1
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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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2
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Cypionka H, Reese JO. Recording and Simulating Proton-Related Metabolism in Bacterial Cell Suspensions. Front Microbiol 2021; 12:654065. [PMID: 33995312 PMCID: PMC8117226 DOI: 10.3389/fmicb.2021.654065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/29/2021] [Indexed: 11/13/2022] Open
Abstract
Proton release and uptake induced by metabolic activities were measured in non-buffered cell suspensions by means of a pH electrode. Recorded data were used for simulating substrate turnover rates by means of a new freeware app (proton.exe). The program applies Michaelis-Menten or first-order kinetics to the metabolic processes and allows for parametrization of simultaneously ongoing processes. The simulation includes changes of the transmembrane ΔpH, membrane potential and ATP gains, and demonstrates the principles of chemiosmotic energy conservation. In our experiments, the versatile sulfate-reducing bacterium Desulfovibrio desulfuricans CSN (DSM 9104) was used as model organism. We analysed sulfate uptake by proton-sulfate symport, scalar alkalinization by sulfate reduction to sulfide, as well as nitrate and nitrite reduction to ammonia, and electron transport-coupled proton translocation. Two types of experiments were performed: In oxidant pulse experiments, cells were kept under H2, and micromolar amounts of sulfate, nitrate or nitrite were added. For reductant pulse experiments, small amounts of H2-saturated KCl were added to cells incubated under N2 with an excess of one of the above-mentioned electron acceptors. To study electron-transport driven proton translocation, the membrane potential was neutralized by addition of KSCN (100 mM). H+/e– ratios of electron-transport driven proton translocation were calculated by simulation with proton.exe. This method gave lower but more realistic values than logarithmic extrapolation. We could verify the kinetic simulation parameters found with proton.exe using series of increasing additions of the reactants. Our approach allows for studying a broad variety of proton-related metabolic activities at micromolar concentrations and time scales of seconds to minutes.
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Affiliation(s)
- Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Jan-Ole Reese
- Institute for Chemistry and Biology of the Marine Environment, Carl-von-Ossietzky University of Oldenburg, Oldenburg, Germany
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3
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Li GX, Bao P. Transcriptomics analysis of the metabolic mechanisms of iron reduction induced by sulfate reduction mediated by sulfate-reducing bacteria. FEMS Microbiol Ecol 2021; 97:6095723. [PMID: 33439980 DOI: 10.1093/femsec/fiab005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 01/11/2021] [Indexed: 11/12/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) play an important role in sulfur, iron and carbon cycling. The majority of studies have illustrated the role of SRB in biogeochemical cycling in pure cultures. In this study, we established three SRB enrichment cultures (designated HL, NB and WC) from different paddy soils and conducted a transcriptomic analysis of their metabolic characteristics under sulfate and sulfate-free conditions. In the HL cultures, there was no sulfate consumption but ferrihydrite was reduced. This indicated that bacteria in the HL samples can reduce ferrihydrite and preferentially utilize ferrihydrite as the electron acceptor in the absence of both ferrihydrite and sulfate. Sulfate consumption was equal in the NB and the WC cultures, although more ferrihydrite was reduced in the NB cultures. Transcriptomics analysis showed that (i) upregulation of O-acetylserine sulfhydrylase gene expression indicating sulfate assimilation in the WC samples; (ii) the energy conservation trithionate pathway is commonly employed by SRB and (iii) sulfate not only enhanced iron reduction by its conversion to sulfide but also promoted enzymatic electron transfer via c-type cytochromes.
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Affiliation(s)
- Guo-Xiang Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road 1799, Xiamen 361021, P. R. China.,Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Zhongke Road 88, Ningbo 315800, P. R. China.,Center for Applied Geosciences (ZAG), Eberhard Karls University Tuebingen, Hölderlinstr. 12, Tuebingen 72076, Germany
| | - Peng Bao
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Jimei Road 1799, Xiamen 361021, P. R. China.,Ningbo Urban Environment Observation and Station, Chinese Academy of Sciences, Zhongke Road 88, Ningbo 315800, P. R. China
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4
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Zheng R, Wu S, Sun C. Pseudodesulfovibrio cashew sp. Nov., a Novel Deep-Sea Sulfate-Reducing Bacterium, Linking Heavy Metal Resistance and Sulfur Cycle. Microorganisms 2021; 9:429. [PMID: 33669756 PMCID: PMC7922080 DOI: 10.3390/microorganisms9020429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022] Open
Abstract
Sulfur cycling is primarily driven by sulfate reduction mediated by sulfate-reducing bacteria (SRB) in marine sediments. The dissimilatory sulfate reduction drives the production of enormous quantities of reduced sulfide and thereby the formation of highly insoluble metal sulfides in marine sediments. Here, a novel sulfate-reducing bacterium designated Pseudodesulfovibrio cashew SRB007 was isolated and purified from the deep-sea cold seep and proposed to represent a novel species in the genus of Pseudodesulfovibrio. A detailed description of the phenotypic traits, phylogenetic status and central metabolisms of strain SRB007 allowed the reconstruction of the metabolic potential and lifestyle of a novel member of deep-sea SRB. Notably, P. cashew SRB007 showed a strong ability to resist and remove different heavy metal ions including Co2+, Ni2+, Cd2+ and Hg2+. The dissimilatory sulfate reduction was demonstrated to contribute to the prominent removal capability of P. cashew SRB007 against different heavy metals via the formation of insoluble metal sulfides.
