUSIONS:This study permitted the identification of genes likely involved in diploid-specific biomineralization, haploid-specific motility, and transcriptional control. Greater transcriptome richness in diploid cells suggests they may be more versatile for exploiting a diversity of rich environments whereas haploid cells are intrinsically more streamlined.},
	keywords = {2009, rcc, RCC1216, rcc1217, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1186/gb-2009-10-10-r114},
	url = {http://genomebiology.com/2009/10/10/R114},
	author = {von Dassow, Peter and Ogata, Hiroyuki and Probert, Ian and Wincker, Patrick and Da Silva, Corinne and Audic, St{\'e}phane and Claverie, Jean-Michel and de Vargas, Colomban}
}
@article {Frada2008,
	title = {The {\textquotedblleft}Cheshire Cat{\textquotedblright} escape strategy of the coccolithophore Emiliania huxleyi in response to viral infection},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto?ppo},
	pages = {15944{\textendash}15949},
	abstract = {The coccolithophore is one of the most successful eukaryotes in modern oceans. The two phases in its haplodiploid life cycle exhibit radically different phenotypes. The diploid calcified phase forms extensive blooms, which profoundly impact global biogeochemical equilibria. By contrast, the ecological role of the noncalcified haploid phase has been completely overlooked. Giant phycodnaviruses ( viruses, EhVs) have been shown to infect and lyse diploid-phase cells and to be heavily implicated in the regulation of populations and the termination of blooms. Here, we demonstrate that the haploid phase of is unrecognizable and therefore resistant to EhVs that kill the diploid phase. We further show that exposure of diploid to EhVs induces transition to the haploid phase. Thus we have clearly demonstrated a drastic difference in viral susceptibility between life cycle stages with different ploidy levels in a unicellular eukaryote. Resistance of the haploid phase of provides an escape mechanism that involves separation of meiosis from sexual fusion in time, thus ensuring that genes of dominant diploid clones are passed on to the next generation in a virus-free environment. These {\^a}{\texteuro}{\oe}Cheshire Cat{\^a}{\texteuro} ecological dynamics release host evolution from pathogen pressure and thus can be seen as an opposite force to a classic {\^a}{\texteuro}{\oe}Red Queen{\^a}{\texteuro} coevolutionary arms race. In , this phenomenon can account for the fact that the selective balance is tilted toward the boom-and-bust scenario of optimization of both growth rates of calcifying cells and infectivity of EhVs.},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1073/pnas.0807707105},
	author = {Frada, Miguel and Probert, Ian and Allen, Michael J and Wilson, William H and de Vargas, Colomban}
}
@article {Jancek2008,
	title = {Clues about the genetic basis of adaptation emerge from comparing the proteomes of two Ostreococcus ecotypes (Chlorophyta, Prasinophyceae)},
	journal = {Molecular Biology and Evolution},
	volume = {25},
	number = {11},
	year = {2008},
	note = {Edition: 2008/08/06 ISBN: 1537-1719 (Electronic) 0737-4038 (Linking) tex.mendeley-tags: RCC,rcc},
	pages = {2293{\textendash}2300},
	abstract = {We compared the proteomes of two picoplanktonic Ostreococcus unicellular green algal ecotypes to analyze the genetic basis of their adaptation with their ecological niches. We first investigated the function of the species-specific genes using Gene Ontology databases and similarity searches. Although most species-specific genes had no known function, we identified several species-specific functions involved in various cellular processes, which could be critical for environmental adaptations. Additionally, we investigated the rate of evolution of orthologous genes and its distribution across chromosomes. We show that faster evolving genes encode significantly more membrane or excreted proteins, consistent with the notion that selection acts on cell surface modifications that is driven by selection for resistance to viruses and grazers, keystone actors of phytoplankton evolution. The relationship between GC content and chromosome length also suggests that both strains have experienced recombination since their divergence and that lack of recombination on the two outlier chromosomes could explain part of their peculiar genomic features, including higher rates of evolution.},
	keywords = {adaptation, Base Composition, Chlorophyta/*genetics, Ecosystem, Physiological/*genetics, Phytoplankton/genetics, Proteome/*genetics, rcc, Species Specificity},
	doi = {10.1093/molbev/msn168},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18678753},
	author = {Jancek, S and Gourbiere, S and Moreau, H and Piganeau, G}
}
@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 {Vaulot2008,
	title = {The diversity of small eukaryotic phytoplankton ({\textexclamdown}3 {\textmu}m) in marine ecosystems},
	volume = {32},
	number = {5},
	year = {2008},
	note = {Publication Title: FEMS microbiology reviews tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {795{\textendash}820},
	abstract = {Small cells dominate photosynthetic biomass and primary production in many marine ecosystems. Traditionally, picoplankton refers to cells {\textexclamdown} or =2 microm. Here we extend the size range of the organisms considered to 3 microm, a threshold often used operationally in field studies. While the prokaryotic component of picophytoplankton is dominated by two genera, Prochlorococcus and Synechococcus, the eukaryotic fraction is much more diverse. Since the discovery of the ubiquitous Micromonas pusilla in the early 1950s, just over 70 species that can be {\textexclamdown}3 microm have been described. In fact, most algal classes contain such species. Less than a decade ago, culture-independent approaches (in particular, cloning and sequencing, denaturing gradient gel electrophoresis, FISH) have demonstrated that the diversity of eukaryotic picoplankton is much more extensive than could be assumed from described taxa alone. These approaches revealed the importance of certain classes such as the Prasinophyceae but also unearthed novel divisions such as the recently described picobiliphytes. In the last couple of years, the first genomes of photosynthetic picoplankton have become available, providing key information on their physiological capabilities. In this paper, we discuss the range of methods that can be used to assess small phytoplankton diversity, present the species described to date, review the existing molecular data obtained on field populations, and end up by looking at the promises offered by genomics.},
	keywords = {2008, diversity, genomics, Marine ecosystems, Micro-algae, picoplankton, rcc, sbr?hyto$_\textrmd$ipo, taxonomy},
	author = {Vaulot, Daniel and Eikrem, Wenche and Viprey, Manon and Moreau, Herv{\'e}}
}
@article {Foulon2008,
	title = {Ecological niche partitioning in the picoplanktonic green alga Micromonas pusilla: evidence from environmental surveys using phylogenetic probes},
	journal = {Environmental Microbiology},
	volume = {10},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {2433{\textendash}2443},
	keywords = {2008, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1111/j.1462-2920.2008.01673.x},
	author = {Foulon, E and Not, F and Jalabert, F and Cariou, T and Massana, R and Simon, N}
}
@article {Claquin2008,
	title = {Effects of temperature on photosynthetic parameters and TEP production in eight species of marine microalgae},
	journal = {Aquatic Microbial Ecology},
	volume = {51},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc},
	pages = {1{\textendash}11},
	keywords = {2008, rcc, SBR$_\textrmP$hyto},
	doi = {10.3354/ame01187},
	author = {Claquin, Pascal and Probert, Ian and Lefebvre, S{\'e}bastien and Veron, Benoit}
}
@article {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 {Descles2008,
	title = {New tools for labeling silica in living diatoms},
	journal = {New Phytologist},
	volume = {177},
	number = {3},
	year = {2008},
	note = {ISBN: 0028-646X tex.mendeley-tags: rcc},
	pages = {822{\textendash}829},
	abstract = {Silicon biomineralization is a widespread mechanism found in several kingdoms that concerns both unicellular and multicellular organisms. As a result of genomic and molecular tools, diatoms have emerged as a good model for biomineralization studies and have provided most of the current knowledge on this process. However, the number of techniques available to study its dynamics at the cellular level is still rather limited. Here, new probes were developed specifically to label the pre-existing or the newly synthesized silica frustule of several diatoms species. It is shown that the LysoTracker Yellow HCK-123, which can be used to visualize silica frustules with common filter sets, presents an enhanced signal-to-noise ratio and allows details of the frustules to be imaged without of the use of ionophores. It is also demonstrated that methoxysilane derivatives can be coupled to fluorescein-5-isothiocyanate (FITC) to preferentially label the silica components of living cells. The coupling of labeling procedures might help to address the challenging question of the process of frustule exocytosis.},
	keywords = {3D-imaging, BACILLARIOPHYCEAE, BIOLOGY, biomineralization, DEPOSITION, diatoms, exocytosis, FLUORESCENT, nanopattern, pH, phaeodactylum-tricornutum, PLANTS, rcc, THALASSIOSIRA-PSEUDONANA, ultrastructure, VESICLE},
	doi = {10.1111/j.1469-8137.2007.02303.x},
	author = {Descles, J and Vartanian, M and El Harrak, A and Quinet, M and Bremond, N and Sapriel, G and Bibette, J and Lopez, P J}
}
@article {Cardol2008,
	title = {An original adaptation of photosynthesis in the marine green alga Ostreococcus},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {105},
	number = {22},
	year = {2008},
	note = {tex.mendeley-tags: RCC745,RCC809},
	pages = {7881{\textendash}7886},
	abstract = {Adaptation of photosynthesis in marine environment has been examined in two strains of the green, picoeukaryote : OTH95, a surface/high-light strain, and RCC809, a deep-sea/low-light strain. Differences between the two strains include changes in the light-harvesting capacity, which is lower in OTH95, and in the photoprotection capacity, which is enhanced in OTH95. Furthermore, RCC809 has a reduced maximum rate of O evolution, which is limited by its decreased photosystem I (PSI) level, a possible adaptation to Fe limitation in the open oceans. This decrease is, however, accompanied by a substantial rerouting of the electron flow to establish an HO-to-HO cycle, involving PSII and a potential plastid plastoquinol terminal oxidase. This pathway bypasses electron transfer through the cytochrome complex and allows the pumping of {\^a}{\texteuro}{\oe}extra{\^a}{\texteuro} protons into the thylakoid lumen. By promoting the generation of a large {\^I}{\textquotedblright}pH, it facilitates ATP synthesis and nonphotochemical quenching when RCC809 cells are exposed to excess excitation energy. We propose that the diversion of electrons to oxygen downstream of PSII, but before PSI, reflects a common and compulsory strategy in marine phytoplankton to bypass the constraints imposed by light and/or nutrient limitation and allow successful colonization of the open-ocean marine environment.},
