Global phylogeography of marine synechococcus in coastal areas reveals strong community shifts

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

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change

Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies

The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change

Analyses de variations génomiques liées à la biogéographie des picoalgues Mamiellales

Mamiellales are an order of unicellular cosmopolitan green algae with ecologically important species such as Bathycoccus, Micromonas or Ostreococcus, major contributors to the primary production. This thesis uses this phytoplankton group with known reference genomes as a study model in order to better analyze the impact of the environment on plankton using samples from the Tara Oceans expedition.To do this, different analyses were carried out to define their biogeography and ecological preferences, first in temperate waters then in the cold, nutrient-rich waters of the Arctic Ocean. In both cases, temperature was shown to be the main factor distinguishing the environment in which the different genomes were found. We then carried out a more detailed study in particular on Bathycoccus prasinos, a species abundant in these two distinct environments, in order to establish its population structure, which proved to be clearly separated into three groups: southern , arctic and temperate samples, again showing an impact of temperature but not only in view of the genomic distance between the first two basins.Finally, our study was extended with various collaborations, allowing us to observe a group of heterotrophic protists, the stramenopiles, and to perform analyses at the much larger scale of communities. All of these results conclude once again, among other things, on the strong impact of temperature, leading us to contribute to the question about the current context of climate change and its impact on plankton.Les Mamiellales sont un ordre d'algues vertes unicellulaires cosmopolites comprenant des espèces d'importance écologique telles que Bathycoccus, Micromonas ou encore Ostreococcus, des contributeurs majeurs à la production primaire. Cette thèse prend pour modèle d'étude ce groupe phytoplanctonique aux génomes de référence connus afin d'analyser au mieux l'impact de l'environnement sur le plancton grâce aux échantillons provenant de l'expédition Tara Oceans.Pour cela, différentes analyses ont été menées afin de définir leur biogéographie et leurs préférences écologiques, d'abord dans les eaux tempérées puis dans les eaux froides et riches en nutriments de l'océan Arctique. Dans les deux cas, il a été montré que la température était le principal facteur distinguant l'environnement dans lequel les différentes espèces ont été trouvées. Nous avons ensuite réalisé une étude plus poussée en particulier sur Bathycoccus prasinos, une espèce abondante dans ces deux milieux distincts afin d'établir la structure de ses populations, qui s'avère séparer clairement trois groupes: les échantillons austral, arctiques et tempérés, montrant encore une fois un impact de la température mais pas uniquement au vu de la distance génomique entre les deux premiers bassins.Finalement, notre étude a pu être étendue avec diverses collaborations, nous permettant d'observer également un groupe de protistes hétérotrophes, les straménopiles, et de réaliser des analyses à l'échelle beaucoup plus large des communautés. L'ensemble de ces résultats concluent encore une fois, entre autre, à un fort impact de la température, menant à un questionnement sur le contexte actuel de changements climatiques et son potentiel impact sur le plancton

Analysis of genomic variations related the biogeography of Mamiellales picoalgae

Les Mamiellales sont un ordre d'algues vertes unicellulaires cosmopolites comprenant des espèces d'importance écologique telles que Bathycoccus, Micromonas ou encore Ostreococcus, des contributeurs majeurs à la production primaire. Cette thèse prend pour modèle d'étude ce groupe phytoplanctonique aux génomes de référence connus afin d'analyser au mieux l'impact de l'environnement sur le plancton grâce aux échantillons provenant de l'expédition Tara Oceans.Pour cela, différentes analyses ont été menées afin de définir leur biogéographie et leurs préférences écologiques, d'abord dans les eaux tempérées puis dans les eaux froides et riches en nutriments de l'océan Arctique. Dans les deux cas, il a été montré que la température était le principal facteur distinguant l'environnement dans lequel les différentes espèces ont été trouvées. Nous avons ensuite réalisé une étude plus poussée en particulier sur Bathycoccus prasinos, une espèce abondante dans ces deux milieux distincts afin d'établir la structure de ses populations, qui s'avère séparer clairement trois groupes: les échantillons austral, arctiques et tempérés, montrant encore une fois un impact de la température mais pas uniquement au vu de la distance génomique entre les deux premiers bassins.Finalement, notre étude a pu être étendue avec diverses collaborations, nous permettant d'observer également un groupe de protistes hétérotrophes, les straménopiles, et de réaliser des analyses à l'échelle beaucoup plus large des communautés. L'ensemble de ces résultats concluent encore une fois, entre autre, à un fort impact de la température, menant à un questionnement sur le contexte actuel de changements climatiques et son potentiel impact sur le plancton.Mamiellales are an order of unicellular cosmopolitan green algae with ecologically important species such as Bathycoccus, Micromonas or Ostreococcus, major contributors to the primary production. This thesis uses this phytoplankton group with known reference genomes as a study model in order to better analyze the impact of the environment on plankton using samples from the Tara Oceans expedition.To do this, different analyses were carried out to define their biogeography and ecological preferences, first in temperate waters then in the cold, nutrient-rich waters of the Arctic Ocean. In both cases, temperature was shown to be the main factor distinguishing the environment in which the different genomes were found. We then carried out a more detailed study in particular on Bathycoccus prasinos, a species abundant in these two distinct environments, in order to establish its population structure, which proved to be clearly separated into three groups: southern , arctic and temperate samples, again showing an impact of temperature but not only in view of the genomic distance between the first two basins.Finally, our study was extended with various collaborations, allowing us to observe a group of heterotrophic protists, the stramenopiles, and to perform analyses at the much larger scale of communities. All of these results conclude once again, among other things, on the strong impact of temperature, leading us to contribute to the question about the current context of climate change and its impact on plankton

Populations structure of the microalgae Bathycoccus prasinos in the open ocean

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Populations structure of the microalgae Bathycoccus prasinos in the open ocean

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Populations structure of the microalgae Bathycoccus prasinos in the open ocean

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Equatorial to Polar genomic description of the cosmopolitan Bathycoccus populations

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