A unique hydrogenase operon observed in the thioautotrophic symbiont of Bathymodiolus mussel in the East Pacific Rise

The mytilid mussel <em>Bathymodiolus thermophilus</em> lives in the deep-sea hydrothermal vent regions due to its symbiotic relationship with chemosynthetic Gammaproteobacteria. It is well established that symbionts in this mussel gill bacteriocytes utilize the vent environment’s hydrogen sulfide, methane, and hydrogen gases. However, some symbiont genomes of mussels either possess or lack genes for hydrogen metabolism within the single-ribotype population and host mussel species level. Here, we observed a unique hydrogenase operon consisting of additional H2-sensing hydrogenase subunits from a complete genome of <em>B. thermophilus</em> symbiont sampled from an individual mussel from the East Pacific Rise (EPR9N). Also, we found methylated regions sparsely distributed throughout the EPR9N genome, mainly in the transposases regions and densely present in the rRNA gene regions. CRISPR diversity analysis confirmed this genome originated from a single symbiont strain. Variation in genome size, gene content, and genome re-arrangements across individual hosts suggest multiple symbiont strains can associate with <em>B. thermophilus</em>. Furthermore, the unique genomic features of the EPR9N symbiont indicate that the acquisition of such a locally adapted symbiotic strain may be an effective mechanism for successfully colonizing diverse chemosynthetic environments across the global oceans by host mussels.