	keywords = {rcc, RCC745, RCC809},
	doi = {10.1073/pnas.0802762105},
	url = {http://www.pnas.org/content/105/22/7881.abstract},
	author = {Cardol, Pierre and Bailleul, Benjamin and Rappaport, Fabrice and Derelle, Evelyne and Baal, Daniel and Breyton, C{\'e}cile and Bailey, Shaun and Wollman, Francis Andr{\'e} and Grossman, Arthur and Moreau, Herv{\'e} and Finazzi, Giovanni}
}
@article {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 {LeGall2008,
	title = {Picoplankton diversity in the south-east pacific ocean from cultures},
	journal = {Biogeosciences},
	volume = {5},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo,sbr?hyto?app},
	pages = {203{\textendash}214},
	keywords = {2008, PICOFUNPAC, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo, sbr?hyto?app},
	doi = {10.5194/bg-5-203-2008},
	author = {Le Gall, F and Rigaut-Jalabert, F and Marie, D and Garczareck, L and Viprey, M and Godet, A and Vaulot, D}
}
@article {Jouenne2008,
	title = {Plankton taxonomy in the computer age},
	journal = {Cahiers de Biologie Marine},
	volume = {49},
	year = {2008},
	note = {tex.mendeley-tags: 2008,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {355{\textendash}367},
	abstract = {<p>Preservation of biodiversity starts with knowledge of biodiversity. Based on this principle, numerous projects combining taxonomy and web-based technologies have developed over the last fifteen years, often with the aim of listing all living organisms described to date. Individual lists have been progressively incorporated into federative projects, such as Species 2000 or the Global Biodiversity Information Facility (GBIF). Nowadays, modern taxonomy is splited up between traditionalism and pragmatism. The Internet can provide new advantages to taxonomy (accessibility and efficiency) without reducing quality. In the future, it would be highly desirable to ba able to publish species descriptions and revisions on permanent web-sites on the model of GENBANK. Biodiversity inventory projects should converge to a very limited number of portals (e.g. Encyclopedia of Life). We illustrate these concepts by presenting Plankton*Net an interactive web site dedicated to the taxonomy and images of plankton.</p>
},
	keywords = {2008, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	author = {Jouenne, F and Probert, I and Vaulot, D}
}
@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 {Six2007,
	title = {Diversity and evolution of phycobilisomes in marine Synechococcus spp. - a comparative genomics study},
	journal = {Genome Biology},
	volume = {8},
	year = {2007},
	note = {tex.mendeley-tags: 2007,rcc,sbr?hyto?app},
	pages = {R259},
	keywords = {2007, rcc, SBR$_\textrmP$hyto, sbr?hyto?app},
	doi = {10.1186/gb-2007-8-12-r259},
	author = {Six, C and Thomas, J.-C. and Garczarek, L and Ostrowski, M and Dufresne, A and Blot, N and Scanlan, D J and Partensky, F}
}
@article {Waters2007,
	title = {Evolutionary analysis of the small heat shock proteins in five complete algal genomes},
	journal = {Journal of Molecular Evolution},
	volume = {65},
	number = {2},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {162{\textendash}174},
	abstract = {Small heat shock proteins (sHSPs) are chaperones that are crucial in the heat shock response but also have important nonstress roles within the cell. sHSPs are found in all three domains of life (Bacteria, Archaea, and Eukarya). These proteins are particularly diverse within land plants and the evolutionary origin of the land plant sHSP families is still an open question. Here we describe the identification of 17 small sHSPs from the complete genome sequences of five diverse algae: Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ostreococcus lucimarinus, Ostreococcus tauri, and Thalassiosira pseudonana. Our analysis indicates that the number and diversity of algal sHSPs are not correlated with adaptation to extreme conditions. While all of the algal sHSPs identified are members of this large and important superfamily, none of these sHSPs are members of the diverse land plant sHSP families. The evolutionary relationships among the algal sHSPs and homologues from bacteria and other eukaryotes are consistent with the hypothesis that the land plant chloroplast and mitochondrion sHSPs did not originate from the endosymbionts of the chloroplast and mitochondria. In addition the evolutionary history of the sHSPs is very different from that of the HSP70s. Finally, our analysis of the algal sHSPs sequences in light of the known sHSP crystal structures and functional data suggests that the sHSPs possess considerable structural and functional diversity.},
	keywords = {*Evolution, *Genome, algae, Algae/classification/*genetics, Algal Proteins/*genetics, Amino Acid Sequence, Animals, Chlamydomonas reinhardtii/genetics, Diatoms/genetics, Green/genetics, Heat-Shock Proteins, Molecular, Molecular Sequence Data, phylogeny, Protein, rcc, Red/genetics, Sequence Alignment, Sequence Analysis, Small/*genetics, Species Specificity},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17684698},
	author = {Waters, E R and Rioflorido, I}
}
@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 {Dimier2007,
	title = {Photophysiological properties of the marine picoeukaryote Picochlorum RCC 237 (Trebouxiophyceae, Chlorophyta)},
	journal = {Journal of Phycology},
	volume = {43},
	number = {2},
	year = {2007},
	note = {ISBN: 0022-3646 tex.mendeley-tags: RCC,rcc},
	pages = {275{\textendash}283},
	abstract = {The photophysiological properties of strain RCC 237 belonging to the marine picoplanktonic genus Picochlorum, first described by Henley et al., were investigated under different photon flux densities (PFD), ranging from 40 to 400 mu mol photons. m(-2).s(-1), mainly focusing on the development of the xanthophyll cycle and its relationship with the nonphotochemical quenching of fluorescence (NPQ). The functioning of the xanthophyll cycle and its photoprotective role was investigated by applying a progressive increase of PFD and using dithiotreitol and norflurazon to block specific enzymatic reactions in order to study in depth the relationship between xanthophyll cycle and NPQ. These two processes were significantly related only during the gradually increasing light periods and not during stable light periods, where NPQ and zeaxanthin were decoupled. This result reveals that NPQ is a photoprotective process developed by algae only when cells are experiencing increasing PFD or in response to stressful light variations, for instance after a sudden light shift. Results showed that the photobiological properties of Picochlorum strain RCC 237 seem to be well related to the surface water characteristics, as it is able to maintain its photosynthetic characteristics under different PFDs and to quickly activate the xanthophyll cycle under high light.},
	keywords = {A FLUORESCENCE, CHLAMYDOMONAS-REINHARDTII, DIATOM PHAEODACTYLUM-TRICORNUTUM, ENERGY-DISSIPATION, fluctuating light, fluorescence quantum yield, MANTONIELLA-SQUAMATA, nonphotochemical quenching of fluorescence, photoacclimation, PHOTOSYNTHETIC APPARATUS, picoplankton, POOL SIZE, rcc, VIOLAXANTHIN DE-EPOXIDASE, Xanthophyll cycle, XANTHOPHYLL-CYCLE, zeaxanthin},
	doi = {10.1111/j.1529-8817.2007.00327.x},
	author = {Dimier, C and Corato, F and Saviello, G and Brunet, C}
}
@article {Khan2007,
	title = {Plastid genome sequence of the cryptophyte alga Rhodomonas salina CCMP1319: lateral transfer of putative DNA replication machinery and a test of chromist plastid phylogeny},
	journal = {Molecular Biology and Evolution},
	volume = {24},
	number = {8},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1832{\textendash}1842},
	abstract = {Cryptophytes are a group of unicellular algae with chlorophyll c-containing plastids derived from the uptake of a secondary (i.e., eukaryotic) endosymbiont. Biochemical and molecular data indicate that cryptophyte plastids are derived from red algae, yet the question of whether or not cryptophytes acquired their red algal plastids independent of those in heterokont, haptophyte, and dinoflagellate algae is of long-standing debate. To better understand the origin and evolution of the cryptophyte plastid, we have sequenced the plastid genome of Rhodomonas salina CCMP1319: at 135,854 bp, it is the largest secondary plastid genome characterized thus far. It also possesses interesting features not seen in the distantly related cryptophyte Guillardia theta or in other red secondary plastids, including pseudogenes, introns, and a bacterial-derived gene for the tau/gamma subunit of DNA polymerase III (dnaX), the first time putative DNA replication machinery has been found encoded in any plastid genome. Phylogenetic analyses indicate that dnaX was acquired by lateral gene transfer (LGT) in an ancestor of Rhodomonas, most likely from a firmicute bacterium. A phylogenomic survey revealed no additional cases of LGT, beyond a noncyanobacterial type rpl36 gene similar to that recently characterized in other cryptophytes and haptophytes. Rigorous concatenated analysis of 45 proteins encoded in 15 complete plastid genomes produced trees in which the heterokont, haptophyte, and cryptophyte (i.e., chromist) plastids were monophyletic, and heterokonts and haptophytes were each other{\textquoteright}s closest relatives. However, statistical support for chromist monophyly disappears when amino acids are recoded according to their chemical properties in order to minimize the impact of composition bias, and a significant fraction of the concatenate appears consistent with a sister-group relationship between cryptophyte and haptophyte plastids.},
	keywords = {*DNA Replication, *Gene Transfer, *Genome, Bacteria/*genetics, Cryptophyta/*genetics, DNA, evolution, genes, Horizontal, Molecular, phylogeny, Plant, Plastids/*genetics, rcc, Sequence Analysis, symbiosis},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17522086},
	author = {Khan, H and Parks, N and Kozera, C and Curtis, B A and Parsons, B J and Bowman, S and Archibald, J M}
}
@article {Piganeau2007,
	title = {Screening the Sargasso Sea metagenome for data to investigate genome evolution in Ostreococcus (Prasinophyceae, Chlorophyta)},
	journal = {Gene},
	volume = {406},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {184{\textendash}190},
	abstract = {The Sargasso Sea water shotgun sequencing unveiled an unprecedented glimpse of marine prokaryotic diversity and gene content. The sequence data was gathered from 0.8 ??m filtered surface water extracts, and revealed picoeukaryotic (cell size {\textexclamdown} 2 ??m) sequences alongside the prokaryotic data. We used the available genome sequence of the picoeukaryote Ostreococcus tauri (Prasinophyceae, Chlorophyta) as a benchmark for the eukaryotic sequence content of the Sargasso Sea metagenome. Sequence data from at least two new Ostreococcus strains were identified and analyzed, and showed a bias towards higher coverage of the AT-rich organellar genomes. The Ostreococcus nuclear sequence data retrieved from the Sargasso metagenome is divided onto 731 scaffolds of average size 3917 bp, and covers 23\% of the complete nuclear genome and 14\% of the total number of protein coding genes in O. tauri. We used this environmental Ostreococcus sequence data to estimate the level of constraint on intronic and intergenic sequences in this compact genome.},
