Evolutionary mechanisms of long-term genome diversification associated with niche partitioning in marine picocyanobacteria

Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton

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

Cyanorak v2.1 : a scalable information system dedicated to the visualization and expert curation of marine and brackish picocyanobacteria genomes

Cyanorak v2.1 (http://www.sb-roscoff.fr/cyanorak) is an information system dedicated to visualizing, comparing and curating the genomes of Prochlorococcus, Synechococcus and Cyanobium, the most abundant photosynthetic microorganisms on Earth. The database encompasses sequences from 97 genomes, covering most of the wide genetic diversity known so far within these groups, and which were split into 25,834 clusters of likely orthologous groups (CLOGs). The user interface gives access to genomic characteristics, accession numbers as well as an interactive map showing strain isolation sites. The main entry to the database is through search for a term (gene name, product, etc.), resulting in a list of CLOGs and individual genes. Each CLOG benefits from a rich functional annotation including EggNOG, EC/K numbers, GO terms, TIGR Roles, custom-designed Cyanorak Roles as well as several protein motif predictions. Cyanorak also displays a phyletic profile, indicating the genotype and pigment type for each CLOG, and a genome viewer (Jbrowse) to visualize additional data on each genome such as predicted operons, genomic islands or transcriptomic data, when available. This information system also includes a BLAST search tool, comparative genomic context as well as various data export options. Altogether, Cyanorak v2.1 constitutes an invaluable, scalable tool for comparative genomics of ecologically relevant marine microorganisms

Étude des bases moléculaires de l’adaptation et de l’acclimatation aux changements environnementaux chez les picocyanobactéries marines, des organismes clés du phytoplancton

The two marine picocyanobacteria Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on the planet, their wide distribution being probably linked to their large genomic diversity. The first part of my work has consisted in studying the genetic bases of the adaptation of these organisms to distinct ecological niches and revealed, by comparing 81 genomes of these two genera, the role of gene gains/losses and variations in nucleotide sequences in the diversification of these organisms. A second part has consisted in the analysis of the physiological responses of a Synechococcus model strain (WH7803) and of four other strains, representative of the dominant ecotypes in the field (clades I to IV), to various environmental factors in order to identify the genes that are involved in specific or common responses to these different stresses and/or ecotypes. Finally, the last part of my thesis aimed at identifying the distribution of all picocyanobacterial genes in the world ocean and to link it to environmental parameters and to the distribution of ecotypes, which made it possible to highlight the gene repertoires specific of niches and/or ecotypes. The integration of these results led me to get a better understanding of the adaptation and acclimation mechanisms, which allowed marine picocyanobacteria to colonize virtually all lit ecological niches of the oceans.Les deux picocyanobactéries marines Prochlorococcus et Synechococcus sont les organismes photosynthétiques les plus abondants de la planète, leur vaste distribution étant sans doute liée à leur importante diversité génomique. La première partie de mon travail a consisté à étudier les bases génétiques de l'adaptation de ces organismes à des niches écologiques distinctes et a révélé, en comparant 81 génomes de ces deux genres, le rôle des gains/pertes de gènes et des variations des séquences nucléotidiques dans la diversification de ces organismes. Une deuxième partie a consisté en l'analyse des réponses physiologiques d'une souche modèle de Synechococcus (WH7803) et de quatre autres souches représentatives des écotypes dominants in situ (clades I à IV) à divers stress environnementaux, afin d'identifier les gènes impliqués dans les réponses spécifiques ou communes à ces différents stress et/ou écotypes. Enfin, la dernière partie de ma thèse a visé à identifier la distribution de l’ensemble des gènes de picocyanobactéries dans l'océan mondial et à la relier aux paramètres environnementaux et à la distribution des écotypes, ce qui a permis de mettre en évidence les répertoires de gènes spécifiques de niches et/ou d’écotypes. L’intégration de ces résultats m’a permis de mieux comprendre les mécanismes d'adaptation et d'acclimatation, qui ont permis aux picocyanobactéries de coloniser la quasi-totalité des niches écologiques éclairées des océans

