@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.}
}
@booklet {barton_novel_2023,
	title = {A novel fluoro-electrochemical technique for classifying diverse marine nanophytoplankton},
	year = {2023},
	month = {apr},
	publisher = {Life Sciences},
	type = {preprint},
	abstract = {<p>To broaden our understanding of pelagic ecosystem responses to environmental change, it is essential that we improve the spatio-temporal resolution of in situ monitoring of phytoplankton communities. A key challenge for existing methods is in classifying and quantifying cells within the nanophytoplankton size range (2-20{\textmu}m). This is particularly difficult when there are similarities in morphology, making visual differentiation difficult for both trained taxonomists and machine learning based approaches. Here we present a rapid fluoro-electrochemical technique for classifying nanophytoplankton, and using a library of 52 diverse strains of nanophytoplankton we assess the accuracy of this technique based on two measurements at the individual level: charge required to reduce per cell chlorophyll a fluorescence by 50\%, and cell radius. We demonstrate a high degree of accuracy overall (\&gt;90\%) in categorising cells belonging to widely recognised key functional groups, however this is reduced when we consider the broader diversity of {\textquotedblleft}nano-phytoflagellates{\textquotedblright}. Notably, we observe that some groups, for example calcifying Isochrysidales, have much greater resilience to electrochemically driven oxidative conditions relative to others of a similar size, making them more easily categorised by the technique. The findings of this study present a promising step forward in advancing our toolkit for monitoring phytoplankton communities. We highlight that, for improved categorisation accuracy, future iterations of the method can be enhanced by measuring additional predictor variables with minimal adjustments to the set-up. In doing so, we foresee this technique being highly applicable, and potentially invaluable, for in situ classification and enumeration of the nanophytoplankton size fraction.</p>
},
	keywords = {RCC1, rcc1084, RCC1130, RCC1150, RCC1178, RCC1185, RCC1198, RCC1216, rcc1217, RCC1242, RCC1314, RCC1346, RCC1489, RCC1511, RCC1546, RCC1557, RCC1614, rcc1731, RCC191, RCC2570, RCC3598, RCC3696, RCC3776, RCC3780, RCC4207, RCC4221, RCC4273, RCC4657, RCC4660, RCC6, RCC623, RCC6516, RCC656, RCC678, RCC69, RCC74, RCC76, RCC8, RCC80, RCC81, RCC88, RCC911, RCC950},
	doi = {10.1002/lom3.10572},
	url = {https://aslopubs.onlinelibrary.wiley.com/doi/10.1002/lom3.10572},
	author = {Barton, Samuel and Yang, Minjun and Chen, Haotian and Batchelor-McAuley, Christopher and Compton, Richard and Bouman, Heather and Rickaby, Rosalind}
}
@article {bendif_rapid_2023,
	title = {Rapid diversification underlying the global dominance of a cosmopolitan phytoplankton},
	journal = {The ISME Journal},
	year = {2023},
	note = {Publisher: Nature Publishing Group},
	pages = {1{\textendash}11},
	abstract = {Marine phytoplankton play important roles in the global ecosystem, with a limited number of cosmopolitan keystone species driving their biomass. Recent studies have revealed that many of these phytoplankton are complexes composed of sibling species, but little is known about the evolutionary processes underlying their formation. Gephyrocapsa huxleyi, a widely distributed and abundant unicellular marine planktonic algae, produces calcified scales (coccoliths), thereby significantly affects global biogeochemical cycles via sequestration of inorganic carbon. This species is composed of morphotypes defined by differing degrees of coccolith calcification, the evolutionary ecology of which remains unclear. Here, we report an integrated morphological, ecological and genomic survey across globally distributed G. huxleyi strains to reconstruct evolutionary relationships between morphotypes in relation to their habitats. While G. huxleyi has been considered a single cosmopolitan species, our analyses demonstrate that it has evolved to comprise at least three distinct species, which led us to formally revise the taxonomy of the G. huxleyi complex. Moreover, the first speciation event occurred before the onset of the last interglacial period (\textasciitilde140 ka), while the second followed during this interglacial. Then, further rapid diversifications occurred during the most recent ice-sheet expansion of the last glacial period and established morphotypes as dominant populations across environmental clines. These results suggest that glacial-cycle dynamics contributed to the isolation of ocean basins and the segregations of oceans fronts as extrinsic drivers of micro-evolutionary radiations in extant marine phytoplankton.},
	keywords = {Microbial biooceanography, phylogenomics, population genetics, rcc1212, RCC1216, rcc1220, RCC1239, RCC1240, RCC1242, RCC1245, rcc1252, RCC1253, RCC1266, RCC1304, rcc1731, RCC1754, RCC1813, RCC1823, rcc1824, RCC1830, RCC1838, RCC1840, RCC1853, RCC1856, RCC3746, RCC4027, RCC4028, RCC4030, RCC5134, RCC5137, RCC5141, RCC6381, RCC6421, RCC6427, RCC6566, RCC6660, RCC6666, RCC911, RCC963},
	issn = {1751-7370},
	doi = {10.1038/s41396-023-01365-5},
	url = {https://www.nature.com/articles/s41396-023-01365-5},
	author = {Bendif, El Mahdi and Probert, Ian and Archontikis, Odysseas A. and Young, Jeremy R. and Beaufort, Luc and Rickaby, Rosalind E. and Filatov, Dmitry}
}
@article {storti_tailoring_2023,
	title = {Tailoring confocal microscopy for real-time analysis of photosynthesis at single-cell resolution},
	journal = {Cell Reports Methods},
	year = {2023},
	pages = {100568},
	abstract = {Photoautotrophs{\textquoteright} environmental responses have been extensively studied at the organism and ecosystem level. However, less is known about their photosynthesis at the single-cell level. This information is needed to understand photosynthetic acclimation processes, as light changes as it penetrates cells, layers of cells, or organs. Furthermore, cells within the same tissue may behave differently, being at different developmental/ physiological stages. Here, we describe an approach for single-cell and subcellular photophysiology based on the customization of confocal microscopy to assess chlorophyll fluorescence quenching by the saturation pulse method. We exploit this setup to (1) reassess the specialization of photosynthetic activities in developing tissues of non-vascular plants; (2) identify a specific subpopulation of phytoplankton cells in marine photosymbiosis, which consolidate energetic connections with their hosts; and (3) examine the link between light penetration and photoprotection responses inside the different tissues that constitute a plant leaf anatomy.},
	keywords = {rcc1383},
	issn = {26672375},
	doi = {10.1016/j.crmeth.2023.100568},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2667237523002126},
	author = {Storti, Mattia and Hsine, Haythem and Uwizeye, Clarisse and Bastien, Olivier and Yee, Daniel P. and Chevalier, Fabien and Decelle, Johan and Giustini, C{\'e}cile and B{\'e}al, Daniel and Curien, Gilles and Finazzi, Giovanni and Tolleter, Dimitri}
}
@article {yee_v-type_2023,
	title = {The V-type ATPase enhances photosynthesis in marine phytoplankton and further links phagocytosis to symbiogenesis},
	journal = {Current Biology},
	year = {2023},
	month = {may},
	pages = {S0960982223006152},
	abstract = {Diatoms, dinoflagellates, and coccolithophores are dominant groups of marine eukaryotic phytoplankton that are collectively responsible for the majority of primary production in the ocean.1 These phytoplankton contain additional intracellular membranes around their chloroplasts, which are derived from ancestral engulfment of red microalgae by unicellular heterotrophic eukaryotes that led to secondary and tertiary endosymbiosis.2 However, the selectable evolutionary advantage of these membranes and the physiological significance for extant phytoplankton remain poorly understood. Since intracellular digestive vacuoles are ubiquitously acidified by V-type H+-ATPase (VHA),3 proton pumps were proposed to acidify the microenvironment around secondary chloroplasts to promote the dehydration of dissolved inorganic carbon (DIC) into CO2, thus enhancing photosynthesis.4,5 We report that VHA is localized around the chloroplasts of centric diatoms and that VHA significantly contributes to their photosynthesis across a wide range of oceanic irradiances. Similar results in a pennate diatom, dinoflagellate, and coccolithophore, but not green or red microalgae, imply the co-option of phagocytic VHA activity into a carbon-concentrating mechanism (CCM) is common to secondary endosymbiotic phytoplankton. Furthermore, analogous mechanisms in extant photosymbiotic marine invertebrates6{\textendash}8 provide functional evidence for an adaptive advantage throughout the transition from endosymbiosis to symbiogenesis. Based on the contribution of diatoms to ocean biogeochemical cycles, VHA-mediated enhancement of photosynthesis contributes at least 3.5 Gtons of fixed carbon per year (or 7\% of primary production in the ocean), providing an example of a symbiosis-derived evolutionary innovation with global environmental implications.},
	keywords = {RCC3387},
	issn = {09609822},
	doi = {10.1016/j.cub.2023.05.020},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982223006152},
	author = {Yee, Daniel P. and Samo, Ty J. and Abbriano, Raffaela M. and Shimasaki, Bethany and Vernet, Maria and Mayali, Xavier and Weber, Peter K. and Mitchell, B. Greg and Hildebrand, Mark and Decelle, Johan and Tresguerres, Martin}
}
@article {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 {zhang_intense_2022,
	title = {Intense blooms of Phaeocystis globosa in the South China Sea are caused by a unique {\textquotedblleft}giant-colony{\textquotedblright} ecotype},
	journal = {Harmful Algae},
	volume = {114},
	year = {2022},
	pages = {102227},
