Geology topics

Elisha Kelly Moore

Publications and source records attributed to Elisha Kelly Moore.

9 recordsLinked to original sources

USGS2026

Structural evolution of iron coordination in proteins across Earth’s oxygenation history

Protein metal-binding sites support essential biological functions shaped by protein fold, subunit interactions, and cofactor chemistry. Because these sites encode both biochemical function and environmental constraint, they offer a route to connect protein evolution with changes in Earth’s surface environment through time. Of particular interest is iron (Fe), the most widely used metal in biology and a cofactor central to both anaerobic and aerobic metabolism. Here, we systematically compare the immediate chemical environments of functionally essential Fe-binding sites in three-dimensional protein structures to test whether Fe coordination spheres differ across oxygen contexts. Using a curated dataset of experimentally determined structures, we identify a clear shift in the local chemistry of Fe-binding environments from anaerobic to aerobic proteins. Aerobic Fe sites are significantly more hydrophilic than anaerobic ones, and amino-acid composition analyses show reduced cysteine use in aerobic Fe-binding neighborhoods. These patterns suggest that as Earth’s surface environments became more oxygenated, proteins retained Fe as a core redox metal while reconfiguring local coordination chemistry in ways less vulnerable to oxidative damage. More broadly, this study introduces and applies the Coordination Sphere Analysis and Comparison (CSAC) workflow, an open and archived Python workflow for extracting local metal-binding environments from structure datasets, providing a framework for linking metalloprotein structure to evolutionary and geobiological transitions across Earth history.

Discover Life↗

USGS2026

Diverging mineral chemistry of iron and nickel throughout Earth’s changing redox conditions reveals foundation for their evolution as protein cofactors

Iron (Fe) and nickel (Ni) were both foundational to early metabolism, yet their biological trajectories diverged as Earth’s surface redox state changed. Here, we integrate mineral chemistry network analysis, protein metal-site coordination-sphere analysis, and curated redox comparisons to test how geochemistry and metalloprotein architecture co-evolved. Mineral network analyses show broader electronegativity variation and network diversity for Fe-bearing minerals through time relative to Ni-bearing minerals. In structural analyses of protein metal centers in a combined Fe/Ni protein structure set, it is shown that Fe- and Ni-associated environments differ in amino-acid composition, hydropathy structure, and cysteine representation. The greater chemical diversity and electronegativity variation in Fe minerals mirror the higher redox and structural versatility of Fe-binding proteins. The presence of Fe in a broader range of mineral and protein environments demonstrates the chemical adaptability of the metal, from the anoxic Archean to oxidative Earth surface conditions following the Great Oxidation Event. Iron, with its broad redox potential range in Fe-oxidoreductases, has a central role in both anaerobic and aerobic metabolisms. Nickel, by contrast, is less widespread in biology. Today, Ni is predominantly employed in deeply branching anaerobic pathways and by proteins with narrower redox potential ranges. Our results show that evolutionary processes, constrained by metal chemistry, habitually utilize Fe as a redox generalist while retaining Ni in specialized roles. The divergent paths of Ni and Fe, from rocks to proteins, demonstrate the intimate relationship between planetary geochemistry and metabolic origins on Earth and suggest that Fe/Ni geochemistry may inform habitability assessments in extraterrestrial environments when interpreted within specific planetary environmental contexts.

Life↗

USGS2026

The mineral chemistry networks of tin and tungsten reflect metallogenic eras of the Mesozoic

Continental remobilization is a crucial driver of metallogenesis and the formation of ore deposits. Some of the world’s largest mineral deposits of the economically valuable elements tin (Sn), tungsten (W), gold (Au), copper (Cu), lead (Pb), and zinc (Zn) formed during the Mesozoic Era. Additionally, the chemistry and distribution of the elements Sn and W have been investigated in previous studies to understand planetary formation and differentiation processes. These two elements are largely co-located during certain South China Mesozoic metallogenic events but are not co-located during other time periods in the same regions. Here, we investigated the mineral chemistry network similarities and dissimilarities of Sn and W to understand their mineral formation and distribution during the Mesozoic Era and throughout Earth history. Mineral chemistry network community detection analysis and electronegativity associations among mineral constituent elements of Sn minerals and W minerals indicate that the elements have similar chemistry among their oxide minerals. However, Sn forms a much wider range of minerals that also contain S compared to W, which occurs in a limited number of S-containing minerals. The divergent constituent element interactions among S-containing Sn minerals and W minerals reflect the redox sensitivity and importance of oxygen (O) fugacity in Sn mineral formation. Conversely, extensive W mineral deposits are known to form at both high and low O fugacities. The similarities and differences between the mineral chemistry networks of Sn and W reflect the mineral distribution of the two elements in the Sn-W mineralization event from 160 to 139 Ma vs. the Sn–uranium (U) mineralization event from 125 to 98 million years ago (Ma). The mineral chemistry and distribution of Mesozoic Sn and W deposits illustrate the contrasting importance of redox and O fugacity on the mineral formation of different elements, and the dynamic crustal evolution that took place during this period of Earth history.

