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Löffler M, Schwab L, Dethlefsen F, Lagmöller L, Vogt C, Richnow HH. Anaerobic dihydrogen consumption of nutrient-limited aquifer sediment microbial communities examined by stable isotope analysis. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2024; 60:103-121. [PMID: 38344763 DOI: 10.1080/10256016.2024.2306146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 12/21/2023] [Indexed: 03/20/2024]
Abstract
The biogeochemical consequences of dihydrogen (H2) underground storage in porous aquifers are poorly understood. Here, the effects of nutrient limitations on anaerobic H2 oxidation of an aquifer microbial community in sediment microcosms were determined in order to evaluate possible responses to high H2 partial pressures. Hydrogen isotope analyses of H2 yielded isotope depletion in all biotic setups indicating microbial H2 consumption. Carbon isotope analyses of carbon dioxide (CO2) showed isotope enrichment in all H2-supplemented biotic setups indicating H2-dependent consumption of CO2 by methanogens or homoacetogens. Homoacetogenesis was indicated by the detection of acetate and formate. Consumption of CO2 and H2 varied along the differently nutrient-amended setups, as did the onset of methane production. Plotting carbon against hydrogen isotope signatures of CH4 indicated that CH4 was produced hydrogenotrophically and fermentatively. The putative hydrogenotrophic Methanobacterium sp. was the dominant methanogen. Most abundant phylotypes belonged to typical ferric iron reducers, indicating that besides CO2, Fe(III) was an important electron acceptor. In summary, our study provides evidence for the adaptability of subsurface microbial communities under different nutrient-deficient conditions to elevated H2 partial pressures.
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Affiliation(s)
- Michaela Löffler
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Laura Schwab
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Frank Dethlefsen
- Department of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy (KGE), University of Kiel, Kiel, Germany
| | - Louisa Lagmöller
- Department of Applied Geosciences - Aquatic Geochemistry and Hydrogeology, Institute for Geosciences, Competence Centre for Geoenergy (KGE), University of Kiel, Kiel, Germany
| | - Carsten Vogt
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Isodetect GmbH, Leipzig, Germany
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2
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Marbehan X, Roger M, Fournier F, Infossi P, Guedon E, Delecourt L, Lebrun R, Giudici-Orticoni MT, Delaunay S. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough. Front Microbiol 2024; 15:1336360. [PMID: 38463485 PMCID: PMC10920352 DOI: 10.3389/fmicb.2024.1336360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria that exhibits highly versatile metabolism. By switching from one energy mode to another depending on nutrients availability in the environments" it plays a central role in shaping ecosystems. Despite intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remain far from being fully understood. Alternatively, metabolic modeling is a powerful tool to understand bioenergetics. However, all the current models for D. vulgaris appeared to be not easily adaptable to various environmental conditions. Methods To lift off these limitations, here we constructed a novel transparent and robust metabolic model to explain D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). Results The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. Discussion In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
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Affiliation(s)
| | - Magali Roger
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Pascale Infossi
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Louis Delecourt
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
- LISM-UMR 7255, Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Aix-Marseille Université, CNRS, Marseille, France
| | - Régine Lebrun
- IMM-FR3479, Marseille Protéomique, Aix-Marseille Université, CNRS, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
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Jawaharraj K, Peta V, Dhiman SS, Gnimpieba EZ, Gadhamshetty V. Transcriptome-wide marker gene expression analysis of stress-responsive sulfate-reducing bacteria. Sci Rep 2023; 13:16181. [PMID: 37758719 PMCID: PMC10533852 DOI: 10.1038/s41598-023-43089-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/19/2023] [Indexed: 09/29/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) are terminal members of any anaerobic food chain. For example, they critically influence the biogeochemical cycling of carbon, nitrogen, sulfur, and metals (natural environment) as well as the corrosion of civil infrastructure (built environment). The United States alone spends nearly $4 billion to address the biocorrosion challenges of SRB. It is important to analyze the genetic mechanisms of these organisms under environmental stresses. The current study uses complementary methodologies, viz., transcriptome-wide marker gene panel mapping and gene clustering analysis to decipher the stress mechanisms in four SRB. Here, the accessible RNA-sequencing data from the public domains were mined to identify the key transcriptional signatures. Crucial transcriptional candidate genes of Desulfovibrio spp. were accomplished and validated the gene cluster prediction. In addition, the unique transcriptional signatures of Oleidesulfovibrio alaskensis (OA-G20) at graphene and copper interfaces were discussed using in-house RNA-sequencing data. Furthermore, the comparative genomic analysis revealed 12,821 genes with translation, among which 10,178 genes were in homolog families and 2643 genes were in singleton families were observed among the 4 genomes studied. The current study paves a path for developing predictive deep learning tools for interpretable and mechanistic learning analysis of the SRB gene regulation.
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Affiliation(s)
- Kalimuthu Jawaharraj
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
| | - Vincent Peta
- Biomedical Engineering, University of South Dakota, 4800 N Career Ave, Sioux Falls, SD, 57107, USA
| | - Saurabh Sudha Dhiman
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
- Chemistry, Biology and Health Sciences, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA
| | - Etienne Z Gnimpieba
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Biomedical Engineering, University of South Dakota, 4800 N Career Ave, Sioux Falls, SD, 57107, USA.
| | - Venkataramana Gadhamshetty
- Civil and Environmental Engineering, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- 2D-Materials for Biofilm Engineering, Science and Technology (2D BEST) Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
- Data-Driven Materials Discovery for Bioengineering Innovation Center, South Dakota Mines, 501 E. St. Joseph Street, Rapid City, SD, 57701, USA.
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Darnajoux R, Inomura K, Zhang X. A diazotrophy-ammoniotrophy dual growth model for the sulfate reducing bacterium Desulfovibrio vulgaris var. Hildenborough. Comput Struct Biotechnol J 2023; 21:3136-3148. [PMID: 37293241 PMCID: PMC10244686 DOI: 10.1016/j.csbj.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/10/2023] Open
Abstract
Sulfate reducing bacteria (SRB) comprise one of the few prokaryotic groups in which biological nitrogen fixation (BNF) is common. Recent studies have highlighted SRB roles in N cycling, particularly in oligotrophic coastal and benthic environments where they could contribute significantly to N input. Most studies of SRB have focused on sulfur cycling and SRB growth models have primarily aimed at understanding the effects of electron sources, with N usually provided as fixed-N (nitrate, ammonium). Mechanistic links between SRB nitrogen-fixing metabolism and growth are not well understood, particularly in environments where fixed-N fluctuates. Here, we investigate diazotrophic growth of the model sulfate reducer Desulfovibrio vulgaris var. Hildenborough under anaerobic heterotrophic conditions and contrasting N availabilities using a simple cellular model with dual ammoniotrophic and diazotrophic modes. The model was calibrated using batch culture experiments with varying initial ammonium concentrations (0-3000 µM) and acetylene reduction assays of BNF activity. The model confirmed the preferential usage of ammonium over BNF for growth and successfully reproduces experimental data, with notably clear bi-phasic growth curves showing an initial ammoniotrophic phase followed by onset of BNF. Our model enables quantification of the energetic cost of each N acquisition strategy and indicates the existence of a BNF-specific limiting phenomenon, not directly linked to micronutrient (Mo, Fe, Ni) concentration, by-products (hydrogen, hydrogen sulfide), or fundamental model metabolic parameters (death rate, electron acceptor stoichiometry). By providing quantitative predictions of environment and metabolism, this study contributes to a better understanding of anaerobic heterotrophic diazotrophs in environments with fluctuating N conditions.
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Affiliation(s)
- Romain Darnajoux
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
- High Meadow Environmental Institute, Princeton University, Princeton, NJ 08544, USA
| | - Keisuke Inomura
- Graduate School of Oceanography, University of Rhode Island, Narragansett, RI 02882, USA
| | - Xinning Zhang
- Department of Geosciences, Princeton University, Princeton, NJ 08544, USA
- High Meadow Environmental Institute, Princeton University, Princeton, NJ 08544, USA
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5
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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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6
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Kpebe A, Guendon C, Payne N, Ros J, Khelil Berbar M, Lebrun R, Baffert C, Shintu L, Brugna M. An essential role of the reversible electron-bifurcating hydrogenase Hnd for ethanol oxidation in Solidesulfovibrio fructosivorans. Front Microbiol 2023; 14:1139276. [PMID: 37051519 PMCID: PMC10084766 DOI: 10.3389/fmicb.2023.1139276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The tetrameric cytoplasmic FeFe hydrogenase Hnd from Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans) catalyses H2 oxidation and couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin by using a flavin-based electron-bifurcating mechanism. Regarding its implication in the bacterial physiology, we previously showed that Hnd, which is non-essential when bacteria grow fermentatively on pyruvate, is involved in ethanol metabolism. Under these conditions, it consumes H2 to produce reducing equivalents for ethanol production as a fermentative product. In this study, the approach implemented was to compare the two S. fructosivorans WT and the hndD deletion mutant strains when grown on ethanol as the sole carbon and energy source. Based on the determination of bacterial growth, metabolite consumption and production, gene expression followed by RT-q-PCR, and Hnd protein level followed by mass spectrometry, our results confirm the role of Hnd hydrogenase in the ethanol metabolism and furthermore uncover for the first time an essential function for a Desulfovibrio hydrogenase. Hnd is unequivocally required for S. fructosivorans growth on ethanol, and we propose that it produces H2 from NADH and reduced ferredoxin generated by an alcohol dehydrogenase and an aldehyde ferredoxin oxidoreductase catalyzing the conversion of ethanol into acetate. The produced H2 could then be recycled and used for sulfate reduction. Hnd is thus a reversible hydrogenase that operates in H2-consumption by an electron-bifurcating mechanism during pyruvate fermentation and in H2-production by an electron-confurcating mechanism when the bacterium uses ethanol as electron donor.