	keywords = {rcc},
	doi = {10.1016/j.gene.2007.09.015},
	author = {Piganeau, G and Moreau, H}
}
@article {Palenik2007,
	title = {The tiny eukaryote \textit{Ostreococcus provides genomic insights into the paradox of plankton speciation},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {104},
	number = {18},
	year = {2007},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {7705{\textendash}7710},
	abstract = {The smallest known eukaryotes, at approximately 1-mum diameter, are Ostreococcus tauri and related species of marine phytoplankton. The genome of Ostreococcus lucimarinus has been completed and compared with that of O. tauri. This comparison reveals surprising differences across orthologous chromosomes in the two species from highly syntenic chromosomes in most cases to chromosomes with almost no similarity. Species divergence in these phytoplankton is occurring through multiple mechanisms acting differently on different chromosomes and likely including acquisition of new genes through horizontal gene transfer. We speculate that this latter process may be involved in altering the cell-surface characteristics of each species. In addition, the genome of O. lucimarinus provides insights into the unique metal metabolism of these organisms, which are predicted to have a large number of selenocysteine-containing proteins. Selenoenzymes are more catalytically active than similar enzymes lacking selenium, and thus the cell may require less of that protein. As reported here, selenoenzymes, novel fusion proteins, and loss of some major protein families including ones associated with chromatin are likely important adaptations for achieving a small cell size.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17460045},
	author = {Palenik, B and Grimwood, J and Aerts, A and Rouz{\'e}, P and Salamov, A and Putnam, N and Dupont, C and Jorgensen, R and Derelle, E and Rombauts, S and Zhou, K and Otillar, R and Merchant, S S and Podell, S and Gaasterland, T and Napoli, C and Gendler, K and Manuell, A and Tai, V and Vallon, O and Piganeau, G and Jancek, S and Heijde, M and Jabbari, K and Bowler, C and Lohr, M and Robbens, S and Werner, G and Dubchak, I and Pazour, G J and Ren, Q and Paulsen, I and Delwiche, C and Schmutz, J and Rokhsar, D and Van de Peer, Y and Moreau, H and Grigoriev, I V}
}
@article {Countway2006,
	title = {Abundance and distribution of Ostreococcus sp in the San Pedro Channel, California, as revealed by quantitative PCR},
	journal = {Applied and Environmental Microbiology},
	volume = {72},
	number = {4},
	year = {2006},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {2496{\textendash}2506},
	abstract = {Ostreococcus is a genus of widely distributed marine phytoplankton which are picoplanktonic in size ({\textexclamdown} 2 mu m) and capable of rapid growth. Although Ostreococcus has been detected around the world, little quantitative information exists on its contribution to planktonic communities. We designed and implemented a genus-specific TaqMan-based quantitative PCR (qPCR) assay to investigate the dynamics and ecology of Ostreococcus at the USC Microbial Observatory (eastern North Pacific). Samples were collected from 5 m and the deep chlorophyll maximum (DCM) between September 2000 and August 2002. Ostreococcus abundance at 5 m was generally {\textexclamdown} 5.0 X 10(3) cells ml(-1), with a maximum of 8.2 X 10(4) cells ml(-1). Ostreococcus abundance was typically higher at the DCM, with a maximum of 3.2 X 10(5) cells ml(-1). The vertical distribution of Ostreococcus was examined in March 2005 and compared to the distribution of phototrophic picoeukaryotes (PPE) measured by flow cytometry. The largest contribution to PPE abundance by Ostreococcus was similar to 70\% and occurred at 30 m, near the DCM. Despite its relatively low abundance, the depth-integrated standing stock of Ostreococcus in March 2005 was similar to 30 mg C m(-2). Our work provides a new technique for quantifying the abundance of Ostreococcus and demonstrates the seasonal dynamics of this genus and its contribution to picoeukaryote biomass at our coastal sampling station.},
	keywords = {16s-ribosomal-rna, Biology-, english-channel, eukaryotic-picoplankton, in-situ-hybridization, marine-ecosystems, microbial-populations, microbiology-, Micromonas, pfiesteria-piscicida, rcc, Real-time-pcr, sp-nov, tauri-chlorophyta},
	doi = {10.1128/AEM.72.4.2496-2506.2006},
	author = {Countway, P D and Caron, D A}
}
@article {Fuller2006,
	title = {Analysis of photosynthetic picoeukaryote diversity at open ocean sites in the Arabian Sea using a PCR biased towards marine algal plastids},
	journal = {Aquatic Microbial Ecology},
	volume = {43},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {79{\textendash}93},
	keywords = {2006, PICOCEAN, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.3354/ame043079},
	author = {Fuller, Nicholas J and Campbell, Colin and Allen, David J and Pitt, Frances D and Le Gall, F and Vaulot, Daniel and Scanlan, David J}
}
@article {Everroad2006,
	title = {Biochemical bases of Type IV chromatic adaptation in marine Synechococcus spp.},
	journal = {Journal of Bacteriology},
	volume = {188},
	year = {2006},
	note = {tex.mendeley-tags: 2006,rcc,sbr?hyto?app},
	pages = {3345{\textendash}3356},
	keywords = {2006, rcc, SBR$_\textrmP$hyto, sbr?hyto?app},
	doi = {10.1128/JB.188.9.3345-3356.2006},
	author = {Everroad, C and Six, C and Partensky, F and Thomas, J C and Holtzendorff, J and Wood, A M}
}
@article {Derelle2006,
	title = {Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {31},
	year = {2006},
	note = {tex.mendeley-tags: RCC745},
	pages = {11647{\textendash}11652},
	abstract = {The green lineage is reportedly 1,500 million years old, evolving shortly after the endosymbiosis event that gave rise to early photosynthetic eukaryotes. In this study, we unveil the complete genome sequence of an ancient member of this lineage, the unicellular green alga Ostreococcus tauri (Prasinophyceae). This cosmopolitan marine primary producer is the world{\textquoteright}s smallest free-living eukaryote known to date. Features likely reflecting optimization of environmentally relevant pathways, including resource acquisition, unusual photosynthesis apparatus, and genes potentially involved in C4 photosynthesis, were observed, as was downsizing of many gene families. Overall, the 12.56-Mb nuclear genome has an extremely high gene density, in part because of extensive reduction of intergenic regions and other forms of compaction such as gene fusion. However, the genome is structurally complex. It exhibits previously unobserved levels of heterogeneity for a eukaryote. Two chromosomes differ structurally from the other eighteen. Both have a significantly biased G+C content, and, remarkably, they contain the majority of transposable elements. Many chromosome 2 genes also have unique codon usage and splicing, but phylogenetic analysis and composition do not support alien gene origin. In contrast, most chromosome 19 genes show no similarity to green lineage genes and a large number of them are specialized in cell surface processes. Taken together, the complete genome sequence, unusual features, and downsized gene families, make O. tauri an ideal model system for research on eukaryotic genome evolution, including chromosome specialization and green lineage ancestry.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1073/pnas.0604795103},
	url = {http://www.pnas.org/cgi/content/abstract/103/31/11647},
	author = {Derelle, Evelyne and Ferraz, Conchita and Rombauts, Stephane and Rouze, Pierre and Worden, Alexandra Z and Robbens, Steven and Partensky, Fr{\'e}d{\'e}ric and Degroeve, Sven and Echeynie, Sophie and Cooke, Richard and Saeys, Yvan and Wuyts, Jan and Jabbari, Kamel and Bowler, Chris and Panaud, Olivier and Piegu, Benoit and Ball, Steven G and Ral, Jean-Philippe and Bouget, Fran{\c c}ois-Yves and Piganeau, Gwenael and De Baets, Bernard and Picard, Andr{\'e} and Delseny, Michel and Demaille, Jacques and Van de Peer, Yves and Moreau, Herv{\'e}}
}
@article {Palenik2006,
	title = {Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	volume = {103},
	number = {36},
	year = {2006},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {13555{\textendash}13559},
	abstract = {Coastal aquatic environments are typically more highly productive and dynamic than open ocean ones. Despite these differences, cyanobacteria from the genus Synechococcus are important primary producers in both types of ecosystems. We have found that the genome of a coastal cyanobacterium, Synechococcus sp. strain CC9311, has significant differences from an open ocean strain, Synechococcus sp. strain WH8102, and these are consistent with the differences between their respective environments. CC9311 has a greater capacity to sense and respond to changes in its (coastal) environment. It has a much larger capacity to transport, store, use, or export metals, especially iron and copper. In contrast, phosphate acquisition seems less important, consistent with the higher concentration of phosphate in coastal environments. CC9311 is predicted to have differences in its outer membrane lipopolysaccharide, and this may be characteristic of the speciation of some cyanobacterial groups. In addition, the types of potentially horizontally transferred genes are markedly different between the coastal and open ocean genomes and suggest a more prominent role for phages in horizontal gene transfer in oligotrophic environments.},
	keywords = {rcc},
	doi = {10.1073/pnas.0602963103},
	url = {http://www.pnas.org/cgi/content/abstract/103/36/13555},
	author = {Palenik, Brian and Ren, Qinghu and Dupont, Chris L and Myers, Garry S and Heidelberg, John F and Badger, Jonathan H and Madupu, Ramana and Nelson, William C and Brinkac, Lauren M and Dodson, Robert J and Durkin, A Scott and Daugherty, Sean C and Sullivan, Stephen A and Khouri, Hoda and Mohamoud, Yasmin and Halpin, Rebecca and Paulsen, Ian T}
}
@article {Slapeta2006,
	title = {Global dispersal and ancient cryptic species in the smallest marine eukaryotes},
	journal = {Molecular Biology and Evolution},
	volume = {23},
	number = {1},
	year = {2006},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {23{\textendash}29},