Geosciences↗

USGS2026

Top-down targeted network analysis of critical mineral commodities applied to international geochemistry database

The global demand for critical mineral commodities is rapidly increasing, making domestic production an important factor in supporting the economy and national security. Large scale, publicly available geochemical databases allow for the application of data informatics methods to interrogate critical mineral commodities data for correlations in deposit formation and distribution, particularly for identifying enrichment of multiple critical mineral commodities at the same deposit. In this study, we applied network analysis to the Critical Minerals Mapping Initiative (CMMI) ore geochemistry (Critical Minerals in Ores, CMiO) database to identify the high concentration (defined as 10× bulk crustal abundance) co-occurrence of different critical mineral commodities across a mineral system hierarchy from deposit environments to individual deposits. Identifying patterns or unique outliers in enrichment in network communities will allow for the location of secondary critical mineral commodity resources from under-utilized deposits. We find trends in the enrichment of critical mineral commodities in network-communities between the elements praseodymium (Pr), neodymium (Nd), terbium (Tb), and dysprosium (Dy) across multiple CMiO database deposit environments and groups down to specific deposit types and sites. A separate trend in network community deposition is observed as well between iridium (Ir) and platinum (Pt) in deposit environments, groups, types, and sites. Network analysis focused on critical minerals in magmatic-hydrothermal deposits identified multiple deposit sites from different deposit types within the CMiO database with concentrations of Dy, Nd, Tb, Pr, Ir, and Pt that are at least ten times greater than the crustal average. This approach can be applied to any target element(s) or deposit(s) of interest, allowing broad investigation of co-enriched critical mineral commodities.

Journal of Geochemical Exploration↗

USGS2025

Metaproteomics and metagenomics reveal microbial pathways of organic matter degradation and methanogenesis in a marginally producing natural gas well

The expansion of natural gas production and utilization worldwide has led to the decline of many once-productive wells, eventually resulting in costly well-plugging and unused infrastructure. However, in areas like the Michigan basin, MI, where the majority of natural gas is biogenically produced, microbial communities could potentially be stimulated to generate additional methane, increasing gas supply and reducing the need to drill new wells. In this study, we performed metaproteomic, metagenomic, and geochemical analyses of Antrim Shale formation water from a marginally producing natural gas well to evaluate resident microbial community functions in the context of potential bioenergy production. Functional proteins involved in methanogenesis, degradation/catabolism (including organic matter degradation), biosynthesis, energy utilization, transmembrane transport, and stress response were among the most commonly identified groups. Three metagenome-assembled genomes (MAGs) were characterized, including Methanomicrobiaceae, Methanothrix , and Smithella . For each, the identified proteins involved in methanogenesis and the degradation of diverse organic compounds, strongly suggest their role in utilizing shale-derived organic matter. These findings provide an increased understanding of the microorganisms and their metabolisms generating natural gas in the Antrim Shale and establish a foundation for future stimulation efforts aimed at enhancing biogenic methane production in marginal gas wells.

Michigan↗

USGS2024

Enhanced microplastic fragmentation along human built structures in an urban waterway

Plastic pollution and microplastic (MP, 1 µm to 5 mm) generation are growing problems affecting the global community and a wide range of natural and disturbed environments. Urban and suburban waterways are directly impacted by plastic pollution due to their proximity to population centers and many different types single use plastic waste sources. In this study, plastic waste accumulation and fragmentation was investigated along the Cooper River in Camden County, NJ. Polymer composition was identified for individual plastic waste particles collected along the Cooper River using Fourier transform infrared (FTIR) spectrometry. Multiple human-built structures (Wallworth Lake, Evans Pond and Hopkins Pond dams) along the Cooper River were found to accumulate different types of plastic waste. The accumulation of plastic waste along these structures resulted in the initial stages of plastic fragmentation and the identification of large MP particles (1 to 5 mm). Quantitative analysis revealed that fragmented polystyrene (PS) particles constituted 82.8% of the total plastic fragments identified, most of which were identified at the Wallworth Lake dam. Many other types of fragmented plastic litter, including polyethylene and polypropylene, were identified at the Wallworth Lake dam, as well. This research demonstrates that engineered structures within urban and suburban aquatic ecosystems serve as significant aggregators of plastic debris, thereby catalyzing its breakdown into microplastics. Considering the escalating ecological and human health ramifications of microplastic proliferation, the fragmentation of plastic waste in an urban and suburban waterway observed in this study can also result in potentially toxic smaller MP particles, and increased exposure to aquatic organisms and humans.

