Life\u2019s origins and fate are tightly intertwined. All life as we know it is composed of proteins, carbohydrates, lipids, and nucleic acids. These biomolecules are synthesized today by cellular machinery made of the same components, leaving open questions about the origins of life and prebiotic chemistry. After death, organic remnants are buried in sediments, undergoing microbial reworking, consolidation, and transformation into kerogen. As temperature and pressure increase with depth, kerogen matures, releasing oil and gas before ultimately transforming into graphite. The question remains: can we decipher the traces of life (and non-life) from somewhat altered organic matter from the past or on other planets? This thesis explores the origins and evolution of one of the most fundamental classes of compounds\u2014hydrocarbons\u2014across geological and prebiotic settings through novel applications of intramolecular and clumped isotope analysis.
\r\n\r\nChapter 2 delves into the evolution of isotopic signatures in methane, the simplest hydrocarbon, during the maturation process. By studying the clumped isotope effects of thermogenic methane formation through pyrolysis experiments, this chapter challenges previously held assumptions about abiotic and microbial signatures. The findings offer new opportunities to constrain the thermal maturation of sedimentary organic matter and have implications for the search for extraterrestrial life.
\r\n\r\nTo facilitate high-precision measurements of hydrocarbon isotopic structures, Chapter 3 presents hardware and software developments enabling automated, high-throughput analysis using Orbitrap mass spectrometry. Chapter 4 then introduces a novel method coupling gas chromatography and Orbitrap MS to simultaneously measure intramolecular \u00b9\u00b3C and \u00b2H distributions in n-alkanes, validating the technique for forensic fingerprinting and natural sample characterization.
\r\n\r\nTurning to the impact of thermal maturation, Chapter 5 examines how n-alkane intramolecular isotope patterns evolve through pyrolysis experiments. Kinetic isotope effects control residual n-alkane isotopic compositions, with minimal alteration to intramolecular distributions under the studied conditions, suggesting preservation of primitive signatures.
\r\n\r\nChapter 6 brings together these analytical developments to compare intramolecular isotope compositions of n-nonadecane from sedimentary, abiotic, and biological sources. Distinctive isotopic fingerprints are established for each source, with implications for interpreting organic matter histories and detecting potential signatures of extraterrestrial life.
\r\n\r\nCollectively, this thesis expands the \"molecular detective\" toolkit for tracing hydrocarbon origins across diverse environments, from deep petroleum systems to potential prebiotic reaction pathways. The findings illuminate key processes governing isotopic biosignatures and their preservation through geological time.
", "doi": "10.7907/yw0g-s893", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16204", "collection": "thesis", "collection_id": "16204", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10102023-024622119", "primary_object_url": { "basename": "Wang_Renee_Z_2023_THESIS.pdf", "content": "final", "filesize": 15451019, "license": "other", "mime_type": "application/pdf", "url": "/16204/2/Wang_Renee_Z_2023_THESIS.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "From Photosynthesis to Detoxification: Microbial Metabolisms Shape Earth\u2019s Surface Chemistry", "author": [ { "family_name": "Wang", "given_name": "Ren\u00e9e Zurui", "orcid": "0000-0003-3994-3244", "clpid": "Wang-Ren\u00e9e-Zurui" } ], "thesis_advisor": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Earth\u2019s chemistry, through geologic time and in the present, is inextricably linked with biologically mediated reactions. All major elemental cycles on Earth\u2019s surface have arisen from two competing processes \u2013 life shaping its chemical environment through the evolution of key biochemical pathways, and the environment constraining metabolism by dictating which reactions will occur. Understanding this complicated interplay motivates the research presented in this thesis, which studies this phenomenon over two major elemental cycles \u2013 the modern Nitrogen (N) and ancient Carbon (C) cycle.
\r\n\r\nChapters One and Two focus on the evolution of ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco), the enzyme that catalyzes the key carbon fixation step in modern oxygenic photosynthesis. This reaction also imparts a large kinetic isotope effect (KIE) that causes the fixed carbon to be relatively depleted in natural abundance \u00b9\u00b3C compared to its substrate; this isotopic fingerprint can be seen in both the modern C cycle and in rock records recording the ancient C cycle. Therefore, this KIE has been used both in vitro (outside the cell) by biochemical models to rationalize rubisco\u2019s reaction mechanism, and in vivo (in the cell) as a proxy for environmental CO\u2082 concentrations in the past and present. However, both the in vitro and in vivo measurements are calibrated using modern organisms even though rubisco and oxygenic photosynthesis have undergone profound evolution over geologic time. Therefore, we measured the KIE in vitro and in vivo of a reconstructed ancestral Form IB rubisco dating to >> 1 Ga, and the KIE in vitro of a recently discovered Form I\u2019 rubisco that presents a modern analogue to ancestral Form I rubiscos prior to the evolution of the small subunit. Overall, we find that the KIEs of both rubiscos are smaller than their modern counterparts, which is surprising given that the rock record indicates overall carbon isotope fractionations in vivo are larger in the past. In addition, we find that models strictly based on modern organisms may not apply to the past, questioning the basic assumption that uniformitarianism can be readily applied to biological processes. However, these models can be rescued by accounting for other aspects of cell physiology.
\r\n\r\nChapter Three focuses on disentangling the source of key metabolites, like nitrous oxide (N\u2082O) in the modern N cycle. Like Chapters 1 and 2, an isotopic fingerprint that measures the \u2018preference\u2019 of \u00b9\u2075N for the central or outer nitrogen site in N\u2082O (\u201cSite Preference\u201d or \u201cSP\u201d) has primarily been calibrated using dissimilatory, or energy-generating, nitric oxide (NO) reductases (NORs). However, there exists a much larger and phylogenetically widespread class of NO-detoxifying enzymes; in particular, flavohemoglobin proteins (Fhp/Hmp) produce N\u2082O as a strategy to neutralize damaging NO-radicals in anoxic conditions. This enzyme, which generates N\u2082O in non-growing and anoxic conditions, may be more relevant to natural environments where N\u2082O production has been detected. Surprisingly, we found that Fhp imparts a distinct SP on N\u2082O that differs from both bacterial and eukaryotic NORs, and that this value better aligns with existing in situ measurements of N\u2082O from soils. In addition, we find that in strains with both Fhp and NOR, the Fhp signal dominates when cells are first exposed to high concentrations of NO in oxic conditions while growing before being shifted to an anoxic, non-growing state. Therefore, in addition to telling us \u2018Who\u2019s there,\u2019 the SP fingerprint may also be able to tell us something about cell physiology in vivo. We propose a new framework for interpreting the source of N\u2082O based on SP values.
", "doi": "10.7907/kf85-cq89", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16272", "collection": "thesis", "collection_id": "16272", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01022024-183348243", "primary_object_url": { "basename": "zeichner_sarah_2023_FINAL.pdf", "content": "final", "filesize": 15975875, "license": "other", "mime_type": "application/pdf", "url": "/16272/1/zeichner_sarah_2023_FINAL.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Fates of Carbon", "author": [ { "family_name": "Zeichner", "given_name": "Sarah Soojin", "orcid": "0000-0001-8897-7657", "clpid": "Zeichner-Sarah-Soojin" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Grotzinger", "given_name": "John P.", "orcid": "0000-0001-9324-1257", "clpid": "Grotzinger-J-P" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_gps" } ], "abstract": "This thesis investigates the organic matter relevant to the oldest rocks on the Earth and in the Solar System, along with novel methods for exploring the composition of that organic matter. Chapter II describes a novel method for using a gas chromatography-Orbitrap mass spectrometer system to simultaneously analyze multiple isotopic properties from multiple compounds within a complex mixture. This method is ideal for the study of environmental or extraterrestrial samples and was integral to the study described in Chapter III. Chapters III and IV highlight new isotopic properties that can be measured in extraterrestrial samples to constrain processes of abiotic organic molecule formation: These processes have direct implications for where the carbon on Earth comes from. Chapter III details the measurement of \u00b9\u00b3C, D, and double-\u00b9\u00b3C contents of five polycyclic aromatic hydrocarbons in samples returned by the Hayabusa2 spacecraft mission to the Ryugu asteroid. The findings of this study support the formation of aromatic hydrocarbons---arguably the most abundant molecules in the Milky Way galaxy and other galaxies---through low-temperature reactions within molecular clouds in the interstellar medium. Chapter IV characterizes the position-specific carbon isotopic compositions of three structurally-distinct amino acids-- \u03b1-alanine, \u03b2-alanine and aspartic acid--from the Murchison meteorite, which provide constraints for how they were synthesized abiotically within the meteorite parent body. Chapters V-VI of this thesis relate to organic molecules on the early Earth. Chapter V is a scholarly review of prior data documenting the carbon isotope contents of organic carbon in Archean rocks. It also includes a model for the evolution of the carbon isotopic composition of organic matter as it goes through the rock cycle (i.e., diagenesis, catagenesis, metagenesis and metamorphism), which is then used to re-interpret carbon isotope data based on extant biology and models of metabolic evolution. Chapter VI uses sedimentological experiments to demonstrate that water-soluble organic compounds may have led to the rise of mud deposition concurrent with the evolution of land plants.", "doi": "10.7907/vy9f-k705", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16357", "collection": "thesis", "collection_id": "16357", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04172024-164449548", "primary_object_url": { "basename": "Lim_thesis_2024.pdf", "content": "final", "filesize": 10822139, "license": "other", "mime_type": "application/pdf", "url": "/16357/5/Lim_thesis_2024.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "The Impact of Energy Availability and Substrate Complexity on Anaerobic Microbial Communities in Marine Sediment", "author": [ { "family_name": "Lim", "given_name": "Sujung", "orcid": "0000-0001-6040-729X", "clpid": "Lim-Sujung" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "This thesis probes the interplay of organic matter complexity (Chapters 1 and 2) and local redox gradients (Chapter 3) with the community structure and function of the anaerobic marine sediment microbiome. Deep marine sediments, despite being generally organic-poor, harbor a vast diversity of microorganisms that are critical to the global nutrient cycle. Transient nutrient inputs such as whale falls result in hotspots of microbial community activity in an environment that normally processes heavily degraded organic material from the upper ocean. These organic loading events result in transitions down redox gradients and dynamic shifts in the local energy availability of the microbial communities. Through in situ seafloor and laboratory microcosm experiments, we provide insights into the impact of energy availability and carbon complexity on maintaining hierarchical and complex community interactions, community activity, and systematic and functional diversity.", "doi": "10.7907/67j6-4885", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16420", "collection": "thesis", "collection_id": "16420", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05232024-200019160", "primary_object_url": { "basename": "EPM_ThesisFinal.pdf", "content": "final", "filesize": 21001173, "license": "other", "mime_type": "application/pdf", "url": "/16420/1/EPM_ThesisFinal.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Carbon Currencies: Isotopic Constraints on the Biogeochemistry of Organic Acids", "author": [ { "family_name": "Mueller", "given_name": "Elliott Patrick", "orcid": "0000-0002-6837-0409", "clpid": "Mueller-Elliott-Patrick" } ], "thesis_advisor": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" } ], "thesis_committee": [ { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" } ], "local_group": [ { "literal": "3MT Competition (Caltech)" }, { "literal": "div_gps" } ], "abstract": "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:16426", "collection": "thesis", "collection_id": "16426", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05252024-201300283", "primary_object_url": { "basename": "BHD_Dissertation_20240529.pdf", "content": "final", "filesize": 17426893, "license": "other", "mime_type": "application/pdf", "url": "/16426/1/BHD_Dissertation_20240529.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Intermolecular and Intramolecular Stable Isotope Studies in Alanine", "author": [ { "family_name": "Dallas", "given_name": "Brooke Hillary", "orcid": "0000-0002-1313-3270", "clpid": "Dallas-Brooke-Hillary" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "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" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "In Chapter 1 of this thesis, we give an introduction to this body of work, providing some background for context.
\r\n\r\nIn Chapter 2, we present a set of theoretical predictions for the carbon isotope distribution between equilibrated carbon sites of alanine and pyruvate. We start with the simplest possible theoretical treatment, and work progressively through higher levels of theory, showing consistency in the direction and magnitude of expected fractionation across these treatments.
\r\n\r\nIn Chapter 3, we present our experimental work to confirm the predictions made in Chapter 2 by measuring the \u03b413C of the \u03b1 carbon site in alanine that has undergone equilibration with the analogous carbon site in pyruvate via the alanine transaminase enzyme (ALT).
\r\n\r\nIn Chapter 4, we describe the process that led to our (re)discovery of \u03b2-hydrogen-deuterium exchange in amino acids catalyzed by transaminases. We then provide a literature review on the small body of historical work on this system, which took place primarily during the 1960s and 70s. This literature summary provides the background necessary for the reader to appreciate our experimental work presented in the next chapter.