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Affiliation(s)
- Rikuan Zheng
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- College of Earth Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Shimei Wu
- Department of Life Science, Qingdao University, Qingdao 266071, China;
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology & Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China;
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- Center of Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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5
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McCully AL, Spormann AM. Direct cathodic electron uptake coupled to sulfate reduction by Desulfovibrio ferrophilus IS5 biofilms. Environ Microbiol 2020; 22:4794-4807. [PMID: 32939950 DOI: 10.1111/1462-2920.15235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 11/28/2022]
Abstract
Direct electron uptake is emerging as a key process for electron transfer in anaerobic microbial communities, both between species and from extracellular sources, such as zero-valent iron (Fe0 ) or cathodic surfaces. In this study, we investigated cathodic electron uptake by Fe0 -corroding Desulfovibrio ferrophilus IS5 and showed that electron uptake is dependent on direct cell contact via a biofilm on the cathode surface rather than through secreted intermediates. Induction of cathodic electron uptake by lactate-starved D. ferrophilus IS5 cells resulted in the expression of all components necessary for electron uptake; however, protein synthesis was required for full biofilm formation. Notably, proteinase K treatment uncoupled electron uptake from biofilm formation, likely through proteolytic degradation of proteinaceous components of the electron uptake machinery. We also showed that cathodic electron uptake is dependent on SO4 2- reduction. The insensitivity of Fe0 corrosion to proteinase K treatment suggests that electron uptake from a cathode might involve different mechanism(s) than those involved in Fe0 corrosion.
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Affiliation(s)
- Alexandra L McCully
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA.,Department of Chemical Engineering, Stanford University, Stanford, CA, USA
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6
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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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7
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Qian Z, Tianwei H, Mackey HR, van Loosdrecht MCM, Guanghao C. Recent advances in dissimilatory sulfate reduction: From metabolic study to application. WATER RESEARCH 2019; 150:162-181. [PMID: 30508713 DOI: 10.1016/j.watres.2018.11.018] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/25/2018] [Accepted: 11/08/2018] [Indexed: 05/24/2023]
Abstract
Sulfate-reducing bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.
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Affiliation(s)
- Zeng Qian
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Hao Tianwei
- Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China; Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.
| | - Hamish Robert Mackey
- Division of Sustainable Development, College of Science and Engineering, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | | | - Chen Guanghao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Hong Kong, China; Water Technology Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Branch of Chinese National Engineering Research Center for Control & Treatment of Heavy Metal Pollution, The Hong Kong University of Science and Technology, Hong Kong, China; Wastewater Treatment Laboratory, FYT Graduate School, The Hong Kong University of Science and Technology, Nansha, Guangzhou, China.
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8
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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9
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Kirchhoff C, Ebert M, Jahn D, Cypionka H. Chemiosmotic Energy Conservation in Dinoroseobacter shibae: Proton Translocation Driven by Aerobic Respiration, Denitrification, and Photosynthetic Light Reaction. Front Microbiol 2018; 9:903. [PMID: 29867814 PMCID: PMC5954134 DOI: 10.3389/fmicb.2018.00903] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/18/2018] [Indexed: 11/13/2022] Open
Abstract
Dinoroseobacter shibae is an aerobic anoxygenic phototroph and able to utilize light energy to support its aerobic energy metabolism. Since the cells can also grow anaerobically with nitrate and nitrite as terminal electron acceptor, we were interested in how the cells profit from photosynthesis during denitrification and what the steps of chemiosmotic energy conservation are. Therefore, we conducted proton translocation experiments and compared O2-, NO3-, and NO2- respiration during different light regimes and in the dark. We used wild type cells and transposon mutants with knocked-out nitrate- and nitrite- reductase genes (napA and nirS), as well as a mutant (ppsR) impaired in bacteriochlorophyll a synthesis. Light had a positive impact on proton translocation, independent of the type of terminal electron acceptor present. In the absence of an electron acceptor, however, light did not stimulate proton translocation. The light-driven add-on to proton translocation was about 1.4 H+/e- for O2 respiration and about 1.1 H+/e- for NO3- and NO2-. We could see that the chemiosmotic energy conservation during aerobic respiration involved proton translocation, mediated by the NADH dehydrogenase, the cytochrome bc1 complex, and the cytochrome c oxidase. During denitrification the last proton translocation step of the electron transport was missing, resulting in a lower H+/e- ratio during anoxia. Furthermore, we studied the type of light-harvesting and found that the cells were able to channel light from the green–blue spectrum most efficiently, while red light has only minor impact. This fits well with the depth profiles for D. shibae abundance in the ocean and the penetration depth of light with different wavelengths into the water column.
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Affiliation(s)
- Christian Kirchhoff
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Matthias Ebert
- Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Dieter Jahn
- Institute of Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Heribert Cypionka
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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10
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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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11
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Leavitt WD, Cummins R, Schmidt ML, Sim MS, Ono S, Bradley AS, Johnston DT. Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20. Front Microbiol 2014; 5:591. [PMID: 25505449 PMCID: PMC4243691 DOI: 10.3389/fmicb.2014.00591] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 10/20/2014] [Indexed: 11/13/2022] Open
Abstract
Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large ((34)ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite ((34)ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved.
