Stanford University

*** Ph.D. Thesis/ Oral Defense ***

Amanda Semler

Wednesday, April 10th, 2:00pm

Green Earth Science 365 

Department of Earth System Science

Advisor: Dr. Anne Dekas

Marine hydrocarbon seeps, also known as cold seeps, are widespread features of continental margins and sedimentary basins worldwide and are hotspots of microbial activity on the seafloor. At cold seeps, hydrocarbons are released from underlying sediments in large quantities, and due to the nature of the predominant carbon source (and its high carbon to nitrogen ratio), seeps harbor distinct microbial community members capable of oxidizing hydrocarbons and of fixing nitrogen. Despite many recent investigations surrounding one core seep metabolism – the anaerobic oxidation of methane – little is known about the wealth of other metabolic strategies at seeps, nor about the biogeochemical controls on microbial community composition and assembly.

In this dissertation, I analyze molecular and geochemical data from >100 samples across six discrete cold seep sites in the Atlantic and Pacific Oceans. I leverage recent improvements in sequencing technologies to gather millions of DNA and RNA sequences from inside and outside seeps, and I combine the resulting taxonomic information with geochemical data and with measurements of metabolic gene abundances to uncover the controls on microbial community composition and metabolic potential. In Chapter 1, I investigate the process of microbial community assembly in a developing cold seep system on the U.S. Atlantic Margin, which is fed by dissociating methane hydrate. I find that seep communities – unlike those in nearby background sediments – are selected deterministically via specific geochemical parameters, rather than by the composition of nearby seeps or by random dispersal. In Chapter 2, I explore two unusual seeps in Monterey Bay, which, despite high concentrations of methane, do not host canonical methane-oxidizers, perhaps due to competition surrounding inputs of other hydrocarbons. In Chapter 3, I explore the distribution and ecology of nitrogen-fixers at seeps and find that, despite a wide variety of taxa with the ability to fix nitrogen, most are directly involved in hydrocarbon degradation, and their abundance is driven by nitrogen limitation. Together, these studies showcase the heterogeneity of microbial communities at hydrocarbon seeps and the conspicuous impact of local biogeochemical conditions on metabolic potential. Given the role of seep microorganisms in filtering potent greenhouse gases, elucidating the factors governing their presence or absence is critical for assessing the current and future impact of seeps on global climate.