@article {letscher_biodiversity_2023,
	title = {Biodiversity and stoichiometric plasticity increase pico-phytoplankton contributions to marine net primary productivity and the biological pump},
	journal = {Global Biogeochemical Cycles},
	volume = {n/a},
	number = {n/a},
	year = {2023},
	note = {_eprint: https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2023GB007756},
	pages = {e2023GB007756},
	abstract = {Earth System Models generally predict increasing upper ocean stratification from 21st century warming, which will cause a decrease in the vertical nutrient flux forcing declines in marine net primary productivity (NPP) and carbon export. Recent advances in quantifying marine ecosystem carbon to nutrient stoichiometry have identified large latitudinal and biome variability, with low-latitude oligotrophic systems harboring pico-sized phytoplankton exhibiting large phosphorus to carbon cellular plasticity. Climate forced changes in nutrient flux stoichiometry and phytoplankton community composition is thus likely to alter the ocean{\textquoteright}s biogeochemical response and feedback with the carbon-climate system. We have added three pico-phytoplankton functional types within the Biogeochemical Elemental Cycling component of the Community Earth System Model while incorporating variable cellular phosphorus to carbon stoichiometry for all represented phytoplankton types. The model simulates Prochlorococcus and Synechococcus populations that dominate the productivity and sinking carbon export of the tropical and subtropical ocean, and pico-eukaryote populations that contribute significantly to productivity and export within the subtropical to mid-latitude transition zone, with the western subtropical regions of each basin supporting the most P-poor stoichiometries. Subtropical gyre recirculation regions along the poleward flanks of surface western boundary currents are identified as regional hotspots of enhanced carbon export exhibiting C-rich/P-poor stoichiometry, preferentially inhabited by pico-eukaryotes and diatoms. Collectively, pico-phytoplankton contribute \~{}58\% of global NPP and \~{}46\% of global particulate organic carbon export below 100 meters through direct and ecosystem processing pathways. Biodiversity and cellular nutrient plasticity in marine pico-phytoplankton combine to increase their contributions to ocean productivity and the biological carbon pump. This article is protected by copyright. All rights reserved.},
	keywords = {carbon export, net primary productivity, pico-phytoplankton, rcc162, rcc1677, rcc212, rcc289, rcc296, rcc30, rcc438, variable C:P},
	issn = {1944-9224},
	doi = {10.1029/2023GB007756},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1029/2023GB007756},
	author = {Letscher, Robert T. and Moore, J. Keith and Martiny, Adam C. and Lomas, Michael W.}
}
@article {Dore2020,
	title = {Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria},
	journal = {Frontiers in Microbiology},
	volume = {11},
	number = {September},
	year = {2020},
	note = {tex.mendeley-tags: RCC1084,RCC1085,RCC1086,RCC1087,RCC156,RCC158,RCC162,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2374,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2385,RCC2433,RCC2436,RCC2438,RCC2527,RCC2528,RCC2533,RCC2534,RCC2535,RCC2553,RCC2554,RCC2555,RCC2556,RCC2571,RCC2673,RCC278,RCC296,RCC307,RCC328,RCC3377,RCC407,RCC515,RCC539,RCC555,RCC556,RCC752,RCC753,RCC791},
	month = {sep},
	pages = {1{\textendash}23},
	keywords = {amino-acid substitutions, comparative genomics, evolution, genomic islands, marine cyanobacteria, niche adaptation, Prochlorococcus, rcc1084, RCC1085, RCC1086, RCC1087, RCC156, RCC158, rcc162, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2374, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2385, RCC2433, RCC2436, RCC2438, RCC2527, RCC2528, RCC2533, RCC2534, RCC2535, RCC2553, RCC2554, RCC2555, RCC2556, RCC2571, RCC2673, RCC278, rcc296, RCC307, RCC328, RCC3377, RCC407, RCC515, rcc539, rcc555, RCC556, rcc752, RCC753, rcc791, Synechococcus},