Étude des bases moléculaires de l’adaptation et de l’acclimatation aux changements environnementaux chez les picocyanobactéries marines, des organismes clés du phytoplancton

The two marine picocyanobacteria Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on the planet, their wide distribution being probably linked to their large genomic diversity. The first part of my work has consisted in studying the genetic bases of the adaptation of these organisms to distinct ecological niches and revealed, by comparing 81 genomes of these two genera, the role of gene gains/losses and variations in nucleotide sequences in the diversification of these organisms. A second part has consisted in the analysis of the physiological responses of a Synechococcus model strain (WH7803) and of four other strains, representative of the dominant ecotypes in the field (clades I to IV), to various environmental factors in order to identify the genes that are involved in specific or common responses to these different stresses and/or ecotypes. Finally, the last part of my thesis aimed at identifying the distribution of all picocyanobacterial genes in the world ocean and to link it to environmental parameters and to the distribution of ecotypes, which made it possible to highlight the gene repertoires specific of niches and/or ecotypes. The integration of these results led me to get a better understanding of the adaptation and acclimation mechanisms, which allowed marine picocyanobacteria to colonize virtually all lit ecological niches of the oceans.Les deux picocyanobactéries marines Prochlorococcus et Synechococcus sont les organismes photosynthétiques les plus abondants de la planète, leur vaste distribution étant sans doute liée à leur importante diversité génomique. La première partie de mon travail a consisté à étudier les bases génétiques de l'adaptation de ces organismes à des niches écologiques distinctes et a révélé, en comparant 81 génomes de ces deux genres, le rôle des gains/pertes de gènes et des variations des séquences nucléotidiques dans la diversification de ces organismes. Une deuxième partie a consisté en l'analyse des réponses physiologiques d'une souche modèle de Synechococcus (WH7803) et de quatre autres souches représentatives des écotypes dominants in situ (clades I à IV) à divers stress environnementaux, afin d'identifier les gènes impliqués dans les réponses spécifiques ou communes à ces différents stress et/ou écotypes. Enfin, la dernière partie de ma thèse a visé à identifier la distribution de l’ensemble des gènes de picocyanobactéries dans l'océan mondial et à la relier aux paramètres environnementaux et à la distribution des écotypes, ce qui a permis de mettre en évidence les répertoires de gènes spécifiques de niches et/ou d’écotypes. L’intégration de ces résultats m’a permis de mieux comprendre les mécanismes d'adaptation et d'acclimatation, qui ont permis aux picocyanobactéries de coloniser la quasi-totalité des niches écologiques éclairées des océans

Study of the molecular basis of adaptation and acclimation to environmental changes in marine picocyanobacteria, key phytoplankton organisms

Les deux picocyanobactéries marines Prochlorococcus et Synechococcus sont les organismes photosynthétiques les plus abondants de la planète, leur vaste distribution étant sans doute liée à leur importante diversité génomique. La première partie de mon travail a consisté à étudier les bases génétiques de l'adaptation de ces organismes à des niches écologiques distinctes et a révélé, en comparant 81 génomes de ces deux genres, le rôle des gains/pertes de gènes et des variations des séquences nucléotidiques dans la diversification de ces organismes. Une deuxième partie a consisté en l'analyse des réponses physiologiques d'une souche modèle de Synechococcus (WH7803) et de quatre autres souches représentatives des écotypes dominants in situ (clades I à IV) à divers stress environnementaux, afin d'identifier les gènes impliqués dans les réponses spécifiques ou communes à ces différents stress et/ou écotypes. Enfin, la dernière partie de ma thèse a visé à identifier la distribution de l’ensemble des gènes de picocyanobactéries dans l'océan mondial et à la relier aux paramètres environnementaux et à la distribution des écotypes, ce qui a permis de mettre en évidence les répertoires de gènes spécifiques de niches et/ou d’écotypes. L’intégration de ces résultats m’a permis de mieux comprendre les mécanismes d'adaptation et d'acclimatation, qui ont permis aux picocyanobactéries de coloniser la quasi-totalité des niches écologiques éclairées des océans.The two marine picocyanobacteria Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on the planet, their wide distribution being probably linked to their large genomic diversity. The first part of my work has consisted in studying the genetic bases of the adaptation of these organisms to distinct ecological niches and revealed, by comparing 81 genomes of these two genera, the role of gene gains/losses and variations in nucleotide sequences in the diversification of these organisms. A second part has consisted in the analysis of the physiological responses of a Synechococcus model strain (WH7803) and of four other strains, representative of the dominant ecotypes in the field (clades I to IV), to various environmental factors in order to identify the genes that are involved in specific or common responses to these different stresses and/or ecotypes. Finally, the last part of my thesis aimed at identifying the distribution of all picocyanobacterial genes in the world ocean and to link it to environmental parameters and to the distribution of ecotypes, which made it possible to highlight the gene repertoires specific of niches and/or ecotypes. The integration of these results led me to get a better understanding of the adaptation and acclimation mechanisms, which allowed marine picocyanobacteria to colonize virtually all lit ecological niches of the oceans