New Jersey↗

USGS2024

The early Earth as an analogue for exoplanetary biogeochemistry

Planet Earth has evolved over the past 4.5 billion years from an entirely anoxic planet with possibly a different tectonic regime to the oxygenated world with horizontal plate tectonics that we know today. For most of this time, Earth has been inhabited by a purely microbial biosphere albeit with seemingly increasing complexity over time. A rich record of this geobiological evolution over most of Earth’s history thus provides insights into the remote detectability of microbial life under a variety of planetary conditions. Here we leverage Earth’s geobiological record with the aim of (a) illustrating the current state of knowledge and key knowledge gaps about the early Earth as a reference point in exoplanet science research; (b) compiling biotic and abiotic mechanisms that controlled the evolution of the atmosphere over time; and (c) reviewing current constraints on the detectability of Earth’s early biosphere with state-of-the-art telescope technology. We highlight that life may have originated on a planet with a different (stagnant lid) tectonic regime and strong hydrothermal activity, and under these conditions, biogenic CH 4 gas was perhaps the most detectable atmospheric biosignature. Oxygenic photosynthesis, which is responsible for essentially all O 2 gas in the modern atmosphere, appears to have emerged concurrently with the establishment of modern plate tectonics and the emergence of continental crust, but O 2 accumulation to modern levels only occurred late in Earth’s history, perhaps tied to the rise of land plants. Nutrient limitation in anoxic oceans, promoted by hydrothermal Fe fluxes, may have limited biological productivity and O 2 production. N 2 O is an alternative biosignature that was perhaps significant on the redox-stratified Proterozoic Earth. We conclude that the detectability of atmospheric biosignatures on Earth was not only dependent on biological evolution but also strongly controlled by the evolving tectonic context.

Reviews in Mineralogy and Geochemistry↗

USGS2024

Uranium redox and deposition transitions embedded in deep-time geochemical models and mineral chemistry networks

Uranium (U) is an important global energy resource and a redox sensitive trace element that reflects changing environmental conditions and geochemical cycling. The redox evolution of U mineral chemistry can be interrogated to understand the formation and distribution of U deposits and the redox processes involved in U geochemistry throughout Earth history. In this study, geochemical modeling using thermodynamic data, and mineral chemistry network analysis are used to investigate U geochemistry and deposition through time. The number of U 6+ mineral localities surpasses the number of U 4+ mineral localities in the Paleoproterozoic. Moreover, the number of sedimentary U 6+ mineral localities increases earlier in the Phanerozoic than the number of U 4+ sedimentary mineral localities, likely due to the necessity of sufficient sedimentary organic matter to reduce U 6+ –U 4+ . Indeed, modeling calculations indicate that increased oxidative weathering due to surface oxygenation limited U 4+ uraninite (UO 2 ) formation from weathered granite and basalt. Louvain network community detection shows that U 6+ forms minerals with many more shared elements and redox states than U 4+ . The range of weighted Mineral Element Electronegativity Coefficient of Variation (wMEE CV ) values of U 6+ minerals increases through time, particularly during the Phanerozoic. Conversely, the range of wMEE CV values of U 4+ minerals is consistent through time due to the relative abundance of uraninite, coffinite, and brannerite. The late oxidation and formation of U 6+ minerals compared to S 6+ minerals illustrates the importance of the development of land plants, organic matter deposition, and redox-controlled U deposition from ground water in continental sediments during this time-period.

Geochemistry, Geophysics, Geosystems↗

USGS2024

Characterizing sulfur redox state and geochemical implications in deep-time using mineral chemistry network analysis

Sulfur (S) is a central element in global biogeochemical cycling and Earth’s redox evolution. Minerals that contain S are an important record of local environmental conditions at the time of their formation based on chemical speciation and redox. However, the oxidation state of S for hundreds of different S-containing minerals and thousands of S-containing mineral localities is unknown, largely sulfides and sulfosalts, and the redox state alone does not fully capture mineral chemistry diversity, thus limiting understanding of S redox evolution. Here, we use mineral chemistry network analysis and the weighted Mineral Element Electronegativity Coefficient of Variation (wMEE CV ) metric to investigate the element interactions and localities of S-containing minerals from the Mineral Evolution Database (MED) to infer the redox state of S in minerals where the redox state is unknown (S U ). Louvain community detection of the S mineral chemistry redox network reveals that there are three main network communities that are separated by redox state. The S 6+ community includes minerals that contain the S 6+ redox state and a small number of S 4+ and S 2+ minerals, the S 2− community includes S 2− -containing minerals, and the S U community includes minerals in which the redox state of S is unknown. The wMEE CV values of the S U community closely overlap with the wMEE CV values of the S 2− community, and do not overlap with the wMEE CV values of the S 6+ community, indicating the S U community minerals contain predominately reduced S. Assuming that S U community minerals contain reduced S, as supported by their network chemical associations and wMEE CV values, then reduced S-containing minerals make up approximately 81 % of S-containing mineral localities in the S mineral chemistry network, even though the majority of all mineral localities (S-containing and non-S-containing) are oxygen (O)-containing minerals. Additionally, reduced S-containing minerals make up the majority (∼75 %) of all non-O containing mineral localities in the MED, representing the importance of reduced S as an electron source and substrate in the evolution of microbial metabolic networks. The range wMEE CV values of S 6+ community minerals expands through time due primarily to formation of chemically diverse sulfate minerals, coinciding with crustal oxidation from the late Proterozoic to Phanerozoic and the expansion of the marine sulfate reservoir. The intersection of shared constituent elements among reduced and oxidized S in the mineral chemistry network represents redox convergence of weathered S in the geosphere that was crucial in the formation of natural resource deposits and the evolution of biogeochemical cycles.

Geochimica et Cosmochimica Acta↗