Résumé
Life around deep hydrothermal vents is based on chemosynthetic primary production, and symbiotic associations with chemosynthetic bacteria are widespread in the deep-sea . The shrimp Rimicaris exoculata dominates the fauna of hydrothermal sites along the Mid Atlantic ridge. The species harbors a complex bacterial community including Epsilon-, Gamma- and some recently discovered Zetaproteobacteria within its gill chamber, as well as long microbial filaments within the digestive tract. While in vivo experiments provide evidence for direct nutritional transfers from bacteria to the host across the gill chamber and therefore show a true mutualistic association, in silico analyses suggest four metabolic pathways (iron, sulfide, methane and hydrogen oxidation) may co-occur within this community. Here, we build on these previous studies and use shotgun metagenomics to reconstruct novel Rimicaris exoculata symbiotic genomes, and unravel their metabolic potential. By comparing four metagenomes originating from the contrasted ultramafic Rainbow and the mafic TAG sites along the Mid Atlantic Ridge, we could detect and recover seven abundant and site-specific draft genomes. Bacterial single-copy genes predict a relatively complex environment, with the presence of 48 bacterial genomes above our detection limit in the raw metagenomic assembly. The characterization of these vital, energy-harvesting symbionts, will likely provide new and important insights into the fundamental ecological and evolutionary mechanisms underlying the intimate host-microbe associations and geobiological interactions in extreme environments.