@article {wang_aggregating_2024,
	title = {Aggregating Synechococcus contributes to particle organic carbon export in coastal estuarine waters: Its lineage features and assembly processes},
	journal = {Science of The Total Environment},
	year = {2024},
	month = {jan},
	pages = {170368},
	issn = {00489697},
	doi = {10.1016/j.scitotenv.2024.170368},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0048969724005035},
	author = {Wang, Ting and Li, Jialin and Xu, Yandong and Zou, Tao and Qin, Song}
}
@article {ruan_different_2023,
	title = {Different photosynthetic responses of haploid and diploid Emiliania huxleyi (Prymnesiophyceae) to high light and ultraviolet radiation},
	journal = {Bioresources and Bioprocessing},
	volume = {10},
	number = {1},
	year = {2023},
	month = {jul},
	pages = {40},
	abstract = {Solar radiation varies quantitatively and qualitatively while penetrating through the seawater column and thus is one of the most important environmental factors shaping the vertical distribution pattern of phytoplankton. The haploid and diploid life-cycle phases of coccolithophores might have different vertical distribution preferences. Therefore, the two phases respond differently to high solar photosynthetically active radiation (PAR, 400{\textendash}700~nm) and ultraviolet radiation (UVR, 280{\textendash}400~nm). To test this, the haploid and diploid Emiliania huxleyi were exposed to oversaturating irradiance. In the presence of PAR alone, the effective quantum yield was reduced by 10\% more due to the higher damage rate of photosystem II in haploid cells than in diploid cells. The addition of UVR resulted in further inhibition of the quantum yield for both haploid and diploid cells in the first 25~min, partly because of the increased damage of photosystem II. Intriguingly, this UVR-induced inhibition of the haploid cells completely recovered half an hour later. This recovery was confirmed by the comparable maximum quantum yields, maximum relative electron transport rates and yields of the haploid cells treated with PAR and PAR + UVR. Our data indicated that photosynthesis of the haploid phase was more sensitive to high visible light than the diploid phase but resistant to UVR-induced inhibition, reflecting the ecological niches to which this species adapts.},
	keywords = {Diploid phase, Effective quantum yield, Emiliania huxleyi, Haploid phase, rcc1217, Ultraviolet radiation (UVR)},
	issn = {2197-4365},
	doi = {10.1186/s40643-023-00660-5},
	url = {https://doi.org/10.1186/s40643-023-00660-5},
	author = {Ruan, Zuoxi and Lu, Meifang and Lin, Hongmin and Chen, Shanwen and Li, Ping and Chen, Weizhou and Xu, Huijuan and Qiu, Dajun}
}
@article {ferrieux_comparative_2022,
	title = {Comparative Thermophysiology of Marine Synechococcus CRD1 Strains Isolated From Different Thermal Niches in Iron-Depleted Areas},
	journal = {Frontiers in Microbiology},
	volume = {13},
	year = {2022},
	abstract = {Marine Synechococcus cyanobacteria are ubiquitous in the ocean, a feature likely related to their extensive genetic diversity. Amongst the major lineages, clades I and IV preferentially thrive in temperate and cold, nutrient-rich waters, whilst clades II and III prefer warm, nitrogen or phosphorus-depleted waters. The existence of such cold (I/IV) and warm (II/III) thermotypes is corroborated by physiological characterization of representative strains. A fifth clade, CRD1, was recently shown to dominate the Synechococcus community in iron-depleted areas of the world ocean and to encompass three distinct ecologically significant taxonomic units (ESTUs CRD1A-C) occupying different thermal niches, suggesting that distinct thermotypes could also occur within this clade. Here, using comparative thermophysiology of strains representative of these three CRD1 ESTUs we show that the CRD1A strain MITS9220 is a warm thermotype, the CRD1B strain BIOS-U3-1 a cold temperate thermotype, and the CRD1C strain BIOS-E4-1 a warm temperate stenotherm. Curiously, the CRD1B thermotype lacks traits and/or genomic features typical of cold thermotypes. In contrast, we found specific physiological traits of the CRD1 strains compared to their clade I, II, III, and IV counterparts, including a lower growth rate and photosystem II maximal quantum yield at most temperatures and a higher turnover rate of the D1 protein. Together, our data suggests that the CRD1 clade prioritizes adaptation to low-iron conditions over temperature adaptation, even though the occurrence of several CRD1 thermotypes likely explains why the CRD1 clade as a whole occupies most iron-limited waters.},