	abstract = {Small eukaryotic species ({\textexclamdown}1 mm) are thought to behave as prokaryotes in that, lacking geographical barriers to their dispersal due to their tiny size, they are ubiquitous. Accordingly, the absence of geographical insulation would imply the existence of a relatively small number of microeukaryotic species. To test these ideas, we sequenced and compared several nuclear, mitochondrial, and chloroplast genes from the isolates of a marine picoeukaryotic alga ([\~]2 microm), Micromonas pusilla, collected worldwide. Independent and combined phylogenetic analyses demonstrate that this traditional single morphospecies actually comprises several independent lineages, some of which are shown to be ubiquitous in oceans. However, while some lineages group closely related strains, others form distant clusters, revealing the existence of cryptic species. Moreover, molecular dating using a relaxed clock suggests that their first diversification may have started as early as during the Late Cretaceous ([\~]65 MYA), implying that "M. pusilla" is the oldest group of cryptic species known to date. Our results illustrate that global dispersal of a picoeukaryote is possible in oceans, but this does not imply a reduced species number. On the contrary, we show that the morphospecies concept is untenable because it overlooks a large genetic and species diversity and may lead to incorrect biological assumptions.},
	keywords = {Micromonas, rcc},
	doi = {10.1093/molbev/msj001},
	url = {http://mbe.oxfordjournals.org/cgi/content/abstract/23/1/23},
	author = {Slapeta, Jan and L{\'o}pez-Garc{\'\i}a, P and Moreira, David}
}
@article {Worden2006,
	title = {Picoeukaryote diversity in coastal waters of the Pacific Ocean},
	journal = {Aquatic Microbial Ecology},
	volume = {43},
	number = {2},
	year = {2006},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {165{\textendash}175},
	abstract = {The extraordinary molecular phylogenetic diversity of picoeukaryotes and their contributions to marine processes have been highlighted recently. Herein, picoeukaryotic diversity in the coastal Pacific Ocean is characterized for the first time, Close to full length small subunit ribosomal RNA (ssu rRNA) gene amplicons were cloned and sequenced from size fractionated samples ({\textexclamdown} 2 mu m) taken between September 2000 and October 2001. Sequences belonging to the order Mamiellales were abundant, with Micromonas pusilla-like sequences in all 5 libraries (4 operational taxonomic units, OTUs, at {\textquestiondown}= 99\% sequence similarity), Ostreococcus in 4 (1 OTU) and Bathycoccus in 2 (1 OTU). Phylogenetic reconstruction showed distinct Micromonas clades at this site (although not for other Mamiellales), supporting the idea that the designation M pusilla harbors cryptic species. In combination with picophytoplankton dynamics previously reported for the same period, the data indicates that picoplanktonic primary production at this site is likely to be dominated by prasinophytes. Furthermore, a Micromonas-clade with no cultured representatives was identified bearing highest identity to Sargasso Sea shotgun clone sequences. Comparison of the Pacific sequences with the shotgun clones showed Ostreococcus and Micromonas at 1 Sargasso site with elevated chlorophyll (chl) levels, but not at other Sargasso sites. Other Pacific clones were primarily Novel Alveolate Group II, which were highly diverse based on OTU analyses. Novel Alveolate Group 1, Ciliophora, Cercozoa-like and stramenopile sequences were also retrieved. Although picoeukaryotic diversity has been characterized in only 1 other Pacific Ocean sample (equatorial Pacific), most stramenopile and alveolate sequences corresponded to previously identified phylogenetic clades from studies conducted in other oceans and for which no cultured representatives exist.},
	keywords = {18s rdna sequences, 18S rRNA, community structure, diversity, english-channel, eukaryotic picoplankton, global dispersal, Micromonas, north-atlantic, phylogenetic analysis, picoeukaryotes, picophytoplankton, picoplankton, prasinophytes, pusilla, rcc, RIBOSOMAL-RNA GENE, sargasso sea, small subunit, vibrio-cholerae},
	doi = {10.3354/ame043165},
	author = {Worden, A Z}
}
@article {Bruyant2005,
	title = {Diel variations in the photosynthetic parameters of Prochlorococcus strain PCC 9511: combined effects of light and cell cycle},
	journal = {Limnology and Oceanography},
	volume = {50},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {850{\textendash}863},
	keywords = {2005, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.4319/lo.2005.50.3.0850},
	author = {Bruyant, F and Babin, M and Genty, B and Prasil, O and Behrenfeld, M J and Claustre, H and Bricaud, A and Holtzendorff, J and Koblizek, M and Garczareck, L and Partensky, F}
}
@article {Rodriguez2005h,
	title = {Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae).},
	journal = {Environmental Microbiology},
	volume = {7},
	year = {2005},
	note = {tex.mendeley-tags: RCC113,RCC143,RCC343,RCC356,RCC371,RCC393,RCC410,RCC420,RCC434,RCC501,RCC658,RCC745,Rcc141},
	pages = {853{\textendash}859},
	keywords = {rcc, RCC113, Rcc141, RCC143, RCC343, RCC356, RCC371, RCC393, rcc410, RCC420, RCC434, rcc501, RCC658, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1111/j.1462-2920.2005.00758.x},
	author = {Rodriguez, F and Derelle, E and Guillou, L and Le Gall, F and Vaulot, D and Moreau, H}
}
@article {Robbens2005,
	title = {Genome-wide analysis of core cell cycle genes in the unicellular green alga Ostreococcus tauri},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {3},
	year = {2005},
	note = {tex.mendeley-tags: RCC745},
	pages = {589{\textendash}597},
	abstract = {The cell cycle has been extensively studied in various organisms, and the recent access to an overwhelming amount of genomic data has given birth to a new integrated approach called comparative genomics. Comparing the cell cycle across species shows that its regulation is evolutionarily conserved; the best-known example is the pivotal role of cyclin-dependent kinases in all the eukaryotic lineages hitherto investigated. Interestingly, the molecular network associated with the activity of the CDK-cyclin complexes is also evolutionarily conserved, thus, defining a core cell cycle set of genes together with lineage-specific adaptations. In this paper, we describe the core cell cycle genes of Ostreococcus tauri, the smallest free-living eukaryotic cell having a minimal cellular organization with a nucleus, a single chloroplast, and only one mitochondrion. This unicellular marine green alga, which has diverged at the base of the green lineage, shows the minimal yet complete set of core cell cycle genes described to date. It has only one homolog of CDKA, CDKB, CDKD, cyclin A, cyclin B, cyclin D, cyclin H, Cks, Rb, E2F, DP, DEL, Cdc25, and Wee L We have also added the APC and SCF E3 ligases to the core cell cycle gene set. We discuss the potential of genome-wide analysis in the identification of divergent orthologs of cell cycle genes in different lineages by mining the genomes of evolutionarily important and strategic organisms.},
	keywords = {Anaphase Promoting Complex, Arabidopsis Thaliana, Cdk Activity, cell division cycle, Chlorophyta, cyclin, cyclin dependant kinase, Green alga, Kinase, Ostreococcus tauri, Plant, Prasinophyceae, rcc, RCC745, Retinoblastoma Protein, Saccharomyces Cerevisiae, Yeast},
	doi = {10.1093/molbev/msi044},
	author = {Robbens, S and Khadaroo, B and Camasses, A and Derelle, E and Ferraz, C and Inze, D and Van, de Peer Y and Moreau, H}
}
@article {Zhu2005,
	title = {Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene},
	journal = {FEMS Microbiology Ecology},
	volume = {52},
	number = {1},
	year = {2005},
	note = {tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {79{\textendash}92},
	abstract = {A quantitative PCR (QPCR) assay based on the use of SYBR Green I was developed to assess the abundance of specific groups of picoeukaryotes in marine waters. Six primer sets were designed targeting four different taxonomic levels: domain (Eukaryota), division (Chlorophyta), order (Mamiellales) and genus (Bathycoccus, Micromonas, and Ostreococcus). Reaction conditions were optimized for each primer set which was validated in silico, on agarose gels, and by QPCR against a variety of target and non-target cultures. The approach was tested by estimating gene copy numbers for Micromonas, Bathycoccus, and Ostreococcus in seawater samples to which cultured cells were added in various concentrations. QPCR was then used to determine that rRNA gene (rDNA) copy number varied from one to more than 12,000 in 18 strains of phytoplankton. Finally, QPCR was applied to environmental samples from a Mediterranean Sea coastal site and the results were compared to those obtained by Fluorescent in situ hybridization (FISH). The data obtained demonstrate that Chlorophyta and more specifically Mamiellales were important in these waters, especially during the winter picoplankton bloom. The timing of major abundance peaks of the targeted species was similar by QPCR and FISH. When used in conjunction with other techniques such as FISH or gene clone libraries, QPCR appears as very promising to quickly obtain data on the ecological distribution of important phytoplankton groups. Data interpretation must take into account primer specificity and the varying rRNA gene copy number among eukaryotes. ?? 2004 Federation of European Microbiological Societies. Published by Elsevier B.V. All rights reserved.},
	keywords = {Coastal ecosystems, Ecology, Fluorescent in situ hybridization, Micromonas, picoplankton, prasinophytes, Quantitative PCR, rcc},
	author = {Zhu, Fei and Massana, Ramon and Not, Fabrice and Marie, Dominique and Vaulot, Daniel}
}
@article {Six2005a,
	title = {New insights into the nature and phylogeny of prasinophyte antenna proteins: Ostreococcus tauri, a case study},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {11},
	year = {2005},
	note = {tex.mendeley-tags: RCC113,RCC114,RCC745: RCC417},
	pages = {2217{\textendash}2230},
	abstract = {The basal position of the Mamiellales (Prasinophyceae) within the green lineage makes these unicellular organisms key to elucidating early stages in the evolution of chlorophyll a/b{\textendash}binding light-harvesting complexes (LHCs). Here, we unveil the complete and unexpected diversity of Lhc proteins in Ostreococcus tauri, a member of the Mamiellales order, based on results from complete genome sequencing. Like Mantoniella squamata, O. tauri possesses a number of genes encoding an unusual prasinophyte-specific Lhc protein type herein designated "Lhcp". Biochemical characterization of the complexes revealed that these polypeptides, which bind chlorophylls a, b, and a chlorophyll c{\textendash}like pigment (Mg-2,4-divinyl-phaeoporphyrin a5 monomethyl ester) as well as a number of unusual carotenoids, are likely predominant. They are retrieved to some extent in both reaction center I (RCI){\textendash} and RCII-enriched fractions, suggesting a possible association to both photosystems. However, in sharp contrast to previous reports on LHCs of M. squamata, O. tauri also possesses other LHC subpopulations, including LHCI proteins (encoded by five distinct Lhca genes) and the minor LHCII polypeptides, CP26 and CP29. Using an antibody against plant Lhca2, we unambiguously show that LHCI proteins are present not only in O. tauri, in which they are likely associated to RCI, but also in other Mamiellales, including M. squamata. With the exception of Lhcp genes, all the identified Lhc genes are present in single copy only. Overall, the discovery of LHCI proteins in these prasinophytes, combined with the lack of the major LHCII polypeptides found in higher plants or other green algae, supports the hypothesis that the latter proteins appeared subsequent to LHCI proteins. The major LHC of prasinophytes might have arisen prior to the LHCII of other chlorophyll a/b{\textendash}containing organisms, possibly by divergence of a LHCI gene precursor. However, the discovery in O. tauri of CP26-like proteins, phylogenetically placed at the base of the major LHCII protein clades, yields new insight to the origin of these antenna proteins, which have evolved separately in higher plants and green algae. Its diverse but numerically limited suite of Lhc genes renders O. tauri an exceptional model system for future research on the evolution and function of LHC components.},
