Ecogenomics of small Phytoplankton & large Virus Interactions in response to changing salinity and phosphate concentrations – ELVIRA

Despite their major ecological role at the base of the food chain in oceanic ecosystems, the variation in phytoplankton-virus interactions as a function of abiotic factors is under studied. Indeed, efforts have focused on estimating the extraordinary interspecific diversity of these communities populating the surface of our oceans. While previous studies on phytoplankton x virus x environment interactions have analysed the effects of temperature, a key factor of climate change, there is a lack of knowledge about the effect of other abiotic factors, also impacted by global change, such as variations in nutrients and salinity.
The objective of the ELVIRA project is to understand how these abiotic factors influence the phytoplankton-virus interaction quantitatively and qualitatively. This is in order to (1) characterize the phenotypic evolution, (2) identify the genomic and transcriptomic bases of these phenotypic changes and (3) establish a predictive model of the dynamics of the phytoplankton-virus system.
We propose to deploy an interdisciplinary approach combining population genomics, high-throughput experimental phenotyping and modeling on an ecologically relevant phytoplankton-virus system with a worldwide distribution.
In order to meet the ambitious objective of integrating the genome x phenotype x environment levels, ELVIRA brings together an international consortium composed of two French teams and a German team with complementary skills in population genomics, phytoplankton eco-physiology and theoretical biology. The ideal location of the partners in the immediate vicinity of the North, the Baltic and the Mediterranean Seas allows us to take advantage of the natural spatial variation in salinity and phosphate concentration between these sites. This lets us test whether the geographical origin impacts the genomic and phenotypic variation of microalgae isolated from these different environments, including their susceptibility to different viruses from these same sites.
The project’s deliverables arise from four tasks carried out in close collaboration between the 3 teams. First, a sampling effort in the North, Baltic and Mediterranean Seas will increase the number of microalgae in the collection previously established by the consortium. This biological resource is the basis of the ELVIRA's genomic resource consisting of transcriptomes and genomes by long and short read technologies for the whole collection. Task 2 will be devoted to high-throughput phenotyping of this collection, with an exceptional exploration of the space of phytoplankton x virus x environment interactions for different conditions of salinity and phosphate concentrations. Task 3 will allow the characterization of the phenotype x genotype linkage through association analyses (GWAS) between the genomic and phenotypic resources obtained. We will first associate nucleotide variants with variations in gene expression between strains (eQTL). Then, we will associate genomic variants (nucleotide and structural) with phenotypes, with particular attention to cases of changes in phytoplankton-virus susceptibility as a function of abiotic variables. Finally, Task 4 will be devoted to the integration of the obtained phenotype x environment space into a multi-host multi-virus epidemiological model in order to predict population dynamics under current and future conditions of salinity and phosphate concentration.
We believe the expected results from the analysis of these genome x phenotype x environment interactions in an original biological system will have implications for integrative biology of host-parasite interactions, population and evolutionary genomics, microbiology and integrative molecular-to-ecosystem approaches.