@article {dufour_differential_2024,
	title = {Differential acclimation kinetics of the two forms of type IV chromatic acclimaters occurring in marine Synechococcus cyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {15},
	year = {2024},
	pages = {1349322},
	abstract = {Synechococcus , the second most abundant marine phytoplanktonic organism, displays the widest variety of pigment content of all marine oxyphototrophs, explaining its ability to colonize all spectral niches occurring in the upper lit layer of oceans. Seven Synechococcus pigment types (PTs) have been described so far based on the phycobiliprotein composition and chromophorylation of their light-harvesting complexes, called phycobilisomes. The most elaborate and abundant PT (3d) in the open ocean consists of cells capable of type IV chromatic acclimation (CA4), i.e., to reversibly modify the ratio of the blue light-absorbing phycourobilin (PUB) to the green light-absorbing phycoerythrobilin (PEB) in phycobilisome rods to match the ambient light color. Two genetically distinct types of chromatic acclimaters, so-called PTs 3dA and 3dB, occur at similar global abundance in the ocean, but the precise physiological differences between these two types and the reasons for their complementary niche partitioning in the field remain obscure. Here, photoacclimation experiments in different mixes of blue and green light of representatives of these two PTs demonstrated that they differ by the ratio of blue-to-green light required to trigger the CA4 process. Furthermore, shift experiments between 100\% blue and 100\% green light, and vice-versa , revealed significant discrepancies between the acclimation pace of the two types of chromatic acclimaters. This study provides novel insights into the finely tuned adaptation mechanisms used by Synechococcus cells to colonize the whole underwater light field.},
	keywords = {RCC2319, RCC2369, RCC2374, RCC2533, RCC2553, RCC2571, RCC515, rcc555, RCC751},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2024.1349322},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2024.1349322/full},
	author = {Dufour, Louison and Garczarek, Laurence and Gouriou, Bastian and Clairet, Julia and Ratin, Morgane and Partensky, Fr{\'e}d{\'e}ric}
}
@article {coello-camba_design_2023,
	title = {Design and use of a new primer pair for the characterization of the cyanobacteria Synechococcus and Prochlorococcus communities targeting petB gene through metabarcoding approaches.},
	journal = {MethodsX},
	year = {2023},
	month = {oct},
	pages = {102444},
	abstract = {During the last years, the application of next-generation sequencing (NGS) technologies to search for specific genetic markers has become a crucial method for the characterization of microbial communities. Illumina MiSeq, likely the most widespread NGS platform for metabarcoding experiments and taxonomic classification, allows processing shorter reads than the classical SANGER sequencing method and therefore requires specific primer pairs that produce shorter amplicons. Specifically, for the analysis of the commonly studied Prochlorococcus and Synechococcus communities, the petB marker gene has recently stood out as able to provide deep coverage to determine the microdiversity of the community.. However, current petB primer set produce a 597 bp amplicon that is not suitable for MiSeq chemistry. Here, we designed and tested a petB primer pair that targets both Prochlorococcus and Synechococcus communities producing an appropriate amplicon to be used with state-of-the-art Illumina MiSeq. This new primer set allows the classification of both groups to a low taxonomic level and is therefore suitable for high throughput experiments using MiSeq technologies, therefore constituting a useful, novel tool to facilitate further studies on Prochlorococcus and Synechococcus communities. {\textbullet} This work describes the de novo design of a Prochlorococcus and Synechococcus-specific petB primer pair, allowing the characterization of both populations to a low taxonomic level. {\textbullet} This primer pair is suitable for widespread Illumina MiSeq sequencing technologies. {\textbullet} petB was confirmed as an adequate target for the characterization of both picocyanobacteria.},
	keywords = {cyanobacteria, Illumina MiSeq, RCC156, rcc162, RCC2319, RCC2372, RCC2378, RCC2383, RCC2384, RCC2455, RCC2529, RCC2531, RCC2554, RCC3377, RCC407, RCC408, sequencing},
	issn = {2215-0161},
	doi = {10.1016/j.mex.2023.102444},
	url = {https://www.sciencedirect.com/science/article/pii/S2215016123004405},
	author = {Coello-Camba, Alexandra and D{\'\i}az-R{\'u}a, Rub{\'e}n and Agusti, Susana}
}
@article {saide_diatom_2023,
	title = {The Diatom Cylindrotheca closterium and the Chlorophyll Breakdown Product Pheophorbide a for Photodynamic Therapy Applications},
	journal = {Applied Sciences},
	volume = {13},
	number = {4},
	year = {2023},
	note = {Number: 4 Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {2590},
	abstract = {Microalgae, eukaryotic unicellular plants that are distributed worldwide, have been shown to exert anti-proliferative and anticancer activities on various human cancer cell lines. An example of a microalgal bioactive compound is a chlorophyll breakdown product named Pheophorbide a (Ppa), which has been reported to have anti-proliferative properties against various cell lines. This compound has also been tested with light exposure in photodynamic therapy for cancer treatment. In this paper, we screened eleven marine microalgae against a panel of cancer cells, and evaluated the synergistic anti-proliferative effect with Pheophorbide a, with and without photo-activation. The results showed significant anti-proliferative activity against melanoma cells when Ppa was combined with fraction E of the diatom Cylindrotheca closterium plus 1 h photo-activation. Its activity was also analyzed using gene expression and Western blot experiments. Altogether, these data give new insights into the possible application of microalgae for photodynamic therapy.},
	keywords = {biotechnological applications, cancer, Microalgae, Pheophorbide \textita, photodynamic therapy, RCC1712, \textitCylindrotheca closterium},
	issn = {2076-3417},
	doi = {10.3390/app13042590},
	url = {https://www.mdpi.com/2076-3417/13/4/2590},
	author = {Saide, Assunta and Riccio, Gennaro and Ianora, Adrianna and Lauritano, Chiara}
}
@article {ruan_different_2023,
	title = {Different photosynthetic responses of haploid and diploid Emiliania huxleyi (Prymnesiophyceae) to high light and ultraviolet radiation},
	journal = {Bioresources and Bioprocessing},
	volume = {10},
	number = {1},
	year = {2023},
	month = {jul},
	pages = {40},
