If life evolved in the oceans and marine environments offered a haven for rapid adaptation during biotic crises, then similar reservoirs should exist today where genomic diversification allows population survival during environmental disturbances. Seafloor methane seep ecosystems might represent key sources for both ancient and modern biological diversification. The potential transfer of energy and genetic information among seep microbiota remains understudied and is the focus of this dissertation.

Seep organisms that obtain energy via hydrocarbon oxidation establish a diverse benthic community where microbial assemblages exhibit myriad trophic interactions. At a shallow hydrocarbon seep, offshore Goleta, CA, benthic microbial mats grow in close proximity to actively venting gas. Bacterial methanotrophs and secondary consumers of methane-derived carbon were identified in the microbial mats using a combination of genetic assays and stable isotope tracking under both natural and enrichment conditions. Direct methane consumption was linked to the family Methylococcaceae, while secondary consumers and chemoautotrophic bacteria were inferred by taxonomic affiliations.

Chemosynthetic microbial communities form the foundation for deep methane seep ecosystems in the Santa Monica Basin, offshore Los Angeles, CA. Here, diverse viral lifestyles from seafloor and pelagic environments were examined through a metagenomic lens. A bacteriophage genome from seep sediments was found to encode a mechanism for self-directed protein evolution, known as a diversity generating retroelement. Similar retroelement patterns of targeted mutagenesis were identified in public sequences from a coastal methane seep, offshore Norway and from an estuarine environment at the Galapagos Islands.

Viral genomes were examined from seawater near a Santa Monica Basin cold seep. Pelagic viral genomes (ssDNA) were differentiated from assembled metagenomic sequences, including bacteriophage and eukaryotic viruses. This mesopelagic virome offers insights about the simplest of encapsulated genomes that have been previously described.