	abstract = {The haptophyte Phaeocystis globosa, an important causative agent of harmful algal blooms globally, exhibits varying morphological and physiological features and high genetic diversity, yet the relationship among these has never been elucidated. In this study, colony sizes and pigment profiles of 19 P. globosa isolates from the Pacific and Atlantic Oceans were determined. Genetic divergence of these strains was analyzed using the chloroplast rbcS-rpl27 intergenic spacer, a novel high-resolution molecular marker. Strains could be divided into four genetic clades based on these sequences, or two groups based on colony size and the identity of diagnostic pigments (19{\textquoteright}-hexanoyloxyfucoxanthin, hex-fuco, and 19{\textquoteright}-butanoyloxyfucoxanthin, but-fuco). Three strains from the South China Sea (SCS), all belonging to the same genetic clade, have unique biological features in forming giant colonies and possessing but-fuco as their diagnostic pigment. Based on these findings, we propose that these SCS strains should be a unique {\textquotedblleft}giant-colony{\textquotedblright} ecotype of P. globosa. During the period 2016-2021, more than 1000 rbcS-rpl27 sequences were obtained from 16 P. globosa colony samples and 18 phytoplankton samples containing solitary P. globosa cells in the SCS. Phylogenetic analysis indicated that >95\% of the sequences from P. globosa colonies in the SCS were comprised of the {\textquotedblleft}giant-colony{\textquotedblright} ecotype, whereas the genetic diversity of solitary cells was much higher. Results demonstrated that intense blooms of P. globosa featuring giant colonies in the SCS were mainly caused by this giant-colony P. globosa ecotype.},
	keywords = {ecotype, genetic diversity, Giant colony, Marker pigment, RCC1736, RCC2055, RCC678, RCC736},
	issn = {1568-9883},
	doi = {10.1016/j.hal.2022.102227},
	url = {https://www.sciencedirect.com/science/article/pii/S1568988322000555},
	author = {Zhang, Qing-Chun and Liu, Chao and Wang, Jin-Xiu and Kong, Fan-Zhou and Niu, Zhuang and Xiang, Ling and Yu, Ren-Cheng}
}
@article {carrigee_phycoerythrobilin_2022,
	title = {The phycoerythrobilin isomerization activity of MpeV in Synechococcus sp. WH8020 is prevented by the presence of a histidine at position 141 within its phycoerythrin-I β-subunit substrate},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	pages = {1011189},
	abstract = {Marine Synechococcus efficiently harvest available light for photosynthesis using complex antenna systems, called phycobilisomes, composed of an allophycocyanin core surrounded by rods, which in the open ocean are always constituted of phycocyanin and two phycoerythrin (PE) types: PEI and PEII. These cyanobacteria display a wide pigment diversity primarily resulting from differences in the ratio of the two chromophores bound to PEs, the green-light absorbing phycoerythrobilin and the blue-light absorbing phycourobilin. Prior to phycobiliprotein assembly, bilin lyases post-translationally catalyze the ligation of phycoerythrobilin to conserved cysteine residues on α- or β-subunits, whereas the closely related lyase-isomerases isomerize phycoerythrobilin to phycourobilin during the attachment reaction. MpeV was recently shown in Synechococcus sp. RS9916 to be a lyase-isomerase which doubly links phycourobilin to two cysteine residues (C50 and C61; hereafter C50, 61) on the β-subunit of both PEI and PEII. Here we show that Synechococcus sp. WH8020, which belongs to the same pigment type as RS9916, contains MpeV that demonstrates lyase-isomerase activity on the PEII β-subunit but only lyase activity on the PEI β-subunit. We also demonstrate that occurrence of a histidine at position 141 of the PEI β-subunit from WH8020, instead of a leucine in its counterpart from RS9916, prevents the isomerization activity by WH8020 MpeV, showing for the first time that both the substrate and the enzyme play a role in the isomerization reaction. We propose a structural-based mechanism for the role of H141 in blocking isomerization. More generally, the knowledge of the amino acid present at position 141 of the β-subunits may be used to predict which phycobilin is bound at C50, 61 of both PEI and PEII from marine Synechococcus strains.},
	keywords = {RCC2437, RCC307, RCC751},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.1011189},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2022.1011189/full},
	author = {Carrigee, Lyndsay A. and Frick, Jacob P. and Liu, Xindi and Karty, Jonathan A. and Trinidad, Jonathan C. and Tom, Irin P. and Yang, Xiaojing and Dufour, Louison and Partensky, Fr{\'e}d{\'e}ric and Schluchter, Wendy M.}
}
@article {fan_quantifying_2022,
	title = {Quantifying the Extent of Calcification of a Coccolithophore Using a Coulter Counter},
	journal = {Analytical Chemistry},
	year = {2022},
	month = {sep},
	pages = {acs.analchem.2c01971},
	abstract = {Although, in principle, the Coulter Counter technique yields an absolute measure of particle volume, in practice, calibration is nearuniversally employed. For regularly shaped and non-biological samples, the use of latex beads for calibration can provide sufficient accuracy. However, this is not the case with particles encased in biogenically formed calcite. To date, there has been no effective route by which a Coulter Counter can be calibrated to enable the calcification of coccolithophores�single cells encrusted with biogenic calcite�to be quantified. Consequently, herein, we seek to answer the following question: to what extent can a Coulter Counter be used to provide accurate information regarding the calcite content of a singlespecies coccolithophore population? Through the development of a new calibration methodology, based on the measurement and dynamic tracking of the acid-driven calcite dissolution reaction, a route by which the cellular calcite content can be determined is presented. This new method allows, for the first time, a Coulter Counter to be used to yield an absolute measurement of the amount of calcite per cell.},
	keywords = {RCC1198, RCC1216, RCC1314},
	issn = {0003-2700, 1520-6882},
	doi = {10.1021/acs.analchem.2c01971},
	url = {https://pubs.acs.org/doi/10.1021/acs.analchem.2c01971},
	author = {Fan, Xinmeng and Batchelor-McAuley, Christopher and Yang, Minjun and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {park_bioluminescence_2021,
	title = {Bioluminescence capability and intensity in the dinoflagellate Alexandrium species},
	journal = {ALGAE},
	volume = {36},
	year = {2021},
	abstract = {Some species in the dinoflagellate genus Alexandrium are bioluminescent. Of the 33 formally described Alexandrium species, the bioluminescence capability of only nine species have been tested, and eight have been reported to be bioluminescent. The present study investigated the bioluminescence capability of seven Alexandrium species that had not been tested. Alexandrium mediterraneum, A. pohangense, and A. tamutum were bioluminescent, but A. andersonii, A. hiranoi, A. insuetum, and A. pseudogonyaulax were not. We also measured the bioluminescent intensity of A. affine, A. fraterculus, A. mediterraneum, A. ostenfeldii, A. pacificum, A. pohangense, A. tamarense, and A. tamutum. The mean 200-second-integrated bioluminescence intensity per cell ranged from 0.02 to 32.2 {\texttimes} 104 relative luminescence unit per cell (RLU cell-1), and the mean maximum bioluminescence intensity per cell per second (BLMax) ranged from 0.01 to 10.3 {\texttimes} 104 RLU cell-1 s-1. BLMax was significantly correlated with the maximum growth rates of Alexandrium species, except for A. tamarense. A phylogenetic tree based on large subunit ribosomal DNA (LSU rDNA), showed that the bioluminescent species A. affine, A. catenella, A. fraterculus, A. mediterraneum, A. pacificum, and A. tamarense formed a large clade. However, the toxicity or mixotrophic capability of these species was split. Thus, their bioluminescence capability in this clade was more consistent than their toxicity or mixotrophic capability. Phylogenetic trees based on LSU rDNA and the luciferase gene of Alexandrium were consistent except for A. pohangense. The results of the present study can provide a basis for understanding the interspecific diversity in bioluminescence of Alexandrium.},
	keywords = {RCC4104},
	doi = {10.4490/algae.2021.36.12.6},
	author = {Park, Sang Ah and Jeong, Hae Jin and Ok, Jin and Kang, Heechang and You, Jihyun and Eom, Se and Yoo, Yeong and Lee, Moo Joon}
}
@article {thomy_combining_2021,
	title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri},
	journal = {Cells},
	volume = {10},
	number = {3},
	year = {2021},
	pages = {664},
	abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.},
	keywords = {RCC1115, RCC7079, RCC7080, RCC7081, RCC7082, RCC7083, RCC7084, RCC7085},
	issn = {2073-4409},
	doi = {10.3390/cells10030664},
	url = {https://www.mdpi.com/2073-4409/10/3/664},
	author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree}
}
@booklet {thomy_combining_2021,
	title = {Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri},
	year = {2021},
	month = {feb},
	publisher = {LIFE SCIENCES},
	type = {preprint},
	abstract = {Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration appears to be random, occurring mainly at a single locus, and thus confirming the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci, and often within the vector sequence itself. From these observations, we speculate that a non-homologous end joining-like mechanism is required during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in ecologically important marine algae.},
	keywords = {RCC1115},
	doi = {10.20944/preprints202102.0506.v1},
	url = {https://www.preprints.org/manuscript/202102.0506/v1},
	author = {Thomy, Julie and Sanchez, Fr{\'e}d{\'e}ric and Gut, Marta and Cruz, Fernando and Alioto, Tyler and Piganeau, Gwenael and Grimsley, Nigel and Yau, Sheree}
}
@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 {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 {yang_opto-electrochemical_2021,
	title = {Opto-Electrochemical Dissolution Reveals Coccolith Calcium Carbonate Content},
	journal = {Angewandte Chemie International Edition},
	volume = {60},
	number = {38},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.202108435},
	pages = {20999{\textendash}21006},
