Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits

Abstract

Background: When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal vent deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018, and document their potential implications in biogeochemical cycles. Results: Our dataset represents 3,635 metagenome-assembled genomes encompassing 511 novel genera, with 395 Bacteria and 116 Archaea, providing many targets for cultivation of novel archaeal and bacterial families. Notably, 52% (206) of the novel bacterial genera and 72% (84) of the novel archaeal genera were found at the deep-sea Brothers volcano, many of which were endemic to the volcano. We report some of the first examples of medium to high-quality MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur and hydrogen metabolic processes across all sites, and illustrates sulfur and nitrogen metabolic "handoffs" in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment. Conclusion: Our study of globally-distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa.

Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes

“…The extensive occurrence of metabolic handoffs in hydrothermal plume communities provides functional interdependency between microbes, leading to auxotrophies. Thus, the community achieves efficient energy and substrate transformations 62 .…”