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Pi K, Xie X, Sun S, Van Cappellen P, Xiao Z, Zhang D, Wang Y. Arsenic redox disequilibrium in geogenic contaminated groundwater: Bioenergetic insights from organic molecular characterization and gene-informed modeling. WATER RESEARCH 2024; 267:122459. [PMID: 39316964 DOI: 10.1016/j.watres.2024.122459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 09/02/2024] [Accepted: 09/14/2024] [Indexed: 09/26/2024]
Abstract
Biotransformation of arsenic (As) influences its speciation and mobility, obscuring mechanistic comprehension on spatiotemporal variation of As concentration in geogenic contaminated groundwater. In particular, unresolved processes underlying As redox disequilibrium in comparison to major redox couples discourage practical efforts to rehabilitate the As-contaminated groundwater. Here, quantitative metagenomic sequencing and ultrahigh-resolution mass spectrometry (FT-ICR-MS) were jointly applied to reveal the links between vertical distribution of As metabolic gene assemblages and that of free energy density of dissolved organic matter (DOM) in As-contaminated groundwater of Datong Basin. Observed small excess of Gibbs free energy available by DOM relative to that required for As(V)-to-As(III) reduction exerts thermodynamic constraint on metabolism-mediated redox transformation of As. Accordingly, the vertical distribution of dissolved As(V)/As(III) ratio correlated significantly with that of ars+acr3 and arr encoding As(V) reduction and aio encoding As(III) oxidation in the moderately/strongly reducing groundwater. Further gene-informed biogeochemical modeling suggests that a net effect of these kinetics-restricted bidirectional metabolic pathways leads to co-preservation of As(V) and As(III) even at relatively high rates of ars+acr3 encoded As(V) reduction. This study therefore provides new insights into bioenergetic constraints on As hydrobiogeochemical behavior, with implications for other redox-sensitive contaminants in the groundwater systems.
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Affiliation(s)
- Kunfu Pi
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, China; MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, 430074 Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, China
| | - Xianjun Xie
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, China; MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, 430074 Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, China
| | - Shige Sun
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, China
| | - Philippe Van Cappellen
- Ecohydrology Research Group, Department of Earth and Environmental Sciences, University of Waterloo, N2L 3G1 Waterloo, Canada; Water Institute, University of Waterloo, N2L 3G1 Waterloo, Canada
| | - Ziyi Xiao
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, China
| | - Duo Zhang
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, China
| | - Yanxin Wang
- School of Environmental Studies, China University of Geosciences, 430074 Wuhan, China; MOE Key Laboratory of Groundwater Quality and Health, China University of Geosciences, 430074 Wuhan, China; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 430074 Wuhan, China.
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Karadagli F, Marcus A, Rittmann BE. Microbiological hydrogen (H 2 ) thresholds in anaerobic continuous-flow systems: Effects of system characteristics. Biotechnol Bioeng 2023. [PMID: 37148477 DOI: 10.1002/bit.28415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/20/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
Hydrogen (H2 ) concentrations that were associated with microbiological respiratory processes (RPs) such as sulfate reduction and methanogenesis were quantified in continuous-flow systems (CFSs) (e.g., bioreactors, sediments). Gibbs free energy yield (ΔǴ ~ 0) of the relevant RP has been proposed to control the observed H2 concentrations, but most of the reported values do not align with the proposed energetic trends. Alternatively, we postulate that system characteristics of each experimental design influence all system components including H2 concentrations. To analyze this proposal, a Monod-based mathematical model was developed and used to design a gas-liquid bioreactor for hydrogenotrophic methanogenesis with Methanobacterium bryantii M.o.H. Gas-to-liquid H2 mass transfer, microbiological H2 consumption, biomass growth, methane formation, and Gibbs free energy yields were evaluated systematically. Combining model predictions and experimental results revealed that an initially large biomass concentration created transients during which biomass consumed [H2 ]L rapidly to the thermodynamic H2 -threshold (≤1 nM) that triggerred the microorganisms to stop H2 oxidation. With no H2 oxidation, continuous gas-to-liquid H2 transfer increased [H2 ]L to a level that signaled the methanogens to resume H2 oxidation. Thus, an oscillatory H2 -concentration profile developed between the thermodynamic H2 -threshold (≤1 nM) and a low [H2 ]L (~10 nM) that relied on the rate of gas-to-liquid H2 -transfer. The transient [H2 ]L values were too low to support biomass synthesis that could balance biomass losses through endogenous oxidation and advection; thus, biomass declined continuously and disappeared. A stable [H2 ]L (1807 nM) emerged as a result of abiotic H2 -balance between gas-to-liquid H2 transfer and H2 removal via advection of liquid-phase.