	abstract = {Coccoliths are plates of biogenic calcium carbonate secreted by calcifying marine phytoplankton; annually these phytoplankton are responsible for exporting >1 billion tonnes (1015 g) of calcite to the deep ocean. Rapid and reliable methods for assessing the degree of calcification are technically challenging because the coccoliths are micron sized and contain picograms (pg) of calcite. Here we pioneer an opto-eletrochemical acid titration of individual coccoliths which allows 3D reconstruction of each individual coccolith via in situ optical imaging enabling direct inference of the coccolith mass. Coccolith mass ranging from 2 to 400 pg are reported herein, evidencing both inter- and intra-species variation over four different species. We foresee this scientific breakthrough, which is independent of knowledge regarding the species and calibration-free, will allow continuous monitoring and reporting of the degree of coccolith calcification in the changing marine environment.},
	keywords = {analytical methods, calcite dissolution, electrochemistry, global carbonate cycle, marine phytoplankton, RCC1130, RCC1198, RCC1216, RCC1314},
	issn = {1521-3773},
	doi = {10.1002/anie.202108435},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.202108435},
	author = {Yang, Minjun and Batchelor-McAuley, Christopher and Barton, Samuel and Rickaby, Rosalind E. M. and Bouman, Heather A. and Compton, Richard G.}
}
@article {castillo_seasonal_2021,
	title = {Seasonal dynamics of natural Ostreococcus viral infection at the single cell level using VirusFISH},
	journal = {Environmental Microbiology},
	volume = {n/a},
	number = {n/a},
	year = {2021},
	note = {_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.15504},
	abstract = {Ostreococcus is a cosmopolitan marine genus of phytoplankton found in mesotrophic and oligotrophic waters, and the smallest free-living eukaryotes known to date, with a cell diameter close to 1 μm. Ostreococcus has been extensively studied as a model system to investigate viral{\textendash}host dynamics in culture, yet the impact of viruses in naturally occurring populations is largely unknown. Here, we used Virus Fluorescence in situ Hybridization (VirusFISH) to visualize and quantify viral-host dynamics in natural populations of Ostreococcus during a seasonal cycle in the central Cantabrian Sea (Southern Bay of Biscay). Ostreococcus were predominantly found during summer and autumn at surface and 50 m depth, in coastal, mid-shelf and shelf waters, representing up to 21\% of the picoeukaryotic communities. Viral infection was only detected in surface waters, and its impact was variable but highest from May to July and November to December, when up to half of the population was infected. Metatranscriptomic data available from the mid-shelf station unveiled that the Ostreococcus population was dominated by the species O. lucimarinus. This work represents a proof of concept that the VirusFISH technique can be used to quantify the impact of viruses on targeted populations of key microbes from complex natural communities. This article is protected by copyright. All rights reserved.},
	keywords = {RCC2590, RCC4221, RCC809},
	issn = {1462-2920},
	doi = {10.1111/1462-2920.15504},
	url = {http://sfamjournals.onlinelibrary.wiley.com/doi/abs/10.1111/1462-2920.15504},
	author = {Castillo, Yaiza M. and Forn, Irene and Yau, Sheree and Mor{\'a}n, Xos{\'e} Anxelu G. and Alonso-S{\'a}ez, Laura and Arandia-Gorostidi, N{\'e}stor and Vaqu{\'e}, Dolors and Sebasti{\'a}n, Marta}
}
@article {bachy_viruses_2021,
	title = {Viruses infecting a warm water picoeukaryote shed light on spatial co-occurrence dynamics of marine viruses and their hosts},
	journal = {The ISME Journal},
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	month = {may},
	pages = {1{\textendash}19},
	abstract = {The marine picoeukaryote Bathycoccus prasinos has been considered a cosmopolitan alga, although recent studies indicate two ecotypes exist, Clade BI (B. prasinos) and Clade BII. Viruses that infect Bathycoccus Clade BI are known (BpVs), but not that infect BII. We isolated three dsDNA prasinoviruses from the Sargasso Sea against Clade BII isolate RCC716. The BII-Vs do not infect BI, and two (BII-V2 and BII-V3) have larger genomes (\textasciitilde210 kb) than BI-Viruses and BII-V1. BII-Vs share \textasciitilde90\% of their proteins, and between 65\% to 83\% of their proteins with sequenced BpVs. Phylogenomic reconstructions and PolB analyses establish close-relatedness of BII-V2 and BII-V3, yet BII-V2 has 10-fold higher infectivity and induces greater mortality on host isolate RCC716. BII-V1 is more distant, has a shorter latent period, and infects both available BII isolates, RCC716 and RCC715, while BII-V2 and BII-V3 do not exhibit productive infection of the latter in our experiments. Global metagenome analyses show Clade BI and BII algal relative abundances correlate positively with their respective viruses. The distributions delineate BI/BpVs as occupying lower temperature mesotrophic and coastal systems, whereas BII/BII-Vs occupy warmer temperature, higher salinity ecosystems. Accordingly, with molecular diagnostic support, we name Clade BII Bathycoccus calidus sp. nov. and propose that molecular diversity within this new species likely connects to the differentiated host-virus dynamics observed in our time course experiments. Overall, the tightly linked biogeography of Bathycoccus host and virus clades observed herein supports species-level host specificity, with strain-level variations in infection parameters.},
	keywords = {RCC715, RCC716},
	issn = {1751-7370},
	doi = {10.1038/s41396-021-00989-9},
	url = {https://www.nature.com/articles/s41396-021-00989-9},
	author = {Bachy, Charles and Yung, Charmaine C. M. and Needham, David M. and Gazit{\'u}a, Maria Consuelo and Roux, Simon and Limardo, Alexander J. and Choi, Chang Jae and Jorgens, Danielle M. and Sullivan, Matthew B. and Worden, Alexandra Z.}
}
@article {Bestion2020,
	title = {Abrupt declines in marine phytoplankton production driven by warming and biodiversity loss in a microcosm experiment},
	journal = {Ecology Letters},
	volume = {23},
	number = {3},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {mar},
	pages = {457{\textendash}466},
	abstract = {Rising sea surface temperatures are expected to lead to the loss of phytoplankton biodiversity. However, we currently understand very little about the interactions between warming, loss of phytoplankton diversity and its impact on the oceans{\textquoteright} primary production. We experimentally manipulated the species richness of marine phytoplankton communities under a range of warming scenarios, and found that ecosystem production declined more abruptly with species loss in communities exposed to higher temperatures. Species contributing positively to ecosystem production in the warmed treatments were those that had the highest optimal temperatures for photosynthesis, implying that the synergistic impacts of warming and biodiversity loss on ecosystem functioning were mediated by thermal trait variability. As species were lost from the communities, the probability of taxa remaining that could tolerate warming diminished, resulting in abrupt declines in ecosystem production. Our results highlight the potential for synergistic effects of warming and biodiversity loss on marine primary production.},
	keywords = {biodiversity, biodiversity loss, climate change, ecosystem functioning, phytoplankton, RCC1303, rcc1512, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal per-},
	issn = {1461-023X},
	doi = {10.1111/ele.13444},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13444},
	author = {Bestion, Elvire and Barton, Samuel and Garc{\'\i}a, Francisca C. and Warfield, Ruth and Yvon-Durocher, Gabriel},
	editor = {Hillebrand, Helmut}
}
@article {Liao2020,
	title = {C41 methyl and C42 ethyl alkenones are biomarkers for Group II Isochrysidales},
	journal = {Organic Geochemistry},
	volume = {147},
	year = {2020},
	note = {Publisher: Elsevier Ltd tex.mendeley-tags: RCC1207,RCC1346,RCC3483},
	month = {sep},
	pages = {104081},
	abstract = {Alkenones are polyunsaturated long-chain methyl or ethyl ketones produced by species in the Isochrysidales, an order of haptophyte algae. Based on phylogenetic data, members of the Isochrysidales have been classified into three groups with each group showing significant differences in alkenone profiles and preferred growth environments. Common carbon chain lengths of alkenones range from 37 to 40. Extended C41 methyl (C41Me) and C42 ethyl (C42Et) alkenones have been reported in hypersaline lakes in China (Lake Alahake and Lake Balikun), Canada (Lake Snakehole) and marine sediments (e.g., \~95 Ma in Blake-Bahama Basin). It is unclear, however, if these extended alkenones are produced by one or more groups of Isochrysidales. Here, we systematically examined alkenones from cultures of Group II (Isochrysis nuda, Isochrysis litoralis, Ruttnera lamellosa, Isochrysis galbana and Tisochrysis lutea) and Group III (Emiliania huxleyi and Gephyrocapsa oceanica) Isochrysidales and environmental samples of Group I Isochysidales. C41Me and C42Et alkenones were found in all Group II species with Isochrysis nuda producing the highest percentages, but not in alkenones produced by Group I nor Group III Isochrysidales. Our results indicate that extended C41Me and C42Et alkenones are specific biomarkers for Group II Isochrysidales. We also report the first temperature calibrations of alkenones for Isochrysis nuda and Isochrysis litoralis using culture experiments, and find temperatures inferred from extended alkenones in Balikun and Alahake surface sediments match warm-season temperatures based on Isochrysis nuda calibrations, which is further corroborated by genomic data indicating the dominance of Isochrysis nuda Isochrysidales.},
	keywords = {18S rDNA, Biomarkers, C41 and C42 alkenones, culture, evolution, Isochrysidales, RCC1207, RCC1346, RCC3483},
	issn = {01466380},
	doi = {10.1016/j.orggeochem.2020.104081},
	author = {Liao, Sian and Yao, Yuan and Wang, Li and Wang, Karen J. and Amaral-Zettler, Linda and Longo, William M. and Huang, Yongsong}
}
@article {Barton2020,
	title = {Evolutionary temperature compensation of carbon fixation in marine phytoplankton},
	journal = {Ecology Letters},
	year = {2020},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC1773,RCC4221,RCC623,RCC626,RCC652,RCC80,RCC834},
	month = {feb},
