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Carbonate-Associated Microbial Ecology at Methane Seeps: Assemblage Composition, Response to Changing Environmental Conditions, and Implications for Biomarker Longevity

Citation

Case, David Hamilton (2016) Carbonate-Associated Microbial Ecology at Methane Seeps: Assemblage Composition, Response to Changing Environmental Conditions, and Implications for Biomarker Longevity. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9TD9V84. https://resolver.caltech.edu/CaltechTHESIS:05262016-170051580

Abstract

Methane seeps are globally distributed geologic features in which reduced fluid from below the seafloor is advected upward and meets the oxidized bottom waters of Earth’s oceans. This redox gradient fuels chemosynthetic communities anchored by the microbially-mediated anaerobic oxidation of methane (AOM). Both today and in Earth’s past, methane seeps have supported diverse biological communities extending from microorgansisms to macrofauna and adding to the diversity of life on Earth. Simultaneously, the carbon cycling associated with methane seeps may have played a significant role in modulating ancient Earth’s climate, particularly by acting as a control on methane emissions.

The AOM metabolism generates alkalinity and dissolved inorganic carbon (DIC) and at a 2:1 ratio, promoting the abiogenic, or authigenic, precipitation of carbonate minerals. Over time, these precipitates can grow into pavements covering hundreds of square meters on the seafloor and dominating the volumetric habitat space available in seep ecosystems. Importantly, carbonates are incorporated into the geologic record and therefore preserve an inorganic (i.e., d13C) and organic (i.e., lipid biomarker) history of methane seepage. However, the extent to which preserved biomarkers represent a snapshot of microorganisms present at the time of primary precipitation, a time-integrated history of microbial assemblages across the life cycle of a methane seep, or a view of the final microorganisms inhabiting a carbonate prior to incorporation in the sedimentary record is unresolved.

This thesis addresses the ecology of carbonate-associated seep microorganisms. Chapters One and Two contextualize the extant microbial diversity on seep carbonates versus within seep sediments, as determined through 16S rRNA gene biomarkers. Small, protolithic carbonate “nodules” recovered from within seep sediments are observed to be capable of capturing surrounding sediment-hosted microbial diversity, but in some cases also diverge from sediments. Meanwhile, lithified carbonate blocks recovered from the seafloor host microbial assemblages demonstrably distinct from seep sediments (and seep nodules). Microbial 16S rRNA gene diversity within carbonate samples is well-differentiated by the extent of contemporary seepage. In situ seafloor transplantation experiments further demonstrated the microbial assemblages associated with seep carbonates to be sensitive to seep quiescence and activation on short (13-month) timescales. This was particularly true for organisms whose 16S rRNA genes imply physiologies dependent on methane or sulfur oxidation. With an improved understanding of the modern ecology of carbonate-associated microorganisms, Chapter Three applies intact polar lipid (IPL) and core lipid analyses to begin describing whether, and to what extent, geologically relevant biomarkers mimic short-term dynamics observed in 16S rRNA gene profiles versus archive a record of historic microbial diversity. Biomarker longevity is determined to increase from 16S rRNA genes to IPLs to core lipids, with IPLs preserving microbial diversity history on timescales more similar to 16S rRNA genes than core lipids. Ultimately, individual IPL biomarkers are identified which may be robust proxies for determining whether the biomarker profile recorded in a seep carbonate represents vestiges of active seepage processes, or the profile of a microbial community persisting after seep quiescence.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Environmental microbiology; Ecology
Degree Grantor:California Institute of Technology
Division:Geological and Planetary Sciences
Major Option:Geochemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Orphan, Victoria J.
Thesis Committee:
  • Fischer, Woodward W. (chair)
  • Adkins, Jess F.
  • Leadbetter, Jared R.
  • Levin, Lisa A.
  • Orphan, Victoria J.
Defense Date:12 May 2016
Funders:
Funding AgencyGrant Number
National Science Foundation Graduate Research FellowshipUNSPECIFIED
National Science FoundationBIO-OCE 0825791
Department of EnergyDE-SC0003940
NASA Astrobiology InstituteNNA13AA92A
Gordon and Betty Moore Foundation3780
National Science FoundationOCE-0826254
National Science FoundationOCE-0939557
National Science FoundationEAPSI-2013
Japan Society for the Promotion of ScienceEAPSI-2013
Record Number:CaltechTHESIS:05262016-170051580
Persistent URL:https://resolver.caltech.edu/CaltechTHESIS:05262016-170051580
DOI:10.7907/Z9TD9V84
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.​1007/​s00248-015-0615-6DOIArticle adapted for Chapter 1
http://dx.doi.org/10.1128/mBio.01348-15DOIArticle adapted for Chapter 2
ORCID:
AuthorORCID
Case, David Hamilton0000-0002-1023-0040
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9776
Collection:CaltechTHESIS
Deposited By: David Case
Deposited On:31 May 2016 16:03
Last Modified:04 Oct 2019 00:13

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