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Affiliation(s)
- Fatih Karadagli
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
| | - Andrew Marcus
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Skyology Inc., San Francisco, California, USA
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
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3
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Wessels HJCT, de Almeida NM, Kartal B, Keltjens JT. Bacterial Electron Transfer Chains Primed by Proteomics. Adv Microb Physiol 2016; 68:219-352. [PMID: 27134025 DOI: 10.1016/bs.ampbs.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Electron transport phosphorylation is the central mechanism for most prokaryotic species to harvest energy released in the respiration of their substrates as ATP. Microorganisms have evolved incredible variations on this principle, most of these we perhaps do not know, considering that only a fraction of the microbial richness is known. Besides these variations, microbial species may show substantial versatility in using respiratory systems. In connection herewith, regulatory mechanisms control the expression of these respiratory enzyme systems and their assembly at the translational and posttranslational levels, to optimally accommodate changes in the supply of their energy substrates. Here, we present an overview of methods and techniques from the field of proteomics to explore bacterial electron transfer chains and their regulation at levels ranging from the whole organism down to the Ångstrom scales of protein structures. From the survey of the literature on this subject, it is concluded that proteomics, indeed, has substantially contributed to our comprehending of bacterial respiratory mechanisms, often in elegant combinations with genetic and biochemical approaches. However, we also note that advanced proteomics offers a wealth of opportunities, which have not been exploited at all, or at best underexploited in hypothesis-driving and hypothesis-driven research on bacterial bioenergetics. Examples obtained from the related area of mitochondrial oxidative phosphorylation research, where the application of advanced proteomics is more common, may illustrate these opportunities.
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Affiliation(s)
- H J C T Wessels
- Nijmegen Center for Mitochondrial Disorders, Radboud Proteomics Centre, Translational Metabolic Laboratory, Radboud University Medical Center, Nijmegen, The Netherlands
| | - N M de Almeida
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - B Kartal
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands; Laboratory of Microbiology, Ghent University, Ghent, Belgium
| | - J T Keltjens
- Institute of Water and Wetland Research, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Maňáková B, Kuta J, Svobodová M, Hofman J. Effects of combined composting and vermicomposting of waste sludge on arsenic fate and bioavailability. JOURNAL OF HAZARDOUS MATERIALS 2014; 280:544-551. [PMID: 25209831 DOI: 10.1016/j.jhazmat.2014.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 08/04/2014] [Accepted: 08/07/2014] [Indexed: 06/03/2023]
Abstract
Composting and vermicomposting are traditional processes for the treatment of sludge. During these processes, the humification of organic matter has a significant effect on the physicochemical form and distribution of heavy metals. In this study, industrial sludge (groundwater treatment waste) contaminated by arsenic (396 ± 1 mg kg(-1)) was used. Such sludge poses a significant challenge with respect to effective treatment. Composting, vermicomposting (with Eisenia fetida), and the combined approach of composting and vermicomposting were performed to determine the evolution of arsenic speciation, mobility and bioavailability. The composting/vermicomposting was done with sludge, horse manure, and grass in the ratios of 3:6:1. A solution of 0.1M NH4COOCH3 was used as a single extraction solvent for determination of the mobile arsenic pool and targeted arsenic species (As(III), As(V), monomethylarsenic acid - MMA(V), dimethylarsenic acid - DMA(V)). The analysis of arsenic in the extracts was carried out by means of HPLC-ICP-MS spectrometry. In addition, the earthworm species E. fetida was used for bioaccumulation tests that followed the compost and vermicompost processes. The obtained results indicate a reduction in arsenic mobility and bioavailability in all matured composts and vermicomposts. The combined process exhibited a greater effect than compost or vermicompost alone.