	keywords = {RCC2374, RCC2385, RCC2533, RCC2534, RCC2571, RCC515, rcc539, rcc791},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2022.893413},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.893413},
	author = {Ferrieux, Mathilde and Dufour, Louison and Dor{\'e}, Hugo and Ratin, Morgane and Gu{\'e}neugu{\`e}s, Audrey and Chasselin, L{\'e}o and Marie, Dominique and Rigaut-jalabert, Fabienne and Le Gall, Florence and Sciandra, Th{\'e}o and Monier, Garance and Hoebeke, Mark and Corre, Erwan and Xia, Xiaomin and Liu, Hongbin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {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 {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 {wang_moderating_2021,
	title = {The moderating role of population succession in the adaptive responses of Synechococcus assemblages: evidence from light intensity simulation experiment},
	journal = {Photosynthetica},
	volume = {59},
	number = {4},
	year = {2021},
	pages = {587{\textendash}599},
	abstract = {Synechococcus is one of the most abundant photoautotrophic picoplankton in the marine ecosystem. However, it is not clear how Synechococcus assemblages respond to light intensity variation in a genus group. Here, enriched Synechococcus assemblages from in situ coastal seawater were subjected to light intensity simulation experiments in a range of 9-243 μmol(photon) m{\textendash}2 s{\textendash}1. Characteristics concerning physiology, genomics, and metatranscriptomics were analyzed. Physiologically, the fitting model predicted photosynthesis indications and pigment contents increased with different trends following the light intensity. Genomic sequencing demonstrated that both the phylogenetic and phenotypic compositions of Synechococcus assemblage exhibited population succession. Especially, the proportion of Synechococcus pigment type 2 was changed significantly. In metatranscriptomics, most genes were downregulated in the high-light intensity group, while photosynthesis-related genes were entirely upregulated. The high upregulation of photosynthesis-related genes, such as psbO, psbA, apcB, and cpcB, corresponded to the succession of Synechococcus genotype and was responsible for the physiological shift in response to light intensity.},
	issn = {03003604, 15739058},
	doi = {10.32615/ps.2021.050},
	url = {http://ps.ueb.cas.cz/doi/10.32615/ps.2021.050.html},
	author = {Wang, T. and Chen, X. and Li, J.L. and Qin, S. and Cui, Y.L. and Xu, F.}
}
@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 {Roesler2017,
	title = {Recommendations for obtaining unbiased chlorophyll estimates from in situ chlorophyll fluorometers: A global analysis of WET Labs ECO sensors},
	journal = {Limnology and Oceanography: Methods},
	volume = {15},
	number = {6},
	year = {2017},
	note = {tex.mendeley-tags: RCC233,RCC42,RCC834},
	pages = {572{\textendash}585},
