@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 {dore_global_2022,
	title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts},
	journal = {mSystems},
	year = {2022},
	note = {Publisher: American Society for Microbiology},
	pages = {e00656{\textendash}22},
	abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21st, 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of {\textquotedblleft}who is where{\textquotedblright} by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.},
	keywords = {RCC1086, RCC1695, RCC2369, rcc2380, RCC2553, RCC2556, RCC2570, rcc791},
	doi = {10.1128/msystems.00656-22},
	url = {https://journals.asm.org/doi/full/10.1128/msystems.00656-22},
	author = {Dor{\'e}, Hugo and Leconte, Jade and Guyet, Ulysse and Breton, Sol{\`e}ne and Farrant, Gregory K. and Demory, David and Ratin, Morgane and Hoebeke, Mark and Corre, Erwan and Pitt, Frances D. and Ostrowski, Martin and Scanlan, David J. and Partensky, Fr{\'e}d{\'e}ric and Six, Christophe and Garczarek, Laurence}
}
@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 {Grebert2018,
	title = {Light color acclimation is a key process in the global ocean distribution of Synechococcus cyanobacteria},
	journal = {Proceedings of the National Academy of Sciences},
	volume = {in press},
	year = {2018},
	note = {tex.mendeley-tags: 2018,RCC1016,RCC1017,RCC1018,RCC1020,RCC1023,RCC1027,RCC1030,RCC1031,RCC1084,RCC1085,RCC1086,RCC1087,RCC1096,RCC1097,RCC1649,RCC1661,RCC1688,RCC2032,RCC2033,RCC2035,RCC2319,RCC2366,RCC2368,RCC2369,RCC2370,RCC2372,RCC2373,RCC2374,RCC2375,RCC2376,RCC2378,RCC2379,RCC2380,RCC2381,RCC2382,RCC2383,RCC2384,RCC2385,RCC2415,RCC2432,RCC2433,RCC2434,RCC2435,RCC2436,RCC2437,RCC2438,RCC2457,RCC2525,RCC2526,RCC2527,RCC2528,RCC2529,RCC2530,RCC2532,RCC2533,RCC2534,RCC2536,RCC2553,RCC2554,RCC2555,RCC2556,RCC2567,RCC2568,RCC2569,RCC2570,RCC2571,RCC2673,RCC30,RCC3010,RCC3012,RCC3014,RCC307,RCC316,RCC318,RCC325,RCC326,RCC328,RCC37,RCC44,RCC46,RCC47,RCC515,RCC539,RCC542,RCC543,RCC550,RCC552,RCC553,RCC555,RCC556,RCC557,RCC558,RCC559,RCC62,RCC650,RCC66,RCC752,RCC753,RCC790,RCC791,RCC792,RCC793,RCC794,sbr?hyto?app},
	month = {feb},
	pages = {201717069},
	abstract = {Marine Synechococcus cyanobacteria are major contributors to global oceanic primary production and exhibit a unique diversity of photosynthetic pigments, allowing them to exploit a wide range of light niches. However, the relationship between pigment content and niche partitioning has remained largely undetermined so far due to the lack of a single-genetic marker resolving all pigment types (PT). Here, we developed a novel and robust method based on three distinct marker genes to estimate the relative abundance of all Synechococcus PTs from metagenomes. Analysis of the Tara Oceans dataset allowed us to unveil for the first time the global distribution of Synechococcus PTs and to decipher their realized environmental niches. Green-light specialists (PT 3a) dominated in warm, green equatorial waters, whereas blue-light specialists (PT 3c) were particularly abundant in oligotrophic areas. Type IV chromatic acclimaters (CA4-A/B), which are able to dynamically modify their light absorption properties to maximally absorb green or blue light, were unexpectedly the most abundant PT in our dataset and predominated at depth and high latitudes. We also identified local populations in which CA4 might be inactive due to the lack of specific CA4 genes, notably in warm high nutrient low chlorophyll areas. Major ecotypes within clades I-IV and CRD1 were preferentially associated with a particular PT, while others exhibited a wide range of PTs. Altogether, this study brings unprecedented insights into the ecology of Synechococcus PTs and highlights the complex interactions between vertical phylogeny, pigmentation and environmental parameters that shape Synechococcus populations and evolution.},
	keywords = {2018, RCC1016, RCC1017, RCC1018, RCC1020, RCC1023, RCC1027, RCC1030, RCC1031, rcc1084, RCC1085, RCC1086, RCC1087, RCC1096, RCC1097, RCC1649, RCC1661, RCC1688, RCC2032, RCC2033, RCC2035, RCC2319, RCC2366, RCC2368, RCC2369, RCC2370, RCC2372, RCC2373, RCC2374, RCC2375, RCC2376, RCC2378, RCC2379, rcc2380, RCC2381, rcc2382, RCC2383, RCC2384, RCC2385, RCC2415, RCC2432, RCC2433, RCC2434, RCC2435, RCC2436, RCC2437, RCC2438, RCC2457, RCC2525, RCC2526, RCC2527, RCC2528, RCC2529, RCC2530, RCC2532, RCC2533, RCC2534, RCC2536, RCC2553, RCC2554, RCC2555, RCC2556, RCC2567, RCC2568, RCC2569, RCC2570, RCC2571, RCC2673, rcc30, RCC3010, RCC3012, RCC3014, RCC307, RCC316, RCC318, RCC325, RCC326, RCC328, RCC37, RCC44, RCC46, RCC47, RCC515, rcc539, RCC542, RCC543, RCC550, RCC552, RCC553, rcc555, RCC556, RCC557, RCC558, RCC559, RCC62, RCC650, RCC66, rcc752, RCC753, RCC790, rcc791, RCC792, RCC793, RCC794, sbr?hyto?app},
	issn = {0027-8424},
	doi = {10.1073/pnas.1717069115},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1717069115},
	author = {Gr{\'e}bert, Th{\'e}ophile and Dor{\'e}, Hugo and Partensky, Fr{\'e}d{\'e}ric and Farrant, Gregory K. and Boss, Emmanuel S. and Picheral, Marc and Guidi, Lionel and Pesant, St{\'e}phane and Scanlan, David J. and Wincker, Patrick and Acinas, Silvia G. and Kehoe, David M. and Garczarek, Laurence}
}
