Diversité des prasinovirus (phycodnaviridae) et contrôle par les facteurs environnementaux.

Viruses are the most abundant biological entities in oceans and they every member of the marine biosphere is affected by them, they influence the composition of communities and influence biogeochemical cycles. However, the influence of environmental conditions on complex viral populations is still poorly understood. The aim of this study is to understand how environmental factors influence viral communities. We followed viral communities monthly from March 2013 to April 2014 and investigated the host-virus system of Mamiellophyceae communities and their prasinoviruses, a model sytem that is abundant and widespread. Prasinovirus-host populations from the Gulf of Lion were quantified by PCR amplification and analysis of genetic marker genes and high throughput sequencing. Photosynthetic populations of picoeukaryotes were dominated by populations of Mamiellophyceae showing high levels of quantitative and qualitative annual variations that were related to environmental factors. Prasinovirus communities mimed host dynamics, but viral dispersion and persistence appeared to be impacted directly by environmental conditions such as temperature and hydrodynamics. Several viral groups, such as Ostreococcus viruses, were specific to lagoonal and coastal areas, suggesting that their dispersal is limited by host occurrence.Les virus sont les entités les plus abondantes dans les océans et ces parasitoïdes interagissent avec chaque composante de la biosphère marine, soit par la sélection des communautés d'hôte, soit en influençant les cycles biogéochimiques. Cependant, l'impact des conditions environnementales sur ces assemblages viraux complexes est encore mal compris. L'objectif de ce travail est de comprendre comment les assemblages viraux sont influencés par les facteurs environnementaux. Durant un suivi mensuel des communautés de mars 2013 à avril 2014, nous nous sommes intéressés à un système hôte-virus abondant et largement répandu, les communautés de microalgues Mamiellophyceae et leurs Prasinovirus. Durant ces études, des approches de PCR quantitative et de séquençage massif ont été développées afin de décrire les populations environnementales présentes au sein du Golfe du Lion. Les populations de Mamiellophyceae dominent le compartiment des picoeucaryotes photosynthétiques, avec des dynamiques fortes au cours de l'année. Les communautés de Prasinovirus reflètent les dynamiques de leurs hôtes, elles-mêmes en lien avec les facteurs environnementaux. En revanche, la dispersion ainsi que le maintien des virions semblent directement impacté par les conditions environnementales, comme la température et l'hydrodynamisme. Certains groupes viraux, comme les virus d'Ostreococcus, sont inféodés aux lagunes et aux zones côtières, suggérant ainsi que la dispersion des populations virales est limitées par la présence des hôtes

Genome analyses of the microalga Picochlorum provide insights into the evolution of thermotolerance in the green lineage

While the molecular events involved in cell responses to heat stress have been extensively studied, our understanding of the genetic basis of basal thermotolerance, and particularly its evolution within the green lineage, remains limited. Here, we present the 13.3-Mb haploid genome and transcriptomes of a halotolerant and thermotolerant unicellular green alga, Picochlorum costavermella (Trebouxiophyceae) to investigate the evolution of the genomic basis of thermotolerance. Differential gene expression at high and standard temperatures revealed that more of the gene families containing up-regulated genes at high temperature were recently evolved, and less originated at the ancestor of green plants. Inversely, there was an excess of ancient gene families containing transcriptionally repressed genes. Interestingly, there is a striking overlap between the thermotolerance and halotolerance transcriptional rewiring, as more than one-third of the gene families up-regulated at 35 degrees C were also up-regulated under variable salt concentrations in Picochlorum SE3. Moreover, phylogenetic analysis of the 9,304 protein coding genes revealed 26 genes of horizontally transferred origin in P. costavermella, of which five were differentially expressed at higher temperature. Altogether, these results provide new insights about how the genomic basis of adaptation to halo- and thermotolerance evolved in the green lineage

Diversity and environmental control of Prasinoviruses (Phycodnaviridae)

