What can metagenomes tell us about deep-sea protists? A global perspective

Abstract

The deep ocean is the largest habitat on Earth and its microbiome is essential for oceanic ecosystem functioning, particularly for organic matter remineralization. Yet, our knowledge on deep-sea microbes, in particular protists, is clearly limited. Here, we investigate 58 Illumina-sequenced metagenomes from 4,000m depth originating from 32 sampling stations distributed across the global ocean that were part of the Malaspina 2010 expedition. In analyses of 18S rDNA sequences extracted from metagenomes, Rhizaria, Alveolata, Fungi, Stramenopiles and Excavata emerged as predominant lineages. In all these groups except Alveolates we found dominance of a few Operational Taxonomic Units (OTUs). Community analyses indicated that large extensions of the deep ocean are populated by comparable protistan assemblages, which allowed recovering long contigs in global metagenome assemblies. In particular, we identified 2.6Mbp of fungal contigs (>50Kbp) likely originating from a single OTU that seems relatively abundant and widely distributed in the South Pacific and Indian oceans. Further analysis of rD/RNA amplicons and functional annotation of these contigs support the observed community structuring patterns and suggest, for the analyzed fungus, low metabolic activity and pathogenicity