Protists, or eukaryotic microbes, are key players in marine ecosystems, encompassing primary producers (phytoplankton), mixotrophs, and heterotrophs. Similar to their prokaryotic microbial counterparts (bacteria and archaea), many protists cannot be cultured, making the direct study of their biology in the lab challenging. Molecular and genomic approaches, particularly those applied to whole, mixed communities (e.g. metagenomics), have shed light on the ecological roles, evolutionary histories, and physiological capabilities of these organisms. Metagenomic analyses have traditionally focused on the analysis of species and gene content and shifts in relative abundance between samples. Recently, new computational approaches have been developed to facilitate the retrieval of nearly complete prokaryotic genomes from metagenomes, a process referred to as ‘binning’ that generates Metagenome Assembled Genomes (MAGs). Genome binning approaches have yet to be applied to metagenomic data to specifically isolate eukaryotic MAGs.
This year the metagenomic data corresponding to protist size fractions (0.8 m - 2000 m) from Tara Oceans were published, spanning the world’s oceans. These data represent the largest metagenomic sequencing initiative focused on protists and provide the unique opportunity to retool existing prokaryotic binning approaches to construct new eukaryotic genomes. We are working to capitalize on the release of these data and the high-memory computational power available at WHOI to (1) establish a eukaryotic MAG pipeline for the assembly and binning of eukaryotic genomes from marine metagenomes, (2) test the efficacy this pipeline with a series of mock community metagenomes, and (3) apply the eukaryotic MAG pipeline to extract eukaryotic genomes out of the Tara Oceans metagenomes. This work will establish new computational approaches for the analysis of eukaryotic metagenomes that will be broadly applicable to all metagenomic samples.