CE02 - Terre vivante

Phytoplankton-virus interactions: from ‘multi-omic’ determinants of antiviral resistance to ecological and evolutionary dynamics – PHYTOMICS

Submission summary

Half the Earth’s photosynthetic activity is mediated by oceanic phytoplankton that is regulated by a large diversity of viruses. Among them, large algae-infecting double-stranded DNA viruses, or phycoDNAviruses, are ubiquitous and key regulators of Mamiellophyceae, i.e. unicellular eukaryotes constituting the dominant green algae in most coastal waters. Their interaction is so tight that Mamiellophyceae-infecting prasinoviruses have been shown to be associated with carbon export at a pan-oceanic scale. Strikingly, the effects of antiviral resistance on phytoplankton-virus interactions remain consistently under-investigated and they are not accounted for in the models attempting to predict marine photosynthetic activity and carbon/nutrient cycling.

The PHYTOMICS project aims at resolving the ‘multi-omic’ bases of such resistance and predicting its ecological and evolutionary implications on phytoplanction-virus interactions. Our working hypothesis is that the effects of antiviral resistance on the short- and long-term phytoplankton-virus interactions indeed depend on its molecular determinants. To this end, we propose an original integrative approach relying on several -omic and modelling tasks. We focus on the Ostreococcus-prasinovirus system, on which all PHYTOMICS partners are working, and that comprises i) cosmopolitan Mamiellophyceae, for which complete reference genomes are available, and ii) well-studied phycoDNAviruses.

We will first build an unprecedented genomic and phenotypic dataset by seeking to obtain high quality annotated genomes for 50 hosts and 50 virus strains. Those, combined with already available genomic resources, will provide a set of 80 hosts and 50 viruses genomes and we will determine the outcome of cross-infections experiments between all of them (Task 1). We will then aim to identify the genomic bases of host-virus compatibility by a joint genome-association study using all those host and viral populations (Task 2). Along with the identification of these long-term signatures of their interactions, we will investigate the multi-omic determinants and dynamics of phenotypic switches, i.e. rapid gain and loss of antiviral resistance observed upon infection and once the virus is removed from a culture. We will focus on two highly genetically divergent Ostreococcus species and seek to identify the common and species-specific molecular bases of such changes. A pioneering experimental evolution study will allow concomitant tracking of the genomic, transcriptional and translational changes, as well as the host-virus population dynamics, during i) the infection of susceptible algae lines and ii) the removal of viruses from resistant cultures (Task 3). The metabolomic profiling of resistant and susceptible algae will then allow identification of key metabolites for resistance to viral infection that will be linked to gene expression patterns to decipher the gene network involved in metabolite production (Task 4). Finally, we aim at integrating the knowledge gained about the Ostreococcus-prasinovirus system into epidemiological models to further understand the impact of antiviral resistance on the ecology and evolution of phytoplankton-virus interactions. We will combine phenotypic and ‘multi-omic’ modelling to perform in silico experiments and assess the antiviral resistance effects on host-virus population dynamics and its (resulting) adaptive evolution according to the underlying molecular mechanisms at work.

Overall, PHYTOMICS will provide an unrivalled molecular knowledge of these host-virus interactions and conceptual advances on integrative approaches required to link such molecular mechanisms to the eco-evolutionary dynamics of natural populations. This interdisciplinary expertise, increasingly critical to assist public policies, will undoubtedly strenghten our ability to predict the impact of (antiviral resistance of) marine viruses and their regulatory role of global biogeochemical cycles.

Project coordination

Sebastien Gourbiere (Laboratoire Génome et développement des plantes)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

LGDP Laboratoire Génome et développement des plantes
LBBM Laboratoire de Biodiversité et Biotechnologies Microbiennes
BIOM Biologie intégrative des organismes marins

Help of the ANR 597,269 euros
Beginning and duration of the scientific project: January 2022 - 48 Months

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