	issn = {1664-302X},
	doi = {10.3389/fmicb.2020.567431},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2020.567431/full},
	author = {Dor{\'e}, Hugo and Farrant, Gregory K. and Guyet, Ulysse and Haguait, Julie and Humily, Florian and Ratin, Morgane and Pitt, Frances D. and Ostrowski, Martin and Six, Christophe and Brillet-Gu{\'e}guen, Loraine and Hoebeke, Mark and Bisch, Antoine and Le Corguill{\'e}, Gildas and Corre, Erwan and Labadie, Karine and Aury, Jean-Marc and Wincker, Patrick and Choi, Dong Han and Noh, Jae Hoon and Eveillard, Damien and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Garczarek, Laurence}
}
@article {Delmont2018,
	title = {Linking pangenomes and metagenomes: the Prochlorococcus metapangenome},
	journal = {PeerJ},
	volume = {6},
	year = {2018},
	note = {ISBN: 2167-8359 tex.mendeley-tags: RCC156,RCC158,RCC162,RCC269,RCC278,RCC296,RCC3377,RCC407},
	pages = {e4320},
	abstract = {Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.},
	keywords = {RCC156, RCC158, rcc162, RCC269, RCC278, rcc296, RCC3377, RCC407},
	issn = {2167-8359},
	doi = {10.7717/peerj.4320},
	url = {https://peerj.com/articles/4320},
	author = {Delmont, Tom O. and Eren, A. Murat}
}
@article {Soitamo2017,
	title = {Photoinhibition in marine picocyanobacteria},
	journal = {Physiologia Plantarum},
	volume = {161},
	number = {1},
	year = {2017},
	note = {Publisher: John Wiley \& Sons, Ltd (10.1111) tex.mendeley-tags: RCC156,RCC2366,RCC296,RCC407},
	month = {sep},
	pages = {97{\textendash}108},
	abstract = {Marine Synechococcus and Prochlorococcus cyanobacteria have different antenna compositions although they are genetically near to each other, and different strains thrive in very different illumination conditions. We measured growth and photoinhibition of PSII in two low-light and one high-light Prochlorococcus strains and in one Synechococcus strain. All strains were found to be able to shortly utilize moderate or even high light, but the low-light strains bleached rapidly in moderate light. Measurements of photoinhibition in the presence of the antibiotic lincomycin showed that a low-light Prochlorococcus strain was more sensitive than a high-light strain and both were more sensitive than the marine Synechococcus. The action spectrum of photoinhibition showed an increase from blue to ultraviolet wavelengths in all strains, suggesting contribution of manganese absorption to photoinhibition, but blue light caused less photoinhibition in marine cyanobacteria than expected on the basis of earlier results from plants and cyanobacteria. The visible-light part of the action spectrum resembled the absorption spectrum of the organism, suggesting that photosynthetic antenna pigments, especially divinyl chlorophylls, have a more important role as photoreceptors of visible-light photoinhibition in marine cyanobacteria than in other photoautotrophs.},
	keywords = {RCC156, RCC2366, rcc296, RCC407},
	issn = {0031-9317},
	doi = {10.1111/ppl.12571},
	url = {https://doi.org/10.1111/ppl.12571},
	author = {Soitamo, Arto and Havurinne, Vesa and Tyystj{\"a}rvi, Esa}
}
@article {Stawiarski2016,
	title = {The physiological response of picophytoplankton to temperature and its model representation},
	journal = {Fronitiers in Marine Science},
	volume = {3},
	number = {164},
	year = {2016},
	note = {tex.mendeley-tags: rcc162,rcc1677,rcc212,rcc289,rcc296,rcc30,rcc361,rcc438,rcc503},
	pages = {1{\textendash}13},
	keywords = {chlorophyll a to carbon, chlorophyll a to carbon ratio, Eppley, frontiers in marine science, frontiersin, org, physiological parameterization, phytoplankton growth rates, phytoplankton size scaling, picoeukaryotes, picophytoplankton, ratio, rcc162, rcc1677, rcc212, rcc289, rcc296, rcc30, rcc361, rcc438, rcc503, temperature tolerance, www},
	issn = {2296-7745},
	doi = {10.3389/fmars.2016.00164},
	author = {Stawiarski, Beate and Buitenhuis, Erik T and Qu{\'e}r{\'e}, Corinne Le}
}