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Affiliation(s)
- Blanka Maňáková
- Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500, Czech Republic
| | - Jan Kuta
- Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500, Czech Republic
| | - Markéta Svobodová
- Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500, Czech Republic
| | - Jakub Hofman
- Research Centre for Toxic Compounds in the Environment (RECETOX), Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500, Czech Republic.
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Shani N, Rossi P, Holliger C. Correlations between environmental variables and bacterial community structures suggest Fe(III) and vinyl chloride reduction as antagonistic terminal electron-accepting processes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:6836-6845. [PMID: 23484639 DOI: 10.1021/es304017s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Natural attenuation of anaerobic aquifers contaminated with tetrachloroethene (PCE) often results in the accumulation of the intermediates cis-dichloroethene and vinyl chloride (VC) which are even more toxic than the parent compound. Reasons for this accumulation were investigated in a PCE-contaminated aquifer in which VC accumulation has previously been shown to occur using stable isotope techniques. Multifactorial analysis of bacterial community structure data and environmental variables showed that in general terminal electron-accepting processes were shaping the bacterial community structures. Both VC and Fe(III) reduction were key but antagonistic terminal electron-accepting processes. The phylogenetic affiliation of terminal restriction fragments (T-RFs), together with correlation analyses, showed that T-RFs having significant correlation with VC reduction were closely affiliated to the genus Dehalococcoides and to uncultured bacteria belonging to the "Lahn Cluster" within the class Dehalococcoidetes. A T-RF that negatively correlated with a "Lahn Cluster" T-RF was affiliated to the genus Rhodoferax that contains members identified as iron-reducing bacteria. The higher affinity of Fe(III)-reducing bacteria for hydrogen compared with VC-reducing bacteria might explain why VC accumulated locally at the studied site. In conclusion, the combination of molecular and numerical ecology approaches was helpful to identify reasons for the accumulation of toxic dechlorination intermediates and could become a useful tool for characterizing contaminated sites in general.
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Affiliation(s)
- Noam Shani
- Laboratory for Environmental Biotechnology, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Fédérale de Lausanne, EPFL ENAC IIE LBE, Station 6, 1015, Lausanne, Switzerland
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Rauschenbach I, Bini E, Häggblom MM, Yee N. Physiological response of Desulfurispirillum indicum S5 to arsenate and nitrate as terminal electron acceptors. FEMS Microbiol Ecol 2012; 81:156-62. [DOI: 10.1111/j.1574-6941.2012.01351.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 02/28/2012] [Accepted: 02/28/2012] [Indexed: 11/30/2022] Open
Affiliation(s)
- Ines Rauschenbach
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Max M. Häggblom
- Department of Biochemistry and Microbiology; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
| | - Nathan Yee
- Department of Environmental Sciences; School of Environmental and Biological Sciences; Rutgers University; New Brunswick; NJ; USA
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Blodau C. Thermodynamic Control on Terminal Electron Transfer and Methanogenesis. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1071.ch004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christian Blodau
- School of Environmental Sciences, University of Guelph, N1G 2W1, Guelph, Canada
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Heimann A, Jakobsen R, Blodau C. Energetic constraints on H2-dependent terminal electron accepting processes in anoxic environments: a review of observations and model approaches. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:24-33. [PMID: 20039730 DOI: 10.1021/es9018207] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Microbially mediated terminal electron accepting processes (TEAPs) to a large extent control the fate of redox reactive elements and associated reactions in anoxic soils, sediments, and aquifers. This review focuses on thermodynamic controls and regulation of H2-dependent TEAPs, case studies illustrating this concept, and the quantitative description of thermodynamic controls in modeling. Other electron transfer processes are considered where appropriate. The work reviewed shows that thermodynamics and microbial kinetics are connected near thermodynamic equilibrium. Free energy thresholds for terminal respiration are physiologically based and often near -20 kJ mol(-1), depending on the mechanism of ATP generation; more positive free energy values have been reported under "starvation conditions" for methanogenesis and lower values for TEAPs that provide more energy. H2-dependent methanogenesis and sulfate reduction are under direct thermodynamic control in soils and sediments and generally approach theoretical minimum energy thresholds. If H2 concentrations are lowered by thermodynamically more potent TEAPs, these processes are inhibited. This principle is also valid for TEAPS providing more free energy, such as denitrification and arsenate reduction, but electron donor concentration cannot be lowered so that the processes reach theoretical energy thresholds. Thermodynamics and kinetics have been integrated by combining traditional descriptions of microbial kinetics with the equilibrium constant K and reaction quotient Q of a process, taking into account process-specific threshold energies. This approach is dynamically evolving toward a general concept of microbially driven electron transfer in anoxic environments and has been used successfully in applications ranging from bioreactor regulation to groundwater and sediment biogeochemistry.