	abstract = {Solar radiation varies quantitatively and qualitatively while penetrating through the seawater column and thus is one of the most important environmental factors shaping the vertical distribution pattern of phytoplankton. The haploid and diploid life-cycle phases of coccolithophores might have different vertical distribution preferences. Therefore, the two phases respond differently to high solar photosynthetically active radiation (PAR, 400{\textendash}700~nm) and ultraviolet radiation (UVR, 280{\textendash}400~nm). To test this, the haploid and diploid Emiliania huxleyi were exposed to oversaturating irradiance. In the presence of PAR alone, the effective quantum yield was reduced by 10\% more due to the higher damage rate of photosystem II in haploid cells than in diploid cells. The addition of UVR resulted in further inhibition of the quantum yield for both haploid and diploid cells in the first 25~min, partly because of the increased damage of photosystem II. Intriguingly, this UVR-induced inhibition of the haploid cells completely recovered half an hour later. This recovery was confirmed by the comparable maximum quantum yields, maximum relative electron transport rates and yields of the haploid cells treated with PAR and PAR + UVR. Our data indicated that photosynthesis of the haploid phase was more sensitive to high visible light than the diploid phase but resistant to UVR-induced inhibition, reflecting the ecological niches to which this species adapts.},
	keywords = {Diploid phase, Effective quantum yield, Emiliania huxleyi, Haploid phase, rcc1217, Ultraviolet radiation (UVR)},
	issn = {2197-4365},
	doi = {10.1186/s40643-023-00660-5},
	url = {https://doi.org/10.1186/s40643-023-00660-5},
	author = {Ruan, Zuoxi and Lu, Meifang and Lin, Hongmin and Chen, Shanwen and Li, Ping and Chen, Weizhou and Xu, Huijuan and Qiu, Dajun}
}
@article {yu_does_2023,
	title = {Does the life cycle stage matter for distinguishing phytoplankton via fluoro-electrochemical microscopy?},
	journal = {Cell Reports Physical Science},
	year = {2023},
	pages = {101223},
	abstract = {Phytoplankton have species-specific responses toward electrogenerated oxidants, allowing high-throughput species analysis. Herein, a fluoro-electrochemical method is used to expose single Chlamydomonas concordia vegetative cells at different points within their life cycle to electro-generated oxidants from seawater. The resulting decay in fluorescence from chlorophyll-a is measured as a function of time and drops to zero for phytoplankton adjacent to the electrode over a period of a few seconds. The chlorophyll-a transient timescale allows mother cells, which are distinctively larger and require a larger quantity of oxidants, to be distinguished from either zoospores or {\textquotedblleft}growing{\textquotedblright} cells, while all the cells show the same intrinsic susceptibility modulated only by the size of the phytoplankton. These observations are essential for the future automated characterization of the speciation of phytoplankton populations as they show that there is no need to manually identify the life cycle stage.},
	keywords = {electrogenerated radicals, fluoro-electrochemistry, Green algae, life cycle, marine phytoplankton, oxidative damage, RCC1, remote sensing, susceptibility library},
	issn = {2666-3864},
	doi = {10.1016/j.xcrp.2022.101223},
	url = {https://www.sciencedirect.com/science/article/pii/S2666386422005410},
	author = {Yu, Jiahao and Yang, Minjun and Batchelor-McAuley, Christopher and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {yung_diversity_2022,
	title = {Diversity and Evolution of Mamiellophyceae: Early-Diverging Phytoplanktonic Green Algae Containing Many Cosmopolitan Species},
	journal = {Journal of Marine Science and Engineering},
	volume = {10},
	number = {2},
	year = {2022},
	note = {Number: 2 Publisher: Multidisciplinary Digital Publishing Institute},
	month = {feb},
	pages = {240},
	abstract = {The genomic revolution has bridged a gap in our knowledge about the diversity, biology and evolution of unicellular photosynthetic eukaryotes, which bear very few discriminating morphological features among species from the same genus. The high-quality genome resources available in the class Mamiellophyceae (Chlorophyta) have been paramount to estimate species diversity and screen available metagenomic data to assess the biogeography and ecological niches of different species on a global scale. Here we review the current knowledge about the diversity, ecology and evolution of the Mamiellophyceae and the large double-stranded DNA prasinoviruses infecting them, brought by the combination of genomic and metagenomic analyses, including 26 metabarcoding environmental studies, as well as the pan-oceanic GOS and the Tara Oceans expeditions.},
	keywords = {Biogeography, evolution, genomics, mamiellophyceae, metagenomics, microalgae{\textendash}virus interactions, phycoDNAvirus, RCC809},
	issn = {2077-1312},
	doi = {10.3390/jmse10020240},
	url = {https://www.mdpi.com/2077-1312/10/2/240},
	author = {Yung, Charmaine C. M. and Rey Redondo, Elvira and Sanchez, Fr{\'e}d{\'e}ric and Yau, Sheree and Piganeau, Gwenael}
}
@article {grebert_diversity_2022,
	title = {Diversity and evolution of pigment types in marine \textit{Synechococcus cyanobacteria},
	journal = {Genome Biology and Evolution},
	year = {2022},
	pages = {evac035},
	abstract = {DNA integration and site-specific recombination, suggesting that their genomic variability relies D in part on a {\textquoteleft}tycheposon{\textquoteright}-like mechanism. Comparison of the phylogenies obtained for PBS and E core genes revealed that the evolutionary history of PBS rod genes differs from the core T genome and is characterized by the co-existence of different alleles and frequent allelic P exchange. We propose a scenario for the evolution of the different pigment types and highlight E the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in C different Synechococcus lineages despite multiple speciation events.},
	keywords = {RCC307, to add},
	issn = {1759-6653},
	doi = {10.1093/gbe/evac035},
	url = {https://academic.oup.com/gbe/advance-article/doi/10.1093/gbe/evac035/6547267},
	author = {Gr{\'e}bert, Th{\'e}ophile and Garczarek, Laurence and Daubin, Vincent and Humily, Florian and Marie, Dominique and Ratin, Morgane and Devailly, Alban and Farrant, Gregory K. and Mary, Isabelle and Mella-Flores, Daniella and Tanguy, Gwenn and Labadie, Karine and Wincker, Patrick and Kehoe, David M. and Partensky, Fr{\'e}d{\'e}ric},
	editor = {Angert, Esther}
}
@article {sorokina_draft_2022,
	title = {Draft genome assembly and sequencing dataset of the marine diatom Skeletonema costatum RCC75},
	journal = {Data in Brief},
	year = {2022},
	month = {feb},
	pages = {107931},
