On both human and geologic timescales, the microbial degradation of organic carbon in anoxic environments significantly influences the Earth\u2019s 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.
\r\n\r\nFirst, 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.
", "doi": "10.7907/qdbh-zr32", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:14239", "collection": "thesis", "collection_id": "14239", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06042021-142625243", "primary_object_url": { "basename": "AAPThesisV3.pdf", "content": "final", "filesize": 16107902, "license": "other", "mime_type": "application/pdf", "url": "/14239/8/AAPThesisV3.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Sulfur Cycling in the Water Columns of Lakes and Oceans", "author": [ { "family_name": "Phillips", "given_name": "Alexandra Atlee", "orcid": "0000-0001-5959-5238", "clpid": "Phillips-Alexandra-Atlee" } ], "thesis_advisor": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" } ], "thesis_committee": [ { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Sulfur is a critical bioelement central to many of Earth\u2019s biogeochemical cycles. Studies of sulfur have overwhelmingly focused on sediments, where transformations between organic and inorganic sulfur phases drive short-term biological reactions and long-term climate cycles. However, sulfur cycling in the water column is just as dynamic and exerts similar controls over biogeochemical cycles in lakes and oceans \u2013 although the exact dynamics are only beginning to be understood. This thesis provides new understanding of sulfur cycling in aquatic environments through three chapters that span laboratory developments and field observations. Chapter 1 presents a time-series in enigmatic Mono Lake, CA, where the temporal dynamics of sulfur cycling microbes was investigated. This study, published in Geobiology, highlights the dependency of sulfate reduction and oxidation on lake chemistry and the need for studies to move beyond \u201csnapshots\u201d of microbial diversity. Chapter 2, published in Rapid Communications in Mass Spectrometry, presents development of a highly sensitive (1-10 \u00b5g S) mass spectrometry technique that allows, for the first time, sulfur isotope measurements of amino acids. These new measurements permitted discovery of new connections between metabolism and sulfur isotope signatures. Chapter 3 further applies these novel methods, making the first sulfur isotope measurements of marine dissolved organic matter. The data indicated that marine organic sulfur is entirely produced by phytoplankton and implied that heterotrophic bacteria rapidly and efficiently recycle reduced sulfur compounds, even in the water column. Taken together, these three chapters significantly advanced available tools for studying sulfur in the environment and expanded our understanding of modern aquatic sulfur cycling. The final chapter represents a departure from oceans, lakes, mass spectrometry, and sulfur. Here, I evaluate the success and impacts of my outreach project, the popular Women Doing Science Instagram, in portraying diverse, international women scientists, noting the powerful potential for social media to bolster STEM identity for graduate students.
", "doi": "10.7907/tmxk-7f90", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:9766", "collection": "thesis", "collection_id": "9766", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262016-125832967", "primary_object_url": { "basename": "Raven_2016_thesis-final.pdf", "content": "final", "filesize": 4694191, "license": "other", "mime_type": "application/pdf", "url": "/9766/1/Raven_2016_thesis-final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Organic Matter Sulfurization in the Modern Ocean", "author": [ { "family_name": "Raven", "given_name": "Morgan Reed", "orcid": "0000-0003-4953-9966", "clpid": "Raven-Morgan-Reed" } ], "thesis_advisor": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" } ], "thesis_committee": [ { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" }, { "family_name": "Lyons", "given_name": "Timothy W.", "clpid": "Lyons-T-W" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Only a tiny fraction of the carbon fixed by primary producers in the surface ocean is preserved in sediments, but this organic matter (OM) burial is one of the main processes linking the short and long-term carbon cycles, giving it important roles in global biogeochemistry. OM-rich deposits often contain abundant organic S (OS), and sulfur incorporation is thought to make OM less available for heterotrophs and more likely to be preserved. Still, we have few constraints on the significance of sulfurization for OM burial in the modern ocean, and fewer on how that flux might have differed in the past. This thesis applies a new generation of analytical tools for S-isotope analysis to investigate the timescales and mechanisms of OM sulfurization in the modern ocean. By measuring the \u03b434S values of minor S phases and individual S-bearing organic compounds as well as major sedimentary phases, we are able to make progress on long-standing questions about the distribution of S isotopes among organic and inorganic S phases in sediments.