\r\n\r\nIn Chapter 5, we present novel 1H NMR and 13C NMR experimental observations of intermolecular hydrogen isotope exchange between water and the \u03b1 and \u03b2 carbon sites of alanine, as well as intramolecular hydrogen isotope exchange between the \u03b1 and \u03b2 carbons, all of which is catalyzed by alanine transaminase (ALT). These experiments track the abundances of eight isotopically distinct alanine species varying in their position and/or number of hydrogen isotopes over a series of reactions differing in initial alanine isotopic composition and initial water isotopic composition. With the data collected we are able to determine up to thirteen rate constants and ten equilibrium constants describing the transfer of hydrogen and deuterium amongst these eight isotopic variants and water, as well as the thermodynamic equilibrium constants between them.
", "doi": "10.7907/xqdx-pp86", "publication_date": "2024", "thesis_type": "phd", "thesis_year": "2024" }, { "id": "thesis:16101", "collection": "thesis", "collection_id": "16101", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06092023-201353115", "primary_object_url": { "basename": "DOR_Caltech_Thesis (2).pdf", "content": "final", "filesize": 55514775, "license": "other", "mime_type": "application/pdf", "url": "/16101/1/DOR_Caltech_Thesis (2).pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Microbial Transformations of Sulfur: Environmental and (Paleo) Ecological Implications", "author": [ { "family_name": "Osorio Rodr\u00edguez", "given_name": "Daniela", "orcid": "0000-0001-6676-4124", "clpid": "Osorio Rodr\u00edguez-Daniela" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Grotzinger", "given_name": "John P.", "orcid": "0000-0001-9324-1257", "clpid": "Grotzinger-J-P" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "This thesis is centered around the role that sulfur plays in the cycling of carbon and in microbial energetics. In the oceans, sulfate is the most important electron acceptor for the remineralization of organic matter after oxygen has been depleted, and sulfate reduction is particularly relevant in coastal environments and in marine and freshwater sediments. The opposite process, reduced sulfur oxidation, allows autotrophic microorganisms to fix carbon in environments where oxygen is scarce. Organic sulfur is also a relevant component of the sulfur cycle, since sulfur is the sixth most abundant element in biomass, it can protect organic matter from degradation, and it is composed of hundreds of molecules that are produced mainly by microorganisms, with potentially relevant ecological roles.
\r\n\r\nThis work has been divided into two parts. In the first one, we attempt to expand our understanding on different aspects of the sulfur cycle. In Chapter 2, published in Limnology and Oceanography, we focus on dimethylsulfoniopropionate (DMSP), the most abundant organic sulfur compound in the oceans with roles of UV, cryo, and osmoprotection, and involved in the formation of sulfate aerosols. We propose a framework to differentiate between the microbial degradation pathways of DMSP based on the sulfur isotope fractionations imprinted by each one of them. In Chapter 3, we perform a survey of sulfate, sulfide, and reduced sulfur intermediates, as well as redox-sensitive elements, in porewaters of a ~40 cm core from the San Clemente Basin (California) and three 1.2-2 m cores near Cocos Ridge (Costa Rica). We correlate these concentrations with the sediment microbial community composition to unveil the specifics of organic matter and sulfur cycling at these localities. In Chapter 4, we explore the utility of sulfur isotope fractionations to characterize different pathways involved in microbial sulfur oxidation (MSO), and examine the role of nutrient limitation and growth rates on the magnitude of the fractionation.
\r\n\r\nIn the second part of this thesis, we aim at understanding biomineralization by consortia between anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB), which comprise more than 90% of the microbial biomass in deep sea sediments around hydrocarbon seeps. In Chapter 5 (in review at Proceedings of the National Academy of Sciences) we establish that modern ANME-SRB aggregates precipitate amorphous silica in undersaturated solutions in sediments and carbonates, often in the form of rims, which pinpoints to a potentially new microbial biomineralization mechanism. In Chapter 6, we posit the use of this proxy, together with distinctive spectral and isotopic signals, to find potential microfossils of ANME-SRB aggregates in the rock record of the Earth and other planetary bodies where methane seepage has occurred throughout geologic time. This suite of tools is used in conjunction to identify ANME-SRB aggregates in the Tepee Buttes (Colorado, 75 Mya) seep carbonates.
", "doi": "10.7907/9bn5-z794", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:15118", "collection": "thesis", "collection_id": "15118", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:03132023-113800696", "primary_object_url": { "basename": "Yi_Zhang_Thesis_Final.pdf", "content": "final", "filesize": 5182026, "license": "other", "mime_type": "application/pdf", "url": "/15118/2/Yi_Zhang_Thesis_Final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Application of Heterojunction Ni-Sb-SnO\u2082 Anodes for Electrochemical Water Treatment", "author": [ { "family_name": "Zhang", "given_name": "Yi", "orcid": "0000-0002-9062-5201", "clpid": "Zhang-Yi" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Frankenberg", "given_name": "Christian", "orcid": "0000-0002-0546-5857", "clpid": "Frankenberg-Christian" }, { "family_name": "See", "given_name": "Kimberly", "orcid": "0000-0002-0133-9693", "clpid": "See-Kimberly" }, { "family_name": "Gschwend", "given_name": "Philip M.", "orcid": "0000-0002-9497-4492", "clpid": "Gschwend-Philip-M" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_gps" } ], "abstract": "Clean water supply and adequate sanitation services are critical for public health as well as for food production. Small-scale decentralized treatment represents an attractive alternative that can provide necessary water treatment in many parts of the developing world where centralized wastewater treatment facilities are not practical owing to financial, geographical, or political constraints. Electrochemical oxidation (EO) is a suitable technique for decentralized treatment settings since it does not require the addition of auxiliary chemicals and offers fast reaction kinetics and modular treatment capacity. EO is considered a versatile technology since it can degrade a wide array of contaminants and inactivate waterborne pathogens. The chemical composition of the anode, where EO takes place, is a key factor that controls reactive species production and thus treatment efficiency and energy consumption. Ideal anodes for wastewater treatment should have high overpotential for oxygen evolution (\u201cnonactive\u201d anodes) and favor complete organics oxidation through direct electron transfer and/or reactions with potent oxidants such as hydroxyl radical and ozone. Common nonactive anodes including antimony-doped tin oxide (Sb-SnO\u2082), lead oxide (PbO\u2082), and boron-doped diamond (BDD) have attracted wide research interests. The work presented in this thesis centered around a newly designed heterojunction Ni-Sb-SnO\u20822-based anode (NAT/AT) and its various applications in decentralized water and wastewater treatment. Direct treatment using NAT/AT has proved to be efficient for chemical oxygen demand removal, trace organic compound degradation, and microbial disinfection. Detailed investigation into pharmaceutical degradation kinetics and transformation products further established NAT/AT as a potential treatment alternative for the control of pharmaceuticals and their metabolites in hospital wastewaters. NAT/AT is also capable of synthesizing ferrates (e.g., FeO\u2084\u00b2\u207b) in circumneutral conditions, the high oxidation state iron species that represents another group of powerful oxidants well-suited for decentralized treatment purposes. In an additional effort to tackle high concentrations of ammonium often present in latrine wastewaters, functionalized metal-organic framework (MOF), a class of materials featuring high porosity, abundant active sites, and highly tunable physical and chemical properties, was used to recover the ammonium nitrogen. Various modifications of MOF-808, a highly water stable MOF, were designed and synthesized to achieve urea hydrolysis, ammonium capture, and real-time ammonium sensing in sequence. In combination, the described works provide a powerful toolkit that can be used in treating various waste streams before discharge and/or reuse.", "doi": "10.7907/dmrd-w489", "publication_date": "2023", "thesis_type": "phd", "thesis_year": "2023" }, { "id": "thesis:14354", "collection": "thesis", "collection_id": "14354", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:09072021-015258902", "type": "thesis", "title": "Investigation of the Roles of Hopanoids in the Lifecycle of Bradyrhizobium diazoefficiens in the Context of Climate Change", "author": [ { "family_name": "Tookmanian", "given_name": "Elise M.", "clpid": "Tookmanian-Elise-M" } ], "thesis_advisor": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "thesis_committee": [ { "family_name": "Ondrus", "given_name": "Alison E.", "orcid": "0000-0002-6023-3290", "clpid": "Ondrus-A-E" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Rees", "given_name": "Douglas C.", "orcid": "0000-0003-4073-1185", "clpid": "Rees-D-C" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "local_group": [ { "literal": "div_chem" } ], "abstract": "Rhizobia are a group of bacteria that participate in plant-growth promoting symbioses with legumes, where the bacteria supply the plant with a source of useable nitrogen. In agriculture, crop rotation capitalizes on this symbiosis by planting legumes to restore the nitrogen content of depleted soils. The effects of climate change, such as increased temperature and changing precipitation patterns, threaten the future viability of agriculture. Rhizobia exemplify the role bacteria can play to improve agriculture\u2019s resilience to climate change and prevent land degradation and food insecurity. However, in order for bacteria to realize this potential, they need to survive the challenges of climate change. In my thesis, I detail the environments that rhizobia experience throughout their lifecycle and how the soil environment will likely change as the climate changes. Then, I connect these environmental parameters, especially hypo and hyperosmolarity, to the outer membrane. The outer membrane is the first line of defense for bacteria against external assaults. Rhizobia make many changes to their outer membrane compared to commonly studied enteric bacteria. For example, the ability to synthesize hopanoids, steroid-like lipids, is overrepresented in rhizobia.
\r\n\r\nHopanoids are known to help protect bacteria against a wide range of stresses \u2013 but, surprisingly, we found that the extended hopanoid class is not required for a moderately successful symbiosis between rhizobia strain Bradyrhizobium diazoefficiens and the tropical legume Aeschynomene afraspera. The main defect was in the initiation of the symbiosis, perhaps due to motility defects in the extended hopanoid\u2014deficient mutant. As we investigated this paradox, we discovered that hopanoids are conditionally essential in B. diazoefficiens depending on the medium in which the organism is grown. Specifically, we investigated the role of hypoosmolarity and divalent cation concentration, discovering that extended hopanoids confer robustness to the physicochemical environment. This property indicates that extended hopanoids may be important in the soil environment, which is prone to osmotic variability, especially as the climate changes. This work increases our understanding of the role of the outer membrane and hopanoids in bacterial resilience which may help with engineering or selection of better crop additives in the future.
", "doi": "10.7907/h0xe-jb65", "publication_date": "2022", "thesis_type": "phd", "thesis_year": "2022" }, { "id": "thesis:14241", "collection": "thesis", "collection_id": "14241", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06042021-184017139", "primary_object_url": { "basename": "Thesis_Alison Xunyi Wu_0606.pdf", "content": "final", "filesize": 4004030, "license": "other", "mime_type": "application/pdf", "url": "/14241/1/Thesis_Alison Xunyi Wu_0606.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Novel, Rapid and Cost-effective Methods for Concentration, Detection and Monitoring of Waterborne Pathogens in Resource-Limited Settings", "author": [ { "family_name": "Wu", "given_name": "Xunyi", "orcid": "0000-0001-9710-6896", "clpid": "Wu-Xunyi" } ], "thesis_advisor": [ { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "thesis_committee": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Tirrell", "given_name": "David A.", "orcid": "0000-0003-3175-4596", "clpid": "Tirrell-D-A" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "orcid": "0000-0001-6495-1946", "clpid": "Hoffmann-M-R" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Waterborne pathogenic organisms including bacteria, viruses, protozoa and helminths, are responsible for a series of diseases which is a major public health concern worldwide. This issue is extremely severe in developing regions due to the scarcity of clean water supply and poor sanitation. Therefore, point-of-use (POU) detection and quantification processes as well as a monitoring program of waterborne pathogens are needed to ensure the safety of water and protect human health. However, the polymerase chain reaction (PCR) technology and its related detection platforms rely on complicated thermal cycling, centralized laboratory equipment and trained personnel, thus making PCR-based systems incapable of POU testing of environmental waters. In this dissertation, we develop a portable 3D-printed system with super-absorbent polymer (SAP) microspheres for sample enrichment, and a membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system for absolute quantification of pathogens. We also explored the interactions between microbial indicator of Escherichia coli (E. coli) and waterborne pathogen Vibrio Cholerae (V. Cholerae). The main results are as follows:
\r\n\r\n1. The application of detection and quantification methods is often hindered by the low pathogen concentrations in natural waters. Rapid and efficient sample concentration methods are urgently needed. Here we present a novel method to pre-concentrate microbial pathogens in water using a portable 3D-printed system with super-absorbent polymer (SAP) microspheres, which can effectively reduce the actual volume of water in a collected sample. The SAP microspheres absorb water while excluding bacteria and viruses by size exclusion and charge repulsion. The 3D-printed system with optimally-designed SAP microspheres could rapidly achieve a 10-fold increase in the concentration of E. coli and bacteriophage MS2 within 20 minutes with concentration efficiencies of 87% and 96%, respectively. Fold changes between concentrated and original samples from qPCR and RT-qPCR results were found to be 11.34-22.27 for E. coli with original concentrations of 104-106 cell\u00b7mL-1; and 8.20-13.81 for MS2 with original concentrations of 104-106 PFU\u00b7mL-1. Furthermore, SAP microspheres can be reused 20 times without performance loss thereby significantly decreasing the cost of our concentration system.