	abstract = {Diatoms (Bacillariophyceae) are a major constituent of the phytoplankton and have a universally recognized ecological importance. Between 1,000 and 1,300 diatom genera have been described in the literature, but only 10 nuclear genomes have been published and made available to the public up to date. Skeletonema costatum is a cosmopolitan marine diatom, principally occurring in coastal regions, and is one of the most abundant members of the Skeletonema genus. Here we present a draft assembly of the Skeletonema costatum RCC75 genome, obtained from PacBio and Illumina NovaSeq data. This dataset will expand the knowledge of the Bacillariophyceae genetics and contribute to the global understanding of phytoplankton{\textquoteright}s physiological, ecological, and environmental functioning.},
	keywords = {Algal genome, BACILLARIOPHYCEAE, diatoms, genome sequencing, Illumina sequencing, PacBio sequencing, RCC75},
	issn = {2352-3409},
	doi = {10.1016/j.dib.2022.107931},
	url = {https://www.sciencedirect.com/science/article/pii/S2352340922001433},
	author = {Sorokina, Maria and Barth, Emanuel and Zulfiqar, Mahnoor and Kwantes, Michiel and Pohnert, Georg and Steinbeck, Christoph}
}
@article {morais_detection_2021,
	title = {Detection of Alexandrium minutum dinoflagellate in environ- mental samples using electrochemical genosensor},
	journal = {Chemistry Proceedings},
	year = {2021},
	pages = {7},
	abstract = {Dinoflagellates are aquatic microorganisms that inhabit both salt and fresh waters. These microorganisms are mostly harmless, however, under certain conditions, some species rapidly reproduce forming water blooms that not only discolor the waters but also compromise the health of every organism in the vicinity, as some dinoflagellates produce potent toxins deemed unsafe for human health (e.g. Alexandrium minutum). In this work, a disposable electrochemical genosensor for the detection of the toxic dinoflagellate Alexandrium minutum was developed. The analytical platform methodology consisted in a sandwich format heterogeneous hybridization of complementary DNA sequences assay. The 70 bp A. minutum-specific targeting probe, the 45 bp fluorescein isothiocyanate-labelled signaling DNA probe and the 25 bp thiolated-DNA-capture probe were designed, after analyzing public databases. To maximize the complementary DNA hybridization and to avoid the formation of strong secondary structures, a mixed mercaptohexanol (MCH) and self-assembled monolayer (SAM) A. minutum-specific DNA-capture probe was immobilized onto disposable screen-printed gold electrodes (SPGE). Using chronoamperometric measurements, the enzymatic amplification of the electrochemical signal was obtained with a concentration range from 0.12 to 1.0 nM, a LD of 24.78 pM with a RSD < 5.2 \%. This electrochemical genosensor was successfully applied to the selective analysis of the targeted A. minutum specific region of denatured genomic DNA, extracted from toxic dinoflagellates present in the Atlantic Ocean.},
	keywords = {? No DOI found, RCC3029},
	author = {Morais, Stephanie L and Barros, Piedade and Santos, Marlene and Delerue-Matos, Cristina and Gomes, Andreia C and Barroso, M F{\'a}tima}
}
@article {robla_determination_2021,
	title = {Determination of the efficiency of filtration of cultures from microalgae and bacteria using hollow fiber filters},
	journal = {Environmental Science: Water Research \& Technology},
	volume = {7},
	number = {7},
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
	month = {jul},
	pages = {1230{\textendash}1239},
	abstract = {The most important question in sampling is {\textquotedblleft}Is the sample representative of the target population?{\textquotedblright} This question is necessary to understand how valid the sample taken is to the original population and if generalizations can be made from the sample. Samples taken for water quality measurement range from 1 mL for bacterial contamination to 100 mL or up to 1000 L for protozoan parasites. With larger samples taken, the confidence in detecting rare events increases dramatically. Here we illustrate that hollow fiber filters as routinely used for kidney dialysis can be adapted for environmental use. The filters retain all organisms down to viral particles and organic matter above 70 kDA, the molecular cutoff for urea, one of the waste products removed in kidney dialysis. With these filters, 50 liters of water can be filtered in about 90 minutes. Backflush of the filters recovers viable cells with minimal cell lysis that can be processed downstream for molecular analysis. Recovery rates were as high as 89\% and 75\% for phytoplankton and bacteria, respectively.},
	keywords = {rcc, RCC1507},
	issn = {2053-1419},
	doi = {10.1039/D0EW00927J},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/ew/d0ew00927j},
	author = {Robla, J. and Garc{\'\i}a-Hierrro, J. and Alguacil, F. J. and Dittami, S. M. and Marie, D. and Villa, E. and Deragon, E. and Guillebault, D. and Mengs, G. and Medlin, L. K.}
}
@mastersthesis {wislon_development_2021,
	title = {Development of automated nucleic acid technologies for marine point of sample diagnostics},
	year = {2021},
	school = {University of Southampton},
	type = {phd},
	address = {Southampton},
	keywords = {RCC1513},
	url = {https://eprints.soton.ac.uk/447354/1/Wilson_Matthew_Thesis_final_Jan21.pdf},
	author = {Wislon, Matthew}
}
@article {zhang_development_2021,
	title = {Development of high-resolution chloroplast markers for intraspecific phylogeographic studies of Phaeocystis globosa},
	journal = {Journal of Oceanology and Limnology},
	volume = {39},
	number = {2},
	year = {2021},
	month = {mar},
	pages = {508{\textendash}524},
	abstract = {Phaeocystis globosa is an important harmful algal bloom causative species distributing widely in temperate and tropical coastal waters in the world. The morphological, physiological, and biochemical characteristics are different among geographic strains, which can not be distinguished with nuclear ribosomal DNA markers at present. Therefore, the genetic distance and phylogeographic relationships of nuclear 28S rDNA D1{\textendash}D2 and ITS regions, and three chloroplast intergenic spacers (petN-trnS1, trnM1-psbA, and rbcS-rpl27) were analyzed and compared among 13 strains of P. globosa isolated from the Pacific Ocean and Atlantic Ocean in this study. In addition, the nucleotide polymorphisms of 28S rDNA D1{\textendash}D2, ITS, and rbcS-rpl27 regions were evaluated in two P. globosa strains. The various levels of nucleotide polymorphism were in the nuclear 28S rDNA D1{\textendash}D2 region and ITS region, but no polymorphism was in the chloroplast rbcS-rpl27 intergenic spacer. A reasonable intraspecific phylogeographic relationship was presented by rbcS-rpl27 intergenic spacer, which had the strongest distinction to geographic strains compared to those of 28S rDNA D1{\textendash}D2 and ITS regions. In the phylogenetic tree of rbcS-rpl27 intergenic spacer, the two strains from the North Sea of the Atlantic Ocean were divided firstly from the species of P. globosa, and then formed an independent clade, while the other Atlantic strains and all of Pacific strains joined up to build the other clade. It was implied that at least two genetically distant populations of P. globosa existed in the Atlantic coastal regions. This study provided a high-resolution chloroplast marker to analyze intraspecific phylogeographic populations of P. globosa, and preliminarily clarified the genetic relationships of the Pacific and Atlantic strains of P. globosa.},