	pages = {ele.13469},
	abstract = {The efficiency of carbon sequestration by the biological pump could decline in the coming decades because respiration tends to increase more with temperature than photosynthesis. Despite these differences in the short-term temperature sensitivities of photosynthesis and respiration, it remains unknown whether the long-term impacts of global warming on metabolic rates of phytoplankton can be modulated by evolutionary adaptation. We found that respiration was consistently more temperature dependent than photosynthesis across 18 diverse marine phytoplankton, resulting in universal declines in the rate of carbon fixation with short-term increases in temperature. Long-term experimental evolution under high temperature reversed the short-term stimulation of metabolic rates, resulting in increased rates of carbon fixation. Our findings suggest that thermal adaptation may therefore have an ameliorating impact on the efficiency of phytoplankton as primary mediators of the biological carbon pump.},
	keywords = {climate change, evolutionary ecology, metabolism, phytoplankton physiology, RCC1303, rcc1512, RCC1773, RCC4221, RCC623, RCC626, RCC652, RCC80, RCC834, thermal performance curves},
	issn = {1461-023X},
	doi = {10.1111/ele.13469},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ele.13469},
	author = {Barton, Samuel and Jenkins, James and Buckling, Angus and Schaum, C.-Elisa and Smirnoff, Nicholas and Raven, John A. and Yvon-Durocher, Gabriel},
	editor = {Ezenwa, Vanessa}
}
@article {Belisle2020,
	title = {Genome sequences of synechococcus sp. Strain MIT S9220 and cocultured cyanophage SynMITS9220M01},
	journal = {Microbiology Resource Announcements},
	volume = {9},
	number = {30},
	year = {2020},
	note = {tex.mendeley-tags: RCC2571},
	month = {jul},
	pages = {28{\textendash}30},
	abstract = {Synechococcus bacteria are unicellular cyanobacteria that contribute significantly to global marine primary production. We report the nearly complete genome sequence of Synechococcus sp. strain MIT S9220, which lacks the nitrate utilization genes present in most marine Synechococcus genomes. Assembly also produced the complete genome sequence of a cyanophage present in the MIT S9220 culture.},
	keywords = {RCC2571},
	issn = {2576-098X},
	doi = {10.1128/MRA.00481-20},
	url = {https://mra.asm.org/content/9/30/e00481-20},
	author = {Belisle, B. Shafer and Avila Paz, Andres A. and Carpenter, Angelina R. and Cormier, Tayla C. and Lewis, Adam J. and Menin, Linnea S. and Oliveira, Daniel R and Song, Bukyung and Szeto, Amy and Tchantouridze, Elizabeth I and Watson, Kayleigh A and Yohannes, Mary T and Ahlgren, Nathan A},
	editor = {Putonti, Catherine}
}
@article {Yau2020,
	title = {Virus-host coexistence in phytoplankton through the genomic lens},
	journal = {Science Advances},
	volume = {6},
	number = {14},
	year = {2020},
	note = {tex.mendeley-tags: RCC2590,RCC2596},
	month = {apr},
	pages = {eaay2587},
	abstract = {Virus-microbe interactions in the ocean are commonly described by {\textquotedblleft}boom and bust{\textquotedblright} dynamics, whereby a numerically dominant microorganism is lysed and replaced by a virus-resistant one. Here, we isolated a microalga strain and its infective dsDNA virus whose dynamics are characterized instead by parallel growth of both the microalga and the virus. Experimental evolution of clonal lines revealed that this viral production originates from the lysis of a minority of virus-susceptible cells, which are regenerated from resistant cells. Whole-genome sequencing demonstrated that this resistant-susceptible switch involved a large deletion on one chromosome. Mathematical modeling explained how the switch maintains stable microalga-virus population dynamics consistent with their observed growth pattern. Comparative genomics confirmed an ancient origin of this {\textquotedblleft}accordion{\textquotedblright} chromosome despite a lack of sequence conservation. Together, our results show how dynamic genomic rearrangements may account for a previously overlooked coexistence mechanism in microalgae-virus interactions.},
	keywords = {RCC2590, RCC2596},
	issn = {2375-2548},
	doi = {10.1126/sciadv.aay2587},
	url = {https://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aay2587},
	author = {Yau, Sheree and Krasovec, Marc and Benites, L. Felipe and Rombauts, Stephane and Groussin, Mathieu and Vancaester, Emmelien and Aury, Jean-Marc and Derelle, Evelyne and Desdevises, Yves and Escande, Marie-Line and Grimsley, Nigel and Guy, Julie and Moreau, Herv{\'e} and Sanchez-Brosseau, Sophie and Van de Peer, Yves and Vandepoele, Klaas and Gourbi{\`e}re, S{\'e}bastien and Piganeau, Gwenael}
}
@article {Castillo2020,
	title = {Visualization of viral infection dynamics in a unicellular eukaryote and quantification of viral production using virus fluorescence in situ hybridization},
	journal = {Frontiers in Microbiology},
	volume = {11},
	year = {2020},
	note = {Publisher: Frontiers Media S.A. tex.mendeley-tags: RCC4221},
	month = {jul},
	pages = {1559},
	abstract = {One of the major challenges in viral ecology is to assess the impact of viruses in controlling the abundance of specific hosts in the environment. To this end, techniques that enable the detection and quantification of virus-host interactions at the single-cell level are essential. With this goal in mind, we implemented virus fluorescence in situ hybridization (VirusFISH) using as a model the marine picoeukaryote Ostreococcus tauri and its virus Ostreococcus tauri virus 5 (OtV5). VirusFISH allowed the visualization and quantification of the proportion of infected cells during an infection cycle in experimental conditions. We were also able to quantify the abundance of free viruses released during cell lysis, discriminating OtV5 from other mid-level fluorescence phages in our non-axenic infected culture that were not easily distinguishable with flow cytometry. Our results showed that although the major lysis of the culture occurred between 24 and 48 h after OtV5 inoculation, some new viruses were already produced between 8 and 24 h. With this work, we demonstrate that VirusFISH is a promising technique to study specific virus-host interactions in non-axenic cultures and establish a framework for its application in complex natural communities.},
	keywords = {culture system, marine picoeukaryote, Ostreococcus tauri, Ostreococcus tauri virus 5, RCC4221, virus fluorescence in situ hybridization, virus-host interactions},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.01559},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.01559/full},
	author = {Castillo, Yaiza M. and Sebasti{\'a}n, Marta and Forn, Irene and Grimsley, Nigel and Yau, Sheree and Moraru, Cristina and Vaqu{\'e}, Dolors}
}
@article {Barton2019,
	title = {Quantifying the temperature dependence of growth rate in marine phytoplankton within and across species},
	journal = {Limnology and Oceanography},
	year = {2019},
	note = {tex.mendeley-tags: RCC1303,RCC1512,RCC1731,RCC1773,RCC4221,RCC539,RCC6,RCC623,RCC626,RCC652,RCC653,RCC655,RCC834,RCC88},
	abstract = {Abstract Models of marine biogeochemistry capture the effects of temperature on phytoplankton growth via the monotonic, exponential Eppley coefficient, without considering the physiological or evolutionary processes that underpin this emergent, across-species temperature response. Here, we investigated both the within- and across-species temperature dependence of growth rate for 18 species of marine phytoplankton. We found that the temperature dependence of growth rate derived across species was lower than the average temperature response within species. This finding supports a {\textquotedblleft}partial compensation{\textquotedblright} model of thermal adaptation and suggests that adaptation can partially compensate for the underlying thermodynamic effects of temperature on physiological rates observed within species. We also found that thermal tolerance traits (e.g. the optimum temperature for growth) systematically covaried with a host of key functional traits (e.g. cell size, elemental composition). Consequently, turnover in species composition in a warmer ocean, linked to interspecific variability in thermal tolerance traits, could be associated with major shifts in the functional trait composition of marine phytoplankton communities with far reaching implications for ecosystem functioning.},
	keywords = {RCC1303, rcc1512, rcc1731, RCC1773, RCC4221, rcc539, RCC6, RCC623, RCC626, RCC652, RCC653, RCC655, RCC834, RCC88},
	issn = {0024-3590},
	doi = {10.1002/lno.11170},
	author = {Barton, Samuel and Yvon-Durocher, Gabriel}
}
@article {bendif_repeated_2019,
	title = {Repeated species radiations in the recent evolution of the key marine phytoplankton lineage Gephyrocapsa},
	journal = {Nature Communications},
	volume = {10},
	number = {1},
	year = {2019},
	pages = {4234},
	abstract = {Abstract Phytoplankton account for nearly half of global primary productivity and strongly affect the global carbon cycle, yet little is known about the forces that drive the evolution of these keystone microscopic organisms. Here we combine morphometric data from the fossil record of the ubiquitous coccolithophore genus Gephyrocapsa with genomic analyses of extant species to assess the genetic processes underlying Pleistocene palaeontological patterns. We demonstrate that all modern diversity in Gephyrocapsa (including Emiliania huxleyi ) originated in a rapid species radiation during the last 0.6 Ma, coincident with the latest of the three pulses of Gephyrocapsa diversification and extinction documented in the fossil record. Our evolutionary genetic analyses indicate that new species in this genus have formed in sympatry or parapatry, with occasional hybridisation between species. This sheds light on the mode of speciation during evolutionary radiation of marine phytoplankton and provides a model of how new plankton species form.},
	keywords = {RCC1253, RCC1296, RCC3370, RCC3711, RCC4028, RCC4030, RCC4032, RCC4033, RCC4034},
	issn = {2041-1723},
	doi = {10.1038/s41467-019-12169-7},
	url = {https://www.nature.com/articles/s41467-019-12169-7},