\r\n\r\n2. Following sample concentration, accurate quantification methods for waterborne pathogens are needed, especially at the point of sample collection. The surge of COVID-19 in late 2019 called for a more urgent need for a rapid and cost-effective quantification of SARS-CoV-2 in environmental waters. Quantification results contribute to wastewater-based epidemiology (WBE) which helps the monitoring of prevalent infections within a community and early detections of contamination. Here we demonstrated the usage of our portable membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system for absolute quantification of SARS CoV-2 in wastewater samples within a one-hour timeframe for point-of-use (POU) testing and data management. The limit of detection (LOD) of mgLAMP for SARS-CoV-2 quantification in Milli-Q water was observed to be down to 1 copy/mL, and that in surface water collected from Kathmandu, Nepal was down to 100 copies/mL. Both were 100-fold lower than that of RT-qPCR in corresponding matrices. Compared to alternative detection methods, our platform has a very high level of tolerance against inhibitors thanks to the restriction of the hydrogel matrix. This enables the highly sensitive detection in either clinical or environmental samples.
\r\n\r\n3. Regular environmental surveillance of waterborne pathogens is key to ensure the safety of water and protect public health. Due to the diversity of pathogenic bacteria in environmental waters, regular monitoring of so many pathogens for individuality is impractical. Therefore, microbial indicators are used to gauge the total pathogen concentration; and manage waterborne health risks. In this study, the interactions of V. cholerae, the etiologic agent of reemerging cholera, with E. coli, the most commonly used indicator for waterborne pathogens. Specifically, we investigated through evaluating the survival and growth of both bacteria under different temperature and nutrition deprivation using plate culturing and real-time polymerase chain reaction (qPCR). During co-growth, it was challenging for V. Cholerae to maintain initial population advantages as E. coli consumes nutrition more effectively. Whereas during co-existence, V. Cholerae soon fell into a viable-but\u2013non-culturable state under environmental stress in 3-5 days while E. coli stay viable more than 14 days. We found that V. cholerae interacts with E. coli differently depending on the composition of the water that is sampled and analyzed. This suggests that bacterium-bacterium interactions influenced by the intrinsic chemical and biological parameters of ambient water will be a contributing mechanism in regulating the proliferation of V. cholerae.
\r\n\r\nIn summary, two platforms for environmental sample concentration and detection have been developed and tested using ambient and engineered waters. In addition, interactions between a microbial indicator, E. coli, and the pathogenic bacteria, V. Cholerae, were studied. The chapters in this thesis describe in detail: (1) A hand-pressed 3D-printed system to produce SAP microspheres was developed with the goal of achieving efficient concentrations of environmental microorganisms for subsequent analysis. The simplified concentration procedure and can be easily integrated into various detection platforms; (2) A portable membrane-based in-gel loop-mediated isothermal amplification (mgLAMP) system was developed for absolute quantification of SARS-CoV-2 in environmental water samples within one hour, enabling a 100-fold lower detection limit compared to the gold-standard of RT-qPCR; and (3) Differences in bacterium-bacterium interactions of V. cholerae and E. coli under as a function of water composition indicated that environmental stress presented in ambient water matrices should be taken into consideration while using a microbial indicator such as E. coli to estimate the risk of waterborne pathogens. These collective advances allow for the rapid and ultrasensitive POU testing of waterborne pathogens that should provide for more effective monitoring strategies in terms of the use of indicator microorganisms.
", "doi": "10.7907/fwhf-a510", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:14050", "collection": "thesis", "collection_id": "14050", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01102021-045431757", "type": "thesis", "title": "Prebiotic Fingerprints", "author": [ { "family_name": "Chimiak", "given_name": "Laura Marie", "orcid": "0000-0002-5047-5421", "clpid": "Chimiak-Laura-Marie" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Blake", "given_name": "Geoffrey A.", "orcid": "0000-0003-0787-1610", "clpid": "Blake-G-A" }, { "family_name": "Burnett", "given_name": "Donald S.", "clpid": "Burnett-D-S" }, { "family_name": "Rossman", "given_name": "George Robert", "orcid": "0000-0002-4571-6884", "clpid": "Rossman-G-R" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Meteorites contain organic compounds that occur in all known life. These compounds, commonly referred to as prebiotic compounds, include \u03b1-amino acids and are most prevalent on carbonaceous chondrites. As carbonaceous chondrites are pristine samples from early in the solar system that have not had living organisms on them, we can study the chemistry that produced \u03b1-amino acids on them to better understand the processes by which they might have formed on early Earth or on other bodies. Multiple syntheses have been put forth as routes to form amino acids on meteorites and include ice-grain chemistry on interstellar ices and Strecker synthesis in meteorite parent bodies. Prior measurements of molecular-average carbon isotope ratios (\u00b9\u00b3C/\u00b9\u00b2C) have found \u00b9\u00b3C enrichments of up to 53\u2030 in certain \u03b1-amino acids and molecular-average hydrogen isotope ratios (D/H) have found enrichments of 100s of \u2030. With this data, it has been suggested that Strecker synthesis\u2014a synthesis in which an aldehyde or ketone reacts with ammonia and cyanide to produce an \u03b1-aminonitrile that is hydrolyzed into an \u03b1-amino amide and then an \u03b1-amino acid\u2014is the primary pathway to produce \u03b1-amino acids on aqueously altered meteorites.
\r\n\r\nHere, we develop an instrument that can measure site-specific isotope ratios (SSIR) for carbon \u2014 that is the \u00b9\u00b2C/\u00b9\u00b3C at each site in a molecule \u2014 and use it to first constrain the site-specific isotope effects associated with Strecker synthesis and then the carbon SSIR of an alanine sample extracted from the Murchison meteorite. The instrument, the Q-Exactive Orbitrap, is a Fourier Transform Mass Spectrometer that has resolution of 240,000 full width-half maximum and can measure site-specific carbon isotope ratios on samples as small as 1 picomole. When we use it to measure the carbon SSIR in multiple samples of alanine produced by Strecker synthesis, we find a -20 \u2030 equilibrium isotope effect between the product alanine's C-2 site (amine carbon, \u00b9\u00b3C-depleted) reactant acetaldehyde\u2019s carbonyl carbon (\u00b9\u00b3C-enriched), a potential -15 \u2030 kinetic isotope effect on the C-1 site (eventual carboxyl carbon) for the first hydrolysis of \u03b1-aminopropanenitrile (\u00b9\u00b3C-enriched) into alaninamide (\u00b9\u00b3C-depleted), and a -15.4 \u2030 kinetic isotope effect on the C-1 carbon for the second hydrolysis step in which \u03b1-alaninamide (\u00b9\u00b3C-enriched) becomes alanine (\u00b9\u00b3C-depleted). Through conventional isotope ratio mass spectrometry, we also measure a +56.4 \u2030 equilibrium isotope effect between ammonia (\u00b9\u2075N-depleted) and the amine site on alanine (\u00b9\u2075N-enriched). When we measure the sample of alanine from the Murchison meteorite, we find site-specific carbon isotope ratios of -29 \u00b1 10 \u2030, 142 \u00b1 20 \u2030, and -36 \u00b1 20 \u2030 for the C-1, C-2, and C-3 (methyl) sites, respectively. This pattern agrees with the hypothesis that Strecker synthesis created alanine in Murchison. Combining these data with the isotope effects found for Strecker synthesis, we find initial site values of -7 \u00b1 10 \u2030, 162 \u00b1 20 \u2030, and 36 \u00b1 20 \u2030 for the C-1, C-2, and C-3 sites, respectively. With these values, we create a model of potential organic synthesis on the Murchison parent body that predicts the molecular-average \u03b4\u00b9\u00b3C values of 19 other prebiotic compounds.
\r\n\r\nFinally, we create a model that uses the previously measured molecular average carbon and deuterium isotope ratios for organics on Murchison to create models that predict site-specific and molecular average isotope ratios for organic compounds. This model finds that organic compounds with have methyl sites that are enriched in deuterium by up to 3000 \u2030 relative to other sites in the compound and that the degree of enrichment scales both with a compound class\u2019s solubility in water and with a sample\u2019s degree of aqueous alteration and terrestrial weathering. These patterns suggest that a primordial ISM-derived deuterium signal exchanges with water and that the methyl site hosts the highest amount of this enrichment due to its low acidity. The carbon model demonstrates that using only the aldehyde and cyanide values measured on Murchison and isotope effects inferred from other studies, we can predict 59 of 82 organic compounds on it (72%) that have \u03b4\u00b9\u00b3C values spanning over 149 \u2030 with an average residual of 6 \u2030. To achieve this level of prediction, the model combines Strecker synthesis, reductive amination, and oxidation of aldehydes to create straight-chain \u03b1-H hydroxy and amino acids, amines, and monocarboxylic acids with subsequent formaldehyde addition to these compounds to create branches.
", "doi": "10.7907/0hvh-xz81", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "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:14113", "collection": "thesis", "collection_id": "14113", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:04012021-045507416", "primary_object_url": { "basename": "Hao Thesis_FINAL.pdf", "content": "final", "filesize": 4400065, "license": "other", "mime_type": "application/pdf", "url": "/14113/1/Hao Thesis_FINAL.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Road to Equilibrium: Stable Isotope Distribution in Gaseous Alkanes and Thermal History of Geological Hydrocarbons", "author": [ { "family_name": "Xie", "given_name": "Hao", "orcid": "0000-0001-5656-2035", "clpid": "Xie-Hao" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Farley", "given_name": "Kenneth A.", "orcid": "0000-0002-7846-7546", "clpid": "Farley-K-A" }, { "family_name": "Miller", "given_name": "Thomas F.", "orcid": "0000-0002-1882-5380", "clpid": "Miller-T-F" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Naturally occurring hydrocarbon fluids have economic, geological, and environmental significance. Most of the natural hydrocarbon on Earth is formed by thermal alteration of organic matter in the sedimentary basin. My dissertation study is motivated by this question: can we track generation, transformation, storage, and destruction of these subsurface hydrocarbon fluids with isotopic proxies? The conventional geochemical toolkit includes relative compositional abundances, such as wetness and C1/(C2+C3) ratio, and stable isotope ratios of 13C/12C and 2H/1H, on both the bulk (material-average) and compound-specific (molecular-average) levels. However, these signatures often rely on empirical categorizations and calibrations, so they can be prone to ambiguities, errors, and inconsistencies. This thesis presents a series of work that develops and refines stable isotope proxies of gaseous hydrocarbon (C1-C5) molecules. My approaches overcome the problems in mainly two ways. (1) I add new analytical techniques to acquire isotopologue ratios of compounds. I establish two new analytical proxies, multiply substituted isotopologues (clumped isotopes) of methane, and position-specific isotope ratios of propane, using recently advanced high-resolution isotope ratio mass spectrometry. (2) I use rigorous thermodynamic and kinetic constraints of isotope distribution in hydrocarbon molecules to interpret isotopic data in natural samples. These constraints are determined by theories and experiments. For thermodynamic control, I conducted catalytic exchange experiments to calibrate equilibrium isotope effect for propane position-specific hydrogen isotopes (Chapter 2) and compound-specific hydrogen isotope fractionation between alkanes (Chapter 4) and tested quantum chemical calculations. For expression of kinetic isotope effects, I implemented a statistical approach, the kinetic Monte Carlo method, to calculate the intramolecular and intermolecular stable isotope composition of alkanes generated by radical cracking mechanism in catagenesis (Chapter 6). I measured position-specific hydrogen isotopes of propane (Chapter 3) and methane clumped isotopes (Chapter 5) in natural gas samples from global reservoirs, and compiled compound-specific isotope data in the literatures (Chapter 5 and 6). Results show similarities in isotope ordering of these molecules, which is that gas formed at lower temperature/depth expresses kinetic isotope effects, but gas formed or buried at higher temperature for longer times is in equilibrium. The switch from kinetic control to thermodynamic control is likely a result of thermally-activated hydrogen exchange. This trend provides the foundation for tracking generation and thermal evolution of subsurface hydrocarbons with stable isotope proxies.