	keywords = {RCC2055, RCC736},
	issn = {2096-5508, 2523-3521},
	doi = {10.1007/s00343-020-9304-5},
	url = {https://link.springer.com/10.1007/s00343-020-9304-5},
	author = {Zhang, Qingchun and Niu, Zhuang and Wang, Jinxiu and Liu, Chao and Kong, Fanzhou and Hu, Xiaokun and Zhao, Jiayu and Yu, Rencheng}
}
@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 {Avrahami2020,
	title = {Detection of phagotrophy in the marine phytoplankton group of the coccolithophores (calcihaptophycidae, haptophyta) during Nutrient-replete and Phosphate-limited growth},
	journal = {Journal of Phycology},
	year = {2020},
	note = {tex.mendeley-tags: RCC1130,RCC1131,RCC1178,RCC1216,RCC1217,RCC3779},
	month = {apr},
	pages = {jpy.12997},
	abstract = {Mixotrophic algae that combine photoautotrophy with phagotrophy in a single cell are prevalent in marine ecosystems. Here, we assessed the ability of food ingestion in coccolithophores, an important group of calcifying haptophytes inhabiting the oceans. We tested four species from different coccolithophore lineages (Emiliania huxleyi, Calcidiscus leptoporus, Coccolithus braarudii, and Calyptrosphaera sphaeroidea). For both E. huxleyi and C. leptoporus we included different life phases (haploid and diploid). For C. braarudii we only tested diploid heterococcolithophore cells, while for C. sphaeroidea we only tested haploid holococcolithophore cells. Phagotrophy was assessed using fluorescently labeled bacteria (FLB) as model prey item, under nutrient-replete and phosphate-limited conditions. We detected by microscopy ingestion of FLB by all species, except the diploid C. braarudii strain. However, a previous study detected ingestion by haploid cells of C. braarudii. These overall results indicate that mixotrophy and the ability to ingest prey is widespread in coccolithophores. Yet, in all tested species the ingestion of FLB was low ({\textexclamdown}1\% of the population contained prey at all time points over 2 days), namely for E. huxleyi and the diploid cells from C. leptoporus where detection of ingestion was sporadic. Moreover, no clear differences were detected between life phases in E. huxleyi and C. leptoporus under equal circumstances, or between replete and limited growth conditions.},
	keywords = {bacterivory, coccolithophores, life cycle, mixotrophy, phytoplankton, RCC1130, RCC1131, RCC1178, RCC1216, rcc1217, RCC3779},
	issn = {0022-3646},
	doi = {10.1111/jpy.12997},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jpy.12997},
	author = {Avrahami, Yoav and Frada, Miguel J.},
	editor = {Mock, T.}
}
@article {Connell2020,
	title = {Diel oscillations in the feeding activity of heterotrophic and mixotrophic nanoplankton in the North Pacific Subtropical Gyre},
	journal = {Aquatic Microbial Ecology},
	volume = {85},
	year = {2020},
	note = {Publisher: Inter-Research Science Center tex.mendeley-tags: RCC80},
	month = {dec},
	pages = {167{\textendash}181},
	abstract = {Daily oscillations in photosynthetically active radiation strongly influence the timing of metabolic processes in picocyanobacteria, but it is less clear how the light-dark cycle affects the activities of their consumers. We investigated the relationship between marine picocyanobacteria and nanoplanktonic consumers throughout the diel cycle to determine whether heterotrophic and mixotrophic protists (algae with phagotrophic ability) display significant periodicity in grazing pressure. Carbon biomass of Prochlorococcus and Synechococcus was estimated continuously from abundances and cell size measurements made by flow cytometry. Picocyanobacterial dynamics were then compared to nanoplankton abundances and ingestion of fluorescently labeled bacteria measured every 4 h during a 4 d survey in the North Pacific Subtropical Gyre. Grazing of the labeled bacteria by heterotrophic nanoplankton was significantly greater at night than during the day. The grazing activity of mixotrophic nanoplankton showed no diel periodicity, suggesting that they may feed continuously, albeit at lower rates than heterotrophic nanoplankton, to alleviate nutrient limitation in this oligotrophic environment. Diel changes in Prochlorococcus biomass indicated that they could support substantial growth of nanoplankton if those grazers are the main source of picocyanobacterial mortality, and that grazers may contribute to temporally stable abundances of picocyanobacteria.},
	keywords = {bacterivory, diel cycles, mixotrophy, nanoplankton grazing, picocyanobacteria, RCC80},
	issn = {0948-3055},
	doi = {10.3354/ame01950},
	url = {http://dx.doi.org/10.3354/ame01950 https://www.int-res.com/abstracts/ame/v85/p167-181/},
	author = {Connell, PE and Ribalet, F and Armbrust, EV and White, A and Caron, DA}
}
@article {Wittek2020,
	title = {Dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO) cell quotas variations arising from sea ice shifts of salinity and temperature in the Prymnesiophyceae Phaeocystis antarctica},
	journal = {Environmental Chemistry},
	year = {2020},
	note = {tex.mendeley-tags: RCC4023},
	abstract = {Environmental context. Dimethylsulfoniopropionate and dimethylsulfoxide could have a climatic influence especially in the polar areas. We investigate the effect of sea ice salinity and temperature on the production of these two sulfur metabolites by a polar microalga, and suggest their potential roles of osmoregulator and cryoprotectant. These results bring new information about the sulfur cycle in sea ice that is useful for climate models.. The Southern Ocean, which includes the seasonal ice zone (SIZ), is a source of large sea-air fluxes of dimethylsulfide (DMS), a climate active gas involved in Earth cooling processes. In this area, the prymnesiophyte Phaeocystis antarctica (P. antarctica) is one of the main producers of dimethylsulfoniopropionate (DMSP) and dimethylsulfoxide (DMSO), two metabolites that are precursors of DMS. These algae are also present in sea ice and contribute substantially to the high DMSP and DMSO concentrations observed in this habitat. DMSP and DMSO production in sea ice by P. antarctica is proposed to be promoted by its ability to live in extreme environmental conditions. We designed cell culture experiments to test that hypothesis, focusing on the impact of shifts of temperature and salinity on the DMSP and DMSO cell quotas. Our experiments show an increase in DMSP and DMSO cell quotas following shifts in salinity (34 to 75, at 4 {\textdegree}C), which suggests a potential osmoregulator function for both DMSP and DMSO. Stronger salinity shifts (up to 100) directly impact cell growth and induce a crash of the cultures. Combining the salinity (34 to 75) and temperature (4 {\textdegree}C to {\textendash}2.3 {\textdegree}C) shifts induces higher increases of DMSP and DMSO cell quotas that also suggests an implication of both metabolites in a cryoprotectant system. Experimental cell quotas (including diatom Fragilariopsis cylindrus quotas from a previous study) are then used to reconstruct DMSP and DMSO profiles in sea ice based on the biomass and taxonomy. Finally, the complexity of the transposition of rates obtained in the experimental domain to the real world is discussed.},
