AtlantECO deliverable D5.2 Report on the All-Atlantic interactome

The main goals of WP5 for Advances in Systems Ecology are to develop cutting-edge network analysis methods, to define an all-Atlantic interactome and ecological niches, and to provide indicators of ecosystem stability and sensitivity to environmental stressors and drivers. The main goal of D5.2, associated with Task 5.2, was to deliver a report on the all-Atlantic interactome by constructing cross-kingdom interaction networks for marine microbiome and plastisphere communities. In this task, we examined the (functional) community organisation of microbiomes and the plastisphere at the scale of the global ocean, using metabarcodes, metagenomes, and metatranscriptomes, and specific traits such as genome size and metabolic potential. In particular, we resolved the global-ocean cross-kingdom interactome of viruses, prokaryotes, and eukaryotes, that is, the viral-host interactome, a crucial regulator of carbon fluxes and plankton community dynamics. We also investigated the diversity and community structure in the North Pacific gyre and the Mediterranean Sea to reveal a niche partitioning of plastics-associated microbial communities. In addition, we leveraged metagenomes and metatranscriptomes into a computational workflow to reconstruct the community metabolic landscape and phenotypes of global ocean microbiomes and demonstrate how they can be used to estimate ecosystem-scale marine biogeochemistry. Finally, we also developed a computational framework, integrating metagenomic and metatranscriptomic information at the genome-scale through ecological and metabolic modelling to improve our functional and mechanistic understanding of microbial interactions driving ecosystem functions in situ.