", "doi": "10.7907/neh6-6c82", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:13982", "collection": "thesis", "collection_id": "13982", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:10202020-173641319", "primary_object_url": { "basename": "johnson_daniel_2020.pdf", "content": "final", "filesize": 25036841, "license": "other", "mime_type": "application/pdf", "url": "/13982/1/johnson_daniel_2020.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Sulfur Isotopic Insights into the Modern and Ancient Marine Sulfur Cycles", "author": [ { "family_name": "Johnson", "given_name": "Daniel Lee", "orcid": "0000-0002-7443-1546", "clpid": "Johnson-Daniel-Lee" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Rosenthal", "given_name": "Yair", "orcid": "000-0002-7546-6011", "clpid": "Rosenthal-Yair" }, { "family_name": "Adkins", "given_name": "Jess F.", "orcid": "0000-0002-3174-5190", "clpid": "Adkins-J-F" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "The marine sulfur cycle plays a key role in regulating Earth's surface oxygen (O\u2082) levels through its interactions with the carbon and iron cycles. Our understanding of the sulfur cycle has traditionally come from measurements of the sulfur isotopic compositions of marine sulfate (SO\u2084\u00b2\u207b) and sulfur-bearing materials in marine sediments. Because the residence time of SO\u2084\u00b2\u207b in seawater is long (Myr) compared to the mixing time of Earth's oceans (kyr), the concentration and sulfur isotopic composition of marine SO\u2084\u00b2\u207b are homogeneous in modern seawater and are assumed to have been homogeneous throughout most of the Phanerozoic Eon (541 Ma to the present). This assumption of homogeneity, when combined with sulfur isotopic composition measurements, has enabled box model reconstructions of the relative fluxes of oxidized versus reduced sulfur leaving the oceans at times in Earth's past. Such reconstructions have informed our understanding of the interactions between Earth's tectonics, climate, and elemental cycles.
\r\n\r\nThis thesis tests some of the key assumptions made in sulfur cycle box models and attempts to better understand sulfur isotopic variability in geologic archives using a combination of measurements and modeling. Measurements of the sulfur isotopic composition (i.e., \u03b4\u00b3\u2074S) of SO\u2084\u00b2\u207b in Permo-Carboniferous brachiopod shells demonstrate that more precise records of SO\u2084\u00b2\u207b \u03b4\u00b3\u2074S may be generated via careful sampling that avoids diagenetically altered phases (Chapter II). Furthermore, measurements of heterogeneous carbonate associated sulfate (CAS) \u03b4\u00b3\u2074S within carbonates deposited across the End-Permian mass extinction (EPME) in South China show that a lack of careful sampling can substantially alter our understanding of the marine sulfur cycle at times in Earth's past (Chapter III). Simple models constructed in each of these studies indicate that changes in the \u03b4\u00b3\u2074S of the sulfur input to the ocean, the \u03b4\u00b3\u2074S offset (i.e., \u0394\u03b4\u00b3\u2074S) between the oxidized and reduced sulfur output fluxes, and the amount of SO\u2084\u00b2\u207b incorporated during diagenetic alteration - all assumed to be negligible in many studies of the marine sulfur cycle - may viably explain these data. Development of a sediment diagenesis model that includes sulfur isotopic species demonstrates that variations in organic matter rain rate, ferric iron input, sedimentation rate, bottom water O\u2082 concentration, and bottom water SO\u2084\u00b2\u207b concentration may all affect \u0394\u03b4\u00b3\u2074S in a given sedimentary environment (Chapter IV). Application of this model to pore water SO\u2084\u00b2\u207b and hydrogen sulfide H\u2082S \u03b4\u00b3\u2074S data from International Ocean Discovery Program (IODP) Expedition 361, IODP Expedition 363, and R.V. Knorr cruise KN223 sites shows that \u0394\u03b4\u00b3\u2074S is ubiquitously large in these deep ocean sedimentary environments (Chapter V). Cluster analysis of pore water [SO\u2084\u00b2\u207b] profiles collected during previous deep ocean cruises successfully extracts and groups profiles that are similar to those observed on these three cruises (Chapter VI). Comparison of cluster data to a compilation of recent marine pyrite (FeS\u2082) \u03b4\u00b3\u2074S data confirms that pyrite burial in shelf sediments constitutes the majority of pyrite burial occurring globally in the modern day. However, changes in sea level or in other variables that affect sediment deposition may plausibly force an increase in deep ocean pyrite burial and a corresponding change in the global \u0394\u03b4\u00b3\u2074S. Future studies of the modern and ancient marine sulfur cycles must carefully consider the geologic and geochemical context of sulfur isotopic measurements - including sea level changes, sedimentation rate changes, and measured or presumed concentrations of other redox-active species - if interpretations of such data are to be robust.
", "doi": "10.7907/vc71-ht05", "publication_date": "2021", "thesis_type": "phd", "thesis_year": "2021" }, { "id": "thesis:11715", "collection": "thesis", "collection_id": "11715", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-145745731", "type": "thesis", "title": "Understanding Geochemical Tracers in Deep-Sea Corals from a Biomineralization Perspective", "author": [ { "family_name": "Chen", "given_name": "Sang", "orcid": "0000-0001-8941-0791", "clpid": "Chen-Sang" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Lea", "given_name": "David W.", "clpid": "Lea-David-W" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Deep-sea corals have been developed as a useful archive of the chemistry and circulation of intermediate and deep waters in past oceans over the last three decades. However, applications of traditional paleoceanographic tracers in deep-sea corals remain a challenge due to our incomplete understanding of the biomineralization mechanisms underlying the incorporation of these tracers and their variabilities in the coral skeletons (a.k.a. the \"vital effects\"). In this thesis, an effort was made to understand the vital effects associated with the stable isotope as well as minor and trace element compositions of the aragonitic skeletons of the deep-sea coral species Desmophyllum dianthus, through a combination of empirical observations and a numerical model of coral calcification. Observations of the chemical and isotopic compositions of the coral skeletons were performed on four different spatial scales in a suite of modern D. dianthus specimens: bulk samples, micromilled samples, SIMS and nanoSIMS. These observations reveal tracer correlations in deep-sea corals that are coherent over different spatial scales and point toward a universal mechanism of the incorporation of these tracers through the biomineralization process. A few tracers emerge as promising proxies for the temperature (Li/Mg, Sr/Ca) and carbonate chemistry (U/Ca, B/Ca, Ba/Ca) of the oceans. The numerical model for coral calcification explains the strong \u03b418O and \u03b413C vital effects in individual deep-sea corals with an updated physicochemical basis, and carbonic anhydrase is found to play a key role in setting the slopes of the strong \u03b418O-\u03b413C correlations in different biogenic carbonates. The model also constrains the key physical parameters in the biomineralization process and is extended to explain the observed minor and trace element variabilities and correlations in deep-sea corals. The model can qualitatively explain the observed correlation patterns between Mg/Ca, Li/Ca, B/Ca and Sr/Ca in the coral skeletons, but quantitative data-model comparison is limited by both deficiencies in high-quality data and a lack of a well-constrained inorganic reference frame for aragonite. Future improvements in the geochemical tracers in biogenic carbonates will benefit from more extended empirical calibrations as well as a more complete mechanistic understanding of the key physicochemical and biological processes underlying the incorporation of tracers.
", "doi": "10.7907/54TA-JK92", "publication_date": "2019", "thesis_type": "phd", "thesis_year": "2019" }, { "id": "thesis:10666", "collection": "thesis", "collection_id": "10666", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01312018-211454203", "type": "thesis", "title": "Clumped and Intramolecular Isotopic Perspectives on the Behavior of Organic and Inorganic Carbon in the Shallow Crust and Deep Biosphere", "author": [ { "family_name": "Lloyd", "given_name": "Max Kaufmann", "orcid": "0000-0001-9367-2698", "clpid": "Lloyd-Max-Kaufmann" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Although the upper crust is the most accessible swath of the subsurface, the geochemical processes therein are challenging to observe. Here, I use site-specific and \u2018clumped\u2019 isotope analyses (where multiple rare, heavy isotopes are bound in single molecules) of carbonates and organic solids to explore petrology, brittle tectonics, diagenesis, and biodegradation in the shallow crust. In carbonates, I employ contact aureoles, regional metamorphic terranes, thermal and geochemical models, and high-pressure experiments, to extract nuanced thermal and chemical histories. In the organic realm, I develop new methods to measure the clumped 13C \u2013 2H composition of methoxyl groups (R \u2013 O \u2013 CH3) from kerogen, lignin, and other complex organic substrates. This work expands the field of clumped isotope geochemistry into the realm of solid compounds, and enables new, site-specific isotopic perspectives on the shallow crustal transformations of organic carbon substrates and the microbial assemblages that live on them.
", "doi": "10.7907/Z96T0JV5", "publication_date": "2018", "thesis_type": "phd", "thesis_year": "2018" }, { "id": "thesis:10330", "collection": "thesis", "collection_id": "10330", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06092017-091849904", "primary_object_url": { "basename": "chemical-controls-dissolution.pdf", "content": "final", "filesize": 128933757, "license": "other", "mime_type": "application/pdf", "url": "/10330/1/chemical-controls-dissolution.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Chemical Controls on the Dissolution Kinetics of Calcite in Seawater", "author": [ { "family_name": "Subhas", "given_name": "Adam Vinay", "orcid": "0000-0002-7688-6624", "clpid": "Subhas-Adam-Vinay" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Berelson", "given_name": "William M.", "clpid": "Berelson-W-M" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "local_group": [ { "literal": "Resnick Sustainability Institute" }, { "literal": "div_gps" } ], "abstract": "Calcium carbonate minerals are abundant on the earth\u2019s surface. Delivery of alkalinity to the oceans is balanced by the production and burial of calcium carbonate in marine sediments, which results in a large reservoir of sedimentary calcium carbonate both in the ocean and in terrestrial rocks. Alkalinity also provides oceanic buffering capacity, which today results in about 60 times more dissolved carbon dioxide in the world oceans than is present as carbon dioxide gas in the atmosphere. Because calcium carbonate formation removes alkalinity from the oceans, calcium carbonate precipitation leads to the outgassing of carbon dioxide from the ocean into the atmosphere. Likewise, the dissolution of calcium carbonate adds alkalinity to the oceans, leading to an increased buffering capacity and a drawdown of atmospheric carbon dioxide concentration.
\r\n\r\nCalcium carbonate precipitation in the form of calcite and aragonite is almost exclusively mediated by biological organisms such as corals, coccoliths, and foraminifera, which use these minerals as components in their shells. calcium carbonate is overproduced by organisms in the ocean relative to the flux of alkalinity delivered to the oceans by rivers. Thus, a significant portion of calcium carbonate must be dissolved back into seawater for the ocean alkalinity cycle to come into steady state. Because of the link between alkalinity and carbon dioxide, the ocean alkalinity cycle has a direct effect on atmospheric carbon dioxide concentration especially on timescales less than 100,000 years.
\r\n\r\nHow fast calcium carbonate dissolves back into seawater is thus a crucial rate in determining the response of the oceanic system to perturbations in either alkalinity or carbon dioxide input to the ocean-atmosphere system. We are testing the kinetics of this system with the large amount of carbon dioxide emitted from fossil fuel burning, about one third of which has dissolved into the surface ocean. This process is known as ocean acidification, as carbon dioxide is an acid, soaking up buffering capacity and dropping ocean pH. This carbon dioxide will eventually be neutralized through the dissolution of carbonate rich deep-sea sediments, but the process will take a long time. This thesis makes new measurements calcite dissolution in seawater, in an attempt to build an understanding of the chemical processes responsible for dissolution kinetics.
\r\n\r\nI first introduce the new method, in which carbon-13 labeled calcium carbonate is dissolved in undersaturated seawater. Mass loss is directly traced by measuring the appearance of carbon-13 in seawater over time. The dissolution rate of calcite is a highly nonlinear function of calcite saturation state.
\r\n\r\nNext, I show that this tracer can tell us about the balance of precipitation and dissolution at the mineral surface. I use this balance to constrain mass fluxes due to precipitation and dissolution as a function of saturation state. I also show that the enzyme Carbonic Anhydrase (CA), which rapidly equilibrates carbon dioxide and carbonic acid, greatly enhances the rate of calcite dissolution especially near equilibrium. A model of dissolution is presented in which CA is most effective in the region where dissolution proceeds via etch pit nucleation at surface defects.
\r\n\r\nThe dissolution behavior of biogenic carbonates is also investigated using the carbon-13 method. I cultured coccoliths, foraminifera, and soft corals in carbon-13-labeled seawater so that their skeletons incorporated the carbon-13 tracer. These skeletons were then used in dissolution experiments. I show that both magnesium and organic matter contained within the calcite lattice have large effects on the dissolution behavior of biogenic carbonates. Magnesium content generally increases dissolution rate, and it is hypothesized that highly soluble magnesium-rich phases are preferentially removed from dissolving carbonates. Organic content generally decreases dissolution rate. It is hypothesized that organic matrices within the calcite lattice promote re-precipitation reactions, due to the balance of dissolution and precipitation rates in our data, and their promotion of precipitation during biomineralization.
