Uncovering Genomic Properties of Microbial Life in the Deepest Portions of the Atlantic and Pacific Oceans One Cell at a Time

This dissertation presents the analyses of twenty-eight single amplified genomes (SAGs) distributed among four major phyla or candidate phyla of archaea and bacteria : Thaumarchaeota, Proteobacteria, Parcubacteria and Marinimicrobia. Samples were obtained from 8,219 m and 10, 908 m depth within the hadal ecosystems of the Puerto Rico Trench (PRT) and Challenger Deep (CHDE) portion of the Mariana Trench, respectively, and microbes associated with seawater, invertebrates and surficial sediments were sorted, amplified by multiple displacement amplification and sequenced using the HiSeq 2000 Illumina platform. Assembled and annotated genomes were analyzed and compared to genomes derived from closely related microbes from other habitats with the goal of understanding PRT and CHDE microbes' metabolic adaptations to deep-sea conditions. Four single amplified genomes (SAGs) were recovered from the PRT: PRT Nitrosopumilus, PRT SAR11, PRT Marinosulfonomonas, and PRT Psychromonas. These microbes are all members of deep-sea phylogenetic clades. The PRT Nitrosopumilus, possesses genes associated with mixotrophy, including those associated with lipoylation and the glycine cleavage pathway, and remarkably, may possess the ability to produce fatty acids and lipids. PRT SAR11 encodes for glycolytic enzymes previously reported to be missing in this highly abundant and cosmopolitan group. The PRT Marinosulfonomonas and PRT Psychromonas SAGs possess genes that may supplement their energy demands through nitrous oxide and hydrogen oxidation. From the CHDE, 13 SAGs were analyzed that belong to the candidate phylum Parcubacteria (OD1), a group of uncultivated microbes characterized by reduced genomes with limited metabolic potential. Comparative genomics was used to examine the metabolic potential harbored by Parcubacteria SAGs (OD1-DSC). Horizontally transferred genes were abundant in the Parcubacteria genomes especially for genes laterally transferred from members of the archaea. Results indicated that some OD1 cells are capable of much greater metabolic versatility and genetic exchange than previously ascribed to this candidate phylum. The other candidate phylum analyzed as part of this dissertation is the Marinimicrobia (Marine Group A, SAR406), which has been suggested to be an abundant contributor in deep ocean microbial communities, but information about their metabolism andphysiology remains minimal. Six Marinimicrobia SAGs were recovered and their phylogenetic and metabolic characteristics were explored. Results revealed two distinct Marinimicrobia clades not associated with previously described Marinimicrobia phylogenetic groups, but mostly associated with sequences obtain from deep-sea environments, particularly sediments. Bioinformatic analyses indicated that Marinimicrobia SAGs take advantage of carbon monoxide and reduced sulfur compounds to supplement their energy requirements. Osmotic and oxidative stress regulation were also found to be over abundant in the hadal Marinimicrobia. Taking all of these genome studies into consideration it is hypothesized that diversified carbon and energy acquisition pathways are a hallmark of many hadal microbes, along with enhanced osmotic pressure adaptation, perhaps as a means to counteract extreme hydrostatic pressure. In all cases this research has expanded the currently available knowledge of the phylogenetic placement and metabolic potential of the microbial groups studie