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Molecular and Geochemical Insights into Microbial Life Centimeters to Kilometers Below the Seafloor


Trembath-Reichert, Elizabeth (2016) Molecular and Geochemical Insights into Microbial Life Centimeters to Kilometers Below the Seafloor. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z96Q1V6Q.


At the broadest scale, this thesis is an investigation of how life modulates the movement of essential elements (carbon, sulfur, nitrogen, and silicon) on modern and geologic timescales. Chapters 1 and 2 explore carbon and sulfur cycling microbial communities found centimeters below the seafloor in hydrocarbon-rich methane seep ecosystems. At the Hydrate Ridge methane seep, we investigated how microbial partnerships direct the flow of methane and sulfide in these benthic oases by using identity-based physical separation methods developed in our lab (Magneto-FISH) in conjunction with community profiling and metagenomic sequencing. This method explores the middle ground between single cell and bulk sediment analysis by separating target microbes and their physically associated community for downstream sequencing applications. Magneto-FISH captures were done at a range of microbial taxonomic group specificities and sequenced with both clone library and next-gen iTag 16S rRNA gene methods. Chapter 1 provides a demonstration of how FISH probe taxonomic specificity correlates to resultant Archaeal taxonomic diversity in Magneto-FISHed seep sediments, with specific attention to preparation of Archaea-enriched samples for downstream metagenomic sequencing. In Chapter 2, a Bacteria-focused parallel environmental isolation and sequencing effort was subjected to co-occurrence analyses which suggested there may be far more microbial associations in methane seep systems than are currently appreciated, including partnerships that do not involve the canonical anaerobic methane oxidizing archaea and sulfate reducing bacteria. With samples from IODP Expedition 337 Shimokita coalbed biosphere, Chapter 3 provides evidence for an active microbial assemblage kilometers below the sea floor in the deepest samples ever collected by marine scientific ocean drilling. Using in situ temperature Stable Isotope Probing (SIP) incubations and NanoSIMS, we investigated whole community activity (with the passive tracer D2O) and substrate specific activity with C1-carbon compounds methylamine and methanol. We found deuterium-based turnover times to be faster (years) than previous deep biosphere estimates (hundreds to thousands of years), but methylotrophy rates to be slower than previous carbon metabolic rates.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:deep biosphere, microbial ecology, Magneto-FISH, coalbed
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:
  • Sessions, Alex L. (chair)
  • Fischer, Woodward W.
  • Leadbetter, Jared R.
  • Orphan, Victoria J.
Defense Date:26 April 2016
Non-Caltech Author Email:eliztr (AT)
Funding AgencyGrant Number
Gordon and Betty Moore FoundationUNSPECIFIED
NIH/NRSA training grant5 T32 GM07616
Record Number:CaltechTHESIS:05262016-132232540
Persistent URL:
Related URLs:
URLURL TypeDescription ItemArticle: Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments ItemArticle: Four hundred million years of silica biomineralization in land plants ItemArticle: Whole Cell Immunomagnetic Enrichment of Environmental Microbial Consortia Using rRNA-Targeted Magneto-FISH
Trembath-Reichert, Elizabeth0000-0002-3979-8676
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9768
Deposited By: Elizabeth Trembath-Reichert
Deposited On:26 May 2016 23:39
Last Modified:04 Oct 2019 00:13

Thesis Files

PDF (Full Thesis) - Final Version
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PDF (Front matter) - Final Version
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PDF (Chapter 1) - Final Version
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PDF (Chapter 2) - Final Version
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PDF (Chapter 3) - Final Version
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PDF (Appendix A) - Final Version
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PDF (Appendix B) - Final Version
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