\r\n\r\nI then analyze in 2- and 3-dimensions dissolved foraminiferal tests to locate where and how mass is being lost. It is shown that dissolution proceeds along specific layers, that are consistent with the size and location of Mg-rich carbonate spherules that are initially deposited during chamber formation. Surface topography generation of foraminiferal tests shows that sub-micron features are formed rapidly and then quickly eroded into larger pits and channels. These larger channels then propagate and cover the test surface at higher amounts of mass loss.
\r\n\r\nFinally, the involvement of CA in carbonate dissolution necessitates the measurement of CA activity in the environment, especially in carbonate-rich ecosystems such as reefs, carbonate-rich sediments, and carbonate-rich marine particles. To this end, I survey a number of available techniques for measuring CA activity. In the end, it is shown that the most effective method is based on measuring the depletion of oxygen-18 from carbon-13- and oxygen-18-labeled DIC, as measured by membrane inlet mass spectrometry (MIMS). This method is promising and shows about 0.1 nM CA present in unfiltered surface seawater collected from San Pedro Basin.
", "doi": "10.7907/Z93X84P3", "publication_date": "2017", "thesis_type": "phd", "thesis_year": "2017" }, { "id": "thesis:9837", "collection": "thesis", "collection_id": "9837", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06032016-150348563", "primary_object_url": { "basename": "Slotznick_Sarah_Thesis_2016.pdf", "content": "final", "filesize": 96312207, "license": "other", "mime_type": "application/pdf", "url": "/9837/7/Slotznick_Sarah_Thesis_2016.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Coupling Textural, Magnetic, and Modeling Techniques to Understand Precambrian Paleoenvironments", "author": [ { "family_name": "Slotznick", "given_name": "Sarah Pearl", "orcid": "0000-0001-8374-3173", "clpid": "Slotznick-Sarah-Pearl" } ], "thesis_advisor": [ { "family_name": "Kirschvink", "given_name": "Joseph L.", "orcid": "0000-0001-9486-6689", "clpid": "Kirschvink-J-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Kirschvink", "given_name": "Joseph L.", "orcid": "0000-0001-9486-6689", "clpid": "Kirschvink-J-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Grotzinger", "given_name": "John P.", "orcid": "0000-0001-9324-1257", "clpid": "Grotzinger-J-P" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "The oxygenation of our planet is perhaps the greatest transition in its history, dramatically affecting geochemical cycles and the evolution of life. Major first-order questions still remain about late Archean and Proterozoic environments, even as newly developed geochemical techniques provide additional constraints and create subtle conundrums. I apply a new approach to classic localities to understand Precambrian redox character and paleoenvironmental conditions by combining textural observations from optical and electron microscopy, isotopic measurements, and (synchrotron-based) x-ray spectroscopy with scanning magnetic microscopy and bulk rock magnetic experiments. Models paired with data from the literature provide additional context for these measurement results.
\r\n\r\nThe first portion of this dissertation focuses on understanding the predominant microbial metabolism recorded in the 2.72 Ga Tumbiana Formation stromatolites. I proposed that these stromatolites formed in shallow, anoxic waters and record a global signature of unique autotrophy distinct from younger systems dominated by oxygenic photosynthesis. The next portion of this dissertation uses the redox sensitivity of iron as a tool to investigate paleoredox conditions of the 1.45 Ga lower Belt Supergroup during a potentially transitional time-period in surface environments. Observations of primary mineralogy in early diagenetic pyrite and detrital iron oxides suggest an oxygenated water-column overlying anoxic, sulfidic pore-fluids very similar to the modern. The final portion of this dissertation assesses the effects of prevalent secondary overprints on the use of iron as a paleoredox proxy. Theoretical data-driven models combined with trends from the Belt Supergroup highlight the mobility of iron during progressive burial metamorphism as well as in diagenetic transformations and reactions with infiltrating fluids. Applying coupled techniques, specifically including textural methods, is vital for untangling secondary alterations from primary records of environmental conditions during the Precambrian.
\u2003\r\n", "doi": "10.7907/Z9HT2M8X", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "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:9768", "collection": "thesis", "collection_id": "9768", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05262016-132232540", "primary_object_url": { "basename": "ETR_Thesis_Final.pdf", "content": "final", "filesize": 120182434, "license": "other", "mime_type": "application/pdf", "url": "/9768/43/ETR_Thesis_Final.pdf", "version": "v6.0.0" }, "type": "thesis", "title": "Molecular and Geochemical Insights into Microbial Life Centimeters to Kilometers Below the Seafloor", "author": [ { "family_name": "Trembath-Reichert", "given_name": "Elizabeth", "orcid": "0000-0002-3979-8676", "clpid": "Trembath-Reichert-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "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.
", "doi": "10.7907/Z96Q1V6Q", "publication_date": "2016", "thesis_type": "phd", "thesis_year": "2016" }, { "id": "thesis:8864", "collection": "thesis", "collection_id": "8864", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05182015-162708844", "primary_object_url": { "basename": "JohnsonJE-2015_PhdThesis_final.pdf", "content": "final", "filesize": 357112948, "license": "other", "mime_type": "application/pdf", "url": "/8864/84/JohnsonJE-2015_PhdThesis_final.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "Manganese: Minerals, Microbes, and the Evolution of Oxygenic Photosynthesis", "author": [ { "family_name": "Johnson", "given_name": "Jena Elaine", "clpid": "Johnson-Jena-Elaine" } ], "thesis_advisor": [ { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Fischer", "given_name": "Woodward W.", "orcid": "0000-0002-8836-3054", "clpid": "Fischer-W-W" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Webb", "given_name": "Samuel M.", "clpid": "Webb-S-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Oxygenic photosynthesis fundamentally transformed our planet by releasing molecular oxygen and altering major biogeochemical cycles, and this exceptional metabolism relies on a redox-active cubane cluster of four manganese atoms. Not only is manganese essential for producing oxygen, but manganese is also only oxidized by oxygen and oxygen-derived species. Thus the history of manganese oxidation provides a valuable perspective on our planet\u2019s environmental past, the ancient availability of oxygen, and the evolution of oxygenic photosynthesis. Broadly, the general trends of the geologic record of manganese deposition is a chronicle of ancient manganese oxidation: manganese is introduced into the fluid Earth as Mn(II) and it will remain only a trace component in sedimentary rocks until it is oxidized, forming Mn(III,IV) insoluble precipitates that are concentrated in the rock record. Because these manganese oxides are highly favorable electron acceptors, they often undergo reduction in sediments through anaerobic respiration and abiotic reaction pathways.
\r\n\r\nThe following dissertation presents five chapters investigating manganese cycling both by examining ancient examples of manganese enrichments in the geologic record and exploring the mineralogical products of various pathways of manganese oxide reduction that may occur in sediments. The first chapter explores the mineralogical record of manganese and reports abundant manganese reduction recorded in six representative manganese-enriched sedimentary sequences. This is followed by a second chapter that further analyzes the earliest significant manganese deposit 2.4 billon years ago, and determines that it predated the origin of oxygenic photosynthesis and thus is supporting evidence for manganese-oxidizing photosynthesis as an evolutionary precursor prior to oxygenic photosynthesis. The lack of oxygen during this early manganese deposition was partially established using oxygen-sensitive detrital grains, and so a third chapter delves into what these grains mean for oxygen constraints using a mathematical model. The fourth chapter returns to processes affecting manganese post-deposition, and explores the relationships between manganese mineral products and (bio)geochemical reduction processes to understand how various manganese minerals can reveal ancient environmental conditions and biological metabolisms. Finally, a fifth chapter considers whether manganese can be mobilized and enriched in sedimentary rocks and determines that manganese was concentrated secondarily in a 2.5 billion-year-old example from South Africa. Overall, this thesis demonstrates how microbial processes, namely photosynthesis and metal oxide-reducing metabolisms, are linked to and recorded in the rich complexity of the manganese mineralogical record.
", "doi": "10.7907/Z9RF5S0X", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8903", "collection": "thesis", "collection_id": "8903", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05282015-153534197", "primary_object_url": { "basename": "Jessica Ricci Thesis 2015 FINAL.pdf", "content": "final", "filesize": 4770646, "license": "other", "mime_type": "application/pdf", "url": "/8903/1/Jessica Ricci Thesis 2015 FINAL.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Constraining the Interpretation of 2-Methylhopanoids through Genetic and Phylogenetic Methods", "author": [ { "family_name": "Ricci", "given_name": "Jessica Nicole", "clpid": "Ricci-Jessica-Nicole" } ], "thesis_advisor": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "thesis_committee": [ { "family_name": "Sternberg", "given_name": "Paul W.", "orcid": "0000-0002-7699-0173", "clpid": "Sternberg-P-W" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "orcid": "0000-0003-2713-1513", "clpid": "Mazmanian-S-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "orcid": "0000-0002-7033-0844", "clpid": "Leadbetter-J-R" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "local_group": [ { "literal": "div_bbe" } ], "abstract": "Hopanoids are a class of sterol-like lipids produced by select bacteria. Their preservation in the rock record for billions of years as fossilized hopanes lends them geological significance. Much of the structural diversity present in this class of molecules, which likely underpins important biological functions, is lost during fossilization. Yet, one type of modification that persists during preservation is methylation at C-2. The resulting 2-methylhopanoids are prominent molecular fossils and have an intriguing pattern over time, exhibiting increases in abundance associated with Ocean Anoxic Events during the Phanerozoic. This thesis uses diverse methods to address what the presence of 2-methylhopanes tells us about the microbial life and environmental conditions of their ancient depositional settings. Through an environmental survey of hpnP, the gene encoding the C-2 hopanoid methylase, we found that many different taxa are capable of producing 2-methylhopanoids in more diverse modern environments than expected. This study also revealed that hpnP is significantly overrepresented in organisms that are plant symbionts, in environments associated with plants, and with metabolisms that support plant-microbe interactions; collectively, these correlations provide a clue about the biological importance of 2-methylhopanoids. Phylogenetic reconstruction of the evolutionary history of hpnP revealed that 2-methylhopanoid production arose in the Alphaproteobacteria, indicating that the origin of these molecules is younger than originally thought. Additionally, we took genetic approach to understand the role of 2-methylhopanoids in Cyanobacteria using the filamentous symbiotic Nostoc punctiforme. We found that hopanoids likely aid in rigidifying the cell membrane but do not appear to provide resistance to osmotic or outer membrane stressors, as has been shown in other organisms. The work presented in this thesis supports previous findings that 2-methylhopanoids are not biomarkers for oxygenic photosynthesis and provides new insights by defining their distribution in modern environments, identifying their evolutionary origin, and investigating their role in Cyanobacteria. These efforts in modern settings aid the formation of a robust interpretation of 2-methylhopanes in the rock record. ", "doi": "10.7907/Z9MC8X0S", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8923", "collection": "thesis", "collection_id": "8923", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05292015-100107828", "primary_object_url": { "basename": "PiaseckiThesis_final.pdf", "content": "final", "filesize": 6514782, "license": "other", "mime_type": "application/pdf", "url": "/8923/1/PiaseckiThesis_final.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Site-Specific Isotopes in Small Organic Molecules", "author": [ { "family_name": "Piasecki", "given_name": "Alison Martha", "clpid": "Piasecki-Alison-Martha" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Asimow", "given_name": "Paul David", "clpid": "Asimow-P-D" }, { "family_name": "Farley", "given_name": "Kenneth A.", "clpid": "Farley-K-A" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Stable isotope geochemistry is a valuable toolkit for addressing a broad range of problems in the geosciences. Recent technical advances provide information that was previously unattainable or provide unprecedented precision and accuracy. Two such techniques are site-specific stable isotope mass spectrometry and clumped isotope thermometry. In this thesis, I use site-specific isotope and clumped isotope data to explore natural gas development and carbonate reaction kinetics. In the first chapter, I develop an equilibrium thermodynamics model to calculate equilibrium constants for isotope exchange reactions in small organic molecules. This equilibrium data provides a framework for interpreting the more complex data in the later chapters. In the second chapter, I demonstrate a method for measuring site-specific carbon isotopes in propane using high-resolution gas source mass spectrometry. This method relies on the characteristic fragments created during electron ionization, in which I measure the relative isotopic enrichment of separate parts of the molecule. My technique will be applied to a range of organic compounds in the future. For the third chapter, I use this technique to explore diffusion, mixing, and other natural processes in natural gas basins. As time progresses and the mixture matures, different components like kerogen and oil contribute to the propane in a natural gas sample. Each component imparts a distinct fingerprint on the site-specific isotope distribution within propane that I can observe to understand the source composition and maturation of the basin. Finally, in Chapter Four, I study the reaction kinetics of clumped isotopes in aragonite. Despite its frequent use as a clumped isotope thermometer, the aragonite blocking temperature is not known. Using laboratory heating experiments, I determine that the aragonite clumped isotope thermometer has a blocking temperature of 50-100\u00b0C. I compare this result to natural samples from the San Juan Islands that exhibit a maximum clumped isotope temperature that matches this blocking temperature. This thesis presents a framework for measuring site-specific carbon isotopes in organic molecules and new constraints on aragonite reaction kinetics. This study represents the foundation of a future generation of geochemical tools for the study of complex geologic systems. ", "doi": "10.7907/Z9833PZP", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8637", "collection": "thesis", "collection_id": "8637", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:08182014-160835979", "primary_object_url": { "basename": "final_thesis_electronic_format.pdf", "content": "final", "filesize": 28484306, "license": "other", "mime_type": "application/pdf", "url": "/8637/1/final_thesis_electronic_format.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "From Lakes to Lungs: Assessing Microbial Activity in Diverse Environments ", "author": [ { "family_name": "Kopf", "given_name": "Sebastian Hermann", "clpid": "Kopf-Sebastian-Hermann" } ], "thesis_advisor": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "thesis_committee": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "John M.", "orcid": "0000-0001-5768-7593", "clpid": "Eiler-J-M" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "All major geochemical cycles on the Earth\u2019s 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.
