Tara Oceans' approach and new challenges in studying the ocean microbiome at global scale

Drawing an ecosystem-wide picture of community structure, functional diversity and ecological drivers of the ocean microbiome has been a grand challenge. This has been primarily due to the lack of a systematically collected set of samples with associated environmental information at global scale. To address this limitation, Tara Oceans has so far collected more than 35,000 samples for genomic, morphological and environmental analyses from all major oceanic regions. Using an eco-systems biology approach, we analyzed 7.2 terabases of metagenomic data from 243 water samples that were collected at multiple depths to determine the main stratifying factors and environmental drivers of ocean microbial community structure and function. To this end, we constructed and annotated an ocean microbial reference gene catalog with >40 million non-redundant, mostly novel sequences from viruses, prokaryotes and picoeukaryotes. A focus on 139 prokaryote-enriched samples revealed microbiota to be primarily stratified into epipelagic and mesopelagic communities. For epipelagic communities, we disentangled co-correlations of environmental parameters and identified microbial communities composition to be mainly driven by temperature rather than geography. To resolve this overall pattern from community to species-level, we reconstructed clusters of core genes of dominant ocean microbial species and investigate their biogeography based on metagenomic profiling of single nucleotide polymorphisms. The integration of metatranscriptomic data is adding an additional layer of information to study their activity as a function of physicochemical differences of their environment.