	keywords = {RCC4023},
	doi = {10.1071/EN19302},
	url = {https://doi.org/10.1071/EN19302},
	author = {Wittek, Boris and Carnat, Gauthier and Delille, Bruno and Tison, Jean-Louis and Gypens, Nathalie}
}
@article {Altenburger2020,
	title = {Dimorphism in cryptophytes{\textemdash}The case of Teleaulax amphioxeia / Plagioselmis prolonga and its ecological implications},
	journal = {Science Advances},
	volume = {6},
	number = {37},
	year = {2020},
	note = {tex.mendeley-tags: RCC5152},
	month = {sep},
	pages = {eabb1611},
	abstract = {Growing evidence suggests that sexual reproduction might be common in unicellular organisms, but observations are sparse. Limited knowledge of sexual reproduction constrains understanding of protist ecology. Although Teleaulax amphioxeia and Plagioselmis prolonga are common marine cryptophytes worldwide, and are also important plastid donors for some kleptoplastic ciliates and dinoflagellates, the ecology and development of these protists are poorly known. We demonstrate that P. prolonga is the haploid form of the diploid T. amphioxeia and describe the seasonal dynamics of these two life stages. The diploid T. amphioxeia dominates during periods of high dissolved inorganic nitrogen (DIN) and low irradiance, temperature, and grazing (winter and early spring), whereas the haploid P. prolonga becomes more abundant during the summer, when DIN is low and irradiance, temperature, and grazing are high. Dimorphic sexual life cycles might explain the success of this species by fostering high genetic diversity and enabling endurance in adverse conditions.},
	keywords = {RCC5152},
	issn = {2375-2548},
	doi = {10.1126/sciadv.abb1611},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.abb1611},
	author = {Altenburger, A and Blossom, H E and Garcia-Cuetos, L. and Jakobsen, H H and Carstensen, J and Lundholm, N. and Hansen, P. J. and Moestrup, {\O}. and Haraguchi, L.}
}
@article {Kayal2020,
	title = {Dinoflagellate host chloroplasts and mitochondria remain functional during amoebophrya infection},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {December},
	year = {2020},
	note = {tex.mendeley-tags: RCC1627,RCC4398},
	month = {dec},
	pages = {1{\textendash}11},
	abstract = {Dinoflagellates are major components of phytoplankton that play critical roles in many microbial food webs, many of them being hosts of countless intracellular parasites. The phototrophic dinoflagellate Scrippsiella acuminata (Dinophyceae) can be infected by the microeukaryotic parasitoids Amoebophrya spp. (Syndiniales), some of which primarily target and digest the host nucleus. Early digestion of the nucleus at the beginning of the infection is expected to greatly impact the host metabolism, inducing the knockout of the organellar machineries that highly depend upon nuclear gene expression, such as the mitochondrial OXPHOS pathway and the plastid photosynthetic carbon fixation. However, previous studies have reported that chloroplasts remain functional in swimming host cells infected by Amoebophrya . We report here a multi-approach monitoring study of S. acuminata organelles over a complete infection cycle by nucleus-targeting Amoebophrya sp. strain A120. Our results show sustained and efficient photosystem II activity as a hallmark of functional chloroplast throughout the infection period despite the complete digestion of the host nucleus. We also report the importance played by light on parasite production, i.e., the amount of host biomass converted to parasite infective propagules. Using a differential gene expression analysis, we observed an apparent increase of all 3 mitochondrial and 9 out of the 11 plastidial genes involved in the electron transport chains (ETC) of the respiration pathways during the first stages of the infection. The longer resilience of organellar genes compared to those encoded by the nucleus suggests that both mitochondria and chloroplasts remain functional throughout most of the infection. This extended organelle functionality, along with higher parasite production under light conditions, suggests that host bioenergetic organelles likely benefit the parasite Amoebophrya sp. A120 and improve its fitness during the intracellular infective stage.},
	keywords = {amoebophrya, chloroplast, Dinoflagellate, frontiers in microbiology, frontiersin, kleptoplast, marine plankton, org, organelles, parasitism, RCC1627, RCC4398, www},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.600823},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2020.600823/full},
	author = {Kayal, Ehsan and Alves-de-Souza, Catharina and Farhat, Sarah and Velo-Suarez, Lourdes and Monjol, Joanne and Szymczak, Jeremy and Bigeard, Estelle and Marie, Dominique and Noel, Benjamin and Porcel, Betina M and Corre, Erwan and Six, Christophe and Guillou, Laure}
}
@article {Fitzsimons2020,
	title = {Dissolved organic phosphorus uptake by marine phytoplankton is enhanced by the presence of dissolved organic nitrogen},
	journal = {Journal of Experimental Marine Biology and Ecology},
	volume = {530-531},
	number = {July},
	year = {2020},
	note = {Publisher: Elsevier tex.mendeley-tags: RC2563,RCC2565},
	month = {sep},
	pages = {151434},
	abstract = {Organic nutrients can constitute the major fractions (up to 70\%) of aquatic nitrogen (N) and phosphorus (P), but their cycling is poorly understood relative to the inorganic pools. Some phytoplankton species access P from the dissolved organic phosphorus (DOP) pool through expression of alkaline phosphatase (AP), which hydrolyses orthophosphate from organic molecules, and is thought to occur either at low concentrations of dissolved inorganic P (DIP), or elevated ratios of dissolved inorganic N (DIN) to DIP. Three algal strains native to the North-East Atlantic Ocean (coccolithophore, dinoflagellate and diatom species) were grown under representative, temperate conditions, and the dissolved N and P components amended to include dissolved organic N (DON) and DOP. The activity of AP was measured to determine the rate of DOP uptake by each algal species. The addition of DON and DOP enhanced the growth of the algal species, regardless of DIN and DIP concentrations. In cultures where the total concentrations and absolute N: P ratio was unchanged but the N pool included both DON and DIN, an increase in alkaline phosphatase activity (APA) was measured. This suggested that the presence of DON triggered the selective uptake of DOP. The uptake of organic P was confirmed by detection of adenosine in DOP-amended culture media, indicating that P had been cleaved from ADP and ATP added to the media as DOP, and cellular P concentration in these cultures exceeded the calculated concentration based on uptake of DIP only. Our data demonstrates that organic nutrients can enhance and sustain marine algal productivity. The findings have implications for marine ecosystem function and health, since climate change scenarios predict variable riverine inputs to coastal areas, altered N: P ratios, and changes in the inorganic to organic balance of the nutrient pools.},
