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Physical, Metabolic, and Energetic Investigations of Methane-Metabolizing Microbial Communities


Marlow, Jeffrey James (2016) Physical, Metabolic, and Energetic Investigations of Methane-Metabolizing Microbial Communities. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9W66HPS.


Understanding the roles of microorganisms in environmental settings by linking phylogenetic identity to metabolic function is a key challenge in delineating their broad-scale impact and functional diversity throughout the biosphere. This work addresses and extends such questions in the context of marine methane seeps, which represent globally relevant conduits for an important greenhouse gas. Through the application and development of a range of culture-independent tools, novel habitats for methanotrophic microbial communities were identified, established settings were characterized in new ways, and potential past conditions amenable to methane-based metabolism were proposed. Biomass abundance and metabolic activity measures – both catabolic and anabolic – demonstrated that authigenic carbonates associated with seep environments retain methanotrophic activity, not only within high-flow seep settings but also in adjacent locations exhibiting no visual evidence of chemosynthetic communities. Across this newly extended habitat, microbial diversity surveys revealed archaeal assemblages that were shaped primarily by seepage activity level and bacterial assemblages influenced more substantially by physical substrate type. In order to reliably measure methane consumption rates in these and other methanotrophic settings, a novel method was developed that traces deuterium atoms from the methane substrate into aqueous medium and uses empirically established scaling factors linked to radiotracer rate techniques to arrive at absolute methane consumption values. Stable isotope probing metaproteomic investigations exposed an array of functional diversity both within and beyond methane oxidation- and sulfate reduction-linked metabolisms, identifying components of each proposed enzyme in both pathways. A core set of commonly occurring unannotated protein products was identified as promising targets for future biochemical investigation. Physicochemical and energetic principles governing anaerobic methane oxidation were incorporated into a reaction transport model that was applied to putative settings on ancient Mars. Many conditions enabled exergonic model reactions, marking the metabolism and its attendant biomarkers as potentially promising targets for future astrobiological investigations. This set of inter-related investigations targeting methane metabolism extends the known and potential habitat of methanotrophic microbial communities and provides a more detailed understanding of their activity and functional diversity.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Environmental Microbiology, Methane, Proteomics, Methane Seep
Degree Grantor:California Institute of Technology
Division:Geological and Planetary Sciences
Major Option:Geobiology
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Orphan, Victoria J.
Thesis Committee:
  • Orphan, Victoria J. (chair)
  • Newman, Dianne K.
  • Fischer, Woodward W.
  • Rees, Douglas C.
  • Hoehler, Tori M.
Defense Date:5 June 2015
Record Number:CaltechTHESIS:07212015-103405937
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for chapter 1 adapted for chapter 3 adapted for chapter 5 adapted for appendix 2
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9064
Deposited By: Jeff Marlow
Deposited On:05 Aug 2015 17:45
Last Modified:04 Oct 2019 00:09

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