@article {LopesdosSantos2016,
	title = {Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters},
	journal = {The ISME Journal},
	volume = {11},
	number = {2},
	year = {2017},
	note = {tex.mendeley-tags: 2016,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {feb},
	pages = {512{\textendash}528},
	keywords = {2016, MACUMBA, MicroB3, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.120},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.120},
	author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Tragin, Margot and No{\"e}l, Mary-H{\'e}l{\`e}ne and Decelle, Johan and Romac, Sarah and Vaulot, Daniel}
}
@article {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 {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 {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 {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 {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 {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 {Marie2014,
	title = {An improved protocol for flow cytometry analysis of phytoplankton cultures and natural samples},
	journal = {Cytometry},
	volume = {85},
	year = {2014},
	note = {tex.mendeley-tags: RCC100,RCC1085,RCC114,RCC156,RCC168,RCC174,RCC180,RCC190,RCC263,RCC365,RCC400,RCC432,RCC446,RCC475,RCC480,RCC504,RCC745,RCC91},
	pages = {962{\textendash}968},
	abstract = {Preservation of cells, choice of fixative, storage, and thawing conditions are recurrent issues for the analysis of phytoplankton by flow cytometry. We examined the effects of addition of the surfactant Pluronic F68 to glutaraldehyde-fixed photosynthetic organisms in cultures and natural samples. In particular, we examined cell losses and modifications of side scatter (a proxy of cell size) and fluorescence of natural pigments. We found that different marine phytoplankton species react differently to the action of Pluronic F68. In particular, photosynthetic prokaryotes are less sensitive than eukaryotes. Observed cell losses may result from cell lysis or from cell adhesion to the walls of plastic tubes that are commonly used for flow cytometry analysis. The addition of the surfactant, Pluronic F68, has a positive effect on cells for long-term storage. We recommend to modify current protocols for preservation of natural marine planktonic samples, by fixing them with glutaraldehyde 0.25\% (final concentration) and adding Pluronic F68 at a final concentration of 0.01\% in the samples before preservation. Pluronic F68 also appears effective for preserving samples without fixation for subsequent sorting, e.g. for molecular biology analyses. (c) 2014 International Society for Advancement of Cytometry},
	keywords = {ASSEMBLE, MACUMBA, RCC100, RCC1085, RCC114, RCC156, RCC168, rcc174, RCC180, RCC190, RCC263, RCC365, RCC400, RCC432, RCC446, RCC475, RCC480, RCC504, RCC745, RCC91, RCC?o?dd, SBR$_\textrmP$hyto$_\textrmD$PO},
	doi = {10.1002/cyto.a.22517},
	author = {Marie, D and Rigaut-Jalabert, F and Vaulot, D}
}
@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 {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 {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}
}