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Affiliation(s)
- William D. Leavitt
- Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA
- Department of Earth and Planetary Sciences, Washington University in St. LouisSt. Louis, MO, USA
| | - Renata Cummins
- Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA
| | - Marian L. Schmidt
- Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA
- Department of Ecology and Evolutionary Biology, University of MichiganAnn Arbor, MI, USA
| | - Min S. Sim
- Department of Earth, Atmosphere and Planetary Science, Massachusetts Institute of TechnologyCambridge, MA, USA
- Division of Geological Sciences, California Institute of TechnologyPasadena, CA, USA
| | - Shuhei Ono
- Department of Earth, Atmosphere and Planetary Science, Massachusetts Institute of TechnologyCambridge, MA, USA
| | - Alexander S. Bradley
- Department of Earth and Planetary Sciences, Washington University in St. LouisSt. Louis, MO, USA
| | - David T. Johnston
- Department of Earth and Planetary Sciences, Harvard UniversityCambridge, MA, USA
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12
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Price MN, Ray J, Wetmore KM, Kuehl JV, Bauer S, Deutschbauer AM, Arkin AP. The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Front Microbiol 2014; 5:577. [PMID: 25400629 PMCID: PMC4215793 DOI: 10.3389/fmicb.2014.00577] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 10/13/2014] [Indexed: 11/13/2022] Open
Abstract
Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy.
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Affiliation(s)
- Morgan N. Price
- Physical Biosciences Division, Lawrence Berkeley LabBerkeley, CA, USA
| | - Jayashree Ray
- Physical Biosciences Division, Lawrence Berkeley LabBerkeley, CA, USA
| | - Kelly M. Wetmore
- Physical Biosciences Division, Lawrence Berkeley LabBerkeley, CA, USA
| | - Jennifer V. Kuehl
- Physical Biosciences Division, Lawrence Berkeley LabBerkeley, CA, USA
| | - Stefan Bauer
- Energy Biosciences Institute, University of CaliforniaBerkeley, CA, USA
| | | | - Adam P. Arkin
- Physical Biosciences Division, Lawrence Berkeley LabBerkeley, CA, USA
- Energy Biosciences Institute, University of CaliforniaBerkeley, CA, USA
- Department of Bioengineering, University of CaliforniaBerkeley, CA, USA
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13
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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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14
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Reardon CL, Magnuson TS, Boyd ES, Leavitt WD, Reed DW, Geesey GG. Hydrogenase activity of mineral-associated and suspended populations of Desulfovibrio desulfuricans Essex 6. MICROBIAL ECOLOGY 2014; 67:318-326. [PMID: 24194097 DOI: 10.1007/s00248-013-0308-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
The interactions between sulfate-reducing microorganisms and iron oxides influence a number of important redox-sensitive biogeochemical processes including the formation of iron sulfides. Enzymes, such as hydrogenase which catalyze the reversible oxidation of molecular hydrogen, are known to mediate electron transfer to metals and may contribute to the formation and speciation of ferrous sulfides formed at the cell-mineral interface. In the present study, we compared the whole cell hydrogenase activity of Desulfovibrio desulfuricans strain Essex 6 growing as biofilms on hematite (hematite-associated) or as suspended populations using different metabolic pathways. Hematite-associated cells exhibited significantly greater hydrogenase activity than suspended populations during sulfate respiration but not during pyruvate fermentation. The enhanced activity of the hematite-associated, sulfate-grown cells appears to be dependent on iron availability rather than a general response to surface attachment since the activity of glass-associated cells did not differ from that of suspended populations. Hydrogenase activity of pyruvate-fermenting cells was stimulated by addition of iron as soluble Fe(II)Cl2 and, in the absence of added iron, both sulfate-reducing and pyruvate-fermenting cells displayed similar rates of hydrogenase activity. These data suggest that iron exerts a stronger influence on whole cell hydrogenase activity than either metabolic pathway or mode of growth. The location of hydrogenase to the cell envelope and the enhanced activity at the hematite surface in sulfate-reducing cells may influence the redox conditions that control the species of iron sulfides on the mineral surface.
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Affiliation(s)
- C L Reardon
- Columbia Plateau Conservation Research Center, USDA Agricultural Research Service, Adams, OR, 97810, USA,
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15
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Ramel F, Amrani A, Pieulle L, Lamrabet O, Voordouw G, Seddiki N, Brèthes D, Company M, Dolla A, Brasseur G. Membrane-bound oxygen reductases of the anaerobic sulfate-reducing Desulfovibrio vulgaris Hildenborough: roles in oxygen defence and electron link with periplasmic hydrogen oxidation. MICROBIOLOGY-SGM 2013; 159:2663-2673. [PMID: 24085836 DOI: 10.1099/mic.0.071282-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytoplasmic membranes of the strictly anaerobic sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough contain two terminal oxygen reductases, a bd quinol oxidase and a cc(b/o)o3 cytochrome oxidase (Cox). Viability assays pointed out that single Δbd, Δcox and double ΔbdΔcox deletion mutant strains were more sensitive to oxygen exposure than the WT strain, showing the involvement of these oxygen reductases in the detoxification of oxygen. The Δcox strain was slightly more sensitive than the Δbd strain, pointing to the importance of the cc(b/o)o3 cytochrome oxidase in oxygen protection. Decreased O2 reduction rates were measured in mutant cells and membranes using lactate, NADH, ubiquinol and menadiol as substrates. The affinity for oxygen measured with the bd quinol oxidase (Km, 300 nM) was higher than that of the cc(b/o)o3 cytochrome oxidase (Km, 620 nM). The total membrane activity of the bd quinol oxidase was higher than that of the cytochrome oxidase activity in line with the higher expression of the bd oxidase genes. In addition, analysis of the ΔbdΔcox mutant strain indicated the presence of at least one O2-scavenging membrane-bound system able to reduce O2 with menaquinol as electron donor with an O2 affinity that was two orders of magnitude lower than that of the bd quinol oxidase. The lower O2 reductase activity in mutant cells with hydrogen as electron donor and the use of specific inhibitors indicated an electron transfer link between periplasmic H2 oxidation and membrane-bound oxygen reduction via the menaquinol pool. This linkage is crucial in defence of the strictly anaerobic bacterium Desulfovibrio against oxygen stress.