	author = {Bendif, El Mahdi and Nevado, Bruno and Wong, Edgar L. Y. and Hagino, Kyoko and Probert, Ian and Young, Jeremy R. and Rickaby, Rosalind E. M. and Filatov, Dmitry A.}
}
@article {Tsuboi2019,
	title = {Short-term changes in marine prokaryotic and eukaryotic microalgal communities exposed to the leachate of a seafloor hydrothermal sulfide},
	journal = {Water, Air, \& Soil Pollution},
	volume = {230},
	year = {2019},
	note = {tex.mendeley-tags: RCC,RCC1089,RCC262},
	pages = {175},
	abstract = {The effects of increased mining of seafloor massive sulfide deposits on marine ecosystems have not been characterized. In this study, the impact of leaching metals from a hydrothermal sulfide on photosynthetic protist and cyanobacterial communities in marine environments was investigated by amplicon analyses of small subunit rDNA (SSU rDNA) and rRNA (SSU rRNA). Seawater samples collected from the Iheya North region and Suruga Bay, Japan, were incubated with or without a leachate containing zinc, copper, cadmium, and manganese, of the actual seafloor hydrothermal sulfide from the Hakurei site in the Izena Hole region. The relative abundances of prasinophytes, diatom protists, and the cyanobacteria Synechococcus decreased substantially during incubation with leachate, indicating the vulnerability of these lineages to the leachate. Phylogenetic analysis based on the cyanobacterial phycocyanin cpcBA/rpcBA operon obtained from samples incubated with or without leachate indicated that the individual lineages of Synechococcus can determine sensitivity to heavy metals in different marine regions as well as particular clades and ecotypes.},
	keywords = {rcc, RCC1089, RCC262},
	doi = {10.1007/s11270-019-4224-8},
	author = {Tsuboi, Shun and Yamaguchi, Haruyo and Fuchida, Shigeshi and Koshikawa, Hiroshi and Kawachi, Masanobu}
}
@article {Sanchez2019,
	title = {Simplified transformation of ostreococcus tauri using polyethylene glycol},
	journal = {Genes},
	volume = {10},
	number = {5},
	year = {2019},
	note = {tex.mendeley-tags: RCC4221},
	month = {may},
	pages = {399},
	abstract = {Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13{\textendash}22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave {\textquestiondown}104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20{\textendash}40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.},
	keywords = {bioluminescence, Chlorophyta, Ecosystem, Gene Expression, luciferase, mamiellophyceae, Ostreococcus, picoeukaryote, plankton, Prasinophyte, promoter, RCC4221},
	issn = {2073-4425},
	doi = {10.3390/genes10050399},
	url = {https://www.mdpi.com/2073-4425/10/5/399},
	author = {Sanchez, Fr{\'e}d{\'e}ric and Geffroy, Sol{\`e}ne and Norest, Manon and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Kashiyama2019,
	title = {Taming chlorophylls by early eukaryotes underpinned algal interactions and the diversification of the eukaryotes on the oxygenated Earth},
	journal = {The ISME Journal},
	year = {2019},
	note = {Publisher: Springer US tex.mendeley-tags: RCC164,RCC22,RCC24,RCC375,RCC916},
	month = {feb},
	pages = {1},
	abstract = {Extant eukaryote ecology is primarily sustained by oxygenic photosynthesis, in which chlorophylls play essential roles. The exceptional photosensitivity of chlorophylls allows them to harvest solar energy for photosynthesis, but on the other hand, they also generate cytotoxic reactive oxygen species. A risk of such phototoxicity of the chlorophyll must become particularly prominent upon dynamic cellular interactions that potentially disrupt the mechanisms that are designed to quench photoexcited chlorophylls in the phototrophic cells. Extensive examination of a wide variety of phagotrophic, parasitic, and phototrophic microeukaryotes demonstrates that a catabolic process that converts chlorophylls into nonphotosensitive 132,173-cyclopheophorbide enols (CPEs) is phylogenetically ubiquitous among extant eukaryotes. The accumulation of CPEs is identified in phagotrophic algivores belonging to virtually all major eukaryotic assemblages with the exception of Archaeplastida, in which no algivorous species have been reported. In addition, accumulation of CPEs is revealed to be common among phototrophic microeukaryotes (i.e., microalgae) along with dismantling of their secondary chloroplasts. Thus, we infer that CPE-accumulating chlorophyll catabolism (CACC) primarily evolved among algivorous microeukaryotes to detoxify chlorophylls in an early stage of their evolution. Subsequently, it also underpinned photosynthetic endosymbiosis by securing close interactions with photosynthetic machinery containing abundant chlorophylls, which led to the acquisition of secondary chloroplasts. Our results strongly suggest that CACC, which allowed the consumption of oxygenic primary producers, ultimately permitted the successful radiation of the eukaryotes throughout and after the late Proterozoic global oxygenation.},
	keywords = {Biochemistry, Biogeochemistry, Cellular microbiology, microbial ecology, RCC164, RCC22, RCC24, RCC375, RCC916},
	issn = {1751-7362},
	doi = {10.1038/s41396-019-0377-0},
	url = {http://www.nature.com/articles/s41396-019-0377-0},
	author = {Kashiyama, Yuichiro and Yokoyama, Akiko and Shiratori, Takashi and Hess, Sebastian and Not, Fabrice and Bachy, Charles and Gutierrez-Rodriguez, Andres and Kawahara, Jun and Suzaki, Toshinobu and Nakazawa, Masami and Ishikawa, Takahiro and Maruyama, Moe and Wang, Mengyun and Chen, Man and Gong, Yingchun and Seto, Kensuke and Kagami, Maiko and Hamamoto, Yoko and Honda, Daiske and Umetani, Takahiro and Shihongi, Akira and Kayama, Motoki and Matsuda, Toshiki and Taira, Junya and Yabuki, Akinori and Tsuchiya, Masashi and Hirakawa, Yoshihisa and Kawaguchi, Akane and Nomura, Mami and Nakamura, Atsushi and Namba, Noriaki and Matsumoto, Mitsufumi and Tanaka, Tsuyoshi and Yoshino, Tomoko and Higuchi, Rina and Yamamoto, Akihiro and Maruyama, Tadanobu and Yamaguchi, Aika and Uzuka, Akihiro and Miyagishima, Shinya and Tanifuji, Goro and Kawachi, Masanobu and Kinoshita, Yusuke and Tamiaki, Hitoshi}
}
@article {Cheng2018,
	title = {10KP: A phylodiverse genome sequencing plan},
	journal = {GigaScience},
	volume = {7},
	number = {3},
	year = {2018},
	pages = {1{\textendash}9},
	keywords = {10kp, 12 february 2018, 2018, 4, accepted, access article distributed under, and reproduction in any, attribution license, biodiversity, by, c the author, creative commons, creativecommons, Distribution, genome sequencing, genomics, http, licenses, medium, mgiseq, open community, org, phylogenomics, PLANTS, press, published by oxford university, received, s, samples, the terms of the, this is an open, which permits unrestricted reuse},
	issn = {2047-217X},
	doi = {10.1093/gigascience/giy013},
	url = {https://academic.oup.com/gigascience/article/7/3/1/4880447},
	author = {Cheng, Shifeng and Melkonian, Michael and Smith, Stephen A and Brockington, Samuel and Archibald, John M and Delaux, Pierre-Marc and Li, Fay-Wei and Melkonian, Barbara and Mavrodiev, Evgeny V and Sun, Wenjing and Fu, Yuan and Yang, Huanming and Soltis, Douglas E and Graham, Sean W and Soltis, Pamela S and Liu, Xin and Xu, Xun and Wong, Gane Ka-Shu}
}
@article {Kuwata2018,
	title = {Bolidophyceae, a sister picoplanktonic group of diatoms {\textendash} a review},
	journal = {Frontiers in Marine Science},
	volume = {5},
	year = {2018},
	note = {tex.mendeley-tags: RCC1657,RCC201,RCC205,RCC206,RCC212,RCC239},
	month = {oct},
	pages = {370},
	keywords = {RCC1657, RCC201, RCC205, RCC206, rcc212, RCC239},
	issn = {2296-7745},
	doi = {10.3389/fmars.2018.00370},
	url = {https://www.frontiersin.org/article/10.3389/fmars.2018.00370/full},
	author = {Kuwata, Akira and Yamada, Kazumasa and Ichinomiya, Mutsuo and Yoshikawa, Shinya and Tragin, Margot and Vaulot, Daniel and Lopes dos Santos, Adriana}
}
@article {Paerl2018,
	title = {Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis},
	journal = {Scientific Reports},
	volume = {8},
	number = {1},
	year = {2018},
	note = {Publisher: Springer US tex.mendeley-tags: RCC4222,RCC745},
	pages = {5940},
	keywords = {RCC4222, RCC745},
	issn = {2045-2322},
	doi = {10.1038/s41598-018-24321-2},
	url = {http://www.nature.com/articles/s41598-018-24321-2},
	author = {Paerl, Ryan W. and Bertrand, Erin M. and Rowland, Elden and Schatt, Phillippe and Mehiri, Mohamed and Niehaus, Thomas D. and Hanson, Andrew D. and Riemann, Lasse and Yves-Bouget, Francois}
}
@article {Yamada2018,
	title = {Ontogenetic analysis of siliceous cell wall formation in Triparma laevis f. inornata (Parmales, Stramenopiles)},
	journal = {Journal of Phycology},
	year = {2018},
	note = {ISBN: 0000000266291 tex.mendeley-tags: RCC4665},
	month = {oct},
	pages = {0{\textendash}2},
	keywords = {RCC4665},
	issn = {00223646},
	doi = {10.1111/jpy.12800},
	url = {http://doi.wiley.com/10.1111/jpy.12800},
	author = {Yamada, Kazumasa and Katsura, Hirotaka and No{\"e}l, Mary-H{\'e}l{\`e}ne and Ichinomiya, Mutsuo and Kuwata, Akira and Sato, Shinya and Yoshikawa, Shinya}
}
@article {yau_rapidity_2018,
	title = {Rapidity of Genomic Adaptations to Prasinovirus Infection in a Marine Microalga},
	journal = {Viruses},
	volume = {10},
	number = {8},
	year = {2018},
	note = {Number: 8 Publisher: Multidisciplinary Digital Publishing Institute},
	pages = {441},
	abstract = {Prasinoviruses are large dsDNA viruses commonly found in aquatic systems worldwide, where they can infect and lyse unicellular prasinophyte algae such as Ostreococcus. Host susceptibility is virus strain-specific, but resistance of susceptible Ostreococcus tauri strains to a virulent virus arises frequently. In clonal resistant lines that re-grow, viruses are usually present for many generations, and genes clustered on chromosome 19 show physical rearrangements and differential expression. Here, we investigated changes occurring during the first two weeks after inoculation of the prasinovirus OtV5. By serial dilutions of cultures at the time of inoculation, we estimated the frequency of resistant cells arising in virus-challenged O. tauri cultures to be 10\&minus;3\&ndash;10\&minus;4 of the inoculated population. Re-growing resistant cells were detectable by flow cytometry 3 days post-inoculation (dpi), visible re-greening of cultures occurred by 6 dpi, and karyotypic changes were visually detectable at 8 dpi. Resistant cell lines showed a modified spectrum of host-virus specificities and much lower levels of OtV5 adsorption.},