\r\n\r\nChapters 2 and 3 focus on Cariaco Basin, where a large proportion of the OS in sediments appears to derive from OM sulfurization in particles sinking through the water column. Rapid sulfurization likely involves polysulfides and is associated with high primary productivity and OM export. In the sediments, low-molecular-weight organosulfur compounds accumulate over longer timescales and have low and distinctive \u03b434S values. Chapter 4 presents records from Santa Barbara Basin, where OS appears to be exchanging with less abundant porewater sulfide and controlling its \u03b434S value. As in many environments, pyrite in these sediments is more 34S-depleted than either OS or sulfide. We attribute this pattern to pyrite formation within sulfide-generating microenvironments prior to equilibration between OS and sulfide in porewater. Chapter 5 tests the feasibility of the proposed OS\u2013sulfide exchange and confirms that sulfide \u03b434S can reflect equilibrium with natural OM. We also find evidence that sulfurization of thiols may involve an interim polysulfide that includes the thiol S atom, providing a mechanism to mix biogenic S into proto-kerogen and potentially helping explain differences between the global pyrite and OS S-isotope records.
\r\n", "doi": "10.7907/Z91Z42B0", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:7535", "collection": "thesis", "collection_id": "7535", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03202013-162430365", "primary_object_url": { "basename": "Osburn_thesis_final.pdf", "content": "final", "filesize": 35915213, "license": "other", "mime_type": "application/pdf", "url": "/7535/1/Osburn_thesis_final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Isotopic Proxies for Microbial and Environmental Change: Insights from Hydrogen Isotopes and the Ediacaran Khufai Formation", "author": [ { "family_name": "Osburn", "given_name": "Magdalena Rose", "clpid": "Osburn-Magdalena-Rose" } ], "thesis_advisor": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Grotzinger", "given_name": "John P.", "clpid": "Grotzinger-J-P" } ], "thesis_committee": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Grotzinger", "given_name": "John P.", "clpid": "Grotzinger-J-P" }, { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" }, { "family_name": "Lyons", "given_name": "Timothy W.", "clpid": "Lyons-T-W" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Microbes have profoundly influenced the Earth\u2019s environments through time. Records of these interactions come primarily from the development and implementation of proxies that relate known modern processes to chemical signatures in the sedimentary record. This thesis is presented in two parts, focusing first on novel proxy development in the modern and second on interpretation of past environments using well-established methods. Part 1, presented in two chapters, builds on previous observations that different microbial metabolisms produce vastly different lipid hydrogen isotopic compositions. Chapter 1 evaluates the potential environmental expression of metabolism-based fractionation differences by exploiting the natural microbial community gradients in hydrothermal springs. We find a very large range in isotopic composition that can be demonstrably linked to the microbial source(s) of the fatty acids at each sample site. In Chapter 2, anaerobic culturing techniques are used to evaluate the hydrogen isotopic fractionations produced by anaerobic microbial metabolisms. Although the observed fractionation patterns are similar to those reported for aerobic cultures for some organisms, others show large differences. Part 2 changes focus from the modern to the ancient and uses classical stratigraphic methods combined with isotope stratigraphy to interpret microbial and environmental changes during the latest Precambrian Era. Chapter 3 presents a detailed characterization of the facies, parasequence development, and stratigraphic architecture of the Ediacaran Khufai Formation. Chapter 4 presents measurements of carbon, oxygen, and sulfur isotopic ratios in stratigraphic context. Large oscillations in the isotopic composition of sulfate constrain the size of the marine sulfate reservoir and suggest incorporation of an enriched isotopic source. Because this data was measured in stratigraphic context, we can assert with confidence that these isotopic shifts are not related to stratigraphic surfaces or facies type but instead reflect the evolution of the ocean through time. This data integrates into the chemostratigraphic global record and contributes to the emerging picture of changing marine chemistry during the latest Precambrian Era.", "doi": "10.7907/KBAN-B073", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "id": "thesis:5319", "collection": "thesis", "collection_id": "5319", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-213942982", "primary_object_url": { "basename": "Revised_Thesis_Ying_Wang.pdf", "content": "final", "filesize": 4389057, "license": "other", "mime_type": "application/pdf", "url": "/5319/1/Revised_Thesis_Ying_Wang.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Equilibrium \u00b2H/\u00b9H Fractionations in Organic Molecules ", "author": [ { "family_name": "Wang", "given_name": "Ying", "clpid": "Wang-Ying" } ], "thesis_advisor": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" } ], "thesis_committee": [ { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Goddard", "given_name": "William A., III", "clpid": "Goddard-W-A-III" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "\r\nCompound-specific H isotope analysis has become widespread over the past decade and stimulated a variety of studies using the H isotopic composition (\u03b4\u00b2H values) of sedimentary organic molecules as paleoenvironmental proxies. Since alkyl H can be affected by a variety of exchange processes that lead to \u03b4\u00b2H changes on geological timescales, interpretation of empirical \u03b4\u00b2H data must account for these changes, which requires quantitative knowledge regarding the endpoint of the isotopic exchange, i.e., equilibrium fractionation factor (\u03b1eq). Nevertheless, to date relevant data have been lacking for molecules larger than methane. This is because the conventional isotope exchange experiments suffer from the slow exchange rates of C-bound H (half-life ~ 105\u2013106 years), whereas theoretical calculations \u2014 a convenient way to cover many organic structures over wide temperature ranges \u2014 are restricted by systematic biases for the H isotope system.
