Microbial Biogeochemistry

Weber Microbial Biogeochemistry and Geomicrobiology Laboratory Home

Karrie A. Weber

Selected Projects:

Feammox: A new pathway in the nitrogen cycle

Feammox is the anaerobic oxidation of ammonium coupled to ferric iron [Fe (III)] reduction. It has the potential to produce inert dinitrogen gas as well as reactive nitrite, which could subsequently be reduced to gaseous or organic nitrogen, or ammonium under anaerobic conditions. Given the potential gaseous loss of nitrogen from terrestrial environments, this pathway may play a significant role in the global nitrogen cycle. The proposed research will place this newly discovered nitrogen transformation pathway in the context of the larger nitrogen cycle by (i) determining if Feammox is mediated by soil microbes, and if so identify the responsible organisms, (ii) determining the relative importance of iron- and nitrogen-containing compounds as controls on Feammox, and (iii) quantifying the role of Feammox in total nitrogen gas emissions from soils.

Microbially-mediated oxidation of Fe(II) carbonates forming Fe(III) Oxide concretions in sandstone aquifers

Our prior research indicates that Fe(II)-carbonate minerals precipitated in the paleoaquifer within the Jurassic Navajo Sandstone of the Colorado Plateau. We recently described that the spheroidal Navajo concretions were first solidly cemented by Fe(II)-carbonate minerals, such as siderite (FeCO3). The present mineralogy and structure was transformed as oxidizing conditions developed and permitted the proliferation of neutrophilic, microaerophilic, Fe(II)-oxidizing microorganisms. Proton generation as a result of iron oxidation continued to dissolve the siderite promoting the generation of aqueous Fe(II) and carbonate, a microbial electron donor and carbon source respectively. Oxygen in the groundwater served as the terminal electron acceptor for microbial respiration. Together, these geochemical conditions supported lithoautotrophic, neutrophilic Fe(II)-oxidizing microorganisms. This proposed research seeks to demonstrate the conceptual model that iron-oxidizing microorganisms will catalyze Fe(II)-carbonate, siderite dissolution, and Fe(III) oxide precipitation surrounding Fe(II)-carbonate spheroids.

Geovirology: viral infection of subsurface microorganisms and metal radionuclide transport

Microbially mediated metabolisms have been identified as a significant factor either directly or indirectly impacting the fate and transport of heavy metal/radionclide contaminants in soils and sedimentary environments. To date several microorganisms have been isolated from these contaminated environments including metal reducing bacteria. Examination of annotated finished genome sequences of isolates G. uraniumreducens Rf4, Geobacter sp. FRC-32, and Anaeromyxobacter sp. Fw109-5, revealed phage genes integrated into the chromosome. To date the role that viruses play influencing microbial mortality and the resulting community structure under varying redox conditions in soils and sedimentary environments remains poorly understood. Similar to bacterial surfaces, viral surfaces could adsorb heavy metals and radionuclides subsequently influencing contaminant transport. The objective of this study is to investigate viral infection of subsurface bacteria and the role of viral surfaces as nucleation sites for metal adsorption and mineral precipitation.

Other Projects.

Nitrate stimulated oxidative dissolution of U(IV) bearing minerals leading to U mobility in Nebraska groundwater

Microbially-mediated coupled biogeochemical reactions: Nitrification and Nitrate-dependent Fe(II) oxidation

Selected Publications:

Loope, D. B., R. M. Kettler, K. A. Weber. Morphologic Clues to the Origins of Iron-Oxide-Cemented spheroids, “Boxworks”, and Pipe-like Concretions, Navajo Sandstone of South-Central Utah, USA. J Geol. (in press)

Weber, K. A., J. C. Thrash, J. I. Van Trump, L. A. Achenbach, J. D. Coates. Environmental and Taxonomic Bacterial Diversity of Anaerobic Uranium(IV) Bio-Oxidation. Appl. Environ. Microbiol. (in press)

Loope, D. B., R. M. Kettler, K. A. Weber. 2010. Follow the Water: Connecting a CO₂ Reservoir and Bleached Sandstone to Iron-Rich Concretions in the Navajo Sandstone of south-central Utah. Geology 38: 999-1002.

Byrne-Bailey, K. G.*, K. A. Weber*, A. H. Chair, S. Bose, T. K. Knox, T. Spanbauer, O. Chertkov, and John D. Coates. 2010. Completed genome sequence of the iron oxidizing bacterium Acidovorax ebreus strain TPSY. J. Bact. 192: 1475-1476.

*These authors contributed equally to this work and have been placed in alphabetical order.

Sun, Y., R. L. Gustavson, N. Ali, K. A. Weber, L. L. Westphal, and J. D. Coates. 2009. Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors. Appl. Microbiol. Biotechnol. 84:955-963.

Weber, K. A., D. B. Hedrick, A. D. Peacock, J. C. Thrash, D. C. White, L. A. Achenbach, J. D. Coates. 2009. Physiological and taxonomic description of the novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp. strain 2002. Appl. Microbiol. Biotechnol. 83:555–565.

Wrighton, K. C., P. Agbo, F. Warnecke, K. A. Weber, E. L. Brodie, T. Z. DeSantis, P. Hugenholtz, G. L. Andersen, J. D. Coates. 2008. A Novel Ecological Role of the Firmicutes Identified in Thermophilic Fuel Cells. ISME J. 2, 1146–1156.

Pollock, J., K. A. Weber, J. Lack, L. A. Achenbach, M. Mormile, and J. D. Coates. 2007. Alkaline iron(III) reduction by a novel alkaliphilic, halotolerant, Bacillus sp. isolated from salt flat sediments of Soap Lake. Appl. Microbiol. Biotechnol. 77, 927-934.

Thrash, J. C., J. I. Van Trump, K. A. Weber, E. Miller, L. A. Achenbach. J. D. Coates. 2007. Electrochemical stimulation of microbial perchlorate reduction. Environ. Sci. Technol. 41, 1740-1746.

Weber, K. A., L. A. Achenbach, and J. D. Coates. 2006. Microbes Pumping Iron: Anaerobic Microbial Iron Oxidation and Reduction. Nat. Rev. Microbiol. 4, 752-764.

Weber, K.A., J. L. Pollock, K.A. Cole, L.A. Achenbach, J.D. Coates. 2006. Nitrate-Dependent Fe(II) Oxidation by a Novel, Lithoautotrophic, Betaproteobacterium, Strain 2002. Appl. Environ. Microbiol. 72(1) 686-694.

Weber, K. A., M.M. Urrutia, P. F. Churchill, R. K. Kukkadapu, and E. E. Roden. 2006. Anaerobic Redox Cycling of Iron by Freshwater Sediment Microorganisms. Environ. Microbiol. 8(1), 100-113.

Weber, K. A., F. W. Picardal, E. E. Roden. 2001. Microbially Catalyzed Nitrate-Dependent Oxidation of Biogenic Solid-Phase Fe(II) Compounds. Environ. Sci. Technol. 35(8), 1644-1650.

Book Chapters and Reviews

Weber, K. A. and J. D. Coates. 2007. Microbially-Mediated Anaerobic Iron(II) Oxidation at Circumneutral pH. In Manual of Environmental Microbiology. Edited by C. J. Hurst, R. L. Crawford, J. L. Garland, D. A. Lipson, A. L. Mills, L. D. Stetzenbach. ASM Press. Section 94.

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