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Affiliation(s)
| | | | - Natalie Payne
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
- CNRS, Aix-Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | - Julien Ros
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
| | - Manel Khelil Berbar
- CNRS, Aix-Marseille Univ, Plate-forme Protéomique de l’IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Régine Lebrun
- CNRS, Aix-Marseille Univ, Plate-forme Protéomique de l’IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | | | - Laetitia Shintu
- CNRS, Aix-Marseille Univ, Centrale Marseille, ISM2, Marseille, France
| | - Myriam Brugna
- CNRS, Aix-Marseille Univ, BIP, Marseille, France
- *Correspondence: Myriam Brugna,
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7
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Payne N, Kpebe A, Guendon C, Baffert C, Maillot M, Haurogné T, Tranchida F, Brugna M, Shintu L. NMR-based metabolomic analysis of the physiological role of the electron-bifurcating FeFe-hydrogenase Hnd in Solidesulfovibrio fructosivorans under pyruvate fermentation. Microbiol Res 2023; 268:127279. [PMID: 36592576 DOI: 10.1016/j.micres.2022.127279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Solidesulfovibrio fructosivorans (formely Desulfovibrio fructosovorans), an anaerobic sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of hydrogen gas (H2) into protons and electrons. One of these, named Hnd, was demonstrated to be an electron-bifurcating hydrogenase Hnd (Kpebe et al., 2018). It couples the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 and whose function has been recently shown to be involved in ethanol production under pyruvate fermentation (Payne 2022). To understand further the physiological role of Hnd in S. fructosivorans, we compared the mutant deleted of part of the hnd gene with the wild-type strain grown on pyruvate without sulfate using NMR-based metabolomics. Our results confirm that Hnd is profoundly involved in ethanol metabolism, but also indirectly intervenes in global carbon metabolism and additional metabolic processes such as the biosynthesis of branched-chain amino acids. We also highlight the metabolic reprogramming induced by the deletion of hndD that leads to the upregulation of several NADP-dependent pathways.
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Affiliation(s)
- Natalie Payne
- Aix Marseille Univ, CNRS, BIP, Marseille, France; Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | | | | | | | | | - Fabrice Tranchida
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France
| | | | - Laetitia Shintu
- Aix Marseille Univ, CNRS, Centrale Marseille, ISM2, Marseille, France.
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8
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Zhang S, Zhang X, Yuan Y, Li K, Liu H. Renewable biohydrogen production from Clostridium sp. LQ25 using different forms of ferric as electron acceptor. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158911. [PMID: 36152847 DOI: 10.1016/j.scitotenv.2022.158911] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/09/2022] [Accepted: 09/17/2022] [Indexed: 06/16/2023]
Abstract
Clostridium sp. LQ25 was cultured in different forms of ferric (ferric citrate and ferric hydroxide) as electron acceptors to investigate growth, ferric reduction, hydrogen production, fermentation products and fermentation process. The growth of the strain LQ25 detected by protein was 82.8 ± 2.1 mg/L and 73.5 ± 1.7 mg/L using ferric citrate and ferric hydroxide as electron acceptors, which was 33.3 % and 18.4 % higher than without ferric, respectively. The accumulation concentration of Fe(II) was 9.0 ± 0.6 mg/L and 5.0 ± 0.2 mg/L when using ferric citrate and ferric hydroxide as electron acceptors, and ferric citrate was 1.8-fold higher than ferric hydroxide, which indicated that the ability of ferric reduction was higher using ferric citrate as electron acceptor. The hydrogen production of strain LQ25 was 238.0 ± 1.0 mmol/mol glucose and 113.0 ± 1.3 mmol/mol glucose under condition of ferric citrate and ferric hydroxide as electron acceptors, which was 2.6 and 1.2-fold higher than without ferric, respectively. The growth and hydrogen production of strain LQ25 was promoted by using ferric as electron acceptor, while the fermentation type of strain did not change and was always butyrate type. The differential expression of the genes of strain LQ25 was significant when using ferric as electron acceptor, mainly in NADH and PFL pathway. This study provided preliminary evidence for hydrogen production by Clostridium sp. LQ25 in the presence of electron acceptor.
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Affiliation(s)
- Shan Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Xiaodan Zhang
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Yuan Yuan
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Kaiqiang Li
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China
| | - Hongyan Liu
- College of Marine and Environmental Sciences, Tianjin University of Science & Technology, China.
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Paiva AR, Pilloni G. Inferring Microbial Biomass Yield and Cell Weight Using Probabilistic Macrochemical Modeling. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:442-454. [PMID: 35038296 DOI: 10.1109/tcbb.2021.3139290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Growth rates and biomass yields are key descriptors used in microbiology studies to understand how microbial species respond to changes in the environment. Of these, biomass yield estimates are typically obtained using cell counts and measurements of the feed substrate. These quantities are perturbed with measurement noise however. Perhaps most crucially, estimating biomass from cell counts, as needed to assess yields, relies on an assumed cell weight. Noise and discrepancies on these assumptions can lead to significant changes in conclusions regarding the microbes' response. This article proposes a methodology to address these challenges using probabilistic macrochemical models of microbial growth. It is shown that a model can be developed to fully use the experimental data, relax assumptions and greatly improve robustness to a priori estimates of the cell weight, and provides uncertainty estimates of key parameters. This methodology is demonstrated in the context of a specific case study and the estimation characteristics are validated in several scenarios using synthetically generated microbial growth data.
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10
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Payne N, Kpebe A, Guendon C, Baffert C, Ros J, Lebrun R, Denis Y, Shintu L, Brugna M. The electron-bifurcating FeFe-hydrogenase Hnd is involved in ethanol metabolism in Desulfovibrio fructosovorans grown on pyruvate. Mol Microbiol 2022; 117:907-920. [PMID: 35066935 DOI: 10.1111/mmi.14881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 11/28/2022]
Abstract
Desulfovibrio fructosovorans, a sulfate-reducing bacterium, possesses six gene clusters encoding six hydrogenases catalyzing the reversible oxidation of H2 into protons and electrons. Among them, Hnd is an electron-bifurcating hydrogenase, coupling the exergonic reduction of NAD+ to the endergonic reduction of a ferredoxin with electrons derived from H2 . It was previously hypothesized that its biological function involves the production of NADPH necessary for biosynthetic purposes. However, it was subsequently demonstrated that Hnd is instead a NAD+ -reducing enzyme, thus its specific function has yet to be established. To understand the physiological role of Hnd in D. fructosovorans, we compared the hnd deletion mutant with the wild-type strain grown on pyruvate. Growth, metabolites production and comsumption, and gene expression were compared under three different growth conditions. Our results indicate that hnd is strongly regulated at the transcriptional level and that its deletion has a drastic effect on the expression of genes for two enzymes, an aldehyde ferredoxin oxidoreductase and an alcohol dehydrogenase. We demonstrated here that Hnd is involved in ethanol metabolism when bacteria grow fermentatively and proposed that Hnd might oxidize part of the H2 produced during fermentation generating both NADH and reduced ferredoxin for ethanol production via its electron bifurcation mechanism.
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Affiliation(s)
| | | | | | | | - Julien Ros
- CNRS, Aix Marseille Univ, BIP, Marseille, France
| | - Régine Lebrun
- CNRS, Aix Marseille Univ, Plate-forme Protéomique de l'IMM, FR 3479, Marseille Protéomique (MaP), Marseille, France
| | - Yann Denis
- CNRS, Aix Marseille Univ, Plate-forme Transcriptomique, Marseille, France
| | - Laetitia Shintu
- CNRS, Aix Marseille Univ, Centrale Marseille, ISM2, Marseille, France
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Anguita J, Pizarro G, Vargas IT. Mathematical modelling of microbial corrosion in carbon steel due to early-biofilm formation of sulfate-reducing bacteria via extracellular electron transfer. Bioelectrochemistry 2022; 145:108058. [DOI: 10.1016/j.bioelechem.2022.108058] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 11/26/2022]
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12
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Response to substrate limitation by a marine sulfate-reducing bacterium. THE ISME JOURNAL 2022; 16:200-210. [PMID: 34285365 PMCID: PMC8692349 DOI: 10.1038/s41396-021-01061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 02/07/2023]
Abstract
Sulfate-reducing microorganisms (SRM) in subsurface sediments live under constant substrate and energy limitation, yet little is known about how they adapt to this mode of life. We combined controlled chemostat cultivation and transcriptomics to examine how the marine sulfate reducer, Desulfobacterium autotrophicum, copes with substrate (sulfate or lactate) limitation. The half-saturation uptake constant (Km) for lactate was 1.2 µM, which is the first value reported for a marine SRM, while the Km for sulfate was 3 µM. The measured residual lactate concentration in our experiments matched values observed in situ in marine sediments, supporting a key role of SRM in the control of lactate concentrations. Lactate limitation resulted in complete lactate oxidation via the Wood-Ljungdahl pathway and differential overexpression of genes involved in uptake and metabolism of amino acids as an alternative carbon source. D. autotrophicum switched to incomplete lactate oxidation, rerouting carbon metabolism in response to sulfate limitation. The estimated free energy was significantly lower during sulfate limitation (-28 to -33 kJ mol-1 sulfate), suggesting that the observed metabolic switch is under thermodynamic control. Furthermore, we detected the upregulation of putative sulfate transporters involved in either high or low affinity uptake in response to low or high sulfate concentration.