\r\n\r\nTo remedy the situation, this project was proposed to use experimental equilibration data to calibrate ab initio calculations of \u03b1eq. To accurately measure the value of \u03b1eq within reasonable experimental timescale, I utilized the keto-enol tautomerism that leads to fast equilibration between H positions adjacent to carbonyl groups (denoted as H\u03b1) and water. By equilibrating ketones with waters of varying \u03b4\u00b2H values, the values of \u03b1eq were measured for H\u03b1 positions in a variety of acyclic and cyclic molecular structures at different temperatures. On the other hand, statistical thermodynamics and ab initio QM computations (B3LYP/6-311G**) were applied to calculate \u03b1eq values for the same ketone molecules. Comparison between experimental and theoretical results yields a temperature-dependent linear calibration curve for linear molecules with slope = 1.081\u22120.00376T and intercept = 8.404\u22120.387T (T is temperature in degrees Celsius). For cyclic structures, the calibration is slightly different with slope of 1.44\u00b10.05 and intercept of 32.8\u00b15.1. Application of these calibration curves to more ab initio calculations generates the \u03b1eq values for various H sites in alkanes, alkenes, ketones, carboxylic acids, esters, alcohols, and ethers, with the uncertainties estimated to be 10\u201325\u2030. The effects of functional groups were found to increase the value of \u03b1eq for H next to electron-donating groups, e.g., \u2212OR, \u2212OH or \u2212O(C=O)R, and to decrease the value of \u03b1eq for H next to electron-withdrawing groups, e.g., \u2212(C=O)R or \u2212(C=O)OR. It is analogous to the well-known substituent effects in the aromatic ring system.
\r\n\r\nOur results provide a modular dataset to calculate equilibrium \u00b2H/\u00b9H fractionations for common molecules found in sediments and oils. By summing over individual H positions, the equilibrium fractionation relative to water between 0 and 100\u00b0C is estimated to be \u221270\u2030 to \u221290\u2030 for n-alkanes, around \u2212100\u2030 for acyclic isoprenoids and \u221275 to \u2212100\u2030 for steroids and hopanoids. The temperature dependence of these molecular fractionations is very weak within the relevant temperature range. The results agree well with field data for thermally mature hydrocarbons (\u03b4\u00b2H values between -80\u2030 and -110\u2030 relative to water; Schimmelmann et al., 2006), suggesting that the observed \u03b4\u00b2H changes in sedimentary organic matter can be confidently attributed to H exchange towards an equilibrium state.
\r\n\r\nBecause of the need to accurately measure the widely-ranging \u03b4\u00b2H values encountered in natural and isotopically-exchanged samples, a side project was conducted to quantitatively investigate the isotopic memory effects in compound-specific \u00b2H/\u00b9H analysis by gas chromatography/pyrolysis/isotope-ratio mass spectrometry (GC/P/IRMS), i.e., the situation in which the \u00b2H/\u00b9H ratio of a given chromatographic peak affects that of the following peak(s). Through a series of experiments that employed synthesized esters with \u03b4\u00b2H varying by up to 1000\u2030, we were able to estimate the isotopic memory to be typically 2\u20134% of the nominal \u03b4\u00b2H difference between two adjacent peaks. It increases with decreasing time separation, increasing analyte abundance of the preceding peak, or increasing age of the pyrolysis reactor. Roughly half of the memory effect can be attributed to the H2-adsorption process in the pyrolytic reactor, and the other half to unknown processes within the GC. Finally, based on our experimental and model study, modifications in routine analyses were proposed to mitigate memory effects.
", "doi": "10.7907/4MPX-MF10", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" } ]