\r\n\r\nPart 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.
\r\n\r\nPart 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.
", "doi": "10.7907/Z9HQ3WV6", "publication_date": "2015", "thesis_type": "phd", "thesis_year": "2015" }, { "id": "thesis:8404", "collection": "thesis", "collection_id": "8404", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05272014-225828922", "primary_object_url": { "basename": "Stolper_Daniel_2014_Thesis.pdf", "content": "final", "filesize": 4137579, "license": "other", "mime_type": "application/pdf", "url": "/8404/1/Stolper_Daniel_2014_Thesis.pdf", "version": "v5.0.0" }, "type": "thesis", "title": "New Insights into the Formation and Modification of Carbonate-Bearing Minerals and Methane Gas in Geological Systems using Multiply Substituted Isotopologues", "author": [ { "family_name": "Stolper", "given_name": "Daniel Aaron", "orcid": "0000-0003-3299-3177", "clpid": "Stolper-Daniel-Aaron" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Grotzinger", "given_name": "John P.", "clpid": "Grotzinger-J-P" } ], "thesis_committee": [ { "family_name": "Fischer", "given_name": "Woodward W.", "clpid": "Fischer-W-W" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Grotzinger", "given_name": "John P.", "clpid": "Grotzinger-J-P" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "This thesis describes the use of multiply-substituted stable isotopologues of carbonate minerals and methane gas to better understand how these environmentally significant minerals and gases form and are modified throughout their geological histories. Stable isotopes have a long tradition in earth science as a tool for providing quantitative constraints on how molecules, in or on the earth, formed in both the present and past. Nearly all studies, until recently, have only measured the bulk concentrations of stable isotopes in a phase or species. However, the abundance of various isotopologues within a phase, for example the concentration of isotopologues with multiple rare isotopes (multiply substituted or 'clumped' isotopologues) also carries potentially useful information. Specifically, the abundances of clumped isotopologues in an equilibrated system are a function of temperature and thus knowledge of their abundances can be used to calculate a sample\u2019s formation temperature. In this thesis, measurements of clumped isotopologues are made on both carbonate-bearing minerals and methane gas in order to better constrain the environmental and geological histories of various samples.
\r\n\r\nClumped-isotope-based measurements of ancient carbonate-bearing minerals, including apatites, have opened up paleotemperature reconstructions to a variety of systems and time periods. However, a critical issue when using clumped-isotope based measurements to reconstruct ancient mineral formation temperatures is whether the samples being measured have faithfully recorded their original internal isotopic distributions. These original distributions can be altered, for example, by diffusion of atoms in the mineral lattice or through diagenetic reactions. Understanding these processes quantitatively is critical for the use of clumped isotopes to reconstruct past temperatures, quantify diagenesis, and calculate time-temperature burial histories of carbonate minerals. In order to help orient this part of the thesis, Chapter 2 provides a broad overview and history of clumped-isotope based measurements in carbonate minerals.
\r\n\r\nIn Chapter 3, the effects of elevated temperatures on a sample\u2019s clumped-isotope composition are probed in both natural and experimental apatites (which contain structural carbonate groups) and calcites. A quantitative model is created that is calibrated by the experiments and consistent with the natural samples. The model allows for calculations of the change in a sample\u2019s clumped isotope abundances as a function of any time-temperature history.
\r\n\t\r\nIn Chapter 4, the effects of diagenesis on the stable isotopic compositions of apatites are explored on samples from a variety of sedimentary phosphorite deposits. Clumped isotope temperatures and bulk isotopic measurements from carbonate and phosphate groups are compared for all samples. These results demonstrate that samples have experienced isotopic exchange of oxygen atoms in both the carbonate and phosphate groups. A kinetic model is developed that allows for the calculation of the amount of diagenesis each sample has experienced and yields insight into the physical and chemical processes of diagenesis.
\r\n\t\r\nThe thesis then switches gear and turns its attention to clumped isotope measurements of methane. Methane is critical greenhouse gas, energy resource, and microbial metabolic product and substrate. Despite its importance both environmentally and economically, much about methane\u2019s formational mechanisms and the relative sources of methane to various environments remains poorly constrained. In order to add new constraints to our understanding of the formation of methane in nature, I describe the development and application of methane clumped isotope measurements to environmental deposits of methane. To help orient the reader, a brief overview of the formation of methane in both high and low temperature settings is given in Chapter 5.
\r\n\t\r\nIn Chapter 6, a method for the measurement of methane clumped isotopologues via mass spectrometry is described. This chapter demonstrates that the measurement is precise and accurate. Additionally, the measurement is calibrated experimentally such that measurements of methane clumped isotope abundances can be converted into equivalent formational temperatures. This study represents the first time that methane clumped isotope abundances have been measured at useful precisions.
\r\n\t\r\nIn Chapter 7, the methane clumped isotope method is applied to natural samples from a variety of settings. These settings include thermogenic gases formed and reservoired in shales, migrated thermogenic gases, biogenic gases, mixed biogenic and thermogenic gas deposits, and experimentally generated gases. In all cases, calculated clumped isotope temperatures make geological sense as formation temperatures or mixtures of high and low temperature gases. Based on these observations, we propose that the clumped isotope temperature of an unmixed gas represents its formation temperature \u2014 this was neither an obvious nor expected result and has important implications for how methane forms in nature. Additionally, these results demonstrate that methane-clumped isotope compositions provided valuable additional constraints to studying natural methane deposits.
\r\n", "doi": "10.7907/Z9CF9N3Q", "publication_date": "2014", "thesis_type": "phd", "thesis_year": "2014" }, { "id": "thesis:7347", "collection": "thesis", "collection_id": "7347", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:12192012-141624638", "primary_object_url": { "basename": "Dekas_Anne_2013_thesis.pdf", "content": "final", "filesize": 52021793, "license": "other", "mime_type": "application/pdf", "url": "/7347/1/Dekas_Anne_2013_thesis.pdf", "version": "v9.0.0" }, "type": "thesis", "title": "Diazotrophy in the Deep: An Analysis of the Distribution, Magnitude, Geochemical Controls, and Biological Mediators of Deep-Sea Benthic Nitrogen Fixation", "author": [ { "family_name": "Dekas", "given_name": "Anne Elizabeth", "orcid": "0000-0001-9548-8413", "clpid": "Dekas-Anne-Elizabeth" } ], "thesis_advisor": [ { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "thesis_committee": [ { "family_name": "Kirschvink", "given_name": "Joseph L.", "orcid": "0000-0001-9486-6689", "clpid": "Kirschvink-J-L" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Howard", "given_name": "James B.", "clpid": "Howard-J-B" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Biological nitrogen fixation (the conversion of N2 to NH3) is a critical process in the oceans, counteracting the production of N2 gas by dissimilatory bacterial metabolisms and providing a source of bioavailable nitrogen to many nitrogen-limited ecosystems. One currently poorly studied and potentially underappreciated habitat for diazotrophic organisms is the sediments of the deep-sea. Although nitrogen fixation was once thought to be negligible in non-photosynthetically driven benthic ecosystems, the present study demonstrates the occurrence and expression of a diversity of nifH genes (those necessary for nitrogen fixation), as well as a widespread ability to fix nitrogen at high rates in these locations. The following research explores the distribution, magnitude, geochemical controls, and biological mediators of nitrogen fixation at several deep-sea sediment habitats, including active methane seeps (Mound 12, Costa Rica; Eel River Basin, CA, USA; Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA), whale-fall sites (Monterey Canyon, CA), and background deep-sea sediment (off-site Mound 12 Costa Rica, off-site Hydrate Ridge, OR, USA; and Monterey Canyon, CA, USA). The first of the five chapters describes the FISH-NanoSIMS method, which we optimized for the analysis of closely associated microbial symbionts in marine sediments. The second describes an investigation of methane seep sediment from the Eel River Basin, where we recovered nifH sequences from extracted DNA, and used FISH-NanoSIMS to identify methanotrophic archaea (ANME-2) as diazotrophs, when associated with functional sulfate-reducing bacterial symbionts. The third and fourth chapters focus on the distribution and diversity of active diazotrophs (respectively) in methane seep sediment from Mound 12, Costa Rica, using a combination of 15N-labeling experiments, FISH-NanoSIMS, and RNA and DNA analysis. The fifth chapter expands the scope of the investigation by targeting diverse samples from methane seep, whale-fall, and background sediment collected along the Eastern Pacific Margin, and comparing the rates of nitrogen fixation observed to geochemical measurements collected in parallel. Together, these analyses represent the most extensive investigation of deep-sea nitrogen fixation to date, and work towards understanding the contribution of benthic nitrogen fixation to global marine nitrogen cycling.
", "doi": "10.7907/H9F5-T161", "publication_date": "2013", "thesis_type": "phd", "thesis_year": "2013" }, { "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:5955", "collection": "thesis", "collection_id": "5955", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:06222010-150731880", "primary_object_url": { "basename": "Thesis.pdf", "content": "final", "filesize": 2618850, "license": "other", "mime_type": "application/pdf", "url": "/5955/1/Thesis.pdf", "version": "v10.0.0" }, "type": "thesis", "title": "Investigating Sources and Sinks of Organic Aerosols: NO\u2083-initiated Oxidation of Isoprene and Heterogeneous Oxidation of Organic Aerosol\r ", "author": [ { "family_name": "Kwan", "given_name": "Alan Jake-Man", "clpid": "Kwan-Alan-Jake-Man" } ], "thesis_advisor": [ { "family_name": "Wennberg", "given_name": "Paul O.", "clpid": "Wennberg-P-O" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Seinfeld", "given_name": "John H.", "clpid": "Seinfeld-J-H" }, { "family_name": "Okumura", "given_name": "Mitchio", "clpid": "Okumura-M" }, { "family_name": "Wennberg", "given_name": "Paul O.", "clpid": "Wennberg-P-O" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Secondary organic aerosol (SOA) are important components in atmospheric processes and significantly impact human health. The complexity of SOA composition and formation processes has hampered efforts to fully characterize their impacts, and to predict how those impacts will be affected by changes in climate and human activity. Here, we explore SOA formation in the laboratory by coupling an environmental chamber with a suite of analytical tools, including a gas-phase mass spectrometry technique that is well suited for tracking the hydrocarbon oxidation processes that drive SOA formation. Focusing on the oxidation of isoprene by the nitrate radical, NO\u2083, we find that reactions of peroxy radicals (RO\u2082) to form ROOR dimers is an important process in SOA formation. The other gas-phase products of these RO\u2082 reactions differ from what is expected from studies of simpler radicals, indicating that more studies are necessary to fully constrain RO\u2082 chemistry. Finally, we examine the role of heterogeneous oxidation as a sink of organic aerosol and a source of oxygenated volatile organic compounds in the free troposphere.", "doi": "10.7907/2ET7-0D89", "publication_date": "2011", "thesis_type": "phd", "thesis_year": "2011" }, { "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" }, { "id": "thesis:5786", "collection": "thesis", "collection_id": "5786", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-142709280", "primary_object_url": { "basename": "XZhang_Complete_Thesis.pdf", "content": "final", "filesize": 24930564, "license": "other", "mime_type": "application/pdf", "url": "/5786/12/XZhang_Complete_Thesis.pdf", "version": "v8.0.0" }, "type": "thesis", "title": "I. Formate Dehydrogenase Gene Diversity in Lignocellulose-Feeding Insect Gut Microbial Communities. II. Metabolic Impacts on the Hydrogen Isotope Content of Bacterial Lipids ", "author": [ { "family_name": "Zhang", "given_name": "Xinning", "orcid": "0000-0003-2763-1526", "clpid": "Zhang-Xinning" } ], "thesis_advisor": [ { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Mazmanian", "given_name": "Sarkis K.", "clpid": "Mazmanian-S-K" }, { "family_name": "Leadbetter", "given_name": "Jared R.", "clpid": "Leadbetter-J-R" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "I.) Symbiotic CO\u2082-reducing acetogens are important bacterial members of lignocellulose-feeding termite and roach gut communities. Acetogens are the major consumers of H\u2082 derived from lignocellulose fermentation and can contribute up to 1/3 of the acetate that serves as fuel for the insect host. Many acetogens in wood-feeding termites belong to a diverse group of relatively unstudied, uncultured spirochetes within the genus Treponema. Here, I use the gene sequence for hydrogenase-linked formate dehydrogenase, an enzyme utilized in sugar fermentation and the acetogenic metabolism of the spirochete isolate Treponema primitia, to investigate the diversity, evolution, and activity of uncultured acetogenic spirochetes in lignocellulose-feeding insect guts. The results suggest that (a) the trace element selenium has shaped the gene content of acetogenic spirochetes in gut communities over evolutionary time scales, (b) acetogenic spirochete populations have undergone extinctions and radiations associated with an evolutionary bottleneck, convergent evolutions, and possibly even invasion during termite evolution, and (c) termite gut acetogenesis is largely mediated by only a few spirochete species, which represent a small portion of total acetogenic spirochete diversity.
