UC San Diego

The indigenous microbial members of deep oceanic environments mediate carbon fluxes in this realm and contribute to major biogeochemical cycles globally, yet their distribution, phylogenetic composition, and functional attributes are not yet well understood. Emerging concepts suggest the prevailing ecological processes and evolutionary constraints acting on these assemblages are more dynamic and heterogeneous than previously thought. In this context, the research presented herein examines the composition and genomic repertoires of bacteria, archaea, and eukarya from an extreme deep ocean environment, 6,000 m depth within the Puerto Rico Trench. The results identify depth-specific taxonomic and functional trends, as well as expanded gene inventories indicative of unique lifestyle strategies divergent from their photic-zone counterparts. The findings indicate significantly different bacterial communities in particle-associated and free-living fractions at depth, which has implication for future sampling practices and diversity estimates from deep ocean habitats. The disparity between the number of cultivated piezophilic ('high-pressure adapted') isolates and the expansive diversity identified using molecular techniques has limited further exploration of the physiological and biochemical properties of diverse piezophiles. This issue has been addressed through the application of dilution to extinction cultivation techniques at high-hydrostatic pressure and low temperature using a natural seawater medium. This work has led to the isolation and subsequent characterization of a unique piezophilic member of the Roseobacter lineage within the Alphaproteobacteria. The results provide further evidence for the temperature- pressure dependence of the growth rate for deep-ocean bacteria and substantiate hypotheses regarding piezophilic traits under nutritionally limiting conditions. This research concludes with the detailed genetic characterization of the unique flagellar motility system of the model piezophilic bacterium Photobacterium profundum SS9. It is the first investigation of motility as a function of high hydrostatic pressure in a deep-sea microbial species and highlights the profound value of genetically tractable systems to test hypotheses regarding high-pressure adaptation