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Affiliation(s)
- F Ramel
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - A Amrani
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - L Pieulle
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - O Lamrabet
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - G Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary T2N 1N4, AB, Canada
| | - N Seddiki
- Laboratoire de Métabolisme Énergétique Cellulaire, IBGC-CNRS, et Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, 33077 Bordeaux CEDEX, France
| | - D Brèthes
- Laboratoire de Métabolisme Énergétique Cellulaire, IBGC-CNRS, et Université Bordeaux Segalen, 1 Rue Camille Saint-Saëns, 33077 Bordeaux CEDEX, France
| | - M Company
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - A Dolla
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
| | - G Brasseur
- Laboratoire de Chimie Bactérienne, CNRS-UMR7283, 31 Chemin Joseph Aiguier, 13402 Marseille CEDEX 20, France
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16
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Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PLoS One 2013; 8:e57487. [PMID: 23526944 PMCID: PMC3587595 DOI: 10.1371/journal.pone.0057487] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/22/2013] [Indexed: 01/10/2023] Open
Abstract
Proteorhodopsin (PR) photoheterotrophy in the marine flavobacterium Dokdonia sp. PRO95 has previously been investigated, showing no growth stimulation in the light at intermediate carbon concentrations. Here we report the genome sequence of strain PRO95 and compare it to two other PR encoding Dokdonia genomes: that of strain 4H-3-7-5 which shows the most similar genome, and that of strain MED134 which grows better in the light under oligotrophic conditions. Our genome analysis revealed that the PRO95 genome as well as the 4H-3-7-5 genome encode a protein related to xanthorhodopsins. The genomic environment and phylogenetic distribution of this gene suggest that it may have frequently been recruited by lateral gene transfer. Expression analyses by RT-PCR and direct mRNA-sequencing showed that both rhodopsins and the complete β-carotene pathway necessary for retinal production are transcribed in PRO95. Proton translocation measurements showed enhanced proton pump activity in response to light, supporting that one or both rhodopsins are functional. Genomic information and carbon source respiration data were used to develop a defined cultivation medium for PRO95, but reproducible growth always required small amounts of yeast extract. Although PRO95 contains and expresses two rhodopsin genes, light did not stimulate its growth as determined by cell numbers in a nutrient poor seawater medium that mimics its natural environment, confirming previous experiments at intermediate carbon concentrations. Starvation or stress conditions might be needed to observe the physiological effect of light induced energy acquisition.
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Affiliation(s)
- Thomas Riedel
- Helmholtz-Centre for Infection Research, Braunschweig, Germany.
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17
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Thorgersen MP, Stirrett K, Scott RA, Adams MWW. Mechanism of oxygen detoxification by the surprisingly oxygen-tolerant hyperthermophilic archaeon, Pyrococcus furiosus. Proc Natl Acad Sci U S A 2012; 109:18547-52. [PMID: 23093671 PMCID: PMC3494905 DOI: 10.1073/pnas.1208605109] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The anaerobic archaeon Pyrococcus furiosus grows by fermenting carbohydrates producing H(2), CO(2), and acetate. We show here that it is surprisingly tolerant to oxygen, growing well in the presence of 8% (vol/vol) O(2). Although cell growth and acetate production were not significantly affected by O(2), H(2) production was reduced by 50% (using 8% O(2)). The amount of H(2) produced decreased in a linear manner with increasing concentrations of O(2) over the range 2-12% (vol/vol), and for each mole of O(2) consumed, the amount of H(2) produced decreased by approximately 2 mol. The recycling of H(2) by the two cytoplasmic hydrogenases appeared not to play a role in O(2) resistance because a mutant strain lacking both enzymes was not more sensitive to O(2) than the parent strain. Decreased H(2) production was also not due to inactivation of the H(2)-producing, ferredoxin-dependent membrane-bound hydrogenase because its activity was unaffected by O(2) exposure. Electrons from carbohydrate oxidation must therefore be diverted to relieve O(2) stress at the level of reduced ferredoxin before H(2) production. Deletion strains lacking superoxide reductase (SOR) and putative flavodiiron protein A showed increased sensitivity to O(2), indicating that these enzymes play primary roles in resisting O(2). However, a mutant strain lacking the proposed electron donor to SOR, rubredoxin, was unaffected in response to O(2). Hence, electrons from sugar oxidation normally used to produce H(2) are diverted to O(2) detoxification by SOR and putative flavodiiron protein A, but the electron flow pathway from ferredoxin does not necessarily involve rubredoxin.|
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Affiliation(s)
- Michael P. Thorgersen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Karen Stirrett
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Robert A. Scott
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
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18
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Fritz G, Einsle O, Rudolf M, Schiffer A, Kroneck PMH. Key Bacterial Multi-Centered Metal Enzymes Involved in Nitrate and Sulfate Respiration. J Mol Microbiol Biotechnol 2006; 10:223-33. [PMID: 16645317 DOI: 10.1159/000091567] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Many essential life processes, such as photosynthesis, respiration, nitrogen fixation, depend on transition metal ions and their ability to catalyze multi-electron redox and hydrolytic transformations. Here we review some recent structural studies on three multi-site metal enzymes involved in respiratory processes which represent important branches within the global cycles of nitrogen and sulfur: (i) the multi-heme enzyme cytochrome c nitrite reductase, (ii) the FAD, FeS-enzyme adenosine-5'-phosphosulfate reductase, and (iii) the siroheme, FeS-enzyme sulfite reductase. Structural information comes from X-ray crystallography and spectroscopical techniques, in special cases catalytically competent intermediates could be trapped and characterized by X-ray crystallography.