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Tang WT, Hao TW, Chen GH. Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms. Biotechnol Bioeng 2021; 118:2676-2693. [PMID: 33844295 DOI: 10.1002/bit.27787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/21/2021] [Accepted: 03/11/2021] [Indexed: 11/07/2022]
Abstract
Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.
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Affiliation(s)
- Wen-Tao Tang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tian-Wei Hao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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14
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Schwarz A, Suárez JI, Aybar M, Nancucheo I, Martínez P, Rittmann BE. A membrane-biofilm system for sulfate conversion to elemental sulfur in mining-influenced waters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:140088. [PMID: 32559542 DOI: 10.1016/j.scitotenv.2020.140088] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 06/06/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
A system of two membrane biofilm reactors (MBfRs) was tested for the conversion of sulfate (1.5 g/L) in mining-process water into elemental sulfur (S0) particles. Initially, a H2-based MBfR reduced sulfate to sulfide, and an O2-based MBfR then oxidized sulfide to S0. Later, the two MBfRs were coupled by a recirculation flow. Surface loading, reactor-coupling configuration, and substrate-gas pressure exerted important controls over performance of each MBfR and the coupled system. Continuously recirculating the liquid between the H2-based MBfR and the O2-based MBfR, compared to series operation, avoided the buildup of sulfide and gave overall greater sulfate removal (99% vs 62%) and production of S0 (61% vs 54%). The trade-off was that recirculation coupling demanded greater delivery of H2 and O2 (in air) due to the establishment of a sulfur cycle catalyzed by Sulfurospirillum spp., which had an average abundance of 46% in the H2-based MBfR fibers and 62% in the O2-based MBfR fibers at the end of the experiments. Sulfate-reducing bacteria (Desulfovibrio and Desulfomicrobium) and sulfur-oxidizing bacteria (Thiofaba, Thiomonas, Acidithiobacillus and Sulfuricurvum) averaged only 22% and 11% in the H2-based MBfR and O2-based MBfR fibers, respectively. Evidence suggests that the undesired Sulfurospirillum species, which reduce S0 to sulfide, can be suppressed by increasing sulfate-surface loading and H2 pressure.
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Affiliation(s)
- Alex Schwarz
- Departamento de Ingeniería Civil, Universidad de Concepción, P.O. Box 160-C, Concepción 4070386, Chile.
| | - José Ignacio Suárez
- Departamento de Ingeniería Civil, Universidad de Concepción, P.O. Box 160-C, Concepción 4070386, Chile
| | - Marcelo Aybar
- Departamento de Ingeniería Civil, Universidad de Concepción, P.O. Box 160-C, Concepción 4070386, Chile
| | - Iván Nancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | | | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, P.O. Box 875701, Tempe, AZ 85287-5701, United States of America
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15
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Stahl DA. The path leading to the discovery of the ammoniaoxidizing archaea. Environ Microbiol 2020; 22:4507-4519. [PMID: 32955155 DOI: 10.1111/1462-2920.15239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 11/28/2022]
Affiliation(s)
- David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, 98195, USA
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16
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. Competition for Hydrogen Prevents Coexistence of Human Gastrointestinal Hydrogenotrophs in Continuous Culture. Front Microbiol 2020; 11:1073. [PMID: 32547517 PMCID: PMC7272605 DOI: 10.3389/fmicb.2020.01073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/29/2020] [Indexed: 01/24/2023] Open
Abstract
Understanding the metabolic dynamics of the human gastrointestinal tract (GIT) microbiota is of growing importance as research continues to link the microbiome to host health status. Microbial strains that metabolize hydrogen have been associated with a variety of both positive and negative host nutritional and health outcomes, but limited data exists for their competition in the GIT. To enable greater insight into the behaviour of these microbes, a mathematical model was developed for the metabolism and growth of the three major hydrogenotrophic groups: sulphate-reducing bacteria (SRB), methanogens and reductive acetogens. In batch culture simulations with abundant sulphate and hydrogen, the SRB outcompeted the methanogen for hydrogen due to having a half-saturation constant 106 times lower than that of the methanogen. The acetogen, with a high model threshold for hydrogen uptake of around 70 mM, was the least competitive. Under high lactate and zero sulphate conditions, hydrogen exchange between the SRB and the methanogen was the dominant interaction. The methanogen grew at 70% the rate of the SRB, with negligible acetogen growth. In continuous culture simulations, both the SRB and the methanogen were washed out at dilution rates above 0.15 h−1 regardless of substrate availability, whereas the acetogen could survive under abundant hydrogen conditions. Specific combinations of conditions were required for survival of more than one hydrogenotroph in continuous culture, and survival of all three was not possible. The stringency of these requirements and the inability of the model to simulate survival of all three hydrogenotrophs in continuous culture demonstrates that factors outside of those modelled are vital to allow hydrogenotroph coexistence in the GIT.
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Affiliation(s)
- Nick W Smith
- School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Ruakura Research Centre, Hamilton, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Paul R Shorten
- Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Ruakura Research Centre, Hamilton, New Zealand
| | - Eric Altermann
- Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Nicole C Roy
- Riddet Institute, Massey University, Palmerston North, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
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17
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Chen J, Wade MJ, Dolfing J, Soyer OS. Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer. J R Soc Interface 2020; 16:20190129. [PMID: 31064258 PMCID: PMC6544901 DOI: 10.1098/rsif.2019.0129] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Methane-producing microbial communities are of ecological and biotechnological interest. Syntrophic interactions among sulfate reducers and aceto/hydrogenotrophic and obligate hydrogenotrophic methanogens form a key component of these communities, yet, the impact of these different syntrophic routes on methane production and their stability against sulfate availability are not well understood. Here, we construct model synthetic communities using a sulfate reducer and two types of methanogens representing different methanogenesis routes. We find that tri-cultures with both routes increase methane production by almost twofold compared to co-cultures and are stable in the absence of sulfate. With increasing sulfate, system stability and productivity decreases and does so faster in communities with aceto/hydrogenotrophic methanogens despite the continued presence of acetate. We show that this is due to a shift in the metabolism of these methanogens towards co-utilization of hydrogen with acetate. These findings indicate the important role of hydrogen dynamics in the stability and productivity of syntrophic communities.
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Affiliation(s)
- Jing Chen
- 1 School of Life Sciences, University of Warwick , Coventry CV4 7AL , UK
| | - Matthew J Wade
- 3 School of Engineering, Newcastle University , Newcastle NE1 7RU , UK.,4 School of Mathematics and Statistics, McMaster University , Hamilton, Ontario , Canada L8S 4K1
| | - Jan Dolfing
- 3 School of Engineering, Newcastle University , Newcastle NE1 7RU , UK
| | - Orkun S Soyer
- 1 School of Life Sciences, University of Warwick , Coventry CV4 7AL , UK.,2 Warwick Integrative Synthetic Biology Centre (WISB), University of Warwick , Coventry CV4 7AL , UK
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18
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Delattre H, Chen J, Wade MJ, Soyer OS. Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis. J R Soc Interface 2020; 17:20200053. [PMID: 32370691 PMCID: PMC7276542 DOI: 10.1098/rsif.2020.0053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Microbial communities are complex dynamical systems harbouring many species interacting together to implement higher-level functions. Among these higher-level functions, conversion of organic matter into simpler building blocks by microbial communities underpins biogeochemical cycles and animal and plant nutrition, and is exploited in biotechnology. A prerequisite to predicting the dynamics and stability of community-mediated metabolic conversions is the development and calibration of appropriate mathematical models. Here, we present a generic, extendable thermodynamic model for community dynamics and calibrate a key parameter of this thermodynamic model, the minimum energy requirement associated with growth-supporting metabolic pathways, using experimental population dynamics data from synthetic communities composed of a sulfate reducer and two methanogens. Our findings show that accounting for thermodynamics is necessary in capturing the experimental population dynamics of these synthetic communities that feature relevant species using low energy growth pathways. Furthermore, they provide the first estimates for minimum energy requirements of methanogenesis (in the range of −30 kJ mol−1) and elaborate on previous estimates of lactate fermentation by sulfate reducers (in the range of −30 to −17 kJ mol−1 depending on the culture conditions). The open-source nature of the developed model and demonstration of its use for estimating a key thermodynamic parameter should facilitate further thermodynamic modelling of microbial communities.