	keywords = {adsorption, Chromosome, host range, karyotype, mamiellophyceae, phycodnaviridae, RCC1105, RCC4221, RCC4223, rearrangement, resistance, specificity, \textitOstreococcus tauri},
	doi = {10.3390/v10080441},
	url = {https://www.mdpi.com/1999-4915/10/8/441},
	author = {Yau, Sheree and Caravello, Ga{\"e}tan and Fonvieille, Nad{\`e}ge and Desgranges, Elodie and Moreau, Herv{\'e} and Grimsley, Nigel}
}
@article {Yoo2017a,
	title = {Mixotrophy in the marine red-tide cryptophyte Teleaulax amphioxeia and ingestion and grazing impact of cryptophytes on natural populations of bacteria in Korean coastal waters},
	journal = {Harmful Algae},
	volume = {68},
	number = {May 2005},
	year = {2017},
	note = {Publisher: Elsevier B.V. tex.mendeley-tags: RCC1086},
	pages = {105{\textendash}117},
	abstract = {Cryptophytes are ubiquitous and one of the major phototrophic components in marine plankton communities. They often cause red tides in the waters of many countries. Understanding the bloom dynamics of cryptophytes is, therefore, of great importance. A critical step in this understanding is unveiling their trophic modes. Prior to this study, several freshwater cryptophyte species and marine Cryptomonas sp. and Geminifera cryophila were revealed to be mixotrophic. The trophic mode of the common marine cryptophyte species, Teleaulax amphioxeia has not been investigated yet. Thus, to explore the mixotrophic ability of T. amphioxeia by assessing the types of prey species that this species is able to feed on, the protoplasms of T. amphioxeia cells were carefully examined under an epifluorescence microscope and a transmission electron microscope after adding each of the diverse prey species. Furthermore, T. amphioxeia ingestion rates heterotrophic bacteria and the cyanobacterium Synechococcus sp. were measured as a function of prey concentration. Moreover, the feeding of natural populations of cryptophytes on natural populations of heterotrophic bacteria was assessed in Masan Bay in April 2006. This study reported for the first time, to our knowledge, that T. amphioxeia is a mixotrophic species. Among the prey organisms offered, T. amphioxeia fed only on heterotrophic bacteria and Synechococcus sp. The ingestion rates of T. amphioxeia on heterotrophic bacteria or Synechococcus sp. rapidly increased with increasing prey concentrations up to 8.6 {\texttimes} 106 cells ml-1, but slowly at higher prey concentrations. The maximum ingestion rates of T. amphioxeia on heterotrophic bacteria and Synechococcus sp. reached 0.7 and 0.3 cells predator-1 h-1, respectively. During the field experiments, the ingestion rates and grazing coefficients of cryptophytes on natural populations of heterotrophic bacteria were 0.3{\textendash}8.3 cells predator-1 h-1 and 0.012{\textendash}0.033 d-1, respectively. Marine cryptophytes, including T. amphioxeia, are known to be favorite prey species for many mixotrophic and heterotrophic dinoflagellates and ciliates. Cryptophytes, therefore, likely play important roles in marine food webs and may exert a considerable potential grazing impact on the populations of marine bacteria.},
	keywords = {Bloom, Flagellate, Grazing impact, Predator-prey relationship, RCC1086, Red tide},
	issn = {18781470},
	doi = {10.1016/j.hal.2017.07.012},
	url = {http://dx.doi.org/10.1016/j.hal.2017.07.012},
	author = {Yoo, Yeong Du and Seong, Kyeong Ah and Jeong, Hae Jin and Yih, Wonho and Rho, Jung Rae and Nam, Seung Won and Kim, Hyung Seop}
}
@article {Blanc-Mathieu2017,
	title = {Population genomics of picophytoplankton unveils novel chromosome hypervariability},
	journal = {Science Advances},
	volume = {3},
	number = {7},
	year = {2017},
	note = {tex.mendeley-tags: RCC1105,RCC1108,RCC1110,RCC1112,RCC1114,RCC1115,RCC1116,RCC1117,RCC1118,RCC1123,RCC1558,RCC1559,RCC1561,RCC299,RCC4221,RCC809},
	month = {jul},
	pages = {e1700239},
	keywords = {RCC1105, RCC1108, RCC1110, RCC1112, RCC1114, RCC1115, RCC1116, RCC1117, RCC1118, RCC1123, RCC1558, RCC1559, RCC1561, RCC299, RCC4221, RCC809},
	issn = {2375-2548},
	doi = {10.1126/sciadv.1700239},
	url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.1700239},
	author = {Blanc-Mathieu, Romain and Krasovec, Marc and Hebrard, Maxime and Yau, Sheree and Desgranges, Elodie and Martin, Joel and Schackwitz, Wendy and Kuo, Alan and Salin, Gerald and Donnadieu, Cecile and Desdevises, Yves and Sanchez-Ferandin, Sophie and Moreau, Herv{\'e} and Rivals, Eric and Grigoriev, Igor V. and Grimsley, Nigel and Eyre-Walker, Adam and Piganeau, Gwenael}
}
@article {Derelle2017,
	title = {Prasinovirus attack of ostreococcus is furtive by day but savage by night},
	journal = {Journal of Virology},
	volume = {92},
	number = {4},
	year = {2017},
	note = {tex.mendeley-tags: RCC4221},
	month = {nov},
	pages = {JVI.01703{\textendash}17},
	abstract = {Prasinoviruses are large DNA viruses that infect diverse genera of green microalgae worldwide in aquatic ecosystems, but molecular knowledge of their life-cycles is lacking. Several complete genomes of both these viruses and their marine algal hosts are now available and have been used to show the pervasive presence of these species in microbial metagenomes. We have analysed the life-cycle of OtV5, a lytic virus, using RNA-Seq from 12 time points of healthy or infected Ostreococcus tauri cells over a day/night cycle in culture. In the day, viral gene transcription remained low while host nitrogen metabolism gene transcription was initially strongly repressed for two successive time points before being induced for 8 hours, but in the night viral transcription increased steeply while host nitrogen metabolism genes were repressed and many host functions that are normally reduced in the night appeared to be compensated either by genes expressed from the virus or by increased expression of a subset of 4.4 \% of the host{\textquoteright}s genes. Some host cells lysed progressively during the night, but a larger proportion lysed the following morning. Our data suggest that the life-cycles of algal viruses mirror the diurnal rhythms of their hosts.},
	keywords = {accepted 9, mamiellophyceae, ncldv, Ostreococcus, phycodnaviridae, prasinophytes, RCC4221, received 28 september 2017},
	issn = {0022-538X},
	doi = {10.1128/JVI.01703-17},
	url = {http://jvi.asm.org/lookup/doi/10.1128/JVI.01703-17},
	author = {Derelle, Evelyne and Yau, Sheree and Moreau, Herv{\'e} and Grimsley, Nigel H.}
}
@article {Andersen2017,
	title = {Rediscovery of the Ochromonas type species Ochromonas triangulata (Chrysophyceae) from its type locality (Lake Veysove, Donetsk region, Ukraine)},
	journal = {Phycologia},
	volume = {56},
	number = {6},
	year = {2017},
	note = {tex.ids= Andersen2017a tex.mendeley-tags: 2017,RCC21},
	pages = {591{\textendash}604},
	abstract = {Ochromonas triangulata, the type species for a genus with over 125 taxa, was collected for only the second time, again from the type locality. Cell morphology, cell division, palmelloid stage and cyst structure generally agreed with the original description. Molecular phylogenetic analysis based on the 18S rRNA gene revealed 13 clades of Ochromonas-like flagellates as well as the clade represented by our O. triangulata strain and the nearly identical strain RCC-21/AC025. We also conducted a concatenated analysis using the 18S rRNA and the rbcL genes, and we recovered the same 14 clades. One clade, containing strains CCAP 933/27 and CCMP1861, previously named Ochromonas tuberculata, was re-identified as Chrysastrella paradoxa and Chrysastrella breviappendiculata, respectively. One clade included the Poterioochromonas strains but we were unable to convincingly connect species names to the strains because authentic strains were unknown or not examined. Organisms in the clade that included the well-known Ochromonas danica were assigned to Chlorochromonas. The generic name Melkoniania gen. nov. was proposed for one distinct clade of marine flagellates. These changes addressed some of the issues associated with the polyphyletic Ochromonas sensu lato but many problems remained.},
	keywords = {2017, RCC21},
	issn = {0031-8884},
	doi = {10.2216/17-15.1},
	url = {http://www.phycologia.org/doi/10.2216/17-15.1},
	author = {Andersen, Robert A. and Graf, Louis and Malakhov, Yuriy and Yoon, Hwan Su}
}
@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 {Zheng2016,
	title = {The geographic impact on genomic divergence as revealed by comparison of nine Citromicrobial genomes},
	journal = {Applied and Environmental Microbiology},
	volume = {82},
	number = {24},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC1878,RCC1885,RCC1897,sbr?hyto?app},
	pages = {AEM.02495{\textendash}16},
	abstract = {Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus Citromicrobium , widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine Citromicrobium strains isolated from the South China Sea, the Mediterranean Sea or the tropical South Atlantic were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs), involved mainly in type IV secretion systems, flagellar biosynthesis, prophage and integrative conjugative elements, were identified by a fine scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the co-existence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for Citromicrobium members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, ANI, SNPs and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea vs Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences, and allow microbes to evolve through local adaptation. Three Citromicrobium strains isolated from the Mediterranean Sea diverged millions of years ago from other strains, and evolved into a novel group.},
	keywords = {2016, RCC1878, RCC1885, RCC1897, sbr?hyto?app},
	issn = {0099-2240},
	doi = {10.1128/AEM.02495-16},
	url = {http://aem.asm.org/lookup/doi/10.1128/AEM.02495-16},
	author = {Zheng, Qiang and Liu, Yanting and Jeanthon, Christian and Zhang, Rui and Lin, Wenxin and Yao, Jicheng and Jiao, Nianzhi}
}
@article {Bendif2016,
	title = {Recent reticulate evolution in the ecologically dominant lineage of coccolithophores},
	journal = {Frontiers in Microbiology},
	volume = {7},
