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Carbon Currencies: Isotopic Constraints on the Biogeochemistry of Organic Acids


Mueller, Elliott Patrick (2024) Carbon Currencies: Isotopic Constraints on the Biogeochemistry of Organic Acids. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/qdbh-zr32.


On both human and geologic timescales, the microbial degradation of organic carbon in anoxic environments significantly influences the Earth’s climate. The rate-limiting step of this process is the initial breakdown of complex organic polymers (e.g. cellulose) into small organic acids (e.g. acetate), which are then rapidly converted into either carbon dioxide or methane. While the steady-state concentration of organic acids is kept low by microbial turnover, the flux of reactions producing and consuming them is large. In my doctoral work, I leveraged this dynamic pool of metabolites as a window into the broader carbon cycle. Specifically, I developed novel analytical and computational tools that quantify and interpret the isotope composition of organic acids. These techniques provide new information about the mechanism and rates of organic acid turnover in nature.

First, in Chapter 2, I adapted electrospray ionization (ESI) Orbitrap mass spectrometry (MS) to simultaneously measure the carbon and hydrogen isotope compositions of acetate. This approach is 50 to 1000-fold more sensitive than established techniques, making measurements of environmental samples feasible for the first time. This technique clearly distinguishes the metabolic sources of acetate (fermentation and acetogenesis). In Chapter 3, I developed a complementary computational tool to interpret this new isotopic information. Quantifying Isotopologue Reaction Networks (QIRN) builds numerical models of complex reaction networks, including metabolic pathways, and predicts the isotope composition of molecules produced by these networks. In Chapter 4, I combined my analytical and computational approaches to investigate the isotopic fractionations of the microbial metabolism that generate organic acids in nature, fermentation. I found that fermentation imposes a significant isotopic fractionation during the degradation of organic matter. By coupling flux-balance analysis and QIRN, I isolated the enzymes responsible for these fractionations. These results suggested that fermentation may have imprinted a carbon isotope trophic enrichment that is observable in the compound-specific carbon isotope composition of Proterozoic biomarkers. In Chapter 5, I used my Orbitrap method to quantify in situ acetate turnover rates based on the exchange of hydrogen atoms between water and acetate's methyl group. I took this tool to the environment, where I studied the biogeochemical drivers of carbon cycling in the deep continental subsurface. In Kidd Creek mine, which has subsurface fracture fluids that have been isolated for over a billion years, I found that acetate is being actively produced and consumed in the subsurface. My analyses of acetate's isotope composition suggested that turnover may be driven by low-temperature water-rock reactions with implications for the habitability of subsurface environments elsewhere in the Solar System. Chapter 6 is a second application of the Orbitrap and QIRN in natural systems. This time I expanded the Orbitrap technique to include not only acetate but also the organic acids propionate and butyrate. I investigated carbon turnover in the rumen fluid of cows, where microbial fermentation breaks down cellulose and transfers organic acids to the animal host. I found clear trends in the carbon and hydrogen isotope composition of acetate and propionate that may hold information about the metabolic strategies of fermenters in the rumen. Finally, in Chapter 7, I highlight the challenges and opportunities of transitioning Orbitrap MS isotopic applications from pure standards to compelx samples. These studies demonstrate bespoke strategies for isolating organic acids, and possibly other ESI-Orbitrap analytes, from environmental samples without fractionating their isotope ratios. Together, these chapters use a combination of novel analytical and computational tools to study the rate and mechanism of organic acid cycling in nature. Elucidating these drivers is necessary to understand the modern and ancient carbon cycle and to predict its response to climate change.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Stable isotopes; fermentation; microbiology; acetate; carbon
Degree Grantor:California Institute of Technology
Division:Geological and Planetary Sciences
Major Option:Geobiology
Awards:Caltech Three Minute Thesis (3MT) competition, 2024, 3rd Place. Patrick Hummel and Harry Gray Travel Fund, 2024.
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Sessions, Alex L.
Group:3MT Competition (Caltech)
Thesis Committee:
  • Eiler, John M.
  • Fischer, Woodward W. (chair)
  • Leadbetter, Jared R.
  • Sessions, Alex L.
Defense Date:3 May 2024
Funding AgencyGrant Number
NSF Graduate Research FellowshipDGE-1745301
Linde Endowment for Global Environmental Science25570006
Resnick Sustainability InstituteRESNICK.SRA
Record Number:CaltechTHESIS:05232024-200019160
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for ch. 2 adapted for ch. 3 adapted for ch. 5 DocumentArticle adapted for ch. 7
Mueller, Elliott Patrick0000-0002-6837-0409
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:16420
Deposited By: Elliott Mueller
Deposited On:03 Jun 2024 23:42
Last Modified:17 Jun 2024 20:01

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