	keywords = {Alkaline phosphatase, COASTAL WATERS, Dissolved organic nitrogen, Dissolved organic phosphorus, Marine algae, P-limitation, RCC2563, RCC2565},
	issn = {00220981},
	doi = {10.1016/j.jembe.2020.151434},
	url = {https://doi.org/10.1016/j.jembe.2020.151434 https://linkinghub.elsevier.com/retrieve/pii/S0022098119304666},
	author = {Fitzsimons, Mark F. and Probert, Ian and Gaillard, Fanny and Rees, Andrew P.}
}
@article {Arsenieff2020,
	title = {Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel},
	journal = {The ISME Journal},
	year = {2020},
	note = {Publisher: Springer US tex.mendeley-tags: RCC4657,RCC4658,RCC4659,RCC4660,RCC4661,RCC4662,RCC4663,RCC4664,RCC4665,RCC4666,RCC5154,RCC5839,RCC5840,RCC5841,RCC5842,RCC5843,RCC5844,RCC5845,RCC5846,RCC5847,RCC5848,RCC5849,RCC5850,RCC5851,RCC5852,RCC5853,RCC5854,RCC5855,RCC5856,RCC5857,RCC5859,RCC5860,RCC5861,RCC5862,RCC5863,RCC5864,RCC5865,RCC5866,RCC5867,RCC5868,RCC5869,RCC5870,RCC5871,RCC5872,RCC5873,RCC5875,RCC5876,RCC5877,RCC5878,RCC5879,RCC5880,RCC5881,RCC5882,RCC5883,RCC5884,RCC5885,RCC5886,RCC5887,RCC5921},
	month = {apr},
	keywords = {RCC4657, RCC4658, RCC4659, RCC4660, RCC4661, RCC4662, RCC4663, RCC4664, RCC4665, RCC4666, RCC5154, RCC5839, RCC5840, RCC5841, RCC5842, RCC5843, RCC5844, RCC5845, RCC5846, RCC5847, RCC5848, RCC5849, RCC5850, RCC5851, RCC5852, RCC5853, RCC5854, RCC5855, RCC5856, RCC5857, RCC5859, RCC5860, RCC5861, RCC5862, RCC5863, RCC5864, RCC5865, RCC5866, RCC5867, RCC5868, RCC5869, RCC5870, RCC5871, RCC5872, RCC5873, RCC5875, RCC5876, RCC5877, RCC5878, RCC5879, RCC5880, RCC5881, RCC5882, RCC5883, RCC5884, RCC5885, RCC5886, RCC5887, RCC5921},
	issn = {1751-7362},
	doi = {10.1038/s41396-020-0659-6},
	url = {http://dx.doi.org/10.1038/s41396-020-0659-6 http://www.nature.com/articles/s41396-020-0659-6},
	author = {Arsenieff, Laure and Le Gall, Florence and Rigaut-jalabert, Fabienne and Mah{\'e}, Fr{\'e}d{\'e}ric and Sarno, Diana and Gouhier, L{\'e}na and Baudoux, Anne-claire and Simon, Nathalie}
}
@article {Kuwata2020,
	title = {Draft whole-genome sequence of triparma laevis f. inornata (parmales, bolidophyceae), isolated from the oyashio region, western north pacific ocean},
	journal = {Microbiology Resource Announcements},
	volume = {9},
	number = {33},
	year = {2020},
	note = {ISBN: 9781493991730 tex.mendeley-tags: RCC4655},
	month = {aug},
	pages = {13{\textendash}14},
	abstract = {We present the first draft whole-genome sequence for the Parmales (Bolidophyceae, Heterokonta), a picoplanktonic sister group of diatoms, using a Triparma laevis f. inornata strain that was isolated from the Oyashio region in the western North Pacific Ocean.},
	keywords = {RCC4655},
	issn = {2576-098X},
	doi = {10.1128/MRA.00367-20},
	url = {https://mra.asm.org/content/9/33/e00367-20},
	author = {Kuwata, Akira and Saitoh, Kenji and Nakamura, Yoji and Ichinomiya, Mutsuo and Sato, Naoki},
	editor = {Stajich, Jason E.}
}
@article {kusch_dead_2019,
	title = {Dead in the Water: The Vicious Cycle of Blanks During Natural Level 14 C Manipulation of Marine Algal Cultures},
	journal = {Frontiers in Marine Science},
	volume = {6},
	year = {2019},
	note = {Publisher: Frontiers},
	abstract = {Authentic biomarker standards were obtained from algal cultures in an attempt to accurately determine blank C added during sample processing for compound-specific radiocarbon analysis. Emiliania huxleyi and Thalassiosira pseudonana were grown under manipulated Δ14C dissolved inorganic carbon (DIC) levels and chlorophyll a and either alkenones (E. huxleyi) or low molecular weight (LMW) alkanoic acids (T. pseudonana) were isolated from the respective biomass using preparative liquid chromatography (LC), wet chemical techniques or preparative gas chromatography, respectively. DI14C in the seawater medium was determined pre- and post-growth. Biomarker Δ14C values mostly agree within 1-2? analytical uncertainties. In those cases where biomarker Δ14C values differ significantly, chlorophyll a is up to 104{\textperthousand} more 14C-depleted than alkenones or LMW alkanoic acids, consistent with a larger LC blank compared to the other purification methods. However, in the majority of experimental setups pre- and post-growth DIC Δ14C values seem to be compromised by an unknown and variable blank C contribution. DIC Δ14C values deviate strongly from the anticipated Δ14C values (by up to ca. 560{\textperthousand}), pre- and post-growth Δ14C values differ significantly (by up to ca. 460{\textperthousand}), and changes are not unidirectional. Accordingly, since the substrate Δ14C value cannot unequivocally be constrained, blank C contributions for the different biomarker purification methods cannot be accurately calculated. This study illustrates the challenges and problems of producing authentic standards that are not readily commercially available and exemplifies how a laborious and time-consuming culturing approach may enter a vicious cycle of blank C contamination hampering accurate blank C determination.},
	keywords = {Algal cultures, Alkanoic acids, alkenones, Authentic standards, Blank, chlorophyll a, Compound-specific radiocarbon analysis, natural level 14 C manipulation, rcc1238},
	issn = {2296-7745},
	doi = {10.3389/fmars.2019.00780},
	url = {https://www.frontiersin.org/articles/10.3389/fmars.2019.00780/full},
	author = {Kusch, Stephanie and Benthien, Albert and Richter, Klaus-Uwe and Rost, Bj{\"o}rn and Mollenhauer, Gesine}
}
@article {Lacour2019,
	title = {Decoupling light harvesting, electron transport and carbon fixation during prolonged darkness supports rapid recovery upon re-illumination in the Arctic diatom Chaetoceros neogracilis},
	journal = {Polar Biology},
	year = {2019},
	note = {ISBN: 0123456789 Publisher: Springer Berlin Heidelberg tex.mendeley-tags: RCC2278},
	month = {may},
	keywords = {Arctic microalgae, Darkness, Diatom, GROWTH RATE, Photosynthesis, Polar night, RCC2278, temperature},
	issn = {0722-4060},
	doi = {10.1007/s00300-019-02507-2},
	url = {https://doi.org/10.1007/s00300-019-02507-2 http://link.springer.com/10.1007/s00300-019-02507-2},
	author = {Lacour, Thomas and Morin, Philippe-Isra{\"e}l and Sciandra, Th{\'e}o and Donaher, Natalie and Campbell, Douglas A. and Ferland, Joannie and Babin, Marcel}
}
@article {Engesmo2018,
