UC San Diego

Though the extreme conditions of the deep sea cover the majority of the Earth's biosphere, the adaptations of organisms that grow there remain a mystery. Of particular interest is adaptation to high pressure, which acts as a unique stress on many physiological processes. The use of genomics has been vital to the study of piezophilic microbes, providing detailed information where traditional lab studies are impractical. This thesis describes genome assemblies and analyses related to deep sea microbiology. The genome assembly of Carnobacterium sp. strain AT7 is the first sequencing project of a gram positive piezophile. The genome consists of a single circular chromosome and two plasmids, including genes thought to be involved in heavy metal, phage, and antimicrobial resistance. Psychromonas sp. strain CNPT3 was the first isolated piezophile and the finishing and annotation of its genome serves as a foundation for the study of deep sea adaptation. The manual annotation of the shallow water strain, Photobacterium profundum strain 3TCK, is presented and is used as a piezosensitive comparison to the piezophile model organism Photobacterium profundum strain SS9. The comparison shows that the deep sea strain has more genes dedicated to metabolism, cellular processes and mobile elements. Protein adaptation to pressure was explored by examining amino acid usage of piezophilic and piezotolerant strains in proteins of pressure-sensitive processes. The primary structures revealed no universal trends in protein adaptation. This thesis provides a foundation for future comparative analyses, necessary to the understanding of deep sea adaptation