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Affiliation(s)
- G Fritz
- Fachbereich Biologie, Universität Konstanz, Konstanz, Germany
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19
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Sydow U, Wohland P, Wolke I, Cypionka H. Bioenergetics of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovorans. MICROBIOLOGY (READING, ENGLAND) 2002; 148:853-860. [PMID: 11882721 DOI: 10.1099/00221287-148-3-853] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Energy metabolism of the alkaliphilic sulfate-reducing bacterium Desulfonatronovibrio hydrogenovorans strain Z-7935 was investigated in continuous culture and in physiological experiments on washed cells. When grown in chemostats with H2 as electron donor, the cells had extrapolated growth yields [Y(max), g dry cell mass (mol electron acceptor)(-1)] of 5.5 with sulfate and 12.8 with thiosulfate. The maintenance energy coefficients were 1.9 and 1.3 mmol (g dry mass)(-1) x h(-1), and the minimum doubling times were 27 and 20 h with sulfate and thiosulfate, respectively. Cell suspensions reduced sulfate, thiosulfate, sulfite, elemental sulfur and molecular oxygen in the presence of H2. In the absence of H2, sulfite, thiosulfate and sulfur were dismutated to sulfide and sulfate. Sulfate and sulfite were only reduced in the presence of sodium ions, whereas sulfur was reduced also in the absence of Na+. Plasmolysis experiments showed that sulfate entered the cells via an electroneutral symport with Na+ ions. The presence of an electrogenic Na+-H+ antiporter was demonstrated in experiments applying monensin (an artificial electroneutral Na+-H+ antiporter) and propylbenzylylcholine mustard.HCl (a specific inhibitor of Na+-H+ antiporters). Sulfate reduction was sensitive to uncouplers (protonophores), whereas sulfite reduction was not affected. Changes in pH upon lysis of washed cells with butanol indicated that the intracellular pH was lower than the optimum pH for growth (pH 9.5). Pulses of NaCl (0.52 M) to cells incubated in the absence of Na+ did not result in ATP formation, whereas HCl pulses (shifting the pH from 9.2 to 7.0) did. Small oxygen pulses, which were reduced within a few seconds, caused a transient alkalinization. The results of preliminary experiments with chemiosmotic inhibitors provided further evidence that the alkalinization was caused by sodium--proton antiport following a primary electron-transport-driven sodium ion translocation. It is concluded that energy conservation in D. hydrogenovorans depends on a proton-translocating ATPase, whereas electron transport appears to be coupled to sodium ion translocation.
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Affiliation(s)
- Ulrike Sydow
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg,D-26111 Oldenburg, Germany1
| | - Pia Wohland
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg,D-26111 Oldenburg, Germany1
| | - Irmgard Wolke
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg,D-26111 Oldenburg, Germany1
| | - Heribert Cypionka
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg,D-26111 Oldenburg, Germany1
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20
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Abstract
Throughout the first 90 years after their discovery, sulfate-reducing bacteria were thought to be strict anaerobes. During the last 15 years, however, it has turned out that they have manifold properties that enable them to cope with oxygen. Sulfate-reducing bacteria not only survive oxygen exposure for at least days, but many of them even reduce oxygen to water. This process can be a true respiration process when it is coupled to energy conservation. Various oxygen-reducing systems are present in Desulfovibrio species. In Desulfovibrio vulgaris and Desulfovibrio desulfuricans, oxygen reduction was coupled to proton translocation and ATP conservation. In these species, the periplasmic fraction, which contains hydrogenase and cytochrome c3, was found to catalyze oxygen reduction with high rates. In Desulfovibrio gigas, a cytoplasmic rubredoxin oxidase was identified as an oxygen-reducing terminal oxidase. Generally, the same substrates as with sulfate are oxidized with oxygen. As additional electron donors, reduced sulfur compounds can be oxidized to sulfate. Sulfate-reducing bacteria are thus able to catalyze all reactions of a complete sulfur cycle. Despite a high respiration rate and energy coupling, aerobic growth of pure cultures is poor or absent. Instead, the respiration capacity appears to have a protective function. High numbers of sulfate-reducing bacteria are present in the oxic zones and near the oxic-anoxic boundaries of sediments and in stratified water bodies, microbial mats and termite guts. Community structure analyses and microbiological studies have shown that the populations in those zones are especially adapted to oxygen. How dissimilatory sulfate reduction can occur in the presence of oxygen is still enigmatic, because in pure culture oxygen blocks sulfate reduction. Behavioral responses to oxygen include aggregation, migration to anoxic zones, and aerotaxis. The latter leads to band formation in oxygen-containing zones at concentrations of </=20% air saturation.