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Affiliation(s)
| | - Jing Chen
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Matthew J Wade
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Orkun S Soyer
- School of Life Sciences, University of Warwick, Coventry, UK
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19
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Murray AM, Maillard J, Jin B, Broholm MM, Holliger C, Rolle M. A modeling approach integrating microbial activity, mass transfer, and geochemical processes to interpret biological assays: An example for PCE degradation in a multi-phase batch setup. WATER RESEARCH 2019; 160:484-496. [PMID: 31177078 DOI: 10.1016/j.watres.2019.05.087] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/22/2019] [Accepted: 05/25/2019] [Indexed: 06/09/2023]
Abstract
The rate at which organic contaminants can be degraded in aquatic environments is not only dependent upon specific degrading bacteria, but also upon the composition of the microbial community, mass transfer of the contaminant, and abiotic processes that occur in the environment. In this study, we present three-phase batch experiments of tetrachloroethene (PCE) degradation by a consortium of organohalide-respiring bacteria, cultivated alone or in communities with iron- and/or sulfate-reducers. We developed a modeling approach to quantitatively evaluate the experimental results, comprised of chemical and biomolecular time series data. The model utilizes the IPhreeqc module to couple multi-phase mass transfer between gaseous, organic and aqueous phases with microbial and aquatic geochemical processes described using the geochemical code PHREEQC. The proposed approach is able to capture the contaminant degradation, the microbial population dynamics, the effects of multi-phase kinetic mass transfer and sample removal, and the geochemical reactions occurring in the aqueous phase. The model demonstrates the importance of aqueous speciation and abiotic reactions on the bioavailability of the substrates. The model-based interpretation allowed us to quantify the reaction kinetics of the different bacterial guilds. The model further revealed that the inclusion of sulfate-reducing bacteria lowers the rate of PCE degradation and that this effect is moderated in the presence of iron-reducing bacteria.
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Affiliation(s)
- Alexandra Marie Murray
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Julien Maillard
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Biao Jin
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Science, China
| | - Mette M Broholm
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark
| | - Christof Holliger
- Laboratory for Environmental Biotechnology, ENAC-IIE, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Massimo Rolle
- Department of Environmental Engineering, Technical University of Denmark, Kgs. Lyngby, DK-2800, Denmark.
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20
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Smith NW, Shorten PR, Altermann E, Roy NC, McNabb WC. A Mathematical Model for the Hydrogenotrophic Metabolism of Sulphate-Reducing Bacteria. Front Microbiol 2019; 10:1652. [PMID: 31379794 PMCID: PMC6653664 DOI: 10.3389/fmicb.2019.01652] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Sulphate-reducing bacteria (SRB) are studied across a range of scientific fields due to their characteristic ability to metabolise sulphate and produce hydrogen sulphide, which can lead to significant consequences for human activities. Importantly, they are members of the human gastrointestinal microbial population, contributing to the metabolism of dietary and host secreted molecules found in this environment. The role of the microbiota in host digestion is well studied, but the full role of SRB in this process has not been established. Moreover, from a human health perspective, SRB have been implicated in a number of functional gastrointestinal disorders such as Irritable Bowel Syndrome and the development of colorectal cancer. To assist with the study of SRB, we present a mathematical model for the growth and metabolism of the well-studied SRB, Desulfovibrio vulgaris in a closed system. Previous attempts to model SRB have resulted in complex or highly specific models that are not easily adapted to the study of SRB in different environments, such as the gastrointestinal tract. We propose a simpler, Monod-based model that allows for easy alteration of both key parameter values and the governing equations to enable model adaptation. To prevent any incorrect assumptions about the nature of SRB metabolic pathways, we structure the model to consider only the concentrations of initial and final metabolites in a pathway, which circumvents the current uncertainty around hydrogen cycling by SRB. We parameterise our model using experiments with varied initial substrate conditions, obtaining parameter values that compare well with experimental estimates in the literature. We then validate our model against four independent experiments involving D. vulgaris with further variations to substrate availability. Further use of the model will be possible in a number of settings, notably as part of larger models studying the metabolic interactions between SRB and other hydrogenotrophic microbes in the human gastrointestinal tract and how this relates to functional disorders.
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Affiliation(s)
- Nick W Smith
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand.,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,School of Food and Advanced Technology, Massey University, Palmerston North, New Zealand
| | - Paul R Shorten
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Eric Altermann
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Nicole C Roy
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand.,Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, The University of Auckland, Auckland, New Zealand
| | - Warren C McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand.,High-Value Nutrition National Science Challenge, The University of Auckland, Auckland, New Zealand
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21
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Löffler M, Kümmel S, Vogt C, Richnow HH. H 2 Kinetic Isotope Fractionation Superimposed by Equilibrium Isotope Fractionation During Hydrogenase Activity of D. vulgaris Strain Miyazaki. Front Microbiol 2019; 10:1545. [PMID: 31354654 PMCID: PMC6636216 DOI: 10.3389/fmicb.2019.01545] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/20/2019] [Indexed: 01/24/2023] Open
Abstract
We determined 2H stable isotope fractionation at natural abundances associated with hydrogenase activity by whole cells of Desulfovibrio vulgaris strain Miyazaki F expressing a NiFe(Se) hydrogenase. Inhibition of sulfate reduction by molybdate inhibited the overall oxidation of hydrogen but still facilitated an equilibrium isotope exchange reaction with water. The theoretical equilibrium isotope exchange δ2H-values of the chemical exchange reaction were identical to the hydrogenase reaction, as confirmed using three isotopically different waters with δ2H-values of – 62, +461, and + 1533‰. Expected kinetic isotope fractionation of hydrogen oxidation by non-inhibited cells was also superimposed by an equilibrium isotope exchange. The isotope effects were solely catalyzed biotically as hydrogen isotope signatures did not change in control experiments without cells of D. vulgaris Miyazaki.
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Affiliation(s)
- Michaela Löffler
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Steffen Kümmel
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hans-Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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22
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Baffert C, Kpebe A, Avilan L, Brugna M. Hydrogenases and H 2 metabolism in sulfate-reducing bacteria of the Desulfovibrio genus. Adv Microb Physiol 2019; 74:143-189. [PMID: 31126530 DOI: 10.1016/bs.ampbs.2019.03.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Hydrogen metabolism plays a central role in sulfate-reducing bacteria of the Desulfovibrio genus and is based on hydrogenases that catalyze the reversible conversion of protons into dihydrogen. These metabolically versatile microorganisms possess a complex hydrogenase system composed of several enzymes of both [FeFe]- and [NiFe]-type that can vary considerably from one Desulfovibrio species to another. This review covers the molecular and physiological aspects of hydrogenases and H2 metabolism in Desulfovibrio but focuses particularly on our model bacterium Desulfovibrio fructosovorans. The search of hydrogenase genes in more than 30 sequenced genomes provides an overview of the distribution of these enzymes in Desulfovibrio. Our discussion will consider the significance of the involvement of electron-bifurcation in H2 metabolism.
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Affiliation(s)
- Carole Baffert
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Arlette Kpebe
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Luisana Avilan
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
| | - Myriam Brugna
- Aix-Marseille University, CNRS, BIP, 31 Chemin Joseph Aiguier, 13402 Marseille, France
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23
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Zhou C, Ontiveros-Valencia A, Nerenberg R, Tang Y, Friese D, Krajmalnik-Brown R, Rittmann BE. Hydrogenotrophic Microbial Reduction of Oxyanions With the Membrane Biofilm Reactor. Front Microbiol 2019; 9:3268. [PMID: 30687262 PMCID: PMC6335333 DOI: 10.3389/fmicb.2018.03268] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/17/2018] [Indexed: 11/20/2022] Open
Abstract
Oxyanions, such as nitrate, perchlorate, selenate, and chromate are commonly occurring contaminants in groundwater, as well as municipal, industrial, and mining wastewaters. Microorganism-mediated reduction is an effective means to remove oxyanions from water by transforming oxyanions into harmless and/or immobilized forms. To carry out microbial reduction, bacteria require a source of electrons, called the electron-donor substrate. Compared to organic electron donors, H2 is not toxic, generates minimal secondary contamination, and can be readily obtained in a variety of ways at reasonable cost. However, the application of H2 through conventional delivery methods, such as bubbling, is untenable due to H2's low water solubility and combustibility. In this review, we describe the membrane biofilm reactor (MBfR), which is a technological breakthrough that makes H2 delivery to microorganisms efficient, reliable, and safe. The MBfR features non-porous gas-transfer membranes through which bubbleless H2 is delivered on-demand to a microbial biofilm that develops naturally on the outer surface of the membranes. The membranes serve as an active substratum for a microbial biofilm able to biologically reduce oxyanions in the water. We review the development of the MBfR technology from bench, to pilot, and to commercial scales, and we elucidate the mechanisms that control MBfR performance, particularly including methods for managing the biofilm's structure and function. We also give examples of MBfR performance for cases of treating single and co-occurring oxyanions in different types of contaminated water. In summary, the MBfR is an effective and reliable technology for removing oxyanion contaminants by accurately providing a biofilm with bubbleless H2 on demand. Controlling the H2 supply in accordance to oxyanion surface loading and managing the accumulation and activity of biofilm are the keys for process success.
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Affiliation(s)
- Chen Zhou
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, United States
| | | | - Robert Nerenberg
- Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Youneng Tang
- Department of Civil and Environmental Engineering, FAMU-FSU College of Engineering, Florida State University, Tallahassee, FL, United States
| | | | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, United States
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, AZ, United States
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24
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Abstract
Hydrogen plays a key role in many microbial metabolic pathways in the human gastrointestinal tract (GIT) that have an impact on human nutrition, health and wellbeing. Hydrogen is produced by many members of the GIT microbiota, and may be subsequently utilized by cross-feeding microbes for growth and in the production of larger molecules. Hydrogenotrophic microbes fall into three functional groups: sulfate-reducing bacteria, methanogenic archaea and acetogenic bacteria, which can convert hydrogen into hydrogen sulfide, methane and acetate, respectively. Despite different energy yields per molecule of hydrogen used between the functional groups, all three can coexist in the human GIT. The factors affecting the numerical balance of hydrogenotrophs in the GIT remain unconfirmed. There is increasing evidence linking both hydrogen sulfide and methane to GIT diseases such as irritable bowel syndrome, and strategies for the mitigation of such health problems through targeting of hydrogenotrophs constitute an important field for further investigation.
