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From Lakes to Lungs: Assessing Microbial Activity in Diverse Environments


Kopf, Sebastian Hermann (2015) From Lakes to Lungs: Assessing Microbial Activity in Diverse Environments. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9HQ3WV6.


All major geochemical cycles on the Earth’s surface are mediated by microorganisms. Our understanding of how these microbes have interacted with their environments (and vice versa) throughout Earth's history, and how they will respond to changes in the future, is primarily based on studying their activity in different environments today. The overarching questions that motivate the research presented in the two parts of this thesis -- how do microorganisms shape their environment (and vice versa)? and how can we best study microbial activity in situ? -- have arisen from the ultimate goal of being able to predict microbial activity in response to changes within their environments both past and future.

Part one focuses on work related to microbial processes in iron-rich Lake Matano and, more broadly, microbial interactions with the biogeochemical cycling of iron. Primarily, we find that the chelation of ferrous iron by organic ligands can affect the role of iron in anoxic environmental systems, enabling photomixotrophic growth of anoxygenic microorganisms with ferrous iron, as well as catalyzing the oxidation of ferrous iron by denitrification intermediates. These results imply that the ability to grow photomixotrophically on ferrous iron might be more widespread than previously assumed, and that the co-occurrence of chemical and biological processes involved in the coupled biogeochemical cycling of iron and nitrogen likely dominate organic-rich environmental systems.

Part two switches focus to in situ measurements of growth activity and comprises work related to microbial processes in the Cystic Fibrosis lung, and more broadly, the physiology of slow growth. We introduce stable isotope labeling of microbial membrane fatty acids and whole cells with heavy water as a new technique to measure microbial activity in a wide range of environments, demonstrate its application in continuous culture in the laboratory at the population and single cell level, and apply the tool to measure the in situ activity of the opportunistic pathogen Staphylococcus aureus within the environment of expectorated mucus from cystic fibrosis patients. We find that the average in situ growth rates of S. aureus fall into a range of generation times between ~12 hours and ~4 days, with substantial heterogeneity at the single-cell level. These data illustrate the use of heavy water as a universal environmental tracer for microbial activity, and highlight the crucial importance of studying the physiology of slow growth in representative laboratory systems in order to understand the role of these microorganisms in their native environments.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:iron oxidation; iron cycling; photoferrotrophy; microbial activity; growth rate; slow growh; isotope labeling; deuterium; cystic fibrosis
Degree Grantor:California Institute of Technology
Division:Geological and Planetary Sciences
Major Option:Geobiology
Awards:Lawrence L. And Audrey W. Ferguson Prize, 2015
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Newman, Dianne K.
Thesis Committee:
  • Orphan, Victoria J. (chair)
  • Sessions, Alex L.
  • Eiler, John M.
  • Newman, Dianne K.
Defense Date:11 June 2014
Non-Caltech Author Email:seb.kopf (AT)
Record Number:CaltechTHESIS:08182014-160835979
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for ch. 3 adapted for ch. 4
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:8637
Deposited By: Sebastian Kopf
Deposited On:30 Sep 2014 17:25
Last Modified:08 Nov 2023 00:46

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