Adaptations of Atribacteria to life in methane hydrates: hot traits for cold life

Gas hydrates harbor gigatons of natural gas, yet their microbiomes remain mysterious. We bioprospected methane hydrate-bearing sediments from under Hydrate Ridge (offshore Oregon, USA, ODP Site 1244) using 16S rRNA gene amplicon, metagenomic, and metaproteomic analysis. Atribacteria (JS-1 Genus 1) sequences rose in abundance with increasing sediment depth. We characterized the most complete JS-1 Genus 1 metagenome-assembled genomic bin (B2) from the deepest sample, 69 meters below the seafloor (E10-H5), within the gas hydrate stability zone. B2 harbors functions not previously reported for Atribacteria, including a primitive respiratory complex and myriad capabilities to survive extreme conditions (e.g. high salt brines, high pressure, and cold temperatures). Several Atribacteria traits, such as a hydrogenase-Na+/H+ antiporter supercomplex (Hun) and di-myo-inositol-phosphate (DIP) synthesis, were similar to those from hyperthermophilic archaea. Expressed Atribacteria proteins were involved in transport of branched chain amino acids and carboxylic acids. Transporter genes were downstream from a novel helix-turn-helix transcriptional regulator, AtiR, which was not present in Atribacteria from other sites. Overall, Atribacteria appear to be endowed with unique strategies that may contribute to its dominance in methane-hydrate bearing sediments. Active microbial transport of amino and carboxylic acids in the gas hydrate stability zone may influence gas hydrate stability.