Killer Immunoglobulin-Like Receptor Allele Determination Using Next-Generation Sequencing Technology

International audienceThe impact of natural killer (NK) cell alloreactivity on hematopoietic stem cell transplantation (HSCT) outcome is still debated due to the complexity of graft parameters, HLA class I environment, the nature of killer cell immunoglobulin-like receptor (KIR)/KIR ligand genetic combinations studied, and KIR+ NK cell repertoire size. KIR genes are known to be polymorphic in terms of gene content, copy number variation, and number of alleles. These allelic polymorphisms may impact both the phenotype and function of KIR+ NK cells. We, therefore, speculate that polymorphisms may alter donor KIR+ NK cell phenotype/function thus modulating post-HSCT KIR+ NK cell alloreactivity. To investigate KIR allele polymorphisms of all KIR genes, we developed a next-generation sequencing (NGS) technology on a MiSeq platform. To ensure the reliability and specificity of our method, genomic DNA from well-characterized cell lines were used; high-resolution KIR typing results obtained were then compared to those previously reported. Two different bioinformatic pipelines were used allowing the attribution of sequencing reads to specific KIR genes and the assignment of KIR alleles for each KIR gene. Our results demonstrated successful long-range KIR gene amplifications of all reference samples using intergenic KIR primers. The alignment of reads to the human genome reference (hg19) using BiRD pipeline or visualization of data using Profiler software demonstrated that all KIR genes were completely sequenced with a sufficient read depth (mean 317× for all loci) and a high percentage of mapping (mean 93% for all loci). Comparison of high-resolution KIR typing obtained to those published data using exome capture resulted in a reported concordance rate of 95% for centromeric and telomeric KIR genes. Overall, our results suggest that NGS can be used to investigate the broad KIR allelic polymorphism. Hence, these data improve our knowledge, not only on KIR+ NK cell alloreactivity in HSCT but also on the role of KIR+ NK cell populations in control of viral infections and diseases

Unveiling membrane thermoregulation strategies in marine picocyanobacteria

International audienceThe wide latitudinal distribution of marine Synechococcus cyanobacteria partly relies on the differentiation of lineages adapted to distinct thermal environments. Membranes are highly thermosensitive cell components, and the ability to modulate their fluidity can be critical for the fitness of an ecotype in a particular thermal niche. We compared the thermophysiology of Synechococcus strains representative of major temperature ecotypes in the field. We measured growth, photosynthetic capacities and membrane lipidome variations. We carried out a metagenomic analysis of stations of the Tara Oceans expedition to describe the latitudinal distribution of the lipid desaturase genes in the oceans. All strains maintained efficient photosynthetic capacities over their different temperature growth ranges. Subpolar and cold temperate strains showed enhanced capacities for lipid monodesaturation at low temperature thanks to an additional, poorly regiospecific Delta 9-desaturase. By contrast, tropical and warm temperate strains displayed moderate monodesaturation capacities but high proportions of double unsaturations in response to cold, thanks to regiospecific Delta 12-desaturases. The desaturase genes displayed specific distributions directly related to latitudinal variations in ocean surface temperature. This study highlights the critical importance of membrane fluidity modulation by desaturases in the adaptive strategies of Synechococcus cyanobacteria during the colonization of novel thermal niches