\r\n\r\nII.) The hydrogen-stable isotope compositions (D/H) of lipids in the environment vary greatly. All variations have been assumed to result from changes in the D/H of water, a source of lipid hydrogen. However, several studies suggest that water D/H may not be the only influential factor. In this study, I report that lipid D/H values can vary by 500\u2030 in bacterial cultures despite constant water D/H. This indicates variations in lipid/water fractionation need to be considered when interpreting environmental data. More significantly, I demonstrate that lipid D/H values are systematically related to the utilization of different central metabolic pathways in bacteria. The results suggest that different cellular mechanisms for NADPH synthesis result in lipids with characteristic D/H. Implications for the use of lipid D/H as an isotopic marker of energy metabolism are discussed.
", "doi": "10.7907/ETXQ-D671", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:5501", "collection": "thesis", "collection_id": "5501", "cite_using_url": "https://resolver.caltech.edu/CaltechTHESIS:01072010-132355433", "primary_object_url": { "basename": "Thesis_Wanwan_Yang_Submitted_Version.pdf", "content": "final", "filesize": 2857578, "license": "other", "mime_type": "application/pdf", "url": "/5501/1/Thesis_Wanwan_Yang_Submitted_Version.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Fast Viability Assessment of Clostridium Spores: Survival in Extreme Environments", "author": [ { "family_name": "Yang", "given_name": "Wanwan", "clpid": "Yang-Wanwan" } ], "thesis_advisor": [ { "family_name": "Ponce", "given_name": "Adrian", "clpid": "Ponce-A" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" }, { "family_name": "Gray", "given_name": "Harry B.", "clpid": "Gray-H-B" }, { "family_name": "Ponce", "given_name": "Adrian", "clpid": "Ponce-A" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Bacterial endospores are formed in genera such as Bacillus and Clostridium in response to adverse environmental changes. Endospores have remarkable resistance to various extreme conditions and can remain dormant for extended periods of time. Clostridium spores are of particular interest due to their significant importance in several industries, such as food processing, wastewater treatment, pharmaceuticals, and health care. They are also the ideal candidates to study Panspermia and potential extraterrestrial life. However, to date, most endospore research has been conducted on Bacillus, and study of the anaerobic spore former, Clostridium, is not adequate.
\r\n\r\nIn this study, we have developed a general protocol to produce and purify Clostridium spores. Spectroscopy and microscopy based Endospore Viability Assay (Spectro EVA and Micro EVA) were developed and validated to assess the viability of Clostridium spores. Germinability was used as an indicator for spore viability. The basic principle of the two EVAs is to measure the release of a unique biomarker, dipicolinic acid (DPA), via germination as a proxy for endospore viability. In particular, a luminescence time-gated microscopy technique (Micro EVA) has been developed to enumerate germinable Clostridium endospores within an hour. Micro EVA is based on energy transfer from DPA to terbium ions doped in a solid matrix upon UV excitation. The distinctive emission and millisecond lifetime enables time-resolved imaging to achieve single endospore sensitivity. Comparing to traditional CFU cultivation, EVA probes the early stage of germination, resulting in a much faster detection rate (within 60 minutes) than CFU measurement (more than 3 days incubation). Micro EVA has also been successfully applied to quantify Clostridium spores in an extreme cold biosphere, Greenland ice core, and a hyper-arid biosphere, Atacama Desert, two Mars analogs on earth.
\r\n\r\nThe development of EVA provides a faster way to assess viability of Clostridium spores, which has significant importance in various industries. It also enables the determination of the limit and longevity of life, and provides insight on the search of extinct or extant life on Mars and other celestial bodies.
\r\n\r\n", "doi": "10.7907/8BBD-7Y02", "publication_date": "2010", "thesis_type": "phd", "thesis_year": "2010" }, { "id": "thesis:1864", "collection": "thesis", "collection_id": "1864", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05182009-162828", "primary_object_url": { "basename": "wildmanthesisallchapters.pdf", "content": "final", "filesize": 2236242, "license": "other", "mime_type": "", "url": "/1864/9/wildmanthesisallchapters.pdf", "version": "v7.0.0" }, "type": "thesis", "title": "Biogeochemical Implications of Changing Groundwater and Surface Water Hydrology at Lake Powell, Utah and Arizona, and the Merced River, California, USA", "author": [ { "family_name": "Wildman", "given_name": "Richard Alan", "clpid": "Wildman-Richard-Alan" } ], "thesis_advisor": [ { "family_name": "Hering", "given_name": "Janet G.", "clpid": "Hering-J-G" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Rossman", "given_name": "George Robert", "clpid": "Rossman-G-R" }, { "family_name": "Hering", "given_name": "Janet G.", "clpid": "Hering-J-G" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "This thesis examines some effects of surface water and groundwater hydrology on the mobility of trace elements and phosphorus in natural environments. Three separate field sites are studied: 1) the shoreline of Lake Powell, a large reservoir on the Colorado River in Utah and Arizona where the surface elevation fluctuates on yearly and multi-yearly timescales, 2) the Colorado River inflow region to Lake Powell, where the sediment delta has been exposed due to low water levels, and 3) the lower Merced River, which is located in the San Joaquin Valley, California, amidst extensive agricultural development.
\r\n\r\nOn the shoreline of Lake Powell, depth profiles of manganese and uranium were used to estimate the redox state of sediment porewater. Samples were collected before and after a fluctuation in reservoir level exposed two sampling locations to air and then resubmerged them. Results indicate that reducing conditions are re-established at different rates in two nearby shoreline locations, and that manganese reduction occurs more rapidly than uranium reduction upon resubmergence.
\r\n\r\nIn the Colorado River inflow region of Lake Powell, sediment samples were collected from the lakebed and shoreline. Measurements indicate that particle size anticorrelates with the concentrations of most elements and clay minerals and explains much, but not all, of the variation in trace elements. Spatial trends of particle size imply that low reservoir levels may induce resuspension of fine sediment, a process that may lead to increased primary productivity observed in monitoring data. Sequential extractions performed on these sediment samples suggest that phosphorus, the limiting nutrient in Lake Powell, is primarily associated with calcite and biogenic apatite. Sorption experiments indicate that fine particles sorb much more phosphorus than coarse particles, and that only a small amount of the sediment-associated phosphorus is desorbed during sediment resuspension. When reservoir levels are low, measurements of dissolved phosphorus suggest that sediment resuspended by the Colorado River may supply phosphorus to the photic zone under specific hydrologic conditions.
\r\n\r\nSamples of groundwater collected from beneath the Merced River were analyzed for a suite of trace elements. Statistical analyses suggest that hydrologic processes generally influence the transport of trace solutes more than redox chemistry, and results vary between strontium, barium, uranium, and phosphorus.
\r\n", "doi": "10.7907/2BQF-KR29", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:5058", "collection": "thesis", "collection_id": "5058", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12182008-115035", "primary_object_url": { "basename": "01Guo2008PhDThesis.pdf", "content": "final", "filesize": 17906569, "license": "other", "mime_type": "application/pdf", "url": "/5058/1/01Guo2008PhDThesis.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Carbonate Clumped Isotope Thermometry: Applications to Carbonaceous Chondrites and Effects of Kinetic Isotope Fractionation", "author": [ { "family_name": "Guo", "given_name": "Weifu", "orcid": "0000-0002-1605-1019", "clpid": "Guo-Weifu" } ], "thesis_advisor": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "thesis_committee": [ { "family_name": "Blake", "given_name": "Geoffrey A.", "clpid": "Blake-G-A" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Burnett", "given_name": "Donald S.", "clpid": "Burnett-D-S" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "'Clumped isotope' thermometry of carbonates in the carbonaceous chondrites (CM, CI, CR and Tagish Lake) demonstrates that aqueous alteration of their parent bodies occurred from -31 to 71\u00b0C and involved reaction with fluids having \u03b418OVSMOW values of -29.7\u2030 to 11.8\u2030 and \u03b417OVSMOW of -14.9\u2030 to 7.6\u2030. Estimated carbonate formation temperatures decrease in the order: calcite > dolomite > breunnerite. Based on independent constraints on the ages of these carbonates and models of the evolution of the oxygen isotope compositions of parent body waters, I estimate that carbonate precipitation during aqueous alteration of the carbonaceous chondrite parent bodies started within 1-2 million years after the accretion of those parent bodies, and that the alteration temperatures decreased from 34\u00b0C to 18\u00b0C in the first ~4 million years and further to -20\u00b0C after a total of ~6.5 million years. Our results provide the first direct measurements of the low-temperature cooling histories of C1 and C2 carbonaceous chondrite parent bodies. Within the CM chondrite group itself, I observe a negative correlation between the \u03b413C values of CM carbonates and the \u03b418O of their formation waters, suggesting formation and escape of 13C-depleted CH4 during aqueous alteration on the CM chondrite parent bodies.
\r\n\r\nI apply ab initio transition state and statistical thermodynamics theory to study the kinetic isotope fractionations of clumped isotopologues (i.e., multiply-substituted isotopologues; I also consider singly-substituted isotopologues) associated with phosphoric acid digestion of carbonate minerals and with the degassing of CO2 from aqueous solutions. Assuming that H2CO3 is the reaction intermediate during phosphoric acid digestion of carbonate minerals, I predict at 25\u00b0C that CO2 derived from acid digestion of carbonate minerals will be 10.72\u2030 and 0.220\u2030 higher, respectively, in 18O/16O ratios and 13C-18O clumped isotope anomaly than the reactant carbonate. These predicted kinetic isotope fractionations associated with phosphoric acid digestion and their temperature dependences (for both oxygen isotope and clumped isotopologues) compare favorably with independent experimental constraints for phosphoric acid digestion of calcite. I evaluate the effect of carbonate cation compositions on phosphoric acid digestion fractionations using cluster models in which disproportionating H2CO3 interacts with adjacent cations. These cluster models underestimate the magnitude of isotope fractionations, but do successfully reproduce the general trend of variations and temperature dependences of oxygen isotope acid digestion fractionations among different carbonate minerals (suggesting I have correctly identified the basic mechanism responsible for a dependence on cation chemistry, but not the exact structural model for cation\u2014H2CO3 clusters). I further integrate our acid digestion fractionation model with previous theoretical evaluations of abundances of 13C-18O bonds in carbonate minerals, and predict the relationship between \u039447 values for CO2 extracted from carbonate minerals and the growth temperatures of those carbonates, including witherite, calcite, aragonite, dolomite and magnesite. I observe reasonable agreement between these predictions and available experimental determinations (e.g., difference of less than 0.05\u2030 over 0-50\u00b0C, for calcite).