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Affiliation(s)
- H Cypionka
- Institut für Chemie und Biologie des Meeres, Universität Oldenburg, D-26111 Oldenburg, Germany.
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21
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Abstract
Aerotaxis of two sulphate-reducing bacteria, the freshwater strain Desulfovibrio desulfuricans CSN (DSM 9104) and the marine strain Desulfovibrio oxyclinae N13 (DSM 11498), was studied using capillary microslides, microscopy and oxygen microsensors. The bacteria formed ring-shaped bands in oxygen diffusion gradients surrounding O2 bubbles, which were placed into anoxic sulphate-free cell suspensions in capillary microslides. The radial expansion of the oxic volume by diffusion was stopped by aerobic respiration. Bands were formed by cells avoiding high O2 levels near the O2 bubble, as well as by cells entering from the surrounding anoxic zone. At the inner edge of the bands, O2 levels of up to 20% air saturation (50 microM O2) were found, while the outer edge always coincided with the oxic-anoxic interface. Ring diameters and O2 concentrations at the inner edge of the band depended on the cell density and the strain used in the suspension. Band formation did not occur in the absence of an electron donor (5mM lactate) or when N2 gas bubbles were used. Both strains were highly motile with velocities of approximately equals 32 microm s(-1) during forward runs, and 7 microm s(-1) during backward runs respectively. Within the bands, cells moved in circles of about 20 microm diameter, while cells outside the band exhibited straighter or only slightly bent traces. It is concluded that the capacity of respiration at high rates and the positive and negative aerotactical responses of Desulfovibrio provide an efficient strategy for removing O2 from the habitat in situations where sufficient electron donors and high cell densities are present.
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Affiliation(s)
- A Eschemann
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany
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22
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Park DH, Zeikus JG. Utilization of electrically reduced neutral red by Actinobacillus succinogenes: physiological function of neutral red in membrane-driven fumarate reduction and energy conservation. J Bacteriol 1999; 181:2403-10. [PMID: 10198002 PMCID: PMC93664 DOI: 10.1128/jb.181.8.2403-2410.1999] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/1998] [Accepted: 02/01/1999] [Indexed: 11/20/2022] Open
Abstract
Neutral red (NR) functioned as an electronophore or electron channel enabling either cells or membranes purified from Actinobacillus succinogenes to drive electron transfer and proton translocation by coupling fumarate reduction to succinate production. Electrically reduced NR, unlike methyl or benzyl viologen, bound to cell membranes, was not toxic, and chemically reduced NAD. The cell membrane of A. succinogenes contained high levels of benzyl viologen-linked hydrogenase (12.2 U), fumarate reductase (13.1 U), and diaphorase (109.7 U) activities. Fumarate reductase (24.5 U) displayed the highest activity with NR as the electron carrier, whereas hydrogenase (1.1 U) and diaphorase (0.8 U) did not. Proton translocation by whole cells was dependent on either electrically reduced NR or H2 as the electron donor and on the fumarate concentration. During the growth of Actinobacillus on glucose plus electrically reduced NR in an electrochemical bioreactor system versus on glucose alone, electrically reduced NR enhanced glucose consumption, growth, and succinate production by about 20% while it decreased acetate production by about 50%. The rate of fumarate reduction to succinate by purified membranes was twofold higher with electrically reduced NR than with hydrogen as the electron donor. The addition of 2-(n-heptyl)-4-hydroxyquinoline N-oxide to whole cells or purified membranes inhibited succinate production from H2 plus fumarate but not from electrically reduced NR plus fumarate. Thus, NR appears to replace the function of menaquinone in the fumarate reductase complex, and it enables A. succinogenes to utilize electricity as a significant source of metabolic reducing power.