	number = {May},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC4032,RCC4033,RCC4034,RCC4035,RCC4036,rcc,sbr?hyto},
	month = {may},
	keywords = {2016, coccolithophores, cyto-nuclear discordance, diversity, Emiliania, evolution, Gephyrocapsa, introgressive hybridization, rcc, RCC4032, RCC4033, RCC4034, RCC4035, RCC4036, Reticulofenestra, sbr?hyto},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2016.00784},
	url = {http://journal.frontiersin.org/article/10.3389/fmicb.2016.00784 http://journal.frontiersin.org/Article/10.3389/fmicb.2016.00784/abstract},
	author = {Bendif, El Mahdi and Probert, Ian and D{\'\i}az-Rosas, Francisco and Thomas, Daniela and van den Engh, Ger and Young, Jeremy R. and von Dassow, Peter}
}
@article {Yau2016,
	title = {A viral immunity chromosome in the marine picoeukaryote, ostreococcus tauri},
	journal = {PLOS Pathogens},
	volume = {12},
	number = {10},
	year = {2016},
	note = {tex.mendeley-tags: 2016,RCC299,RCC4221,RCC809},
	month = {oct},
	pages = {e1005965},
	keywords = {2016, RCC299, RCC4221, RCC809},
	issn = {1553-7374},
	doi = {10.1371/journal.ppat.1005965},
	url = {http://dx.plos.org/10.1371/journal.ppat.1005965},
	author = {Yau, Sheree and Hemon, Claire and Derelle, Evelyne and Moreau, Herv{\'e} and Piganeau, Gwenael and Grimsley, Nigel},
	editor = {Ding, Shou-Wei}
}
@article {Bendif2015,
	title = {Morphological and phylogenetic characterization of new gephyrocapsa isolates suggests introgressive hybridization in the Emiliania/Gephyrocapsa complex (haptophyta)},
	journal = {Protist},
	volume = {166},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: 2015,RCC1281,RCC1282,RCC1284,RCC1286,RCC1292,RCC1300,RCC1305,RCC1307,RCC1316,RCC1317,RCC1318,RCC1319,RCC1320,RCC1562,RCC1839,RCC3370,RCC3862,RCC3898,rcc},
	pages = {323{\textendash}336},
	abstract = {The coccolithophore genus Gephyrocapsa contains a cosmopolitan assemblage of pelagic species, including the bloom-forming Gephyrocapsa oceanica, and is closely related to the emblematic coccolithophore Emiliania huxleyi within the No{\"e}laerhabdaceae. These two species have been extensively studied and are well represented in culture collections, whereas cultures of other species of this family are lacking. We report on three new strains of Gephyrocapsa isolated into culture from samples from the Chilean coastal upwelling zone using a novel flow cytometric single-cell sorting technique. The strains were characterized by morphological analysis using scanning electron microscopy and phylogenetic analysis of 6 genes (nuclear 18S and 28S rDNA, plastidial 16S and tufA, and mitochondrial cox1 and cox3 genes). Morphometric features of the coccoliths indicate that these isolates are distinct from G. oceanica and best correspond to G. muellerae. Surprisingly, both plastidial and mitochondrial gene phylogenies placed these strains within the E. huxleyi clade and well separated from G. oceanica isolates, making Emiliania appear polyphyletic. The only nuclear sequence difference, 1bp in the 28S rDNA region, also grouped E. huxleyi with the new Gephyrocapsa isolates and apart from G. oceanica. Specifically, the G. muellerae morphotype strains clustered with the mitochondrial β clade of E. huxleyi, which, like G. muellerae, has been associated with cold (temperate and sub-polar) waters. Among putative evolutionary scenarios that could explain these results we discuss the possibility that E. huxleyi is not a valid taxonomic unit, or, alternatively the possibility of past hybridization and introgression between each E. huxleyi clade and older Gephyrocapsa clades. In either case, the results support the transfer of Emiliania to Gephyrocapsa. These results have important implications for relating morphological species concepts to ecological and evolutionary units of diversity.},
	keywords = {2015, coccolithophores, Emiliania huxleyi, Gephyrocapsa muellerae, Gephyrocapsa oceanica, hybridization, phylogeny., rcc, RCC1281, RCC1282, RCC1284, RCC1286, RCC1292, RCC1300, RCC1305, RCC1307, RCC1316, RCC1317, RCC1318, RCC1319, RCC1320, RCC1562, RCC1839, RCC3370, RCC3862, RCC3898, species concept},
	issn = {14344610},
	doi = {10.1016/j.protis.2015.05.003},
	url = {http://www.sciencedirect.com/science/article/pii/S1434461015000243},
	author = {Bendif, El Mahdi and Probert, Ian and Young, Jeremy R. and von Dassow, Peter}
}
@article {Potvin2015,
	title = {Morphology , molecular phylogeny , and pigment characterization of a novel phenotype of the dinoflagellate genus Pelagodinium from Korean waters},
	journal = {Algae},
	volume = {30},
	number = {3},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {183{\textendash}195},
	abstract = {The dinoflagellate genus Pelagodinium is genetically classified in distinct sub-clades and subgroups. However, it is dif- ficult to determine whether this genetic diversity represents intra- or interspecific divergence within the genus since only the morphology of the type strain of the genus Pelagodinium, Pelagodinium bei, is available. An isolate associated with the genus Pelagodinium from Shiwha Bay, Korea, was recently cultured. This isolate formed a subgroup with 3 to 4 strains from the Atlantic Ocean, Mediterranean Sea, and Indian Ocean. This subgroup was distinct from the subgroup contain- ing P. bei. The morphology of the isolate was analyzed using optical and scanning electron microscopy and was almost identical to that of P. bei except that this isolate had two series of amphiesmal vesicles (AVs) in the cingulum, unlike P. bei that has one series. When the pigment compositions of the isolate and P. bei were analyzed using high-performance liquid chromatography, these two strains had peridinin as a major accessory pigment and their pigment compositions were almost identical. In addition, the swimming behaviors of these two strains were very similar. The re-examination of the type culture of P. bei revealed two series in the cingulum as for the isolate. The new findings on the number of series of AVs in the cingulum, the pigment composition, and the swimming behaviors suggest that P. bei and the isolate may be conspecific despite their association to genetically different subgroups. This study provides a basis to further understand the molecular classification within Pelagodinium combining genetic, morphological, pigment, and behavioral data.},
	keywords = {foraminifera, gymnodinium bei, pelagic symbiont, rcc, suessiaceae, suessiales},
	doi = {10.4490/algae.2015.30.3.183},
	author = {Potvin, {\'E}ric and Jeong, Hae Jin and Kang, Nam Seon and Noh, Jae Hoon and Yang, Eun Jin}
}
@article {Kamikawa2015,
	title = {Multiple losses of photosynthesis in Nitzschia (Bacillariophyceae)},
	journal = {Phycological Research},
	volume = {63},
	year = {2015},
	note = {tex.mendeley-tags: rcc},
	pages = {19{\textendash}28},
	abstract = {In order to obtain insights into the evolution of colorless (apochlorotic) diatoms, we investigated newly established apochlorotic strains of Nitzschia spp. using light and electron microscopy and molecular phylogenetic analyses. Fluores- cence microscopic observations demonstrated that the apochlorotic diatoms lack chlorophylls. Transmission electron microscopy of two apochlorotic strains also demonstrated that their plastids lacked thylakoids; instead, having four- membrane-bound organelles without thylakoids, similar to nonphotosynthetic plastid remnants. From the apochlorotic strains, we also found plastid small subunit rRNA genes that were unusually long branched in phylogenetic analyses, as observed in other nonphotosynthetic plastids. Molecular phylogenetic analysis of the nucleus-encoded large subunit rRNA genes showed eight distinct lineages for apochlo- rotic diatoms. The eight apochlorotic lineages were not monophyletic, suggesting that the loss of photosynthesis took place multiple times independently within Nitzschia. Several diatoms, including Nitzschia spp., are mixotrophic, which is an expected mode of nutrition that would help explain the evolutionary switch from a photosynthetic lifestyle to a heterotrophic lifestyle. Key},
	keywords = {apochlorotic diatoms, genetic diversity, large subunit rrna, molecular phylogenetic analysis, nonphotosynthetic plastids, plastid 16s rrna, rcc},
	issn = {13220829},
	doi = {10.1111/pre.12072},
	url = {http://doi.wiley.com/10.1111/pre.12072},
	author = {Kamikawa, Ryoma and Yubuki, Naoji and Yoshida, Masaki and Taira, Misaka and Nakamura, Noriaki and Ishida, Ken-ichiro and Leander, Brian S. and Miyashita, Hideaki and Hashimoto, Tetsuo and Mayama, Shigeki and Inagaki, Yuji}
}
@article {Hagino2011,
	title = {New evidence for morphological and genetic variation in the cosmopolitan coccolithophore Emiliana huxleyi (prymnesiophyceae) from the cox1b-ATP4 genes},
	journal = {Journal of Phycology},
	volume = {47},
	year = {2011},
	note = {tex.mendeley-tags: 2011,rcc,sbr?hyto?ppo},
	pages = {1164{\textendash}1176},
	abstract = {Emiliania huxleyi (Lohmann) Hay et Mohler is a cosmopolitan coccolithophore occurring from tropical to subpolar waters and exhibiting variations in morphology of coccoliths possibly related to environmental conditions. We examined morphological characters of coccoliths and partial mitochondrial sequences of the cytochrome oxidase 1b (cox1b) through adenosine triphosphate synthase 4 (atp4) genes of thirty-nine clonal E. huxleyi strains from the Atlantic and Pacific Oceans, Mediterranean Sea and their adjacent seas. Based on the morphological study of culture strains by SEM, Type O, a new morphotype characterized by coccoliths with an open central area, was separated from existing morphotypes A, B, B/C, C, R and var. corona, characterized by coccoliths with central area elements. Molecular phylogenetic studies revealed that E. huxleyi consists of at least two mitochondrial sequence groups with different temperature preferences/tolerances: a cool water group occurring in subarctic North Atlantic and Pacific and a warm water group occurring in the sub-tropical Atlantic and Pacific and in the Mediterranean Sea.},
	keywords = {2011, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	doi = {10.1111/j.1529-8817.2011.01053.x},
	author = {Hagino, K and Bendif, El Mahdi and Young, J and Kogame, K and Takano, Y and Probert, I and Horiguchi, T and de Vargas, C and Okada, H}
