UC San Diego

Hadal trenches, oceanic locations deeper than 6,000 m, are one of the most enigmatic environments on Earth. Characterized by hydrostatic pressures reaching 16,000 pounds per square inch, these sites are expected to contain microbial diversity adapted to in situ conditions and distinct from that found at shallower depths. In this dissertation, we describe the composition and functional potential of microbial communities in the Mariana and Kermadec trenches, two hadal sites in the Pacific Ocean, using high-throughput 16S rRNA gene sequencing, meta- and single-cell genomics, and culture-based analyses. We show that hadopelagic microbial communities, which are distinct from those at abyssal depths, appear adapted to in situ hydrostatic pressure conditions and contain a number of putative hadal bathytypes, including members related to the Marinimicrobia, Rhodobacteraceae, Rhodospirilliceae, and Aquibacter. Hadal sediment consortia contained many novel microbial lineages not previously identified in other datasets, especially within deeper sediment horizons. We characterized the functional potential of these sediment microbes using metagenomics and single-cell sequencing and showed that members of these communities have pathways for diverse carbon utilization and nitrogen and sulfur cycling. Mariana and Kermadec trench pelagic and sediment communities were distinct between one another, in part because of higher primary productivity in the overlying water column in the Kermadec relative to the Mariana Trench. Although trenches are geographically isolated, many abundant lineages in both the pelagic and sediment habitats were related to those found in other hadal and abyssal datasets. Comparisons of genomes from both trenches indicate some members may belong to the same species. These findings show the possibility for dispersal of microbes in the deep-ocean and the connectivity of trenches with each other and shallower sites. Finally, we look to the future of hadal exploration by describing the development of a new full-ocean depth lander and water sampler capable of maintaining high hydrostatic pressure upon recovery. Deployments in the Mariana Trench at depths exceeding 10,700 m and the collection of genomes from the hadal lineages Aquibacter and Marinimicrobia show the power of this instrumentation. This dissertation provides a deep dive into microbial community composition and functional potential within hadal trenches.