	keywords = {rcc, RCC113, RCC114, RCC417, RCC745, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1093/molbev/msi220},
	author = {Six, C and Worden, A Z and Rodriguez, F and Moreau, H and Partensky, F}
}
@inbook {Marie2005,
	title = {Phytoplankton cell counting by flow cytometry},
	booktitle = {Algal culturing techniques},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {253{\textendash}267},
	publisher = {Academic Press},
	organization = {Academic Press},
	keywords = {2005, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto},
	author = {Marie, D and Simon, N and Vaulot, D},
	editor = {Andersen, R A}
}
@article {Six2005,
	title = {Two novel phycoerythrin-associated linker proteins in the marine cyanobacterium synechococcus sp. Strain WH8102},
	journal = {Journal of Bacteriology},
	volume = {187},
	number = {5},
	year = {2005},
	note = {tex.mendeley-tags: 2005,rcc,sbr?hyto},
	pages = {1685{\textendash}1694},
	abstract = {The recent availability of the whole genome of Synechococcus sp. strain WH8102 allows us to have a global view of the complex structure of the phycobilisomes of this marine picocyanobacterium. Genomic analyses revealed several new characteristics of these phycobilisomes, consisting of an allophycocyanin core and rods made of one type of phycocyanin and two types of phycoerythrins (I and II). Although the allophycocyanin appears to be similar to that found commonly in freshwater cyanobacteria, the phycocyanin is simpler since it possesses only one complete set of alpha and beta subunits and two rod-core linkers (CpcG1 and CpcG2). It is therefore probably made of a single hexameric disk per rod. In contrast, we have found two novel putative phycoerythrin-associated linker polypeptides that appear to be specific for marine Synechococcus spp. The first one (SYNW2000) is unusually long (548 residues) and apparently results from the fusion of a paralog of MpeC, a phycoerythrin II linker, and of CpeD, a phycoerythrin-I linker. The second one (SYNW1989) has a more classical size (300 residues) and is also an MpeC paralog. A biochemical analysis revealed that, like MpeC, these two novel linkers were both chromophorylated with phycourobilin. Our data suggest that they are both associated (partly or totally) with phycoerythrin II, and we propose to name SYNW2000 and SYNW1989 MpeD and MpeE, respectively. We further show that acclimation of phycobilisomes to high light leads to a dramatic reduction of MpeC, whereas the two novel linkers are not significantly affected. Models for the organization of the rods are proposed.},
	keywords = {2005, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1128/JB.187.5.1685-1694.2005},
	url = {http://jb.asm.org/cgi/content/abstract/187/5/1685},
	author = {Six, Christophe and Thomas, Jean-Claude and Thion, Laurent and Lemoine, Yves and Zal, Frank and Partensky, Fr{\'e}d{\'e}ric}
}
@article {Romari2004,
	title = {Composition and temporal variability of picoeukaryote communities at a coastal site of the English Channel from 18S rDNA sequences},
	volume = {49},
	number = {3},
	year = {2004},
	note = {Publication Title: Limnology and oceanography ISBN: 0024-3590 tex.mendeley-tags: Micromonas,RCC,rcc},
	pages = {784{\textendash}798},
	abstract = {Abstract We analyzed picoeukaryote assemblages at a French coastal site of the English Channel by sequencing cloned eukaryotic 18S rRNA genes in eight genetic libraries constructed from environmental samples (seven coastal , one estuarine) collected at different periods of the ...},
	keywords = {Micromonas, rcc},
	issn = {00243590},
	doi = {10.4319/lo.2004.49.3.0784},
	author = {Romari, Khadidja and Vaulot, Daniel}
}
@article {Guillou2004,
	title = {Diversity of picoplanktonic prasinophytes assessed by direct nuclear SSU rDNA sequencing of environmental samples and novel isolates retrieved from oceanic and coastal marine ecosystems},
	journal = {Protist},
	volume = {155},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {193{\textendash}214},
	keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto, SOMLIT},
	doi = {10.1078/143446104774199592},
	author = {Guillou, Laure and Eikrem, W and Chr{\'e}tiennot-Dinet, M.-J. and Le Gall, F and Massana, R and Romari, K and Pedr{\'o}s-Ali{\'o}, C and Vaulot, D}
}
@article {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 {Latasa2004,
	title = {Pigment suites and taxonomic groups in Prasinophyceae},
	journal = {Journal of Phycology},
	volume = {40},
	number = {6},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	month = {dec},
	pages = {1149{\textendash}1155},
	keywords = {2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto},
	issn = {00223646},
	doi = {10.1111/j.1529-8817.2004.03136.x},
	url = {http://doi.wiley.com/10.1111/j.1529-8817.2004.03136.x},
	author = {Latasa, Mikel and Scharek, Renate and Gall, Florence Le and Guillou, Laure and Le Gall, F}
}
@article {Vaulot2004,
	title = {The roscoff culture collection (RCC): a collection dedicated to marine picoplankton},
	journal = {Nova Hedwigia},
	volume = {79},
	number = {1/2},
	year = {2004},
	note = {tex.mendeley-tags: 2004,rcc,sbr?hyto},
	pages = {49{\textendash}70},
	keywords = {10$_\textrmb$est, 2004, PICODIV, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto},
	doi = {10.1127/0029-5035/2004/0079-0049},
	author = {Vaulot, D and Le Gall, F and Marie, D and Guillou, L and Partensky, F}
}
@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 {Palenik2003,
	title = {The genome of a motile marine Synechococcus},
	journal = {Nature},
	volume = {424},
	number = {6952},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {1037{\textendash}1042},
	abstract = {Marine unicellular cyanobacteria are responsible for an estimated 20-40\% of chlorophyll biomass and carbon fixation in the oceans(1). Here we have sequenced and analysed the 2.4-megabase genome of Synechococcus sp. strain WH8102, revealing some of the ways that these organisms have adapted to their largely oligotrophic environment. WH8102 uses organic nitrogen and phosphorus sources and more sodium-dependent transporters than a model freshwater cyanobacterium. Furthermore, it seems to have adopted strategies for conserving limited iron stores by using nickel and cobalt in some enzymes, has reduced its regulatory machinery (consistent with the fact that the open ocean constitutes a far more constant and buffered environment than fresh water), and has evolved a unique type of swimming motility. The genome of WH8102 seems to have been greatly influenced by horizontal gene transfer, partially through phages. The genetic material contributed by horizontal gene transfer includes genes involved in the modification of the cell surface and in swimming motility. On the basis of its genome, WH8102 is more of a generalist than two related marine cyanobacteria(2).},
	keywords = {2003, Cyanobacterium Synechococcus, Degradation, Ecology, Gene, IDENTIFICATION, Polypeptide, Prochlorococcus, rcc, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, Sp Pcc7942, Strains},
	doi = {10.1038/nature01943},
	author = {Palenik, B and Brahamsha, B and Larimer, F W and Land, M and Hauser, L and Chain, P and Lamerdin, J and Regala, W and Allen, E E and McCarren, J and Paulsen, I and Dufresne, A and Partensky, F and Webb, E A and Waterbury, J}
}
@article {Biegala2003,
	title = {Quantitative assessment of picoeucaryotes in the natural environment using taxon specific oligonucleotide probes in association with TSA-FISH (Tyramide Signal Amplification - Fluorescent In Situ Hybridization) and flow cytometry},
	journal = {Applied and Environmental Microbiology},
	volume = {69},
	year = {2003},
	note = {tex.mendeley-tags: 2003,rcc,sbr?hyto},
	pages = {5519{\textendash}5529},
	keywords = {2003, PICODIV, rcc, SBR$_\textrmP$hyto, sbr?hyto, SOMLIT},
	doi = {10.1128/AEM.69.9.5519-5529.2003},
	author = {Biegala, I C and Not, F and Vaulot, D and Simon, N}
}
@article {Toledo2003,
	title = {A Synechococcus serotype is found preferentially in surface marine waters},
	journal = {Limnology and Oceanography},
	volume = {48},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1744{\textendash}1755},
	abstract = {In marine ecosystems, gradients of light, temperature, and nutrients occur horizontally (coastal to offshore) and vertically. The extent to which microorganisms acclimate or speciate in response to these gradients is under active investigation. Strain isolation data (e.g., site or depth), environmental DNA clone libraries, and preliminary physiology experiments have indicated that marine Synechococcus strain CC9605 might be adapted to the surface oligotrophic ocean. In the present work, we used an immunofluorescent approach to detect the CC9605 serotype in the California Current during September 1998. At two offshore stations, samples were collected along vertical profiles. The relative abundance of the CC9605 serotype was significantly higher in shallow depths within the mixed layer than in deeper depths at the two stations, with maximum values (+/- standard deviation) of 10.3\% +/- 6.4 and 28.7\% +/- 9.5. Surface samples along an offshore-inshore transect showed higher abundance in the most oligotrophic site (8\% +/- 3), compared with almost 1\% inshore, but one coastal site also had high relative abundance of the CC9605 serotype (7\% +/- 0.5). These data indicate that Synechococcus strains are not uniformly distributed and that some strains, such as CC9605, are more abundant in the mixed layer of the euphotic zone than below the mixed layer.},
	keywords = {Aquatic-sciences, california-current, cyanobacteria-, diversity-, flow-cytometry, immunofluorescence-, North-atlantic-ocean, phytoplankton-, prochlorococcus-populations, rcc, sargasso-sea, strains-},
	doi = {10.4319/lo.2003.48.5.1744},
	author = {Toledo, G and Palenik, B}
}
@article {OKelly2003,
	title = {A transient bloom of {\textexclamdown}i{\textquestiondown}Ostreococcus{\textexclamdown}/i{\textquestiondown} (chlorophyta, prasinophyceae) in west neck bay, long island, new york},
	journal = {Journal of Phycology},
	volume = {39},
	number = {5},
	year = {2003},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {850{\textendash}854},