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Affiliation(s)
- Nick W. Smith
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand,AgResearch, Grasslands Research Centre, Palmerston North, New Zealand,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Paul R. Shorten
- AgResearch, Ruakura Research Centre, Hamilton, New Zealand,Riddet Institute, Massey University, Palmerston North, New Zealand,CONTACT Paul R. Shorten AgResearch, Ruakura Research Centre, Private Bag 3123, Hamilton 3240, New Zealand
| | - Eric H. Altermann
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand,Riddet Institute, Massey University, Palmerston North, New Zealand
| | - Nicole C. Roy
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand,Riddet Institute, Massey University, Palmerston North, New Zealand,High-Value Nutrition National Science Challenge, hosted by The University of Auckland, Auckland, New Zealand
| | - Warren C. McNabb
- Riddet Institute, Massey University, Palmerston North, New Zealand
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25
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Delattre H, Desmond-Le Quéméner E, Duquennoi C, Filali A, Bouchez T. Consistent microbial dynamics and functional community patterns derived from first principles. ISME JOURNAL 2018; 13:263-276. [PMID: 30194430 DOI: 10.1038/s41396-018-0272-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 06/14/2018] [Accepted: 06/20/2018] [Indexed: 01/26/2023]
Abstract
Microbial communities are key engines that drive earth's biogeochemical cycles. However, existing ecosystem models have only limited ability to predict microbial dynamics and require the calibration of multiple population-specific empirical equations. In contrast, we build on a new kinetic "Microbial Transition State" (MTS) theory of growth derived from first principles. We show how the theory coupled to simple mass and energy balance calculations provides a framework with intrinsically important qualitative properties to model microbial community dynamics. We first show how the theory can simultaneously account for the influence of all the resources needed for growth (electron donor, acceptor, and nutrients) while still producing consistent dynamics that fulfill the Liebig rule of a single limiting substrate. We also show consistent patterns of energy-dependent microbial successions in mixed culture without the need for calibration of population-specific parameters. We then show how this approach can be used to model a simplified activated sludge community. To this end, we compare MTS-derived dynamics with those of a widely used activated sludge model and show that similar growth yields and overall dynamics can be obtained using two parameters instead of twelve. This new kinetic theory of growth grounded by a set of generic physical principles parsimoniously gives rise to consistent microbial population and community dynamics, thereby paving the way for the development of a new class of more predictive microbial ecosystem models.
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Affiliation(s)
| | - Elie Desmond-Le Quéméner
- Irstea, UR HBAN, F-92761, Antony, France.,LBE, University of Montpellier, INRA, Narbonne, France
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26
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Li X, Lan SM, Zhu ZP, Zhang C, Zeng GM, Liu YG, Cao WC, Song B, Yang H, Wang SF, Wu SH. The bioenergetics mechanisms and applications of sulfate-reducing bacteria in remediation of pollutants in drainage: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 158:162-170. [PMID: 29684746 DOI: 10.1016/j.ecoenv.2018.04.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/30/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
Sulfate-reducing bacteria (SRB), a group of anaerobic prokaryotes, can use sulfur species as a terminal electron acceptor for the oxidation of organic compounds. They not only have significant ecological functions, but also play an important role in bioremediation of contaminated sites. Although numerous studies on metabolism and applications of SRB have been conducted, they still remain incompletely understood and even controversial. Fully understanding the metabolism of SRB paves the way for allowing the microorganisms to provide more beneficial services in bioremediation. Here we review progress in bioenergetics mechanisms and application of SRB including: (1) electron acceptors and donors for SRB; (2) pathway for sulfate reduction; (3) electron transfer in sulfate reduction; (4) application of SRB for economical and concomitant treatment of heavy metal, organic contaminants and sulfates. Moreover, current knowledge gaps and further research needs are identified.
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Affiliation(s)
- Xin Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Shi-Ming Lan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhong-Ping Zhu
- School of Minerals processing and Bioengineering, Central South University, No. 932 South Lushan road, Changsha, Hunan 410083, PR China
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guang-Ming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yun-Guo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wei-Cheng Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Hong Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Sheng-Fan Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Shao-Hua Wu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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Abstract
Energy conservation via hydrogen cycling, which generates proton motive force by intracellular H2 production coupled to extracellular consumption, has been controversial since it was first proposed in 1981. It was hypothesized that the methanogenic archaeon Methanosarcina barkeri is capable of energy conservation via H2 cycling, based on genetic data that suggest that H2 is a preferred, but nonessential, intermediate in the electron transport chain of this organism. Here, we characterize a series of hydrogenase mutants to provide direct evidence of H2 cycling. M. barkeri produces H2 during growth on methanol, a phenotype that is lost upon mutation of the cytoplasmic hydrogenase encoded by frhADGB, although low levels of H2, attributable to the Ech hydrogenase, accumulate during stationary phase. In contrast, mutations that conditionally inactivate the extracellular Vht hydrogenase are lethal when expression of the vhtGACD operon is repressed. Under these conditions, H2 accumulates, with concomitant cessation of methane production and subsequent cell lysis, suggesting that the inability to recapture extracellular H2 is responsible for the lethal phenotype. Consistent with this interpretation, double mutants that lack both Vht and Frh are viable. Thus, when intracellular hydrogen production is abrogated, loss of extracellular H2 consumption is no longer lethal. The common occurrence of both intracellular and extracellular hydrogenases in anaerobic microorganisms suggests that this unusual mechanism of energy conservation may be widespread in nature.IMPORTANCE ATP is required by all living organisms to facilitate essential endergonic reactions required for growth and maintenance. Although synthesis of ATP by substrate-level phosphorylation is widespread and significant, most ATP is made via the enzyme ATP synthase, which is energized by transmembrane chemiosmotic gradients. Therefore, establishing this gradient across the membrane is of central importance to sustaining life. Experimental validation of H2 cycling adds to a short list of mechanisms for generating a transmembrane electrochemical gradient that is likely to be widespread, especially among anaerobic microorganisms.
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Kushwaha S, Marcus AK, Rittmann BE. pH-dependent speciation and hydrogen (H 2 ) control U(VI) respiration by Desulfovibrio vulgaris. Biotechnol Bioeng 2018; 115:1465-1474. [PMID: 29476629 DOI: 10.1002/bit.26579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 11/06/2022]
Abstract
In situ bioreduction of soluble hexavalent uranium U(VI) to insoluble U(IV) (as UO2 ) has been proposed as a means of preventing U migration in the groundwater. This work focuses on the bioreduction of U(VI) and precipitation of U(IV). It uses anaerobic batch reactors with Desulfovibrio vulgaris, a well-known sulfate, iron, and U(VI) reducer, growing on lactate as the electron donor, in the absence of sulfate, and with a 30-mM bicarbonate buffering. In the absence of sulfate, D. vulgaris reduced >90% of the total soluble U(VI) (1 mM) to form U(IV) solids that were characterized by X-ray diffraction and confirmed to be nano-crystalline uraninite with crystallite size 2.8 ± 0.2 nm. pH values between 6 and 10 had minimal impact on bacterial growth and end-product distribution, supporting that the mono-nuclear, and poly-nuclear forms of U(VI) were equally bioavailable as electron acceptors. Electron balances support that H2 transiently accumulated, but was ultimately oxidized via U(VI) respiration. Thus, D. vulgaris utilized H2 as the electron carrier to drive respiration of U(VI). Rapid lactate utilization and biomass growth occurred only when U(VI) respiration began to draw down the sink of H2 and relieve thermodynamic inhibition of fermentation.
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Affiliation(s)
- Shilpi Kushwaha
- Biodesign Swette Center of Environmental Biotechnology, Arizona State University, Tempe, Arizon
| | - Andrew K Marcus
- Biodesign Swette Center of Environmental Biotechnology, Arizona State University, Tempe, Arizon
| | - Bruce E Rittmann
- Biodesign Swette Center of Environmental Biotechnology, Arizona State University, Tempe, Arizon
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29
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Chen Z, Lu J, Gao SH, Jin M, Bond PL, Yang P, Yuan Z, Guo J. Silver nanoparticles stimulate the proliferation of sulfate reducing bacterium Desulfovibrio vulgaris. WATER RESEARCH 2018; 129:163-171. [PMID: 29149671 DOI: 10.1016/j.watres.2017.11.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 06/07/2023]
Abstract
The intensive use of silver nanoparticles (AgNPs) in cosmetics and textiles causes their release into sewer networks of urban water systems. Although a few studies have investigated antimicrobial activities of nanoparticles against environmental bacteria, little is known about potential impacts of the released AgNPs on sulfate reducing bacteria in sewers. Here, we investigated the effect of AgNPs on Desulfovibrio vulgaris Hidenborough (D. vulgaris), a typical sulfate-reducing bacterium (SRB) in sewer systems. We found AgNPs stimulated the proliferation of D. vulgaris, rather than exerting inhibitory or biocidal effects. Based on flow cytometer detections, both the cell growth rate and the viable cell ratio of D. vulgaris increased during exposure to AgNPs at concentrations of up to 100 mg/L. The growth stimulation was dependent on the AgNP concentration. These results imply that the presence of AgNPs in sewage may affect SRB abundance in sewer networks. Our findings also shed new lights on the interactions of nanoparticles and bacteria.