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Affiliation(s)
- D H Park
- Departments of Biochemistry and Microbiology, Michigan State University, East Lansing, Michigan 48824, USA
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23
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Louie TM, Mohn WW. Evidence for a chemiosmotic model of dehalorespiration in Desulfomonile tiedjei DCB-1. J Bacteriol 1999; 181:40-6. [PMID: 9864310 PMCID: PMC103529 DOI: 10.1128/jb.181.1.40-46.1999] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/1998] [Accepted: 10/19/1998] [Indexed: 11/20/2022] Open
Abstract
Desulfomonile tiedjei DCB-1, a sulfate-reducing bacterium, conserves energy for growth from reductive dehalogenation of 3-chlorobenzoate by an uncharacterized chemiosmotic process. Respiratory electron transport components were examined in D. tiedjei cells grown under conditions for reductive dehalogenation, pyruvate fermentation, and sulfate reduction. Reductive dehalogenation was inhibited by the respiratory quinone inhibitor 2-heptyl-4-hydroxyquinoline N-oxide, suggesting that a respiratory quinoid is a component of the electron transport chain coupled to reductive dehalogenation. Moreover, reductive dehalogenation activity was dependent on 1, 4-naphthoquinone, a possible precursor for a respiratory quinoid. However, no ubiquinone or menaquinone could be extracted from D. tiedjei. Rather, a UV-absorbing quinoid which is different from common respiratory quinones in chemical structure according to mass spectrometric and UV absorption spectroscopic analyses was extracted. ATP sulfurylase, adenosine phosphosulfate reductase, and desulfoviridin sulfite reductase, enzymes involved in sulfate reduction, were constitutively expressed in the cytoplasm of D. tiedjei cells grown under all three metabolic conditions. A periplasmic hydrogenase was detected in cells grown under reductive-dehalogenating and pyruvate-fermenting conditions. A membrane-bound, periplasm-oriented formate dehydrogenase was detected only in cells grown with formate as electron donor, while a cytoplasmic formate dehydrogenase was detected in cells grown under reductive-dehalogenating and pyruvate-fermenting conditions. Results from dehalogenation assays with D. tiedjei whole-cell suspensions and cell extracts suggest that the membrane-bound reductive dehalogenase is cytoplasm oriented. The data clearly demonstrate an enzyme topology in D. tiedjei which produces protons directly in the periplasm, generating a proton motive force by a scalar mechanism.
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Affiliation(s)
- T M Louie
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
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24
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Schumacher W, Holliger C. The proton/electron ration of the menaquinone-dependent electron transport from dihydrogen to tetrachloroethene in "Dehalobacter restrictus". J Bacteriol 1996; 178:2328-33. [PMID: 8636034 PMCID: PMC177941 DOI: 10.1128/jb.178.8.2328-2333.1996] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In the anaerobic respiration chain of "Dehalobacter restrictus," dihydrogen functioned as the electron donor and tetrachloroethene (PCE) functioned as the electron acceptor. The hydrogenase faced the periplasm, and the PCE reductase faced the cytoplasmic side of the membrane. Both activities were associated with the cytoplasmic membrane. UV spectroscopy showed that membrane-bound menaquinone (MQ) was reduced by oxidation of H2 and reoxidized by reduction of PCE, indicating that MQ functions as an electron mediator. Fast proton liberation (t1/2 = 6 +/- 2 s) during electron transport from H2 to PCE and to trichloroethene (TCE) after addition of either PCE or TCE to H2-saturated cells resulted in an extrapolated H+/e- ratio of 1.25 +/- 0.2. This ratio indicated that besides the formation of protons upon oxidation of H2, vectorial translocation of protons from the inside to the outside could also occur. Proton liberation was inhibited by carbonylcyanide m-chlorophenylhydrazone (CCCP), 2-n-heptyl-4-hydroxyquinoline N-oxide (HOQNO), and CuCl2. Fast proton liberation with an H+/e- ratio of 0.65 +/- 0.1 was obtained after addition of the MQ analog 2,3-dimethyl-1,4-naphthoquinone (DMN) as an oxidant pulse. This acidification was also inhibited by CCCP, HOQNO, and CuCl2. Oxidation of reduced DMN by PCE was not associated with fast acidification. The results with DMN indicate that the consumption and release of protons associated with redox reactions of MQ during electron transfer from H2 to PCE both occurred at the cytoplasmic side of the membrane. The PCE reductase was photoreversibly inactivated by 1-iodopropane, indicating that a corrinoid was involved in the PCE reduction.
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Affiliation(s)
- W Schumacher
- Limnological Research Center, Swiss Federal Institute for Environmental Science and Technology, Kastanienbaum, Switzerland
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25
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Steuber J, Arendsen AF, Hagen WR, Kroneck PM. Molecular properties of the dissimilatory sulfite reductase from Desulfovibrio desulfuricans (Essex) and comparison with the enzyme from Desulfovibrio vulgaris (Hildenborough). EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 233:873-9. [PMID: 8521853 DOI: 10.1111/j.1432-1033.1995.873_3.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The dissimilatory sulfite reductase desulfoviridin was purified from the membrane (mSiR) and the soluble fraction (sSiR) of the sulfate-reducing bacterium Desulfovibrio desulfuricans (Essex). Molecular and spectroscopic properties were determined and compared with the properties of the soluble desulfoviridin from Desulfovibrio vulgaris (Hildenborough). The enzymes were isolated as alpha 2 beta 2 gamma n (n = 1-3) multimers with a relative molecular mass of 200 +/- 10 (gel filtration). Both mSiR and sSiR from D. desulfuricans contained 24 +/- 3 Fe and 18 +/- 3 labile sulfide/200 kDa, respectively, and showed identical EPR spectra. Quantification of the high-spin Fe(III) heme resonances at g of approximately 6 indicated that close to 80% of the siroheme moiety in the enzyme from D. desulfuricans was demetallated. D. desulfuricans sulfite reductase showed S = 9/2 EPR signals with the highest apparent g value at g = 17 as reported for SiR from D. vulgaris. Antibodies raised against the alpha, beta and gamma subunit of the D. vulgaris enzyme exhibited cross-reactivity with the subunits of mSiR and sSiR from D. desulfuricans. N-terminal sequences of alpha, beta and gamma subunits of both mSiR and sSiR from D. desulfuricans were identical and showed a high degree of similarity with the sequences of the corresponding subunits obtained from the D. vulgaris enzyme. During gel filtration of sSiR from D. desulfuricans, under non-denaturing conditions, a small protein (molecular mass approximately 11 kDa) was separated. This 11-kDa protein exhibited cross-reactivity with the antibody raised against the gamma subunit of D. vulgaris sulfite reductase. In the case of D. desulfuricans sulfite reductase, the 11-kDa gamma subunit seems not to be an integral part of the protein and can be obtained from the soluble fraction and during purification of the soluble enzyme.