	abstract = {The smallest known eukaryote, Ostreococcus tauri Courties et Chretiennot-Dinet, was first reported as the dominant picoplankter in a French lagoon known for its diverse phytoplankton community and high oyster productivity. Long-term seasonal blooms of this picoeukaryote were observed in association with stable plankton communities. On 5 June 2001, a distinctive monotypic picoplankton bloom was detected by flow cytometry as part of an ongoing study of "brown tide" (Aureococcus anophagefferens) bloom initiation in Long Island bays. The bloom reached a concentration of 5 x 10(5) cells.mL(-1) in West Neck Bay and lasted less than 2 weeks. Epifluorescence microscopy and TEM indicated that the bloom organism was an Ostreococcus-like picoalga, the first ever observed in a Long Island bay. Many cells of this alga contained numerous virus-like particles. The Ostreococcus-like picoalga, which resembles O. tauri, was rare in samples collected the following week. Instead, a substantial increase in the Synechococcus population was observed. Such rapid population changes have not previously been reported for Ostreococcus. Viral lysis and grazing by heterotrophic nanoflagellates may have contributed to the rapid decline of the Ostreococcus-like cells in West Neck Bay.},
	keywords = {Aureococcus Anophagefferens Pelagophyceae, bloom dynamics, Gen, Microalga, Ostreococcus, picoalgae, picoplankton, rcc},
	doi = {10.1046/j.1529-8817.2003.02201.x},
	author = {O{\textquoteright}Kelly, C J and Sieracki, M E and Thier, E C and Hobson, I C}
}
@article {Not2002,
	title = {Application of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA) to assess eukaryotic picoplankton composition},
	volume = {28},
	year = {2002},
	note = {Publication Title: Aquatic microbial ecology tex.mendeley-tags: RCC,rcc},
	pages = {157{\textendash}166},
	abstract = {Photosynthetic picoeukaryotes (phytoplankton cells with a diameter smaller than 2 to 3 ??m) contribute significantly to both biomass and primary production in the oligotrophic open ocean and coastal waters, at certain times of the year. The identification of these organisms is difficult because of their small size and simple morphology, therefore hindering detailed ecological studies of their distribution and role. In this paper, we demonstrate the use of oligonucleotide probes specific to algal classes or to lower order taxa in combination with fluorescent in situ hybridization and tyramide signal amplification (FISH-TSA) to determine eukaryotic picophytoplankton diversity. Target cells were detected and enumerated using epifluorescence microscopy. The sensitivity of the technique and the specificity of the probes were tested on pure and mixed picoplanktonic strains, as well as on natural samples from the English Channel. In these samples, the community was dominated by cells belonging to the division Chlorophyta. Haptophyta, Bolidophyceae and Pelagophyceae were also detected at low abundance. The FISH-TSA method is readily applicable to the study of picoplankton diversity in natural communities.},
	keywords = {rcc},
	issn = {0948-3055},
	doi = {10.3354/ame028157},
	author = {Not, F and Simon, N and Biegala, IC and Vaulot, D}
}
@article {Derelle2002,
	title = {DNA libraries for sequencing the genome of Ostreococcus tauri (Chlorophyta, Prasinophyceae): The smallest free-living eukaryotic cell},
	journal = {Journal of Phycology},
	volume = {38},
	number = {6},
	year = {2002},
	note = {tex.mendeley-tags: RCC745},
	pages = {1150{\textendash}1156},
	abstract = {Ostreococcus tauri is a marine photosynthetic picoeukaryote presenting a minimal cellular organization with one nucleus, one chloroplast, and one mitochondrion. It has the smallest genome described among free-living eukaryotic cells, and we showed by pulsed-field gel electrophoresis (PFGE) that it is divided between 15 bands ranging from 1.2 to 0.15 Mb, giving a total size of 9.7 Mb. A Bacterial Artificial Chromosome (BAC) library was prepared from genomic DNA extracted from a culture of O. tauri. A total of 2457 clones was obtained with an average insert size of around 70 kb, representing an 18-fold coverage of the genome. The library was spotted on high density filters, and several probes of coding sequences were hybridized to both the high density BAC library filters and directly to the dried PFGE gels of the O. tauri genomic DNA. These hybridizations allowed a preliminary organization of the library and the localization of several markers on the chromosomes. Randomly selected fragments were also sequenced, representing 12\% of the O. tauri genome. Many sequences showed significant similarities in data banks, mainly with plant and algae sequences. About 1000 coding sequences could be identified. These data confirmed the position of O. tauri in the green lineage and the hypothesis of a very compact organization of its genome.},
	keywords = {Pico$_\textrmR$eview, rcc, RCC745},
	doi = {10.1046/j.1529-8817.2002.02021.x},
	url = {c:\%5CDV\%5CPapers reprints\%5CPhytoplankton Physiology\%5CDerelle Ostreococcus DNA libraries JPhycol 02.pdf},
	author = {Derelle, E and Ferraz, C and Lagoda, P and Eychenie, S and Cooke, R and Regad, F and Sabau, X and Courties, C and Delseny, M and Demaille, J and Picard, A and Moreau, H}
}
@article {Laloui2002,
	title = {Genotyping of axenic and non-axenic isolates of the genus Prochlorococcus and the OMF-{\textquoteright}Synechococcus{\textquoteright} clade by size, sequence analysis or RFLP of the Internal Transcribed Spacer of the ribosomal operon},
	journal = {Microbiology},
	volume = {148},
	number = {2},
	year = {2002},
	note = {tex.mendeley-tags: 2002,rcc,sbr?hyto},
	pages = {453{\textendash}465},
	abstract = {PCR amplicons of the Internal Transcribed Spacer (ITS) of the rrn operon of three axenic OMF (oceanic, marine and freshwater) strains of {\textquoteright}Synechococcus{\textquoteright} (wH7803, PCC 7001 and PCC 6307, respectively) differ greatly in length from that of the axenic Prochlorococcus marinus subsp. pastoris PCC 9511(T), although these four cyanobacteria cluster relatively closely in phylogenetic trees inferred from 165 rRNA gene sequences. The ITSs of three strains (PCC 9511(T), PCC 6307 and PCC 7001) were sequenced and compared with those available for strains Prochlorococcus MED4 (CCMP 1378) and MIT9313 from genome sequencing projects. In spite of large differences in length, sequence and mean DNA base composition, conserved domains important for transcriptional antitermination and folding of the rRNA transcripts were identified in all ITSs. A new group-specific primer permitted ITS amplification even with non-axenic isolates of Prochlorococcus and one OMF-{\textquoteright}Synechococcus{\textquoteright} strain. Prochlorococcus isolates of the high-light-adapted clade (HL) differed from representatives of the low-light-adapted Glade (LL) by the length of their ITS. Restriction fragment length polymorphism (RFLP) of the ITS amplicons revealed three subclusters among the HL strains. Size, sequence data and RFLP of the ITS amplicons will therefore be valuable markers for the identification of different Prochlorococcus genotypes and for their discrimination from other cyanobacterial relatives with which they often co-exist in oceanic ecosystems.},
	keywords = {2002, Blue Green Alga, Chlorophyll B, community structure, cyanobacteria, Escherichia Coli, Marine Prokaryote, Multiple Evolutionary Origins, North Atlantic Ocean, Pacific Ocean, rcc, Rna Operon, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1099/00221287-148-2-453},
	author = {Laloui, W and Palinska, K A and Rippka, R and Partensky, F and de Marsac, N T and Herdman, M and Iteman, I}
}
@article {Rocap2002,
	title = {Resolution of Prochlorococcus and Synechococcus ecotypes by using 16S-23S ribosomal DNA internal transcribed spacer sequences},
	journal = {Applied and Environmental Microbiology},
	volume = {68},
	number = {3},
	year = {2002},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1180{\textendash}1191},
	abstract = {Cultured isolates of the marine cyanobacteria Prochlorococcus and Synechococcus vary widely in their pigment compositions and growth responses to light and nutrients, yet show greater than 96\% identity in their 16S ribosomal DNA (rDNA) sequences. In order to better define the genetic variation that accompanies their physiological diversity, sequences for the 16S-23S rDNA internal transcribed spacer (ITS) region were determined in 32 Prochlorococcus isolates and 25 Synechococcus isolates from around the globe. Each strain examined yielded one ITS sequence that contained two tRNA genes. Dramatic variations in the length and G+C content of the spacer were observed among the strains, particularly among Prochlorococcus strains. Secondary-structure models of the ITS were predicted in order to facilitate alignment of the sequences for phylogenetic analyses. The previously observed division of Prochlorococcus into two ecotypes (called high and low-B/A after their differences in chlorophyll content) were supported, as was the subdivision of the high-B/A ecotype into four genetically distinct clades. ITS-based phylogenies partitioned marine cluster A Synechococcus into six clades, three of which can be associated with a particular phenotype (motility, chromatic adaptation, and lack of phycourobilin). The pattern of sequence divergence within and between clades is suggestive of a mode of evolution driven by adaptive sweeps and implies that each clade represents an ecologically distinct population. Furthermore, many of the clades consist of strains isolated from disparate regions of the world{\textquoteright}s oceans, implying that they are geographically widely distributed. These results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.},
	keywords = {Divinyl Chlorophyll a, genetic diversity, Marine Cyanobacterium Synechococcus, Multiple Evolutionary Origins, North Atlantic, Nucleotide Sequence, rcc, Region, Rna Operon, sargasso sea, Water Column},
	doi = {10.1128/AEM.68.3.1180-1191.2002},
	author = {Rocap, G and Distel, D L and Waterbury, J B and Chisholm, S W}
}
@article {Jacquet2001,
	title = {Cell cycle regulation by light in Prochlorococcus strains},
	journal = {Applied and Environmental Microbiology},
	volume = {67},
	number = {2},
	year = {2001},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {782{\textendash}790},
	abstract = {<p>The effect of light on the synchronization of cell cycling was investigated in several strains of the oceanic photosynthetic prokaryote Prochlorococcus using flow cytometry. When exposed to a light-dark (L-D) cycle with an irradiance of 25 mu mol of quanta m(-2) s(-1), the low-light-adapted strain SS 120 appeared to be better synchronized than the high-light-adapted strain PCC 9511. Submitting LD-entrained populations to shifts (advances or delays) in the timing of the "light on" signal translated to corresponding shifts in the initiation of the S phase, suggesting that this signal is a key parameter for the synchronization of population cell cycles. Cultures that were shifted from an L-D cycle to continuous irradiance showed persistent diel oscillations of flow-cytometric signals (light scatter and chlorophyll fluorescence) but with significantly reduced amplitudes and a phase shift. Complete darkness arrested most of the cells in the G(1), phase of the cell cycle, indicating that light is required to trigger the initiation of DNA replication and cell division. However, some cells also arrested in the S phase, suggesting that cell cycle controls in Prochlorococcus spp. are not as strict as in marine Synechococcus spp. Shifting Prochlorococcus cells from low to high irradiance translated quasi-instantaneously into an increase of cells in both the S and G(2) phases of the cell cycle and then into faster growth, whereas the inverse shift induced rapid slowing of the population growth rate. These data suggest a close coupling between irradiance levels and cell cycling in Prochloroeoccus spp.</p>