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Affiliation(s)
- Zhaoyu Chen
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Ji Lu
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Shu-Hong Gao
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Min Jin
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Philip L Bond
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Ping Yang
- Department of Environmental Science & Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhiguo Yuan
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Jianhua Guo
- Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
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30
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Zhou C, Zhou Y, Rittmann BE. Reductive precipitation of sulfate and soluble Fe(III) by Desulfovibrio vulgaris: Electron donor regulates intracellular electron flow and nano-FeS crystallization. WATER RESEARCH 2017; 119:91-101. [PMID: 28436827 DOI: 10.1016/j.watres.2017.04.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/15/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Fully understanding the metabolism of SRB provides fundamental guidelines for allowing the microorganisms to provide more beneficial services in water treatment and resource recovery. The electron-transfer pathway of sulfate respiration by Desulfovibrio vulgaris is well studied, but still partly unresolved. Here we provide deeper insight by comprehensively monitoring metabolite changes during D. vulgaris metabolism with two electron donors, lactate and pyruvate, in presence or absence of citrate-chelated soluble FeIII as an additional competing electron acceptor. H2 was produced from lactate oxidation to pyruvate, but pyruvate oxidation produced mostly formate. Accumulation of lactate-originated H2 during lag phases inhibited pyruvate transformation to acetate. Sulfate reduction was initiated by lactate-originated H2, but MQ-mediated e- flow initiated sulfate reduction without delay when pyruvate was the donor. When H2-induced electron flow gave priority to FeIII reduction over sulfate reduction, the long lag phase before sulfate reduction shortened the time for iron-sulfide crystallite growth and led to smaller mackinawite (Fe1+xS) nanocrystallites. Synthesizing all the results, we propose that electron flow from lactate or pyruvate towards SO42- reduction to H2S are through at least three routes that are regulated by the e- donor (lactate or pyruvate) and the presence or absence of another e- acceptor (FeIII here). These routes are not competing, but complementary: e.g., H2 or formate production and oxidation were necessary for sulfite and disulfide/trisulfide reduction to sulfide. Our study suggests that the e- donor provides a practical tool to regulate and optimize SRB-predominant bioremediation systems.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA.
| | - Yun Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA; College of Environmental Science and Engineering, Tongji University, China
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
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31
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Kryachko Y, Hemmingsen SM. The Role of Localized Acidity Generation in Microbially Influenced Corrosion. Curr Microbiol 2017; 74:870-876. [PMID: 28444419 DOI: 10.1007/s00284-017-1254-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/13/2017] [Indexed: 10/19/2022]
Abstract
Microbially influenced corrosion is of great industrial concern. Microbial coupling of metal oxidation to sulfate-, nitrate-, nitrite-, or CO2-reduction is proton-mediated, and some sulfate-reducing prokaryotes are capable of regulating extracellular pH. The analysis of the corrosive processes catalyzed by nitrate reducing bacteria and methanogenic archaea indicates that these microorganisms may be capable of regulating extracellular pH as well. It is proposed that nutrient limitation at metal-biofilm interfaces may induce activation of enzymatic proton-producing/proton-secreting functions in respiratory and methanogenic microorganisms to make them capable of using Fe0 as the electron donor. This can be further verified through experiments involving measurements of ion and gas concentrations at metal-biofilm interfaces, microscopy, and transcriptomics analyses.
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Affiliation(s)
- Yuriy Kryachko
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
| | - Sean M Hemmingsen
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
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32
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Großkopf T, Zenobi S, Alston M, Folkes L, Swarbreck D, Soyer OS. A stable genetic polymorphism underpinning microbial syntrophy. THE ISME JOURNAL 2016; 10:2844-2853. [PMID: 27258948 PMCID: PMC5042321 DOI: 10.1038/ismej.2016.80] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 03/28/2016] [Accepted: 04/01/2016] [Indexed: 12/22/2022]
Abstract
Syntrophies are metabolic cooperations, whereby two organisms co-metabolize a substrate in an interdependent manner. Many of the observed natural syntrophic interactions are mandatory in the absence of strong electron acceptors, such that one species in the syntrophy has to assume the role of electron sink for the other. While this presents an ecological setting for syntrophy to be beneficial, the potential genetic drivers of syntrophy remain unknown to date. Here, we show that the syntrophic sulfate-reducing species Desulfovibrio vulgaris displays a stable genetic polymorphism, where only a specific genotype is able to engage in syntrophy with the hydrogenotrophic methanogen Methanococcus maripaludis. This 'syntrophic' genotype is characterized by two genetic alterations, one of which is an in-frame deletion in the gene encoding for the ion-translocating subunit cooK of the membrane-bound COO hydrogenase. We show that this genotype presents a specific physiology, in which reshaping of energy conservation in the lactate oxidation pathway enables it to produce sufficient intermediate hydrogen for sustained M. maripaludis growth and thus, syntrophy. To our knowledge, these findings provide for the first time a genetic basis for syntrophy in nature and bring us closer to the rational engineering of syntrophy in synthetic microbial communities.
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Affiliation(s)
- Tobias Großkopf
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Simone Zenobi
- School of Life Sciences, The University of Warwick, Coventry, UK
| | - Mark Alston
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Leighton Folkes
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - David Swarbreck
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
| | - Orkun S Soyer
- School of Life Sciences, The University of Warwick, Coventry, UK
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33
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Ontiveros-Valencia A, Penton CR, Krajmalnik-Brown R, Rittmann BE. Hydrogen-fed biofilm reactors reducing selenate and sulfate: Community structure and capture of elemental selenium within the biofilm. Biotechnol Bioeng 2016; 113:1736-44. [DOI: 10.1002/bit.25945] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/16/2016] [Accepted: 01/20/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Aura Ontiveros-Valencia
- Swette Center for Environmental Biotechnology; Biodesign Institute, Arizona State University; 1001 South McAllister Ave. Tempe Arizona 85287-5701
| | | | - Rosa Krajmalnik-Brown
- Swette Center for Environmental Biotechnology; Biodesign Institute, Arizona State University; 1001 South McAllister Ave. Tempe Arizona 85287-5701
- School of Sustainable Engineering and the Built Environment; Arizona State University; Tempe Arizona
| | - Bruce E. Rittmann
- Swette Center for Environmental Biotechnology; Biodesign Institute, Arizona State University; 1001 South McAllister Ave. Tempe Arizona 85287-5701
- School of Sustainable Engineering and the Built Environment; Arizona State University; Tempe Arizona
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34
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A Post-Genomic View of the Ecophysiology, Catabolism and Biotechnological Relevance of Sulphate-Reducing Prokaryotes. Adv Microb Physiol 2015. [PMID: 26210106 DOI: 10.1016/bs.ampbs.2015.05.002] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored.
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35
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Vita N, Valette O, Brasseur G, Lignon S, Denis Y, Ansaldi M, Dolla A, Pieulle L. The primary pathway for lactate oxidation in Desulfovibrio vulgaris. Front Microbiol 2015; 6:606. [PMID: 26167158 PMCID: PMC4481167 DOI: 10.3389/fmicb.2015.00606] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022] Open
Abstract
The ability to respire sulfate linked to lactate oxidation is a key metabolic signature of the Desulfovibrio genus. Lactate oxidation by these incomplete oxidizers generates reductants through lactate dehydrogenase (LDH) and pyruvate-ferredoxin oxidoreductase (PFOR), with the latter catalyzing pyruvate conversion into acetyl-CoA. Acetyl-CoA is the source of substrate-level phosphorylation through the production of ATP. Here, we show that these crucial steps are performed by enzymes encoded by a nonacistronic transcriptional unit named now as operon luo (for lactate utilization operon). Using a combination of genetic and biochemical techniques, we assigned a physiological role to the operon genes DVU3027-28 and DVU3032-33. The growth of mutant Δ26-28 was highly disrupted on D-lactate, whereas the growth of mutant Δ32-33 was slower on L-lactate, which could be related to a decrease in the activity of D-lactate or L-lactate oxidase in the corresponding mutants. The DVU3027-28 and DVU3032-33 genes thus encode functional D-LDH and L-LDH enzymes, respectively. Scanning of the genome for lactate utilization revealed several lactate permease and dehydrogenase homologs. However, transcriptional compensation was not observed in any of the mutants except for lactate permease. Although there is a high degree of redundancy for lactate oxidase, it is not functionally efficient in LDH mutants. This result could be related to the identification of several operon enzymes, including LDHs, in the PFOR activity bands, suggesting the occurrence of a lactate-oxidizing supermolecular structure that can optimize the performance of lactate utilization in Desulfovibrio species.
