Global metagenomics reveals a widespread fungal component of the deep-ocean microbiome

Abstract

The deep ocean is the largest habitat on Earth but our knowledge about its microbiome, microeukaryotes in particular, is limited. Here we investigate a deep-sea fungal Metagenome-Assembled Genome (MAG) with a widespread distribution and a relatively high abundance in specific locations. A total of 83 globally distributed metagenomes recovered from 1,500m to 4,000m depth, which were part of the Malaspina 2010 expedition, were co-assembled and binned using different algorithms. We retrieved 15.61Mb of a putative yeast, phylogenetically related to Tilletiopsis spp., featuring ca. 80% of genome recovery. Gene prediction based on conserved orthologs indicated 4,370 genes, which were annotated using a number of databases. In particular, a total of 2,846 genes were annotated using KEGG, with most matching orthologs originating from other fungi (Pseudozyma flocculosa [47.4%], Ustilago maydis [37.5%] and Malassezia globosa [3%]). Functions related to membrane transporters, endocytosis and potential pathogenicity as well as lysosome-like proteins are currently being analysed to understand the ecology of this uncharacterized fungi. Analyses of 18S rDNA and rRNA amplicons from 13 globally-distributed vertical profiles pointed to geographically heterogeneous abundances that tended to increase with depth. In particular, MAG rRNA detection in the deep ocean points to an active metabolism. Analyses of SNPs and indels indicate fine¿grained genomic change that could reveal ecotypic variation. Overall, our results provide insight on the functional role of fungi in the deep ocean