Les virus sont les entités les plus abondantes dans les océans et ces parasitoïdes interagissent avec chaque composante de la biosphère marine, soit par la sélection des communautés d'hôte, soit en influençant les cycles biogéochimiques. Cependant, l'impact des conditions environnementales sur ces assemblages viraux complexes est encore mal compris. L'objectif de ce travail est de comprendre comment les assemblages viraux sont influencés par les facteurs environnementaux. Durant un suivi mensuel des communautés de mars 2013 à avril 2014, nous nous sommes intéressés à un système hôte-virus abondant et largement répandu, les communautés de microalgues Mamiellophyceae et leurs Prasinovirus. Durant ces études, des approches de PCR quantitative et de séquençage massif ont été développées afin de décrire les populations environnementales présentes au sein du Golfe du Lion. Les populations de Mamiellophyceae dominent le compartiment des picoeucaryotes photosynthétiques, avec des dynamiques fortes au cours de l'année. Les communautés de Prasinovirus reflètent les dynamiques de leurs hôtes, elles-mêmes en lien avec les facteurs environnementaux. En revanche, la dispersion ainsi que le maintien des virions semblent directement impacté par les conditions environnementales, comme la température et l'hydrodynamisme. Certains groupes viraux, comme les virus d'Ostreococcus, sont inféodés aux lagunes et aux zones côtières, suggérant ainsi que la dispersion des populations virales est limitées par la présence des hôtes.Viruses are the most abundant biological entities in oceans and they every member of the marine biosphere is affected by them, they influence the composition of communities and influence biogeochemical cycles. However, the influence of environmental conditions on complex viral populations is still poorly understood. The aim of this study is to understand how environmental factors influence viral communities. We followed viral communities monthly from March 2013 to April 2014 and investigated the host-virus system of Mamiellophyceae communities and their prasinoviruses, a model sytem that is abundant and widespread. Prasinovirus-host populations from the Gulf of Lion were quantified by PCR amplification and analysis of genetic marker genes and high throughput sequencing. Photosynthetic populations of picoeukaryotes were dominated by populations of Mamiellophyceae showing high levels of quantitative and qualitative annual variations that were related to environmental factors. Prasinovirus communities mimed host dynamics, but viral dispersion and persistence appeared to be impacted directly by environmental conditions such as temperature and hydrodynamics. Several viral groups, such as Ostreococcus viruses, were specific to lagoonal and coastal areas, suggesting that their dispersal is limited by host occurrence

Investigating microbial associations from sequencing survey data with co-correspondence analysis

International audienceMicrobial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next‐generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co‐correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co‐occurrence networks and thus investigate the presence of patterns in ecological networks

Investigating microbial associations from sequencing survey data with co-correspondence analysis

Microbial communities, which drive major ecosystem functions, consist of a wide range of interacting species. Understanding how microbial communities are structured and the processes underlying this is crucial to interpreting ecosystem responses to global change but is challenging as microbial interactions cannot usually be directly observed. Multiple efforts are currently focused to combine next-generation sequencing (NGS) techniques with refined statistical analysis (e.g., network analysis, multivariate analysis) to characterize the structures of microbial communities. However, most of these approaches consider a single table of sequencing data measured for several samples. Technological advances now make it possible to collect NGS data on different taxonomic groups simultaneously for the same samples, allowing us to analyse a pair of tables. Here, an analytical framework based on co-correspondence analysis (CoCA) is proposed to study the distributions, assemblages and interactions between two microbial communities. We show the ability of this approach to highlight the relationships between two microbial communities, using two data sets exhibiting various types of interactions. CoCA identified strong association patterns between autotrophic and heterotrophic microbial eukaryote assemblages, on the one hand, and between microalgae and viruses, on the other. We demonstrate also how CoCA can be used, complementary to network analysis, to reorder co-occurrence networks and thus investigate the presence of patterns in ecological networks.</p

Stock structure of the English Channel common cuttlefish Sepia officinalis (Linnaeus, 1758) during the reproduction period

International audienceStock structure of the English Channel common cuttlefish Sepia officinalis (Linnaeus, 1758) during the reproduction period michae ¤l gras 1,2 , georges safi 1,2 , hugo lebredonchel 1,2 , je ' ro ^ me quinquis 3 , e ' ric foucher 3 , noussithe Within the English Channel, the common cuttlefish Sepia officinalis is a semelparous species for which a 2-year life cycle was exclusively described in the 1980s. In the 1990s, new research indicated that whilst a 2-year life cycle was still evident for females and the large majority of males, a small proportion of males were actually maturing at only 1 year of age. Since 1980, the interest of French and UK fishers for this resource has increased and it is nowadays one of the most important demersal species of the area and is considered to be fully exploited. From the start of the 20th century, fishing effort and sea surface temperatures have increased in the English Channel and have probably impacted the life history traits of S. officinalis. A 2-year sampling programme was undertaken at French landing sites of the English Channel during the reproduction season in 2010 and 2011 to estimate if the proportion of 1-year-old mature animals has changed. Age determination was carried out by coupling polymodal decomposition and lipofuscin measurement. Size-at-maturity for each year and each sex was estimated by fitting a binomial error GLM. Results highlight that a variable percentage of males and females belonging to the first cohort are mature and that size-at-maturity was lower than that observed in the 1990s. Finally, different parameters , such as temperature and fishing pressure are explored to discuss changes in life history traits suggesting that cuttlefish could be an indicator of the temperature regime shift in the English Channel