Molecular and genomic approaches that target mixed microbial communities (e.g., metagenomics or metatranscriptomics) provide insight into the ecological roles, evolutionary histories, and physiological capabilities of the microorganisms and the processes in the environment. Computational tools that harness large-scale sequence surveys have become a valuable resource for characterizing the genetic make-up of the bacterial and archaeal component of the marine microbiome. Yet, fewer studies have focused on the unicellular eukaryotic fraction of the community. Here, we developed the EukHeist automated computational pipeline, to retrieve eukaryotic and prokaryotic metagenome assembled genomes (MAGs). We applied EukHeist to the eukaryote-dominated large-size fraction data (0.8-2000 μm) from the Tara Oceans survey to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of more than 900 eukaryotic MAGs representing environmentally-relevant microbial and multicellular eukaryotes in addition to over 4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs retrieved with EukHeist complement previous efforts by expanding the existing phylogenetic diversity through the increase in coverage of many likely particle- and host-associated taxa. We also demonstrate how the novel eukaryotic genomic content recovered from this study might be used to infer functional traits, such as trophic mode. By coupling MAGs and metatranscriptomic data, we explored ecologically-significant protistan groups, such as the Stramenopiles. A global survey of both eukaryotic and prokaryotic MAGs enabled the identification of ecological cohorts, driven by specific environmental factors, and putative host-microbe associations. Accessible and scalable computational tools, such as EukHeist, are likely to accelerate the identification of meaningful genetic signatures from large datasets, ultimately expanding the eukaryotic tree of life.
Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species