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Affiliation(s)
- Nicolas Vita
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Odile Valette
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Gaël Brasseur
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Sabrina Lignon
- CNRS, IMM-FR3479, Plate-forme Protéomique-IBISA Marseille-Protéomique Marseille, France
| | - Yann Denis
- IMM-FR3479, Plate-forme Transcriptomique Marseille, France
| | | | - Alain Dolla
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Laetitia Pieulle
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France ; Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
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36
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Zhou C, Liu Z, Pataranutaporn P, Vannela R, Hayes KF, Rittmann BE. Biogenic nano-particulate iron-sulfide produced through sulfate and Fe(iii)-(hydr)oxide reductions was enhanced by pyruvate as the electron donor. RSC Adv 2015. [DOI: 10.1039/c5ra20556e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In nature, the formation of iron sulfide solids is mainly attributed to reductions of sulfate and ferric minerals by microorganisms such asDesulfovibrio vulgaris.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Zhuolin Liu
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Pat Pataranutaporn
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Raveender Vannela
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Kim F. Hayes
- Department of Civil and Environmental Engineering
- University of Michigan
- USA
| | - Bruce E. Rittmann
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
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37
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Junicke H, Feldman H, van Loosdrecht MCM, Kleerebezem R. Impact of the hydrogen partial pressure on lactate degradation in a coculture of Desulfovibrio sp. G11 and Methanobrevibacter arboriphilus DH1. Appl Microbiol Biotechnol 2014; 99:3599-608. [DOI: 10.1007/s00253-014-6241-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 11/13/2014] [Accepted: 11/16/2014] [Indexed: 11/28/2022]
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38
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Zhou C, Ontiveros-Valencia A, Cornette de Saint Cyr L, Zevin AS, Carey SE, Krajmalnik-Brown R, Rittmann BE. Uranium removal and microbial community in a H2-based membrane biofilm reactor. WATER RESEARCH 2014; 64:255-264. [PMID: 25073000 DOI: 10.1016/j.watres.2014.07.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 05/26/2023]
Abstract
We evaluated a hydrogen-based membrane biofilm reactor (MBfR) for its capacity to reduce and remove hexavalent uranium [U(VI)] from water. After a startup period that allowed slow-growing U(VI) reducers to form biofilms, the MBfR successfully achieved and maintained 94-95% U(VI) removal over 8 months when the U surface loading was 6-11 e(-) mEq/m(2)-day. The MBfR biofilm was capable of self-recovery after a disturbance due to oxygen exposure. Nanocrystalline UO2 aggregates and amorphous U precipitates were associated with vegetative cells and apparently mature spores that accumulated in the biofilm matrix. Despite inoculation with a concentrated suspension of Desulfovibrio vulgaris, this bacterium was not present in the U(VI)-reducing biofilm. Instead, the most abundant group in the biofilm community contained U(VI) reducers in the Rhodocyclaceae family when U(VI) was the only electron acceptor. When sulfate was present, the community dramatically shifted to the Clostridiaceae family, which included spores that were potentially involved in U(VI) reduction.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
| | - Aura Ontiveros-Valencia
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA.
| | - Louis Cornette de Saint Cyr
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA; Institut Sup'Biotech de Paris, France
| | - Alexander S Zevin
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
| | - Sara E Carey
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
| | - Rosa Krajmalnik-Brown
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
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39
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Zhou C, Vannela R, Hayes KF, Rittmann BE. Effect of growth conditions on microbial activity and iron-sulfide production by Desulfovibrio vulgaris. JOURNAL OF HAZARDOUS MATERIALS 2014; 272:28-35. [PMID: 24675611 DOI: 10.1016/j.jhazmat.2014.02.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/21/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
Sulfate-reducing bacteria (SRB) can produce iron sulfide (FeS) solids with mineralogical characteristics that may be beneficial for a variety of biogeochemical applications, such as long-term immobilization of uranium. In this study, the growth and metabolism of Desulfovibrio vulgaris, one of the best-studied SRB species, were comprehensively monitored in batch studies, and the biogenic FeS solids were characterized by X-ray diffraction. Controlling the pH by varying the initial pH, the iron-to-sulfate ratio, or the electron donor - affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH (from initial conditions or a decrease caused by less sulfate reduction, FeS precipitation, or using pyruvate as the electron donor) produced larger-sized mackinawite (Fe1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and particularly stimulated mackinawite transformation to greigite (Fe3S4) when the free sulfide concentration was 29.3mM. Furthermore, sufficient free Fe(2+) led to the additional formation of vivianite [Fe3(PO4)2·8(H2O)]. Thus, microbially relevant conditions (initial pH, choice of electron donor, and excess or deficiency of sulfide) are tools to generate biogenic FeS solids of different characteristics.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA.
| | - Raveender Vannela
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
| | - Kim F Hayes
- Department of Civil and Environmental Engineering, University of Michigan, USA
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
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Meyer B, Kuehl JV, Price MN, Ray J, Deutschbauer AM, Arkin AP, Stahl DA. The energy-conserving electron transfer system used byDesulfovibrio alaskensisstrain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environ Microbiol 2014; 16:3463-86. [DOI: 10.1111/1462-2920.12405] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 01/08/2014] [Accepted: 01/13/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Birte Meyer
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA 98195 USA
| | - Jennifer V. Kuehl
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94704 USA
| | - Morgan N. Price
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94704 USA
| | - Jayashree Ray
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94704 USA
| | - Adam M. Deutschbauer
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94704 USA
| | - Adam P. Arkin
- Physical Biosciences Division; Lawrence Berkeley National Laboratory; Berkeley CA 94704 USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering; University of Washington; Seattle WA 98195 USA
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41
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Morais-Silva FO, Santos CI, Rodrigues R, Pereira IAC, Rodrigues-Pousada C. Roles of HynAB and Ech, the only two hydrogenases found in the model sulfate reducer Desulfovibrio gigas. J Bacteriol 2013; 195:4753-60. [PMID: 23974026 PMCID: PMC3807438 DOI: 10.1128/jb.00411-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/05/2013] [Indexed: 11/20/2022] Open
Abstract
Sulfate-reducing bacteria are characterized by a high number of hydrogenases, which have been proposed to contribute to the overall energy metabolism of the cell, but exactly in what role is not clear. Desulfovibrio spp. can produce or consume H2 when growing on organic or inorganic substrates in the presence or absence of sulfate. Because of the presence of only two hydrogenases encoded in its genome, the periplasmic HynAB and cytoplasmic Ech hydrogenases, Desulfovibrio gigas is an excellent model organism for investigation of the specific function of each of these enzymes during growth. In this study, we analyzed the physiological response to the deletion of the genes that encode the two hydrogenases in D. gigas, through the generation of ΔechBC and ΔhynAB single mutant strains. These strains were analyzed for the ability to grow on different substrates, such as lactate, pyruvate, and hydrogen, under respiratory and fermentative conditions. Furthermore, the expression of both hydrogenase genes in the three strains studied was assessed through quantitative reverse transcription-PCR. The results demonstrate that neither hydrogenase is essential for growth on lactate-sulfate, indicating that hydrogen cycling is not indispensable. In addition, the periplasmic HynAB enzyme has a bifunctional activity and is required for growth on H2 or by fermentation of pyruvate. Therefore, this enzyme seems to play a dominant role in D. gigas hydrogen metabolism.
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Affiliation(s)
- Fabio O Morais-Silva
- Instituto de Tecnologia Química e Biológica-António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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42
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Sim MS, Wang DT, Zane GM, Wall JD, Bosak T, Ono S. Fractionation of sulfur isotopes by Desulfovibrio vulgaris mutants lacking hydrogenases or type I tetraheme cytochrome c 3. Front Microbiol 2013; 4:171. [PMID: 23805134 PMCID: PMC3691511 DOI: 10.3389/fmicb.2013.00171] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/04/2013] [Indexed: 11/13/2022] Open
Abstract
The sulfur isotope effect produced by sulfate reducing microbes is commonly used to trace biogeochemical cycles of sulfur and carbon in aquatic and sedimentary environments. To test the contribution of intracellular coupling between carbon and sulfur metabolisms to the overall magnitude of the sulfur isotope effect, this study compared sulfur isotope fractionations by mutants of Desulfovibrio vulgaris Hildenborough. We tested mutant strains lacking one or two periplasmic (Hyd, Hyn-1, Hyn-2, and Hys) or cytoplasmic hydrogenases (Ech and CooL), and a mutant lacking type I tetraheme cytochrome (TpI-c 3). In batch culture, wild-type D. vulgaris and its hydrogenase mutants had comparable growth kinetics and produced the same sulfur isotope effects. This is consistent with the reported redundancy of hydrogenases in D. vulgaris. However, the TpI-c 3 mutant (ΔcycA) exhibited slower growth and sulfate reduction rates in batch culture, and produced more H2 and an approximately 50% larger sulfur isotope effect, compared to the wild type. The magnitude of sulfur isotope fractionation in the CycA deletion strain, thus, increased due to the disrupted coupling of the carbon oxidation and sulfate reduction pathways. In continuous culture, wild-type D. vulgaris and the CycA mutant produced similar sulfur isotope effects, underscoring the influence of environmental conditions on the relative contribution of hydrogen cycling to the electron transport. The large sulfur isotope effects associated with the non-ideal stoichiometry of sulfate reduction in this study imply that simultaneous fermentation and sulfate reduction may be responsible for some of the large naturally-occurring sulfur isotope effects. Overall, mutant strains provide a powerful tool to test the effect of specific redox proteins and pathways on sulfur isotope fractionation.