}
@article {Franklin2010,
	title = {Dimethylsulphoniopropionate (DMSP), DMSP-lyase activity (DLA) and dimethylsulphide (DMS) in 10 species of coccolithophore},
	journal = {Marine Ecology-Progress Series},
	volume = {410},
	year = {2010},
	note = {ISBN: 0171-8630 tex.mendeley-tags: 2010,rcc},
	pages = {13{\textendash}23},
	abstract = {We investigated dimethylsulphoniopropionate (DMSP) quota (pg DMSP cell(-1)), intracellular DMSP concentration (mM), in vitro and in vivo DMSP-lyase activity (DLA) and dimethylsulphide (DMS) concentration in batch cultures of 10 species of coccolithophore. Species were chosen to span the phylogenetic and size range that exists within the coccolithophores. Our overall objective was to examine if Emiliania huxleyi, considered a {\textquoteright}model{\textquoteright} coccolithophore species, is representative in terms of DMSP, DLA and DMS, because other coccolithophores contribute substantially to phyto-plankton biomass and carbon fluxes in temperate and tropical waters. DMSP was found in all species, and DMSP quotas correlated significantly with cell volume, reflecting the fundamental physiological role of DMSP as a compatible solute in this group. This DMSP quota-cell volume relationship can be used to calculate the relative contribution of different species to total DMSP. Lowered nutrient availability (batch growth at a 10-fold lower nutrient concentration) did not significantly affect DMSP quota. In contrast to DMSP, DLA and DMS concentration were variable between the subset of species investigated. Coccolithophore DLA is known only in E. huxleyi and Gephyrocapsa oceanica, and we found DLA to be restricted to these closely related species. If DLA is restricted to a subset of coccolithophores, then those species are more likely to emit DMS directly in the sea. Our results indicate that in ecosystems where coccolithophores form stable populations, species other than E. huxleyi can make significant contributions to the particulate DMSP pool and hence to the amount of DMSP potentially available to the microbial loop.},
	keywords = {2010, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.3354/meps08596},
	author = {Franklin, D J and Steinke, M and Young, J and Probert, I and Malin, G}
}
@article {Frada2010,
	title = {A guide to extant coccolithophores (Calcihaptophycidae, Haptophyta) using light microscopy.},
	journal = {Journal of Nannoplankton Research},
	volume = {31},
	year = {2010},
	note = {tex.mendeley-tags: 2010,rcc,sbr?hyto?ppo},
	pages = {58{\textendash}112},
	keywords = {2010, ? No DOI found, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO, sbr?hyto?ppo},
	author = {Frada, Miguel and Young, Jeremy and Cach{\~a}o, M{\'a}rio and Lino, S{\'\i}lvia and Martins, Ana and Narciso, {\'A}urea and Probert, Ian and de Vargas, Colomban}
}
@article {Ota2009,
	title = {Partenskyella glossopodia gen. et sp. nov., the first report of chlorarachniophyte that lacks pyrenoid},
	journal = {Protist},
	volume = {160},
	year = {2009},
	note = {tex.mendeley-tags: 2009,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {137{\textendash}150},
	keywords = {2009, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1016/j.protis.2008.09.003},
	author = {Ota, S and Vaulot, D and Le Gall, F and Yabuki, A and Ishida, K}
}
@article {Misumi2008,
	title = {Genome analysis and its significance in four unicellular algae, Cyanidioshyzon merolae, Ostreococcus tauri, Chlamydomonas reinhardtii, and Thalassiosira pseudonana},
	journal = {Journal of Plant Research},
	volume = {121},
	number = {1},
	year = {2008},
	note = {tex.mendeley-tags: RCC,rcc},
	pages = {3{\textendash}17},
	abstract = {Algae play a more important role than land plants in the maintenance of the global environment and productivity. Progress in genome analyses of these organisms means that we can now obtain information on algal genomes, global annotation and gene expression. The full genome information for several algae has already been analyzed. Whole genomes of the red alga Cyanidioshyzon merolae, the green algae Ostreococcus tauri and Chlamydomonas reinhardtii, and the diatom Thalassiosira pseudonana have been sequenced. Genome composition and the features of cells among the four algae were compared. Each alga maintains basic genes as photosynthetic eukaryotes and possesses additional gene groups to represent their particular characteristics. This review discusses and introduces the latest research that makes the best use of the particular features of each organism and the significance of genome analysis to study biological phenomena. In particular, examples of post-genome studies of organelle multiplication in C. merolae based on analyzed genome information are presented.},
	keywords = {rcc},
	url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18074102},
	author = {Misumi, O and Yoshida, Y and Nishida, K and Fujiwara, T and Sakajiri, T and Hirooka, S and Nishimura, Y and Kuroiwa, T}
}
@article {Fountain2008,
	title = {Permeation properties of a P2X receptor in the green algae Ostreococcus tauri},
	journal = {Journal of Biological Chemistry},
	volume = {283},
	number = {22},
	year = {2008},
	note = {ISBN: 0021-9258 tex.mendeley-tags: RCC,rcc},
	pages = {15122{\textendash}15126},
	abstract = {We have cloned a P2X receptor (OtP2X) from the green algae Ostreococcus tauri. The 42-kDa receptor shares similar to 28\% identity with human P2X receptors and 23\% with the Dictyostelium P2X receptor. ATP application evoked flickery single channel openings in outside-out membrane patches from human embryonic kidney 293 cells expressing OtP2X. Whole-cell recordings showed concentration-dependent cation currents reversing close to zero mV; ATP gave a half-maximal current at 250 mu m. alpha beta-Methylene-ATP evoked only small currents in comparison to ATP (EC50 {\textquestiondown} 5 mM). 2{\textquoteright},3{\textquoteright}-O-(4-Benzoylbenzoyl)-ATP, beta gamma-imido-ATP, ADP, and several other nucleotide triphosphates did not activate any current. The currents evoked by 300 mu m ATP were not inhibited by 100 mu m suramin, pyridoxal-phosphate-6-azophenyl-2{\textquoteright},4{\textquoteright}-disulfonic acid, 2{\textquoteright},3{\textquoteright}-O-(2,4,6-trinitrophenol)-ATP, or copper. Ion substitution experiments indicated permeabilities relative to sodium with the rank order calcium {\textquestiondown} choline {\textquestiondown} Tris {\textquestiondown} tetraethylammonium {\textquestiondown} N-methyl-D-glucosamine. However, OtP2X had a low relative calcium permeability (P-Ca/P-Na = 0.4) in comparison with other P2X receptors. This was due at least in part to the presence of an asparagine residue (Asn(353)) at a position in the second transmembrane domain in place of the aspartate that is completely conserved in all other P2X receptor subunits, because replacement of Asn(353) with aspartate increased calcium permeability by similar to 50\%. The results indicate that the ability of ATP to gate cation permeation across membranes exists in cells that diverged in evolutionary terms from animals about I billion years ago.},
	keywords = {CELLS, CHANNELS, EXTRACELLULAR ATP, FAMILY, FUNCTIONAL-CHARACTERIZATION, PERMEABILITY, PHARMACOLOGY, rcc},
	doi = {10.1074/jbc.M801512200},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2397467},
	author = {Fountain, S J and Cao, L S and Young, M T and North, R A}
}
@article {Probert2007a,
	title = {Light and electron microscope observations of Algirosphaera robusta (Prymnesiophyceae)},
	journal = {Journal of Phycology},
	volume = {43},
	year = {2007},
	note = {tex.mendeley-tags: 2007,rcc},
	pages = {319{\textendash}332},
	keywords = {2007, rcc, SBR$_\textrmP$hyto$_\textrmE$PPO},
	doi = {10.1111/j.1529-8817.2007.00324.x},
	author = {Probert, I and Fresnel, J and Billard, C and Geisen, Markus and Young, J R}
}
@article {Fawley2000,
	title = {Phylogenetic analyses of 18S rDNA sequences reveal a new coccoid lineage of the Prasinophyceae (Chlorophyta)},
	journal = {Journal of Phycology},
	volume = {36},
	number = {2},
	year = {2000},
	note = {ISBN: 0022-3646 Publisher: Phycological Soc Amer Inc tex.address: 810 East 10Th St, Lawrence, KS 66044, USA tex.mendeley-tags: RCC,rcc},
	pages = {387{\textendash}393},
	abstract = {Phylogenetic analyses of 18S rDNA sequences from 25 prasinophytes, including 10 coccoid isolates, reveals that coccoid organisms are-found in at least three prasinophyte lineages, The coccoid Ostreococcus tauri is included in the Mamiellales lineage and Pycnococcus provasolii is allied with the f dfellate Pseudoscourfieldia marina. A previously undescribed prasinophyte lineage is comprised of the coccoid Prasinococcus cf. Capsulatus (CCMP 1407) and other isolates tentatively identified as Prasinococcussp. (CCMP 1202, CCMP 1614, and CCMP 1194), as well as three unnamed coccoids (CCMP 1193, CCMP 1413, and CCMP 1220). No flagellate organisms are known from this lineage. Organisms of this new lineage share some characteristics of both the Pycnococcaceae and the Mamiellales, although relationships among these separate lineages were not supported by bootstrap analyses. An additional unnamed coccoid isolate (CCMP 1205) is separate from all major prasinophyte lineages. The analyses did not resolve the relationships among the major prasinophyte lineages, although they support previous conclusions that the Prasinophyceae are not monophyletic.},
	keywords = {ALGAL CAROTENOIDS, coccoid algae, EVOLUTIONARY TREES, Gen, GREEN-ALGAE, LIGHT-HARVESTING COMPLEX, MICROMONADOPHYCEAE CHLOROPHYTA, Prasinophyceae, PRASINOXANTHIN, PSEUDOSCOURFIELDIA-MARINA, rcc, RDNA, RIBOSOMAL-RNA SEQUENCES, Sequence Analysis, sp-nov},
	doi = {10.1046/j.1529-8817.2000.99105.x},
	author = {Fawley, M W and Yun, Y and Qin, M}
}
@article {ISI:A1984AAU2400012,
	title = {Purification and properties of <span class="nocase">ι</span>-carrageenase from a marine bacterium},
	journal = {Canadian Journal of Microbiology},
	volume = {30},
	number = {12},
	year = {1984},
	note = {tex.mendeley-tags: RCC5933},
	month = {dec},
	pages = {1500{\textendash}1506},
	keywords = {RCC5933},
	issn = {0008-4166},
	doi = {10.1139/m84-239},
	url = {http://www.nrcresearchpress.com/doi/10.1139/m84-239},
	author = {Greer, C. W. and Yaphe, W.}
}