},
	keywords = {cyanobacteria, Equatorial Pacific, Gene Expression, Growth, Mediterranean Sea, North Atlantic, Photosynthetic Prokaryote, picoplankton, Populations, rcc, Synechococcus},
	doi = {10.1128/AEM.67.2.782-790.2001},
	author = {Jacquet, S and Partensky, F and Marie, D and Casotti, R and Vaulot, D}
}
@article {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 {Jacquet2001a,
	title = {Diel patterns of growth and division in marine picoplankton in culture},
	journal = {Journal of Phycology},
	volume = {37},
	number = {3},
	year = {2001},
	note = {tex.mendeley-tags: 2001,rcc,sbr?hyto},
	pages = {357{\textendash}369},
	abstract = {{The effect of a 12:12-h light:dark (LD) cycle on the phasing of several cell parameters was explored in a variety of marine picophytoplanktonic strains. These included the photosynthetic prokaryotes Pro-chlorococcus (strains MED 4, PCC 9511, and SS 120) and Synechococcus (strains ALMO 03, ROS 04, WH 7803, and WH 8103) and five picoeukaryotes (Bathycoccus prasinos Eikrem et Throndsen, Bolidomonas pacifica Guillou et Chretiennot-Dinet, Micromonas pusilla Manton et Parke, Pelagomonas calceolata Andersen et Saunders, and Pycnococcus provasolii Guillard et al.). Flow cytometric analysis was used to determine the relationship between cell light scatter, pigment fluorescence, DNA (when possible), and the LD cycle in these organisms. Asexpected, growth and division were tightly coupled to the LD cycle for all of these strains. For both Prochlorococcus and picoeukaryotes, chi and intracellular carbon increased throughout the light period as estimated by chi fluorescence and light scatter, respectively. In response to cell division, these parameters decreased regularly during the early part of the dark period, a decrease that either continued throughout the dark period or stopped for the second half of the dark period. For Synechococcus, the decrease of chi and scatter occurred earlier (in the middle of the light period), and for some strains these cellular parameters remained constant throughout the dark period. The timing of division was very similar for all picoeukaryotes and occurred just before the subjective dusk, whereas it was more variable between the different Prochlorococcus and Synechococcus strains. The burst of division for Prochlorococcus SS 120 and PCC 9511 was recorded at the subjective dusk, whereas the MED 4 strain divided later at night. Synechococcus ALMO 03, ROS 04, and WH 7803, which have a low phycourobilin to phycoerythrobilin (PUB:PEB) ratio, divided earlier, and their division was restricted to the light period. In contrast, the high PUB:PEB Synechococcus strain WH 8103 divided preferentially at night. There was a weak linear relationship between the FALS(max):FALS(min) ratio and growth rate calculated from cell counts (r = 0.83},
	keywords = {2001, Cell Division, Cyanobacteria Synechococcus, Dividing Cells, Equatorial Pacific, flow cytometry, Mediterranean Sea, Natural Populations, North Pacific Ocean, Photosynthetic Picoplankton, Picophytoplankton Dynamics, rcc, SBR$_\textrmP$hyto, sbr?hyto},
	doi = {10.1046/j.1529-8817.2001.037003357.x},
	author = {Jacquet, S and Partensky, F and Lennon, J F and Vaulot, D}
}
@article {Guillou2001,
	title = {Grazing impact of two small heterotrophic flagellates on Prochlorococcus and Synechococcus},
	journal = {Aquatic Microbial Ecology},
	volume = {26},
	number = {2},
	year = {2001},
	note = {tex.mendeley-tags: 2001,rcc,sbr?hyto},
	pages = {201{\textendash}207},
	abstract = {In open oceanic waters, phytoplankton biomass is dominated by organisms below 2 to 3 mum in size (pico- and small nanophytoplankton). The cell concentration of these populations is very stable in time and space as a consequence of nutrient limitation and strong grazing pressure, Although the identity of the organisms that directly graze on picoplankton is largely unknown, they are thought to be very small, i.e. {\textexclamdown}3 to 5 {\textexclamdown}mu{\textquestiondown}m, Here, we analyze the grazing impact of 2 small flagellates, Symbiomonas scintillans and Picophagus flagellatus, upon 2 oceanic cyanobacteria, Prochlorococcus and Synechococcus. S. scintillans does not feed on the 2 cyanobacteria. In contrast, P. flagellatus appears as an active predator capable of drastically reducing prey concentrations. The flagellate displays a substantial division rate of the order of 2 doublings d(-1) when fed on Prochlorococcus cells, but no significant growth is recorded when Synechococcus is used as prey. As the majority ({\textquestiondown} 80\%) of P. flagellatus cells can pass throughout a 2 mum filter, the impact of such tiny predators should be taken into consideration during field experiments that rely on size fractionation to separate grazers from prey.},
	keywords = {2001, Algal Class, Equatorial Pacific, Growth Rates, Laboratory Cultures, Marine, Nanoplankton, PICODIV, picoplankton, Prey, rcc, SBR$_\textrmP$hyto, sbr?hyto, Size, Sp Nov},
	doi = {10.3354/ame026201},
	author = {Guillou, L and Jacquet, S and Chr{\'e}tiennot-Dinet, M.-J. and Vaulot, D}
}
@article {Dupuy2000,
	title = {Feeding rate of the oyster Crassostrea gigas in a natural planktonic community of the Mediterranean Thau Lagoon},
	journal = {Marine Ecology - Progress Series},
	volume = {205},
	year = {2000},
	note = {ISBN: 0171-8630 Publisher: Inter-Research tex.address: Nordbunte 23, D-21385 Oldendorf Luhe, Germany tex.mendeley-tags: RCC,rcc},
	pages = {171{\textendash}184},
	abstract = {The Mediterranean Thau Lagoon is an important oyster farming area in Europe. Oyster growth rates are among the highest in France, although chlorophyll a concentration is low. Previous studies have demonstrated that picophytoplankton, nano-microphytoplankton, dinoflagellates and loricate ciliates such as tintinnids are abundant. However, heterotrophic flagellates and aloricate ciliates have not been investigated. The aim of this study was to assess picophytoplankton, protist and zooplankton abundances in the Lagoon and to investigate the particular structure of the microbial food web, which may explain such paradoxical oyster growth. In oligotrophic waters in the Thau Lagoon, the picoeukaryote Ostreococcus tauri is the dominant autotrophic picoplankter, with an abundance maximum in summer. On 17 August 1998, following a rainfall event, pico- and nanophytoplankton abundances were not as high as expected and we observed a high abundance of large diatoms. At this time, the available carbon resources were produced by microphytoplankton (84.5\%), and picoplank-tonic cells represented only 1.27 \% in terms of carbon. Heterotrophic cells were low in abundance and constituted {\textexclamdown}14\% of carbon resources. In order to evaluate the importance of the {\textquoteright}protozoan trophic link{\textquoteright} for energy transfer from the microbial food web to large benthic suspension feeders, the oyster Crassostrea gigas was offered a planktonic community as potential prey. In the grazing experiment, all {\textquestiondown}5 mum flagellates, microphytoplankton, dinoflagellates, ciliates and large zooplankton were retained by the oyster gills. Only flagellates {\textexclamdown}5 pm and O. Tauri were not very well retained (45 and 2\% respectively). The high clearance rates of C. Gigas found in this experiment can be explained by a low concentration of suspended particulate matter (0.65 mg l(-1)). The oysters adapted their retention mechanism when they Lived in oligotrophic waters. These results indicate that, under the given experimental conditions, picophytoplankton did not represent a valuable trophic resource for farmed oysters because (1) C. Gigas cannot retain picoparticles and (2) the picoplankton represented a poor carbon resource capable of being transferred via a weak heterotrophic protist community. In the oyster pens of the Thau Lagoon during this study, microphytoplanktonic primary producers, in particular diatoms, were the main food sources for bivalve suspension feeders.},
	keywords = {ABUNDANCE, bivalve, carbon, COASTAL WATERS, EPIFLUORESCENCE MICROSCOPY, FILTRATION-RATE, food source, FOOD-CHAINS, GEUKENSIA-DEMISSA, heterotrophic protist, microbial food web, MYTILUS-EDULIS, oyster, PARTICLE SELECTION, picophytoplankton, rcc, RETENTION, Thau Lagoon, trophic link},
	doi = {10.3354/meps205171},
	author = {Dupuy, C and Vaquer, A and LamHoai, T and Rougier, C and Mazouni, N and Lautier, J and Collos, Y and LeGall, S}
}
@article {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 {Guillou1999,
	title = {Bolidomonas: a new genus with two species belonging to a new algal class, the Bolidophyceae (Heterokonta)},
	journal = {Journal of Phycology},
	volume = {35},
	year = {1999},
	note = {tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {368{\textendash}381},
	abstract = {A new algal class, the Bolidophyceae (Heterokonta), is described from one genus, Bolidomonas, gen, nov., and two species, Bolidomonas pacifica, sp, nov and Bolidomonas mediterranea, sp, nov., isolated from the equatorial Pacific Ocean and the Mediterranean Sea, respectively. Both species are approximately 1.2 mu m in diameter and have two unequal flagella; the longer flagellum bears tubular hairs, whereas the shorter is smooth. The flagellar basal apparatus is restricted to two basal bodies, and there is no transitional helix. Cells are naked, devoid of walls or siliceous structures. The internal cellular organization is simple with a single plastid containing a ring genophore and a girdle lamella, one mitochondrion with tubular cristae, and one Golgi apparatus close to the basal bodies. The Mediterranean and the Pacific species differ in the insertion angle between their flagella and their pattern of swimming, these differences possibly being linked to each other. Analyses of the SSU rDNA gene place the two strains as a sister group to the diatoms, Moreover, pigment analyses confirm this position, as fucoxanthin is found as the major carotenoid in both lineages. These data strongly suggest that the ancestral heterokont that gave rise to the diatom lineage was probably a biflagellated unicell.},
	keywords = {10$_\textrmb$est, 1999, Bolidophyceae, CELL-CYCLE, CHRYSOPHYCEAE, diatoms, DIVINYL-CHLOROPHYLL, FINE-STRUCTURE, FLAGELLAR APPARATUS, Heterokonta, Marine, marine picoeukaryotes, oligotrophic ocean, rcc, RNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCE, sp-nov, stramenopiles, ultrastructure},
	doi = {10.1046/j.1529-8817.1999.3520368.x},
	author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Medlin, L K and Claustre, H and Loiseaux-de Go{\"e}r, S and Vaulot, D}
}
@article {Guillou1999a,