	title = {Development of a qPCR assay to detect and quantify ichthyotoxic flagellates along the Norwegian coast, and the first Norwegian record of Fibrocapsa japonica (Raphidophyceae)},
	journal = {Harmful Algae},
	volume = {75},
	year = {2018},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1501,RCC1502},
	pages = {105{\textendash}117},
	abstract = {Blooms of ichthyotoxic microalgae pose a great challenge to the aquaculture industry world-wide, and there is a need for fast and specific methods for their detection and quantification in monitoring programs. In this study, quantitative real-time PCR (qPCR) assays for the detection and enumeration of three ichthyotoxic flagellates: the dinoflagellate Karenia mikimotoi (Miyake \& Kominami ex Oda) Hansen \& Moestrup and the two raphidophytes Heterosigma akashiwo (Hada) Hada ex Hara \& Chihara and Fibrocapsa japonica Toriumi \& Takano were developed. Further, a previously published qPCR assay for the dinoflagellate Karlodinium veneficum (Ballantine) Larsen was used. Monthly samples collected for three years (Aug 2009{\textendash}Jun 2012) in outer Oslofjorden, Norway were analysed, and the results compared with light microscopy cell counts. The results indicate a higher sensitivity and a lower detection limit (down to 1 cell L-1) for both qPCR assays. Qualitative and semi-quantitative results were further compared with those obtained by environmental 454 high throughput sequencing (HTS, metabarcoding) and scanning electron microscopy (SEM) examination from the same samplings. All four species were detected by qPCR and HTS and/or SEM in outer Oslofjorden (Aug 2009{\textendash}Jun 2012); Karlodinium veneficum was present year-round, whereas Karenia mikimotoi, Heterosigma akashiwo and Fibrocapsa japonica appeared mainly during the autumn in all three years. This is the first observation of Fibrocapsa japonica in Norwegian coastal waters. This species has previously been recorded off the Swedish west coast and German Bight, which may suggest a northward dispersal.},
	keywords = {454 high throughput environmental sequencing, Heterosigma akashiwo, Karenia mikimotoi, Karlodinium veneficum, Molecular monitoring, rcc1501, rcc1502, RDNA, SEM},
	issn = {15689883},
	doi = {10.1016/j.hal.2018.04.007},
	url = {https://doi.org/10.1016/j.hal.2018.04.007},
	author = {Engesmo, Anette and Strand, David and Gran-Stadnicze{\~n}ko, Sandra and Edvardsen, Bente and Medlin, Linda K. and Eikrem, Wenche}
}
@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 {Gutierrez-Rodriguez2017,
	title = {Dimethylated sulfur compounds in symbiotic protists: A potentially significant source for marine DMS(P)},
	journal = {Limnology and Oceanography},
	number = {February},
	year = {2017},
	note = {tex.mendeley-tags: 2017,rcc1383,rcc1491,rcc3468,rcc3507,sbr?hyto$_\textrmd$ipo},
	month = {feb},
	keywords = {2017, rcc1383, rcc1491, rcc3468, rcc3507, sbr?hyto$_\textrmd$ipo},
	issn = {00243590},
	doi = {10.1002/lno.10491},
	url = {http://doi.wiley.com/10.1002/lno.10491},
	author = {Gutierrez-Rodriguez, Andres and Pillet, Loic and Biard, Tristan and Said-Ahmad, Ward and Amrani, Alon and Sim{\'o}, Rafel and Not, Fabrice}
}
@article {Organelli2017,
	title = {On the discrimination of multiple phytoplankton groups from light absorption spectra of assemblages with mixed taxonomic composition and variable light conditions},
	journal = {Applied Optics},
	volume = {56},
	number = {14},
	year = {2017},
	note = {tex.mendeley-tags: RCC151,RCC322,RCC904},
	month = {may},
	pages = {3952},
	abstract = {According to recommendations of the international community of phytoplankton functional type algorithm devel- opers, a set of experiments on marine algal cultures was conducted to (1) investigate uncertainties and limits in phytoplankton group discrimination from hyperspectral light absorption properties of assemblages withmixed taxo- nomic composition, and (2) evaluate the extent to which modifications of the absorption spectral features due to variable light conditions affect the optical discrimination of phytoplankton. Results showed that spectral absorption signatures of multiple species can be extracted from mixed assemblages, even at low relative contributions. Errors in retrieved pigment abundances are, however, influenced by the co-occurrence of species with similar spectral features. Plasticity of absorption spectra due to changes in light conditions weakly affects interspecific differences, with errors {\textexclamdown}21\% for retrievals of pigment concentrations from mixed assemblages.},
	keywords = {RCC151, RCC322, RCC904},
	issn = {0003-6935},
	doi = {10.1364/AO.56.003952},
	url = {https://www.osapublishing.org/abstract.cfm?URI=ao-56-14-3952},
	author = {Organelli, Emanuele and Nuccio, Caterina and Lazzara, Luigi and Uitz, Julia and Bricaud, Annick and Massi, Luca}
}
@article {Hennon2017,
	title = {Diverse CO2-Induced responses in physiology and gene expression among eukaryotic phytoplankton},
	journal = {Frontiers in Microbiology},
	volume = {8},
	number = {December},
	year = {2017},
	note = {tex.mendeley-tags: RCC1303},
	month = {dec},
	pages = {1{\textendash}14},
	abstract = {With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. Here we compared the physiological and gene expression responses of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (\~400 ppm) and elevated (\~800 ppm) CO2. Dinoflagellates had significantly slower growth rates and higher, yet variable, chlorophyll a per cell under elevated CO2. The other phytoplankton tended to have increased growth rates and/or decreased chlorophyll a per cell. Carbon and nitrogen partitioning of cells shifted under elevated CO2 in some species, indicating potential changes in energy fluxes due to changes in carbon concentrating mechanisms (CCM) or photorespiration. Consistent with these phenotypic changes, gene set enrichment analyses revealed shifts in energy, carbon and nitrogen metabolic pathways, though with limited overlap between species in the genes and pathways involved. Similarly, gene expression responses across species revealed few conserved CO2-responsive genes within CCM and photorespiration categories, and a survey of available transcriptomes found high diversity in biophysical CCM and photorespiration expressed gene complements between and within the four phyla represented by these species. The few genes that displayed similar responses to CO2 across phyla were from understudied gene families, making them targets for further research to uncover the mechanisms of phytoplankton acclimation to elevated CO2. These results underscore that eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and highlight the value of cross-phyla comparisons for identifying gene families that respond to environmental change.},
