Gill chamber R. exoculata metagenome
Metagenomics of the gill chamber epibiosis of deep-sea shrimp Rimicaris                 exoculata and discovery of zetaproteobacterial epibionts
The shrimp Rimicaris exoculata flourishes on deep-sea hydrothermal                 chimneys along the Mid-Atlantic Ridge (MAR). This species harbors dense community of                 chemoautotrophic epibiotic bacteria associated with mineral oxide deposits in its                 enlarged gill chamber. We used metagenomics on specimens from the Rainbow                 hydrothermal vent site, to investigate the metabolism of the two main                 sulfur-oxidizing epibionts affiliated to the Epsilonproteobacteria and                 Gammaproteobacteria. Both epibionts had genes of the Sox pathway for sulfur                 oxidation and hydrogenases. In the epsilonproteobacterial epibiont, two distinct                 denitrification systems (Nas/Nir and Nap/Nrf) as well as a complete rTCA cycle for                 carbon dioxide fixation were found, while the gammaproteobacterial epibiont was                 found to fix carbon dioxide via the CBB cycle with RuBisCo form II. The shrimp gill                 chamber metagenome provided information on host-epibiont interactions, like on                 virulence gene homologues and genes for surface attachment. Likewise, genes were                 found that might play a role in host nutritional and detoxification processes, and                 thus are of major importance for the survival of the shrimp and its adaptation to                 the hydrothermal vent environment. Interestingly, analysis of the metagenome                 revealed sequences affiliated to the iron-oxidizing class Zetaproteobacteria, which                 would explain gill chamber iron oxyhydroxide deposits. Presence of                 Zetaproteobacteria was confirmed by fluorescence in situ hybridizations and thereby                 provided first evidence for a Zetaproteobacteria-invertebrate                 association.