	title = {Diversity and abundance of Bolidophyceae (Heterokonta) in two oceanic regions},
	journal = {Applied and Environmental Microbiology},
	volume = {65},
	number = {10},
	year = {1999},
	note = {ISBN: 0099-2240 Publisher: Amer Soc Microbiology tex.address: 1325 Massachusetts Avenue, NW, Washington, DC 20005-4171, USA tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {4528{\textendash}4536},
	abstract = {The diversity and abundance of the Bolidophyceae (Heterokonta), a newly described picoplanktonic algal class which is a sister group to the diatoms, was assessed in the equatorial Pacific Ocean and in the Mediterranean Sea by culture isolation, molecular biology techniques, and pigment analyses. Eight strains of Bolidophyceae were isolated in culture from different mesotrophic and oligotrophic areas. The corresponding small subunit (SSU) rRNA gene sequences allowed us to design two probes specific for the Bolidophyceae. These probes have been used in natural samples (i) to selectively amplify and detect Bolidophyceae sequences and (ii) to quantify the relative abundance of Bolidophyceae within the picoeukaryote community. Sequences available to date indicate that the class Bolidophyceae comprises at least three different clades, two corresponding to the previously described species Bolidomonas pacifica and Bolidomonas mediterranea and the third one corresponding to a subspecies of B. Pacifica. Amplification of the SSU rRNA gene from natural samples with universal primers and hybridization using a Bolidomonas-specific probe followed by a eukaryote-specific probe allowed us to estimate the contribution of the Bolidophyceae to the eukaryotic DNA in both Pacific and Mediterranean waters to be lower than 1\%. Similarly, high-performance liquid chromatography analyses of fucoxanthin, the major carotenoid present in Bolidophyceae, indicated that less than 4\% of the total chlorophyll a in the picoplanktonic fraction in the equatorial Pacific was due to Bolidophyceae. Consequently, although strains of Bolidophyceae have been isolated from samples collected at several stations, this new class seems to have been a minor component of the natural picoeukaryotic populations in the ecosystems investigated, at least during the periods sampled.},
	keywords = {1999, ATLANTIC, BACTERIOPLANKTON, community structure, flow-cytometry, MOLECULAR PHYLOGENY, PACIFIC, phytoplankton, PIGMENT SIGNATURES, rcc, RNA GENE SEQUENCE, SBR$_\textrmP$hyto, sbr?hyto, ULTRAPHYTOPLANKTON},
	doi = {10.1128/AEM.65.10.4528-4536.1999},
	author = {Guillou, L and Moon-van der Staay, S Y and Claustre, H and Partensky, F and Vaulot, D}
}
@article {Guillou1999b,
	title = {Symbiomonas scintillans gen. et sp nov and Picophagus flagellatus gen. et sp nov (Heterokonta): Two new heterotrophic flagellates of picoplanktonic size},
	journal = {Protist},
	volume = {150},
	number = {4},
	year = {1999},
	note = {ISBN: 1434-4610 Publisher: Urban \& Fischer Verlag tex.address: Branch Office Jena, P O Box No.100 537, D-07705 Jena, Germany tex.mendeley-tags: 1999,rcc,sbr?hyto},
	pages = {383{\textendash}398},
	abstract = {Two new oceanic free-living heterotrophic Heterokonta species with picoplanktonic size ({\textexclamdown} 2 mu m) are described, Symbiomonas scintillans Guillou et Chretiennot-Dinet gen. Ef sp. Nov, was isolated from samples collected both in the equatorial Pacific Ocean and the Mediterranean Sea. This new species possesses ultrastructural features of the bicosoecids, such as the absence of a helix in the flagellar transitional region (found in Cafeteria roenbergensis and in a few bicosoecids), and a flagellar root system very similar to that of C. Roenbergensis, Acronema sippewissettensis, and Bicosoeca maris. This new species is characterized by a single flagellum with mastigonemes, the presence of endosymbiotic bacteria located close to the nucleus, the absence of a lorica and a R3 root composed of a 6+3+x microtubular structure. Phylogenetical analyses of nuclear-encoded SSU rDNA gene sequences indicate that this species is close to the bicosoecids C. Roenbergensis and Siluania monomastiga. Picophagus flagellatus Guillou et Chretiennot-Dinet gen. Et sp. Nov. Was collected in the equatorial Pacific Ocean, Cells are naked and possess two flagella, This species is characterized by the lack of a transitional helix and lateral filaments on the flagellar tubular hairs, the absence of siliceous scales, two unequal flagella, R1 + R3 roots, and the absence of a rhizoplast. SSU rDNA analyses place this strain at the base of the Chrysophyceae/Synurophyceae lineages.},
	keywords = {1999, APPARATUS, DEVELOPAYELLA-ELEGANS, EMPHASIS, MOLECULAR PHYLOGENY, picophytoplankton, PLASTIDS, rcc, RDNA, SBR$_\textrmP$hyto, sbr?hyto, SEQUENCES},
	doi = {10.1016/S1434-4610(99)70040-4},
	author = {Guillou, L and Chr{\'e}tiennot-Dinet, M.-J. and Boulben, S and Moon-van der Staay, S Y and Vaulot, D}
}
@article {Courties1998,
	title = {Phylogenetic analysis and genome size of Ostreococcus tauri (Chlorophyta, Prasinophyceae)},
	journal = {Journal of Phycology},
	volume = {34},
	number = {5},
	year = {1998},
	note = {tex.mendeley-tags: RCC745},
	pages = {844{\textendash}849},
	abstract = {Ostreococcus tauri Courties et Chretiennot-Dinet is the smallest described autotrophic eukaryote dominating the phytoplanktonic assemblage of the marine Mediterranean Thau lagoon (France). Its taxonomic position was partly elucidated from ultrastructure and high-pressure liquid chromatography (HLPC) pigment analysis. The sequence analysis of the 18S rDNA gene of O. Tauri measured here is available in EMBL Nucleotide Sequence Database (accession number: Y15814) and allowed to clarify its phylogenetic position. O. Tauri belongs to the Prasinophyceae and appears very close to Mantoniella, a typical scaly Prasinophyceae, morphologically very different from the naked and coccoid Ostreococcus. An electrophoretic analysis of O. Tauri shows that the nucleus contains 10.20 mbp. This small genome fragmented into 14 chromosomes ranging in size from 300 to 1500 kbp, confirms the minimalist characteristics of Ostreococcus tauri.},
	keywords = {rcc, RCC745, SBR$_\textrmP$hyto},
	doi = {10.1046/j.1529-8817.1998.340844.x},
	author = {Courties, C and Perasso, R and Chr{\'e}tiennot-Dinet, M.-J. and Gouy, M and Guillou, L and Troussellier, M}
}
@article {Scanlan1996,
	title = {High degree of genetic variation in Prochlorococcus (Prochlorophyta) revealed by RFLP analysis},
	journal = {European Journal of Phycology},
	volume = {31},
	number = {1},
	year = {1996},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1{\textendash}9},
	keywords = {DIVINYL CHLOROPHYLL-A, FAMILY, Marine Synechococcus, Mediterranean Sea, Multiple Evolutionary Origins, north-atlantic, NUCLEOTIDE-SEQUENCE, picoplankton, Prokaryote, rcc, RCC SBR$_\textrmP$hyto, UNICELLULAR CYANOBACTERIUM},
	doi = {10.1080/09670269600651131},
	author = {Scanlan, D J and Hess, W R and Partensky, F and Newman, J and Vaulot, D}
}
@article {Shimada1996,
	title = {Vertical distributions and photosynthetic action spectra of two oceanic picophytoplankers, Prochlorococcus marinus and Synechococcus sp},
	journal = {Marine Biology},
	volume = {127},
	year = {1996},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {15{\textendash}23},
	keywords = {OPTICAL-PROPERTIES, Photosynthesis, rcc, \#PROCHLOROCOCCUS},
	doi = {10.1007/BF00993639},
	author = {Shimada, A and Maruyama, T and Miyachi, S}
}
@article {Moore1995,
	title = {Comparative physiology of Synechococcus and Prochlorococcus: influence of light and temperature on growth, pigments, fluorescence and absorptive properties},
	journal = {Marine Ecology - Progress Series},
	volume = {116},
	year = {1995},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {259{\textendash}275},
	keywords = {GROWTH RATE, Light, MARINE OPTICS, rcc, Synechococcus, temperature, \#PROCHLOROPHYTE},
	doi = {10.3354/meps116259},
	author = {Moore, L R and Goericke, R and Chisholm, S W}
}
@article {Chretiennot-Dinet1995,
	title = {A new marine picoeucaryote: Ostreococcus tauri gen. et sp. nov. (Chlorophyta, Prasinophyceae)},
	journal = {Phycologia},
	volume = {34},
	number = {4},
	year = {1995},
	note = {tex.mendeley-tags: RCC745},
	pages = {285{\textendash}292},
	keywords = {FRESH-WATER ECOSYSTEMS, morphology, picoplankton, pigments, PROCHLOROCOCCUS-MARINUS, Prokaryote, rcc, RCC745, Size},
	doi = {10.2216/i0031-8884-34-4-285.1},
	author = {Chr{\'e}tiennot-Dinet, M.-J. and Courties, C and Vaquer, A and Neveux, J and Claustre, H and Lautier, J and Machado, M C}
}
@article {Simon1994,
	title = {Characterization of oceanic photosynthetic picoeukaryotes by flow cytometry analysis},
	journal = {Journal of Phycology},
	volume = {30},
	year = {1994},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {922{\textendash}935},
	keywords = {flow cytometry, hplc, pigments, rcc, RCC SBR$_\textrmP$hyto, \#PICOPLANKTON},
	doi = {10.1111/j.0022-3646.1994.00922.x},
	author = {Simon, N and Barlow, R G and Marie, D and Partensky, F and Vaulot, D}
}
@article {Vaulot1994,
	title = {Phaeocystis spp.: morphology, ploidy, pigment composition and genome size of cultured strains},
	journal = {Journal of Phycology},
	volume = {30},
	year = {1994},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {1022{\textendash}1035},
	keywords = {rcc, RCC SBR$_\textrmP$hyto},
	doi = {10.1111/j.0022-3646.1994.01022.x},
	author = {Vaulot, D and Birrien, J.-L. and Marie, D and Casotti, R and Veldhuis, M J W and Kraay, G W and Chr{\'e}tiennot-Dinet, M.-J.}
}
@article {Partensky1993,
	title = {Photoacclimation of Prochlorococcus sp. (Prochlorophyta) strains isolated from the North Atlantic and the Mediterranean Sea},
	journal = {Plant Physiology},
	volume = {101},
	year = {1993},
	note = {tex.mendeley-tags: RCC,rcc,sbr?hyto},
	pages = {295{\textendash}296},
	keywords = {hplc, Photosynthesis, Pigment, rcc, RCC SBR$_\textrmP$hyto, sbr?hyto, \#PROCHLOROPHYTE},
	doi = {10.1104/pp.101.1.285},
	author = {Partensky, F and Hoepffner, N and Li, W K W and Ulloa, O and Vaulot, D}
}
@article {Morel1993,
	title = {Prochlorococcus and Synechococcus: a comparative study of their size, pigmentation and related optical properties},
	journal = {Journal of Marine Research},
	volume = {51},
	year = {1993},
	note = {tex.mendeley-tags: 1993,rcc,sbr?hyto},
	pages = {617{\textendash}649},
	keywords = {1993, hplc, OPTICS, Pigment, rcc, SBR$_\textrmP$hyto, sbr?hyto, Synechococcus, \#PROCHLOROPHYTE},
	doi = {10.1357/0022240933223963},
	author = {Morel, A and Ahn, Y.-W. and Partensky, F and Vaulot, Daniel and Claustre, H}
}
@article {Chisholm1992,
	title = {\textit{Prochlorococcus marinus nov. gen. nov. sp.: an oxyphototrophic marine prokaryote containing divinyl chlorophyll a and b},
	journal = {Archives of Microbiology},
	volume = {157},
	year = {1992},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {297{\textendash}300},
	keywords = {rcc, systematics, \#PROCHLOROPHYTE},
	doi = {10.1007/BF00245165},
	author = {Chisholm, S W and Frankel, S L and Goericke, R and Olson, R J and Palenik, B and Waterbury, J B and West-Johnsrud, L and Zettler, E R}
}
@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}
}