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Affiliation(s)
- Min Sub Sim
- Department of Earth and Planetary Sciences, Northwestern University Evanston, IL, USA ; Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology Cambridge, MA, USA
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Tang Y, Ontiveros-Valencia A, Feng L, Zhou C, Krajmalnik-Brown R, Rittmann BE. A biofilm model to understand the onset of sulfate reduction in denitrifying membrane biofilm reactors. Biotechnol Bioeng 2012; 110:763-72. [DOI: 10.1002/bit.24755] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 09/25/2012] [Accepted: 10/01/2012] [Indexed: 11/10/2022]
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Deletion of the Desulfovibrio vulgaris carbon monoxide sensor invokes global changes in transcription. J Bacteriol 2012; 194:5783-93. [PMID: 22904289 DOI: 10.1128/jb.00749-12] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The carbon monoxide-sensing transcriptional factor CooA has been studied only in hydrogenogenic organisms that can grow using CO as the sole source of energy. Homologs for the canonical CO oxidation system, including CooA, CO dehydrogenase (CODH), and a CO-dependent Coo hydrogenase, are present in the sulfate-reducing bacterium Desulfovibrio vulgaris, although it grows only poorly on CO. We show that D. vulgaris Hildenborough has an active CO dehydrogenase capable of consuming exogenous CO and that the expression of the CO dehydrogenase, but not that of a gene annotated as encoding a Coo hydrogenase, is dependent on both CO and CooA. Carbon monoxide did not act as a general metabolic inhibitor, since growth of a strain deleted for cooA was inhibited by CO on lactate-sulfate but not pyruvate-sulfate. While the deletion strain did not accumulate CO in excess, as would have been expected if CooA were important in the cycling of CO as a metabolic intermediate, global transcriptional analyses suggested that CooA and CODH are used during normal metabolism.
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45
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Keller KL, Wall JD. Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. Front Microbiol 2011; 2:135. [PMID: 21747813 PMCID: PMC3129016 DOI: 10.3389/fmicb.2011.00135] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2011] [Accepted: 06/10/2011] [Indexed: 11/25/2022] Open
Abstract
Progress in the genetic manipulation of the Desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. Most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. Both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on H2 with CO2 during sulfate reduction are exhibited by some strains. The ability to produce or consume H2 provides Desulfovibrio strains the capacity to participate as either partner in interspecies H2 transfer. Interestingly the mechanisms of energy conversion, pathways of electron flow and the parameters determining the pathways used remain to be elucidated. Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways. These datasets include (1) gene expression changes measured in microarrays for cells cultured with different electron donors and acceptors, (2) relative mRNA abundances for cells growing exponentially in defined medium with lactate as carbon source and electron donor plus sulfate as terminal electron acceptor, and (3) a random transposon mutant library selected on medium containing lactate plus sulfate supplemented with yeast extract. Studies of directed mutations eliminating apparent key components, the quinone-interacting membrane-bound oxidoreductase (Qmo) complex, the Type 1 tetraheme cytochrome c3 (Tp1-c3), or the Type 1 cytochrome c3:menaquinone oxidoreductase (Qrc) complex, suggest a greater flexibility in electron flow than previously considered. The new datasets revealed the absence of random transposons in the genes encoding an enzyme with homology to Coo membrane-bound hydrogenase. From this result, we infer that Coo hydrogenase plays an important role in D. vulgaris growth on lactate plus sulfate. These observations along with those reported previously have been combined in a model showing dual pathways of electrons from the oxidation of both lactate and pyruvate during sulfate respiration. Continuing genetic and biochemical analyses of key genes in Desulfovibrio strains will allow further clarification of a general model for sulfate respiration.
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Affiliation(s)
- Kimberly L Keller
- Department of Biochemistry, University of Missouri Columbia, MO, USA
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46
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Hydrogen is a preferred intermediate in the energy-conserving electron transport chain of Methanosarcina barkeri. Proc Natl Acad Sci U S A 2009; 106:15915-20. [PMID: 19805232 DOI: 10.1073/pnas.0905914106] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methanogens use an unusual energy-conserving electron transport chain that involves reduction of a limited number of electron acceptors to methane gas. Previous biochemical studies suggested that the proton-pumping F(420)H(2) dehydrogenase (Fpo) plays a crucial role in this process during growth on methanol. However, Methanosarcina barkeri Delta fpo mutants constructed in this study display no measurable phenotype on this substrate, indicating that Fpo plays a minor role, if any. In contrast, Delta frh mutants lacking the cytoplasmic F(420)-reducing hydrogenase (Frh) are severely affected in their ability to grow and make methane from methanol, and double Delta fpo/Delta frh mutants are completely unable to use this substrate. These data suggest that the preferred electron transport chain involves production of hydrogen gas in the cytoplasm, which then diffuses out of the cell, where it is reoxidized with transfer of electrons into the energy-conserving electron transport chain. This hydrogen-cycling metabolism leads directly to production of a proton motive force that can be used by the cell for ATP synthesis. Nevertheless, M. barkeri does have the flexibility to use the Fpo-dependent electron transport chain when needed, as shown by the poor growth of the Delta frh mutant. Our data suggest that the rapid enzymatic turnover of hydrogenases may allow a competitive advantage via faster growth rates in this freshwater organism. The mutant analysis also confirms the proposed role of Frh in growth on hydrogen/carbon dioxide and suggests that either Frh or Fpo is needed for aceticlastic growth of M. barkeri.
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Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough. J Microbiol Methods 2008; 76:159-68. [PMID: 18996155 DOI: 10.1016/j.mimet.2008.10.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 10/04/2008] [Accepted: 10/04/2008] [Indexed: 11/24/2022]
Abstract
Growing anaerobic microorganisms in phenotypic microarrays (PM) and 96-well microtiter plates is an emerging technology that allows high throughput survey of the growth and physiology and/or phenotype of cultivable microorganisms. For non-model bacteria, a method for phenotypic analysis is invaluable, not only to serve as a starting point for further evaluation, but also to provide a broad understanding of the physiology of an uncharacterized wild-type organism or the physiology/phenotype of a newly created mutant of that organism. Given recent advances in genetic characterization and targeted mutations to elucidate genetic networks and metabolic pathways, high-throughput methods for determining phenotypic differences are essential. Here we outline challenges presented in studying the physiology and phenotype of a sulfate-reducing anaerobic delta proteobacterium, Desulfovibrio vulgaris Hildenborough. Modifications of the commercially available OmniLog system (Hayward, CA) for experimental setup, and configuration, as well as considerations in PM data analysis are presented. Also highlighted here is data viewing software that enables users to view and compare multiple PM data sets. The PM method promises to be a valuable strategy in our systems biology approach to D. vulgaris studies and is readily applicable to other anaerobic and aerobic bacteria.
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Baidoo EEK, Benke PI, Neusüss C, Pelzing M, Kruppa G, Leary JA, Keasling JD. Capillary Electrophoresis-Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for the Identification of Cationic Metabolites via a pH-Mediated Stacking-Transient Isotachophoretic Method. Anal Chem 2008; 80:3112-22. [DOI: 10.1021/ac800007q] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Xiao J, VanBriesen JM. Expanded thermodynamic true yield prediction model: adjustments and limitations. Biodegradation 2007; 19:99-127. [PMID: 17562190 DOI: 10.1007/s10532-007-9119-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
Bacterial yield prediction is critical for bioprocess optimization and modeling of natural biological systems. In previous work, an expanded thermodynamic true yield prediction model was developed through incorporating carbon balance and nitrogen balance along with electron balance and energy balance. In the present work, the application of the expanded model is demonstrated in multiple growth situations (aerobic heterotrophs, anoxic, anaerobic heterotrophs, and autolithotrophs). Two adjustments are presented that enable improved prediction when additional information regarding the environmental conditions (pH) or degradation pathway (requirement for oxygenase- or oxidase-catalyzed reactions) is known. A large data set of reported yields is presented and considered for suitability in model validation. Significant uncertainties of literature-reported yield values are described. Evaluation of the model with experimental yield values shows good predictive ability. However, the wide range in reported yields and the variability introduced into the prediction by uncertainty in model parameters, limits comprehensive validation. Our results suggest that the uncertainty of the experimental data used for validation limits further improvement of thermodynamic prediction models.
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Affiliation(s)
- Jinghua Xiao
- Department of Civil and Environmental Engineering, Carnegie Mellon University, Pittsburgh, PA 15213-3890, USA
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50
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Carepo M, Baptista JF, Pamplona A, Fauque G, Moura JJG, Reis MAM. Hydrogen metabolism in Desulfovibrio desulfuricans strain New Jersey (NCIMB 8313)--comparative study with D. vulgaris and D. gigas species. Anaerobe 2007; 8:325-32. [PMID: 16887677 DOI: 10.1016/s1075-9964(03)00007-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2002] [Revised: 12/10/2002] [Accepted: 12/20/2002] [Indexed: 10/27/2022]
Abstract
This article aims to study hydrogen production/consumption in Desulfovibrio (D.) desulfuricans strain New Jersey, a sulfate reducer isolated from a medium undergoing active biocorrosion and to compare its hydrogen metabolism with two other Desulfovibrio species, D. gigas and D. vulgaris Hildenborough. Hydrogen production was followed during the growth of these three bacterial species under different growth conditions: no limitation of sulfate and lactate, sulfate limitation, lactate limitation, pyruvate/sulfate medium and in the presence of molybdate. Hydrogen production/consumption by D. desulfuricans shows a behavior similar to that of D. gigas but a different one from that of D. vulgaris, which produces higher quantities of hydrogen on lactate/sulfate medium. The three species are able to increase the hydrogen production when the sulfate became limiting. Moreover, in a pyruvate/sulfate medium hydrogen production was lower than on lactate/sulfate medium. Hydrogen production by D. desulfuricans in presence of molybdate is extremely high. Hydrogenases are key enzymes on production/consumption of hydrogen in sulfate reducing organisms. The specific activity, number and cellular localization of hydrogenases vary within the three Desulfovibrio species used in this work, which could explain the differences observed on hydrogen utilization.
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Affiliation(s)
- M Carepo
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, 2829-516 Monte da Caparica, Portugal
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