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

Abstract

Deep sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. Ten microbes, including eight bacteria and two archaea, were identified as key contributors. These microorganisms uniquely enhanced the metabolic capabilities of the community by donating metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly from accepting metabolites from other members of the microbiome. Amino acids were the key auxotrophy driving metabolic interactions in the community. Finally, over 200 horizontal gene transfer events were predicted in the community, the majority of which were between Gammaproteobacteria and Alphaproteobacteria. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plumes and deep sea microbiomes.

Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology

“…While this exception may be influenced by the smaller filter size used to sample marine viromes compared to those used to generate the other datasets used here, the environments from which marine samples were collected are perhaps the most distinguished out of the others owing to their origin from hydrothermal vent plumes in the deep sea. These environments have been shown to be composed of ultra-small microbes that can have cell sizes <0.22 μm [69,70,76–78], requiring modified virome extraction methods, just as the other environmental sources here require in other respects [64,65].…”

“…It is possible that the lack of differences observed in marine samples was due to a drastic reduction in cellular community members of Guaymas metagenomes. However, the relatively unique environments from which the marine samples came have shown to be enriched in ultra-small microbes and to have communities quite distinct from other marine environments [69,70], so the reasoning behind the reduced filter sizes is justified. Although there were no differences in the total number of viral contigs, vMAGs, and species richness between marine viromes and metagenomes here, we reiterate that there was a significant difference in viral read and contig enrichment in the marine viromes and metagenomes (Figure 2C-D).…”

Genomic, Functional, and Metabolic Enhancements in Multidrug-ResistantEnterobacter bugandensisFacilitating its Persistence and Succession in the International Space Station

“…This metabolite set combines the minimal medium of each metabolic model with essential cofactors and coenzymes, as reported previously [13]. To determine the minimal media for microbial communities, we employed MetQuest v.2.0, which ensures the necessary components for a minimum growth rate of 0.1 h − 1 of all members in the community [64].…”