Diversity and Environmental Control of Prasinoviruses – DECOVIR

Several complete genomes of viruses of prasinophytes (i.e. prasinoviruses) and their algal hosts are available, allowing to design molecular tools. These tools, along with high throughput sequencing, will be used to quantify and monitor virus and host populations in contrasted environments. We expect a high viral diversity, that will be linked to environmental variables using numerical models, to predict the characteristics of virus populations from environmental descriptors.

We designed isolation techniques for viruses and their hosts, and molecular tools to monitor them in the environment. Some sampling have been carried out, and the first samples will soon be sent for sequencing. We built a sequence database to be used as reference to characterise the data we will produce. We are also isolating and characterising a new viral strain, from a new host species (not planned), that will complete this database, in addition as gaining knowledge on this new virus.

We should receive soon our first sequences, and then validate our technical approaches and start regular sampling throughout a year. We expect to have the first results on viral diversity in a few months, and the first insights on its link with environmental variables. Quantification will follow the assessment of diversity. To date, the project is carried out according to the schedule, and in addition we characterised a new virus, from a new algal host.

No publication is directly issued from this project, after only 6 months, but a recent review by our team exposes the state of the art on genomics of algal-virus associations, at the heart of the DECOVIR and allowing the design of molecular tools to monitor viral diversity: Grimsley Nigel H., Rozenn Thomas, Jessica U. Kegel, Stéphan Jacquet, Hervé Moreau & Yves Desdevises. 2012. Genomics of Algal Host-Virus Interactions. Advances in Botanical Research 64: 343-381.

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.