	abstract = {Chlorophyll fluorometers provide the largest in situ global data set for estimating phytoplankton biomass because of their ease of use, size, power consumption, and relatively low price. While in situ chlorophyll a (Chl) fluorescence is proxy for Chl a concentration, and hence phytoplankton biomass, there exist large natural variations in the relationship between in situ fluorescence and extracted Chl a concentration. Despite this large natural variability, we present here a global validation data set for the WET Labs Environmental Characterization Optics (ECO) series chlorophyll fluorometers that suggests a factor of 2 overestimation in the factory calibrated Chl a estimates for this specific manufacturer and series of sensors. We base these results on paired High Pressure Liquid Chromatography (HPLC) and in situ fluorescence match ups for which non-photochemically quenched fluorescence observations were removed. Additionally, we examined matchups between the factory-calibrated in situ fluorescence and estimates of chlorophyll concentration determined from in situ radiometry, absorption line height, NASA{\textquoteright}s standard ocean color algorithm as well as laboratory calibrations with phytoplankton monocultures spanning diverse species that support the factor of 2 bias. We therefore recommend the factor of 2 global bias correction be applied for the WET Labs ECO sensors, at the user level, to improve the global accuracy of chlorophyll concentration estimates and products derived from them. We recommend that other fluorometer makes and models should likewise undergo global analyses to identify potential bias in factory calibration.},
	keywords = {RCC233, RCC42, RCC834},
	issn = {15415856},
	doi = {10.1002/lom3.10185},
	author = {Roesler, Collin and Uitz, Julia and Claustre, Herv{\'e} and Boss, Emmanuel and Xing, Xiaogang and Organelli, Emanuele and Briggs, Nathan and Bricaud, Annick and Schmechtig, Catherine and Poteau, Antoine and D{\textquoteright}Ortenzio, Fabrizio and Ras, Josephine and Drapeau, Susan and Ha{\"e}ntjens, Nils and Barbieux, Marie}
}
@article {Keeling2014,
	title = {The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing},
	journal = {PLoS biology},
	volume = {12},
	number = {6},
	year = {2014},
	note = {Publisher: Public Library of Science tex.mendeley-tags: 2014,rcc,sbr?hyto$_\textrmd$ipo},
	pages = {e1001889},
	abstract = {Current sampling of genomic sequence data from eukaryotes is relatively poor, biased, and inadequate to address important questions about their biology, evolution, and ecology; this Community Page describes a resource of 700 transcriptomes from marine microbial eukaryotes to help understand their role in the world{\textquoteright}s oceans},
	keywords = {2014, rcc, SBR$_\textrmP$hyto$_\textrmD$PO, sbr?hyto$_\textrmd$ipo},
	doi = {10.1371/journal.pbio.1001889},
	url = {http://dx.doi.org/10.1371\%252Fjournal.pbio.1001889},
	author = {Keeling, Patrick J and Burki, Fabien and Wilcox, Heather M and Allam, Bassem and Allen, Eric E and Amaral-Zettler, Linda A and Armbrust, E Virginia and Archibald, John M and Bharti, Arvind K and Bell, Callum J and Beszteri, Bank and Bidle, Kay D and Cameron, Connor T and Campbell, Lisa and Caron, David A and Cattolico, Rose Ann and Collier, Jackie L and Coyne, Kathryn and Davy, Simon K and Deschamps, Phillipe and Dyhrman, Sonya T and Edvardsen, Bente and Gates, Ruth D and Gobler, Christopher J and Greenwood, Spencer J and Guida, Stephanie M and Jacobi, Jennifer L and Jakobsen, Kjetill S and James, Erick R and Jenkins, Bethany and John, Uwe and Johnson, Matthew D and Juhl, Andrew R and Kamp, Anja and Katz, Laura A and Kiene, Ronald and Kudryavtsev, Alexander and Leander, Brian S and Lin, Senjie and Lovejoy, Connie and Lynn, Denis and Marchetti, Adrian and McManus, George and Nedelcu, Aurora M and Menden-Deuer, Susanne and Miceli, Cristina and Mock, Thomas and Montresor, Marina and Moran, Mary Ann and Murray, Shauna and Nadathur, Govind and Nagai, Satoshi and Ngam, Peter B and Palenik, Brian and Pawlowski, Jan and Petroni, Giulio and Piganeau, Gwenael and Posewitz, Matthew C and Rengefors, Karin and Romano, Giovanna and Rumpho, Mary E and Rynearson, Tatiana and Schilling, Kelly B and Schroeder, Declan C and Simpson, Alastair G B and Slamovits, Claudio H and Smith, David R and Smith, G Jason and Smith, Sarah R and Sosik, Heidi M and Stief, Peter and Theriot, Edward and Twary, Scott N and Umale, Pooja E and Vaulot, Daniel and Wawrik, Boris and Wheeler, Glen L and Wilson, William H and Xu, Yan and Zingone, Adriana and Worden, Alexandra Z}
}
