Proteins in Geobiology: New Approaches for Enzyme Field Detection and Biomarker Visualization
2021-01
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Proteins in Geobiology: New Approaches for Enzyme Field Detection and Biomarker Visualization
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2021-01
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Proteins are the biomolecules that carry out most functions of the cells, yet their impacts and potentials to understand current and past Earth-life interactions are understudied. Here, I attempt to exploit the use of proteins—in the form of antibodies and enzymes—to answer fundamental questions in geobiology through two different approaches: (1) Using field assays to identify enzyme activity in the field that promotes calcium carbonate precipitation in modern environments, and (2) using antibodies to visualize lipid biomarkers in the fossil record. The first objective explores in-field analysis of urease and carbonic anhydrase (CA) activity, two enzymes known to promote carbonate precipitation. Microbes are attributed to drive environmental changes that explain geological phenomena, yet the mechanisms underlying these transformations are poorly studied. Simple, fast, and economical field tests were developed to identify on-site CA and urease in biofilms. The tests were used in microbial samples from calcareous fens, ferruginous springs, and an alkaline lake (Salt Lake) in Minnesota, along with carbonate tufa biofilms from an alkaline lake (Big Soda Lake) in Nevada. Relatively high in situ microbial urease activity in lake samples also promoted carbonate precipitation in microcosm incubation experiments. Active enzymes in tufas, together with community characterization by 16S rRNA gene sequencing and shotgun metagenomics, provided a plausible new mechanism to understand tufa biogenicity and its rapid growth. The second objective explores immunological techniques—antibody-based methods used in life sciences—here used to detect lipid biomarkers in the rock record. A previously known antibody that binds squalane was used to detect biomarkers in crude oil samples and to identify in situ micro-scale signatures in organic-rich rocks and potentially in fish fossil remains from the Eocene Green River Formation. A novel chromatographic method developed to separate and immunodetect hydrocarbon fingerprints showed that the antibodies also bind other soluble hydrocarbons in Green River Formation rocks, likely acyclic isoprenoids. The use of antibodies proved useful for identifying biomarker distributions in the sedimentary fabric that are otherwise difficult to study by current techniques. Future methods aimed at investigating the role of microbial proteins in the environment and their value as detection tools will benefit our understanding of the past and current biosphere and its interactions with the geosphere.
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University of Minnesota Ph.D. dissertation. January 2021. Major: Geological Sciences. Advisor: Jake Bailey. 1 computer file (PDF); vi, 205 pages.
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Medina Ferrer, Fernando. (2021). Proteins in Geobiology: New Approaches for Enzyme Field Detection and Biomarker Visualization. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/253412.
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