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Affiliation(s)
- Axel Heimann
- Institute of Environment and Resources, Bygningstorvet, Bilding 115, Technical University of Denmark, DK-2800 Lyngby, Denmark
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Ruiz-Haas P, Ingle J. Monitoring of redox state in a dechlorinating culture with immobilized redox indicators. JOURNAL OF ENVIRONMENTAL MONITORING : JEM 2009; 11:1028-36. [PMID: 19436861 DOI: 10.1039/b818487a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
During the dechlorination of tetrachloroethene (PCE) to ethene (ETH) in a microcosm bottle containing an enriched chlororespiring culture, redox conditions were spectrophotometrically monitored with the redox indicators thionine (THI) and cresyl violet (CV) immobilized on transparent films. Measurements were taken with a unique flow redox monitoring system based on circulating solution from the bottle through a specially constructed flow cell and returning it to the bottle. An enclosure for a peristaltic pump was constructed to minimize contamination of the solution with atmospheric O(2). The redox monitoring instrumentation was shown to be an excellent tool to evaluate the ability of an enclosure for anoxic samples to prevent diffusion of very small amounts of oxygen from the atmosphere into the sample. With careful design of the apparatus, the O(2) permeation rate into a solution of THI in a microcosm bottle during redox monitoring was reduced to less than 40 nmol h(-1). When monitoring a dechlorinating culture, dechlorination was not observed until immobilized THI was completely reduced and vinyl chloride was not produced until partial reduction of CV.
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Affiliation(s)
- Peter Ruiz-Haas
- Department of Chemistry, Pearce Science Center, Mary Baldwin College, Staunton, VA 24401, USA
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Constant P, Poissant L, Villemur R. Tropospheric H(2) budget and the response of its soil uptake under the changing environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:1809-1823. [PMID: 19155054 DOI: 10.1016/j.scitotenv.2008.10.064] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2008] [Revised: 10/06/2008] [Accepted: 10/26/2008] [Indexed: 05/27/2023]
Abstract
Molecular hydrogen (H(2)) is an indirect greenhouse gas present at the trace level in the atmosphere. So far, the sum of its sources and sinks is close to equilibrium, but its large-scale utilization as an alternative energy carrier would alter its atmospheric burden. The magnitude of the emissions associated with a future H(2)-based economy is difficult to predict and remains a matter of debate. Previous attempts to predict the impact that a future H(2)-based economy would exert on tropospheric chemistry were realized by considering a steady rate of microbial-mediated soil uptake, which is currently responsible of ~80% of the tropospheric H(2) losses. Although soil uptake, also known as dry deposition is the most important sink for tropospheric H(2), microorganisms involved in the activity remain elusive. Given that microbial-mediated H(2) soil uptake is influenced by several environmental factors, global change should exert a significant effect on the activity and then, assuming a steady H(2) soil uptake rate for the future may be mistaken. Here, we present an overview of tropospheric H(2) sources and sinks with an emphasis on microbial-mediated soil uptake process. Future researches are proposed to investigate the influence that global change would exert on H(2) dry deposition and to identify microorganisms involved H(2) soil uptake activity.
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Affiliation(s)
- Philippe Constant
- INRS-Institut Armand-Frappier, 531 boul. des Prairies, Laval, Québec, Canada H7V 1B7.
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Blodau C, Rees R, Flessa H, Rodionov A, Guggenberger G, Knorr KH, Shibistova O, Zrazhevskaya G, Mikheeva N, Kasansky OA. A snapshot of CO2and CH4evolution in a thermokarst pond near Igarka, northern Siberia. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jg000652] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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