	keywords = {algae, biophysical CCM, C4 CCM, carbon concentrating mechanism, carbon concentrating mechanism (CCM), ccm, photorespiration, RCC1303, transcriptomics},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2017.02547},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2017.02547/full},
	author = {Hennon, Gwenn M. M. and Hern{\'a}ndez Lim{\'o}n, Mar{\'\i}a D. and Haley, Sheean T. and Juhl, Andrew R. and Dyhrman, Sonya T.}
}
@article {LopesdosSantos2016,
	title = {Diversity and oceanic distribution of prasinophytes clade VII, the dominant group of green algae in oceanic waters},
	journal = {The ISME Journal},
	volume = {11},
	number = {2},
	year = {2017},
	note = {tex.mendeley-tags: 2016,RCC1019,RCC1021,RCC1032,RCC1043,RCC1124,RCC138,RCC15,RCC1871,RCC19,RCC227,RCC2335,RCC2337,RCC2339,RCC287,RCC297,RCC3368,RCC3373,RCC3374,RCC3375,RCC3376,RCC3402,RCC4429,RCC4430,RCC4434,RCC4656,RCC696,RCC700,RCC701,RCC712,RCC713,RCC717,RCC719,RCC722,RCC726,RCC856,RCC857,RCC917,RCC996,RCC997,RCC998,RCC999,sbr?hyto$_\textrmd$ipo,sbr?hyto?ppo},
	month = {feb},
	pages = {512{\textendash}528},
	keywords = {2016, MACUMBA, MicroB3, RCC1019, RCC1021, RCC1032, RCC1043, RCC1124, RCC138, RCC15, RCC1871, RCC19, RCC227, RCC2335, RCC2337, RCC2339, RCC287, RCC297, RCC3368, RCC3373, RCC3374, RCC3375, RCC3376, RCC3402, RCC4429, RCC4430, RCC4434, RCC4656, RCC696, RCC700, RCC701, RCC712, RCC713, RCC717, RCC719, RCC722, RCC726, RCC856, RCC857, RCC917, RCC996, RCC997, RCC998, RCC999, sbr?hyto$_\textrmd$ipo, sbr?hyto?ppo},
	issn = {1751-7362},
	doi = {10.1038/ismej.2016.120},
	url = {http://www.nature.com/doifinder/10.1038/ismej.2016.120},
	author = {Lopes dos Santos, Adriana and Gourvil, Priscillia and Tragin, Margot and No{\"e}l, Mary-H{\'e}l{\`e}ne and Decelle, Johan and Romac, Sarah and Vaulot, Daniel}
}
@article {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 {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 {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 {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 {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 {Turmel2010,
	title = {A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga pycnococcus provasolii},
	journal = {Journal of Molecular Evolution},
	volume = {70},
	number = {2},
	year = {2010},
	note = {ISBN: 0022-2844 tex.mendeley-tags: RCC299},
	pages = {203{\textendash}214},
	abstract = {Reduction in size of flagellated chlorophytes occurred multiple times during evolution, providing the opportunity to study the consequences of cell reduction on genome architecture. Recent investigations on the chloroplast genomes of the tiny prasinophyceans Ostreococcus tauri (Mamiellales), Micromonas sp. RCC299 (Mamiellales), and Pycnococcus provasolii (Pseudocourfieldiales) highlighted their extreme compaction and reduced gene repertoires. Genome compaction is also exemplified by the Ostreococcus and Micromonas mitochondrial DNAs (mtDNAs) although they have retained almost all of the about 65 genes presumably present in the mitochondria of ancestral prasinophyceans. In this study, the mitochondrial genome of Pycnococcus was sequenced and compared to those of previously examined chlorophytes. Our results document the first case where cellular reduction of a free-living alga was accompanied by marked reduction in gene content of both the mitochondrial and chloroplast genomes. At 24,321 bp, the intronless Pycnococcus mitochondrial genome falls within the lower size range displayed by green algal mtDNAs. The 36 conserved genes, specifying two rRNAs with conventional structures, 16 tRNAs and 18 proteins, are all encoded on the same DNA strand and represent 88\% of the genome. Besides a pronounced codon bias, the protein-coding genes feature a variant genetic code characterized by the use of TGA (normally a stop codon) to code for tryptophan, and the unprecedented use of TTA and TTG (normally leucine codons) as stop codons. We conclude that substantial reduction of the mitochondrial genome occurred in at least three independent chlorophyte lineages and that this process entailed a number of convergent changes in these lineages.},
	keywords = {RCC299},
	doi = {10.1007/s00239-010-9322-6},
	author = {Turmel, Monique and Otis, Christian and Lemieux, Claude}
}
@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 {gile_dna_2010,
	title = {Dna Barcoding of Chlorarachniophytes Using Nucleomorph Its Sequences1},
	journal = {Journal of Phycology},
	volume = {46},
	number = {4},
	year = {2010},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1529-8817.2010.00851.x},
	pages = {743{\textendash}750},
	abstract = {Chlorarachniophytes are a small group of marine photosynthetic protists. They are best known as examples of an intermediate stage of secondary endosymbiosis: their plastids are derived from green algae and retain a highly reduced nucleus, called a nucleomorph, between the inner and outer pairs of membranes. Chlorarachniophytes can be challenging to identify to the species level, due to their small size, complex life cycles, and the fact that even genus-level diagnostic morphological characters are observable only by EM. Few species have been formally described, and many available culture collection strains remain unnamed. To alleviate this difficulty, we have developed a barcoding system for rapid and accurate identification of chlorarachniophyte species in culture, based on the internal transcribed spacer (ITS) region of the nucleomorph rRNA cistron. Although this is a multicopy locus, encoded in both subtelomeric regions of each chromosome, interlocus variability is low due to gene conversion by homologous recombination in this region. Here, we present barcode sequences for 39 cultured strains of chlorarachniophytes (>80\% of currently available strains). Based on barcode data, other published molecular data, and information from culture records, we were able to recommend names for 21 out of the 24 unidentified, partially identified, or misidentified chlorarachniophyte strains in culture. Most strains could be assigned to previously described species, but at least two to as many as five new species may be present among cultured strains.},
	keywords = {Bigelowiella, Chlorarachnion, culture collections, Gymnochlora, internal transcribed spacer, Lotharella, Norrisiella, Partenskyella, RCC337, RCC375, RCC376, RCC435, RCC530, RCC531, RCC623, RCC626},
	issn = {1529-8817},
	doi = {10.1111/j.1529-8817.2010.00851.x},
	url = {http://onlinelibrary.wiley.com/doi/abs/10.1111/j.1529-8817.2010.00851.x},
	author = {Gile, Gillian H. and Stern, Rowena F. and James, Erick R. and Keeling, Patrick J.}
}
@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 {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 {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 {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 {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 {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 {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 {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}
}