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Affiliation(s)
- J Steuber
- Universität Konstanz, Fakultät für Biologie, Konstanz, Germany
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26
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Angell P, White DC. Is metabolic activity by biofilms with sulfate-reducing bacterial consortia essential for long-term propagation of pitting corrosion of stainless steel? ACTA ACUST UNITED AC 1995. [DOI: 10.1007/bf01569987] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Energetics of sulfate transport in Desulfomicrobium baculatum. Arch Microbiol 1995. [DOI: 10.1007/bf00393385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Mechanism of dissimilatory sulfite reduction by Desulfovibrio desulfuricans: purification of a membrane-bound sulfite reductase and coupling iwth cytochrome c 3 and hydrogenase. Arch Microbiol 1994. [DOI: 10.1007/bf00301847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Abstract
Dissimilatory sulfate reduction is carried out by a heterogeneous group of bacteria and archaea that occur in environments with temperatures up to 105 degrees C. As a group together they have the capacity to metabolize a wide variety of compounds ranging from hydrogen via typical organic fermentation products to hexadecane, toluene, and several types of substituted aromatics. Without exception all sulfate reducers activate sulfate to APS; the natural electron donor(s) for the ensuing APS reductase reaction is not known. The same is true for the reduction of the product bisulfite; in addition there is still some uncertainty as to whether the pathway to sulfide is a direct six-electron reduction of bisulfite or whether it involves trithionate and thiosulfate as intermediates. The study of the degradation pathways of organic substrates by sulfate-reducing prokaryotes has led to the discovery of novel non-cyclic pathways for the oxidation of the acetyl moiety of acetyl-CoA to CO2. The most detailed knowledge is available on the metabolism of Desulfovibrio strains, both on the pathways and enzymes involved in substrate degradation and on electron transfer components and terminal reductases. Problems encountered in elucidating the flow of reducing equivalents and energy transduction are the cytoplasmic localization of the terminal reductases and uncertainties about the electron donors for the reactions catalyzed by these enzymes. New developments in the study of the metabolism of sulfate-reducing bacteria and archaea are reviewed.
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Affiliation(s)
- T A Hansen
- Department of Microbiology, University of Groningen, Haren, The Netherlands
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Role of sodium ions for sulfate transport and energy metabolism in Desulfovibrio salexigens. Arch Microbiol 1994. [DOI: 10.1007/bf00248893] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Kreke B, Cypionka H. Protonmotive force in freshwater sulfate-reducing bacteria, and its role in sulfate accumulation in Desulfobulbus propionicus. Arch Microbiol 1992; 158:183-7. [PMID: 1332637 DOI: 10.1007/bf00290814] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The protonmotive force in several sulfate-reducing bacteria has been determined by means of radiolabelled membrane-permeant probes (tetraphenylphosphonium cation, TPP+, for delta psi, and benzoate for delta pH). In six of ten freshwater strains tested only the pH gradient could be determined, while the membrane potential was not accessible due to nonspecific binding of TPP+. The protonmotive force of the other four strains was between -110 and -155 mV, composed of a membrane potential of -80 to -140 mV and a pH gradient between 0.25 and 0.8 (inside alkaline) at pH(out) = 7. In Desulfobulbus propionicus the pH gradient decreased with rising external pH values. This decrease, however, was compensated by an increasing membrane potential. Sulfate, which can be highly accumulated by the cells, did not affect the protonmotive force, if added in concentrations of up to 4 mM. The highest sulfate accumulation observed (2500-fold), which occurred at external sulfate concentrations below 5 microM, could be explained by a symport of three protons per sulfate, if equilibrium with the protonmotive force was assumed. At higher sulfate concentrations the accumulation decreased and suggested an electroneutral symport of two protons per sulfate. At sulfate concentrations above 500 microM, the cells stopped sulfate uptake before reaching an equilibrium with the protonmotive force.
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Affiliation(s)
- B Kreke
- Fakultät für Biologie, Universität Konstanz, Federal Republic of Germany
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Dannenberg S, Kroder M, Dilling W, Cypionka H. Oxidation of H2, organic compounds and inorganic sulfur compounds coupled to reduction of O2 or nitrate by sulfate-reducing bacteria. Arch Microbiol 1992. [DOI: 10.1007/bf00245211] [Citation(s) in RCA: 130] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Na+-dependent accumulation of sulfate and thiosulfate in marine sulfate-reducing bacteria. Arch Microbiol 1991. [DOI: 10.1007/bf00245349] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Fitz RM, Cypionka H. Formation of thiosulfate and trithionate during sulfite reduction by washed cells of Desulfovibrio desulfuricans. Arch Microbiol 1990. [DOI: 10.1007/bf00276538] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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