Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

TL;DR

This study shows that bacteria in the ocean transfer genes more often when they co-occur, even after accounting for their evolutionary relatedness and environment.

Contribution

The study demonstrates that co-occurrence significantly influences horizontal gene transfer in marine bacteria, independent of phylogeny and environmental factors.

Findings

Co-occurrence is significantly associated with horizontal gene transfer in marine bacteria.

The association between co-occurrence and HGT remains after controlling for phylogenetic distance and environmental variables.

Particle-attached prokaryotes show higher HGT levels and environmental variables like chlorophyll a influence HGT patterns.

Abstract

Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring taxa have long been appreciated to undergo HGT more often, this association is confounded with other factors, most notably their phylogenetic relatedness. To disentangle these factors, we analyzed 15 339 marine prokaryotic genomes (mainly bacteria) and their distribution in the global ocean. We identified HGT events across these genomes and enrichments for functions previously shown to be prone to HGT. By mapping metagenomic reads from 1862 ocean samples to these genomes, we also identified co-occurrence patterns and environmental associations. Although we observed an expected negative association between HGT rates and phylogenetic distance, we only detected an association between co-occurrence and phylogenetic distance for closely related taxa. This observation refines the previously reported trend to closely related taxa, rather than a consistent pattern across all taxonomic levels, at least here within marine environments. In addition, we identified a significant association between co-occurrence and HGT, which remains even after controlling for phylogenetic distance and measured environmental variables. In a subset of samples with extended environmental data, we identified higher HGT levels associated with particle-attached prokaryotes and associations of varying directions with specific environmental variables, such as chlorophyll a and photosynthetically available radiation. Overall, our findings demonstrate the significant influence of ecological associations in shaping marine prokaryotic evolution through HGT.

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