\r\n\r\nKinetic isotope fractionation associated with HCO3- dehydration and HCO3- dehydroxylation reactions (the two pathways of CO2 degassing from aqueous solutions) are estimated with ab initio transition state theory calculations. Coupled with models of isotopic fractionations accompanying carbonate precipitation, I predict that kinetic isotope fractionation associated with CO2 degassing reactions will increase the \u03b413C and \u03b418O but decrease the relative proportion of 13C-18O bonds in carbonate minerals that precipitate from degassing solutions. Furthermore, these kinetic isotope effects are correlated with each other. For example, I predict the 13C/12C ratio of carbonate increases by 1.1-3.2\u2030 and its \u039447 value decreases by 0.017-0.026\u2030 for every 1\u2030 kinetic enrichment in its 18O/16O at 25\u00b0C, with the exact values depending on the pathway for CO2 degassing (i.e., HCO3- dehydration vs. HCO3- dehydroxylation) and on the amount of carbonate formation that accompanies CO2 degassing. These predictions compare favorably with the experimental constraints from laboratory synthesized cryogenic carbonates and speleothem-like carbonates and with the isotopic compositions of natural modern speleothems.
", "doi": "10.7907/BWC2-RH54", "publication_date": "2009", "thesis_type": "phd", "thesis_year": "2009" }, { "id": "thesis:1588", "collection": "thesis", "collection_id": "1588", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05022008-220144", "primary_object_url": { "basename": "JMendez_Thesis_.pdf", "content": "final", "filesize": 17876944, "license": "other", "mime_type": "application/pdf", "url": "/1588/18/JMendez_Thesis_.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Iron and Manganese in the Ocean: Investigation of Atmospheric Input by Dust and Coastal Ocean Time Series", "author": [ { "family_name": "Mendez", "given_name": "Jeffrey Michael", "clpid": "Mendez-Jeffrey-Michael" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" }, { "family_name": "Hoffmann", "given_name": "Michael R.", "clpid": "Hoffmann-M-R" }, { "family_name": "Orphan", "given_name": "Victoria J.", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Trace metals such as iron (Fe) and manganese (Mn) are essential micronutrients in the biogeochemistry of the ocean (Turner and Hunter, 2001), and dry deposition is a substantial source of both Fe and Mn to the surface ocean (Duce and Tindale, 1991; Guieu et al., 1994). Kinetic and thermodynamic values for the release of metals from dust are needed for computer models which incorporate dust as part of their ocean system. Here we investigate the thermodynamic and kinetics parameters involved in the dissolution of metals from dust in seawater. We added dust from the Sahara and the Western United States to seawater in a variety of ways to investigate the dissolution patterns of Fe and Mn. Results show different apparent thermodynamic constants for manganese (Mn) and iron (Fe). The final Mn concentrations are proportional to the added dust concentration and light intensity, and independent of initial dissolution rate. Fe concentrations in fresh seawater reach a maximum concentration of less than 2 nM. However, depletion of organic ligands lead to the precipitation of Fe oxide from solution, and the addition of siderophores enhanced both the total Fe capacity of the seawater and the rate of Fe dissolution from dust. The first order rate constant for the dissolution of dust differed by dust source and was dependent on oxalate concentration and intensity of natural UV light. We conclude that final Mn concentrations are limited by available Mn on the dust surface, while Fe concentrations are limited by the ligand concentrations in the seawater, which ultimately are determined by the biological community. Because the coastal ocean plays a significant role in global biogeochemical cycles, (Smith and Hollibaugh, 1993; Tsunogai and Noriki, 1991), we conducted a coastal ocean time series to investigate the basic modes and cycles which characterize the ocean. We found that Mn is highly dependent on seasonal rain events, with surface water concentrations observed as high as 30 nM after rain events. Fe within the coastal ocean is highly variable and can be used as a tool to track water mass movements and mixing patterns.\r\n", "doi": "10.7907/Q7JK-MV77", "publication_date": "2008", "thesis_type": "phd", "thesis_year": "2008" }, { "id": "thesis:3163", "collection": "thesis", "collection_id": "3163", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-08182006-105638", "primary_object_url": { "basename": "nsd_final_thesis.pdf", "content": "final", "filesize": 22849688, "license": "other", "mime_type": "application/pdf", "url": "/3163/1/nsd_final_thesis.pdf", "version": "v2.0.0" }, "type": "thesis", "title": "Soil Uptake of Molecular Hydrogen and Remote Sensing of Soil Freeze and Thaw", "author": [ { "family_name": "Smith Downey", "given_name": "Nicole V.", "clpid": "Smith-Downey-Nicole-V" } ], "thesis_advisor": [ { "family_name": "Randerson", "given_name": "James T.", "clpid": "Randerson-J-T" } ], "thesis_committee": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Randerson", "given_name": "James T.", "clpid": "Randerson-J-T" }, { "family_name": "Wennberg", "given_name": "Paul O.", "clpid": "Wennberg-P-O" } ], "local_group": [ { "literal": "div_eng" } ], "abstract": "Soils play a large role in the cycling of atmospheric trace gases and are an important component of the climate system. The bulk of my thesis was directed at the role of soils in the global molecular hydrogen (H\u2082) cycle. I conducted field measurements of H\u2082 uptake in three Southern California ecosystems, and found that both the diffusion of H\u2082 into soils and the distribution of biological activity with depth controlled uptake rates at the surface. I then moved into the laboratory, where I mapped out the temperature and moisture controls on the biological uptake of H\u2082 in both desert and boreal forest soils. These experiments yielded simple relationships between moisture, temperature, and uptake rate, which I then used to constrain H\u2082 uptake by soils in a mechanistic model. The model is based on the 1D diffusion equation with a sink term, and is driven by a combination of remote sensing products and land surface modeling output. I calculated a mean annual soil H\u2082 sink of 67.3 \u00b1 5.5 Tg. The model was able to reproduce the seasonal cycle at high northern latitudes, and implies that seasonal variability in snow cover is a key process controlling H\u2082 uptake. I found that snow cover and soil moisture control the uptake of H\u2082 globally, which may have important implications for the hydrogen budget in future climate change scenarios.
\r\n\r\nMy second thesis topic involved the development of a remote sensing technique using passive microwave brightness temperatures to identify the freeze-thaw status of soils, which I applied to areas north of 45\u00b0N. I found a significant increase in the growing season length in North America by 3.8 days/decade, driven by both an earlier spring thaw and later fall freeze. The lengthening of the growing season may affect the carbon and hydrogen cycles at high northern latitudes, and is a new metric of global change.
", "doi": "10.7907/BXV8-HH61", "publication_date": "2007", "thesis_type": "phd", "thesis_year": "2007" }, { "id": "thesis:2104", "collection": "thesis", "collection_id": "2104", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-110220", "primary_object_url": { "basename": "SeleneThesisFinal.pdf", "content": "final", "filesize": 120379988, "license": "other", "mime_type": "application/pdf", "url": "/2104/7/SeleneThesisFinal.pdf", "version": "v4.0.0" }, "type": "thesis", "title": "Unraveling Deep-Ocean Connections to Climate with Deep-Sea Coral Records of Radiocarbon and Cd/Ca", "author": [ { "family_name": "Eltgroth", "given_name": "Selene Farrell", "clpid": "Eltgroth-Selene-Farrell" } ], "thesis_advisor": [ { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "thesis_committee": [ { "family_name": "Eiler", "given_name": "John M.", "clpid": "Eiler-J-M" }, { "family_name": "Sessions", "given_name": "Alex L.", "clpid": "Sessions-A-L" }, { "family_name": "Ingersoll", "given_name": "Andrew P.", "clpid": "Ingersoll-A-P" }, { "family_name": "Pasquero", "given_name": "Claudia", "clpid": "Pasquero-C" }, { "family_name": "Adkins", "given_name": "Jess F.", "clpid": "Adkins-J-F" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "We generated records of radiocarbon and trace metals in deep-sea corals to investigate the role of the deep ocean during episodes of rapid environmental change. Our record of radiocarbon ages measured in a modern deep-sea coral from the northeastern Atlantic shows the transfer of bomb radiocarbon from the atmosphere to the deep ocean. We detect bomb radiocarbon at the coral growth site starting in 1975\u20131979. Our record documents a Delta14C increase from \u201380 \u00b1 1\u2030 (average 1930\u20131979) to a plateau at \u201339 \u00b1 2\u2030 (average 1994\u20132001). From a suite of fossil deep-sea corals, variability in North Atlantic intermediate water Delta14C during the Younger Dryas (13.0\u201311.5 ka) supports a link between abrupt climate change and intermediate ocean circulation. We observe rapid shifts in deep-sea Delta14C that require the repositioning of large Delta14C gradients within the North Atlantic. The shifts are consistent with changes in the rate of North Atlantic Deep Water formation. We also observe a decadal scale event at 12.0 ka that is marked by the transient return of radiocarbon to the eastern and western basins of the North Atlantic.
\r\n\r\nTo develop a nutrient proxy for use in deep-sea corals, we measured Cd/Ca in 14 modern corals. Several of these corals had anomalously high Cd/Ca that we explain with a systematic bias in Cd/Ca obscuring the signal of seawater Cd/Ca. When these high Cd/Ca corals are removed from the calibration, the best-fit coral-water partition coefficient is 1.3 \u00b1 0.1. Examining Cd/Ca in fossil deep-sea corals, we find that our coral from the Younger Dryas (12.0 ka) resembles the high Cd/Ca corals of the modern calibration and probably does not reflect seawater Cd/Ca. The Cd/Ca record from a 15.4 ka coral resembles our low Cd/Ca calibration samples and probably reflects average seawater Cd/Ca.
\r\n", "doi": "10.7907/ZXHZ-EH83", "publication_date": "2006", "thesis_type": "phd", "thesis_year": "2006" }, { "id": "thesis:4931", "collection": "thesis", "collection_id": "4931", "cite_using_url": "https://resolver.caltech.edu/CaltechETD:etd-12102004-144939", "primary_object_url": { "basename": "101204.pdf", "content": "final", "filesize": 2856256, "license": "other", "mime_type": "application/pdf", "url": "/4931/1/101204.pdf", "version": "v3.0.0" }, "type": "thesis", "title": "Laboratory Models of Microbial Biosignatures in Carbonate Rocks", "author": [ { "family_name": "Bosak", "given_name": "Tanja", "orcid": "0000-0001-5179-5323", "clpid": "Bosak-Tanja" } ], "thesis_advisor": [ { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" } ], "thesis_committee": [ { "family_name": "Kirschvink", "given_name": "Joseph L.", "orcid": "0000-0001-9486-6689", "clpid": "Kirschvink-J-L" }, { "family_name": "Sessions", "given_name": "Alex L.", "orcid": "0000-0001-6120-2763", "clpid": "Sessions-A-L" }, { "family_name": "Ingersoll", "given_name": "Andrew P.", "orcid": "0000-0002-2035-9198", "clpid": "Ingersoll-A-P" }, { "family_name": "Newman", "given_name": "Dianne K.", "orcid": "0000-0003-1647-1918", "clpid": "Newman-D-K" }, { "family_name": "Orphan", "given_name": "Victoria J.", "orcid": "0000-0002-5374-6178", "clpid": "Orphan-V-J" } ], "local_group": [ { "literal": "div_gps" } ], "abstract": "Enigmatically shaped laminated carbonate rocks called stromatolites dominated shallow marine environments for the first 80% of Earth\u2019s history, and are potentially the oldest macrofossils. While these ancient rocky cones and domes occasionally resemble some modern microbial structures, it is unclear whether their formation required biological processes or they could have been produced abiotically. To develop criteria for assessing the biogenicity of ancient stromatolites, we precipitated calcium carbonate in the laboratory in the presence and absence of modern microorganisms under chemical conditions relevant for the early Earth. Using this novel approach, we disproved the paradigm that microbial sulfate reduction, a metabolism important for the formation of modern stromatolites, was responsible for the precipitation of their ancient counterparts. We also produced the first laboratory evidence that sub-micron and micron-sized pores occured in rapidly precipitating carbonate rocks only when microbes were present. Applying a set of experimentally established criteria to modern environmental samples and ancient stromatolites, we found similar biogenic microporosity in some modern fast-precipitating carbonates and in ancient stromatolites. In our abiotic laboratory precipitates, we observed calcite grains that resembled putatively biogenic features from the rock record called peloids. We explained their shape and growth pattern by purely inorganic parameters, underscoring the need for caution when interpreting seemingly biogenic fabrics in the rock record of Earth and other planets. Finally, we showed that active anoxygenic photosynthesis by Rhodopseudomonas palustris could stimulate the precipitation of calcite even in solutions that were well-buffered by a high concentration of dissolved inorganic carbon. Future studies of the relationship between photosynthetic biofilms, the environmental parameters such as light and currents, and the morphology of carbonate precipitates are key to recognizing potential biosignatures produced by similar organisms in the in situ precipitated stromatolites and other microbialites.", "doi": "10.7907/NJ3F-PJ25", "publication_date": "2005", "thesis_type": "phd", "thesis_year": "2005" } ]