Abstract
Viruses are recognized as major players in planktonic ecosystems. Through their active lysis of microorganisms, they tend to short-circuit nutrient cycling and affect biogeochemical cycles at global scales. Viruses regulate and modify the genetic diversity of their hosts, via lysis and lateral gene transfer, and themselves represent the most important reservoir of genetic diversity on the planet. This diversity in turn is largely uncharacterised, especially for viruses of Eukaryotes. Recent medium to large-scale metagenomic studies of viruses have been done, but data are still scarce, especially in marine environments. To date, most studies on viral diversity were based on culture-dependent approaches, which permit the isolation and characterisation of viral strains, but are limited to viruses infecting host cultures. Moreover, recent works suggest that many (but not all) viral strains attack only specific host strains, emphasizing the bias inherent to host culture-dependent approach to assess viral diversity. However, viral diversity is of such magnitude, that in order to obtain tractable results, a study needs to focus on a well-defined taxonomic scope, such as a given viral family. Algal dsDNA viruses, named Phycodnaviridae, are good candidates for such studies since genomic data and preliminary studies on their diversity are available. Moreover, they exert a significant role in the regulation of primary producers. Within Phycodnaviruses, prasinoviruses are viruses of prasinophytes, an important component of photosynthetic picoplankton in oceans, which dominate picoeukaryotic biomass in several oceanic areas. This algae-virus system has the advantage of including hosts and viruses for which genomic data are available (6 host genomes and 7 viral genomes are currently published), especially in the Gulf of Lion (Northwestern Mediterranean Sea). The Gulf of Lion is characterised by contrasted environments, including eutrophic lagoons connected to the sea, nutrient-rich coastal sites, and oligotrophic open-sea locations allowing the influence of environmental factors on viral diversity to be assessed. Prasinophytes in the Gulf of Lion are mainly composed of three genera, Ostreococcus, Micromonas, and Bathycoccus, and at least one complete genome is available for each genus. Thus, this host-virus system, now comprising several relatively well-characterised host and viral strains, possesses sufficient genomic data to define appropriate tools for the molecular characterisation of viral diversity. Understanding the environmental controls of prasinovirus diversity is the main objective of the DECOVIR project. We will define molecular markers that, along with next generation sequencing (NGS) techniques, will allow the estimation of the level of viral diversity at chosen locations in the Gulf of Lion. This diversity will be monitored through time via gene-targeted environmental sequencing at several contrasted locations (a lagoon, a coastal site, and an open-ocean oligotrophic site), in which many environmental descriptors will be also recorded. Real time quantitative PCR (qPCR) will be used to estimate and to monitor the abundance of key viral and host strains at each sampling stations. This will allow viral diversity and abundance to be related to environmental descriptors using multivariate statistical analyses, and permit a better understanding of the factors controlling the prasinovirus community. Host genetic diversity will be recorded at the same time via gene-targeted environmental sequencing and qPCR, and included in the model. This project will combine recent genomic data with NGS techniques to obtain a precise picture of the actual diversity of a defined virus group, its evolution through time and host interactions, and its relationships with environmental factors.
France