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Kim M, Cha IT, Li M, Park SJ. Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications. CHEMOSPHERE 2024; 361:142588. [PMID: 38866340 DOI: 10.1016/j.chemosphere.2024.142588] [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: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024]
Abstract
Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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2
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Chen G, Wang R, Sun M, Chen J, Iyobosa E, Zhao J. Carbon dioxide reduction to high-value chemicals in microbial electrosynthesis system: Biological conversion and regulation strategies. CHEMOSPHERE 2023; 344:140251. [PMID: 37769909 DOI: 10.1016/j.chemosphere.2023.140251] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/03/2023]
Abstract
Large emissions of atmospheric carbon dioxide (CO2) are causing climatic and environmental problems. It is crucial to capture and utilize the excess CO2 through diverse methods, among which the microbial electrosynthesis (MES) system has become an attractive and promising technology to mitigate greenhouse effects while reducing CO2 to high-value chemicals. However, the biological conversion and metabolic pathways through microbial catalysis have not been clearly elucidated. This review first introduces the main acetogenic bacteria for CO2 reduction and extracellular electron transfer mechanisms in MES. It then intensively analyzes the CO2 bioconversion pathways and carbon chain elongation processes in MES, together with energy supply and utilization. The factors affecting MES performance, including physical, chemical, and biological aspects, are summarized, and the strategies to promote and regulate bioconversion in MES are explored. Finally, challenges and perspectives concerning microbial electrochemical carbon sequestration are proposed, and suggestions for future research are also provided. This review provides theoretical foundation and technical support for further development and industrial application of MES for CO2 reduction.
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Affiliation(s)
- Gaoxiang Chen
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Rongchang Wang
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China.
| | - Maoxin Sun
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Jie Chen
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Eheneden Iyobosa
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
| | - Jianfu Zhao
- Key Laboratory of Yangtze Aquatic Environment (MOE), College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, Shanghai, PR China
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3
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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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4
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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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Prakash O, Mostafa A, Im S, Song YC, Kang S, Kim DH. Enhanced anaerobic treatment of sulfate-rich wastewater by electrical voltage application. BIORESOURCE TECHNOLOGY 2023; 369:128430. [PMID: 36464001 DOI: 10.1016/j.biortech.2022.128430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Treatment of sulfate-rich wastewater with high methane recovery is a major concern due to sulfide inhibition. Here, an electrical voltage (EV) aims to enhance methanogenesis and sulfidogenesis to treat sulfate-rich wastewater. Two (control and EV-applied) reactors were operated with a gradual decrease in chemical oxygen demand (COD)/SO42- ratios (CSR). EV-applied reactor (EVR) demonstrated an increase of ∼30 % in methane production and ∼40 % in sulfate removal, compared to the control till CSR of 2.0. At CSR 1.0, the control failed, while EVR still exhibited a stable performance of 50 % COD-methane recovery. Microbial community results showed that the relative abundance of sulfate-reducing bacteria in EVR was 1.5 times higher than the control. Furthermore, higher relative abundance of dissimilatory sulfate reductase (>50 %) and Ni/Fe hydrogenase (x15) genes demonstrated an improved tolerance against H2S toxicity. This study highlights the importance of EV application by minimizing the byproduct inhibition in sulfate-rich wastewater.
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Affiliation(s)
- Om Prakash
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Alsayed Mostafa
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Seongwon Im
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea
| | - Young-Chae Song
- Department of Environmental Engineering, Korea Maritime and Ocean University, Busan 49112, Republic of Korea
| | - Seoktae Kang
- Department of Civil and Environmental Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dong-Hoon Kim
- Department of Smart-city Engineering, Inha University, 100 Inha-ro, Michuhol-gu, Incheon 22212, Republic of Korea.
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6
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Text-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow. Microorganisms 2023; 11:microorganisms11010119. [PMID: 36677411 PMCID: PMC9867429 DOI: 10.3390/microorganisms11010119] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 01/05/2023] Open
Abstract
A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer. Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.
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7
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Inhibition of Sulfate Reduction and Cell Division by Desulfovibrio desulfuricans Coated in Palladium Metal. Appl Environ Microbiol 2022; 88:e0058022. [PMID: 35638843 DOI: 10.1128/aem.00580-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The growth of sulfate-reducing bacteria (SRB) and associated hydrogen sulfide production can be problematic in a range of industries such that inhibition strategies are needed. A range of SRB can reduce metal ions, a strategy that has been utilized for bioremediation, metal recovery, and synthesis of precious metal catalysts. In some instances, the metal remains bound to the cell surface, and the impact of this coating on bacterial cell division and metabolism has not previously been reported. In this study, Desulfovibrio desulfuricans cells (1g dry weight) enabled the reduction of up to 1500 mmol (157.5 g) palladium (Pd) ions, resulting in cells being coated in approximately 1 μm of metal. Thickly coated cells were no longer able to metabolize or divide, ultimately leading to the death of the population. Increasing Pd coating led to prolonged inhibition of sulfate reduction, which ceased completely after cells had been coated with 1200 mmol Pd g-1 dry cells. Less Pd nanoparticle coating permitted cells to carry out sulfate reduction and divide, allowing the population to recover over time as surface-associated Pd diminished. Overcoming inhibition in this way was more rapid using lactate as the electron donor, compared to formate. When using formate as an electron donor, preferential Pd(II) reduction took place in the presence of 100 mM sulfate. The inhibition of important metabolic pathways using a biologically enabled casing in metal highlights a new mechanism for the development of microbial control strategies. IMPORTANCE Microbial reduction of sulfate to hydrogen sulfide is highly undesirable in several industrial settings. Some sulfate-reducing bacteria are also able to transform metal ions in their environment into metal phases that remain attached to their outer cell surface. This study demonstrates the remarkable extent to which Desulfovibrio desulfuricans can be coated with locally generated metal nanoparticles, with individual cells carrying more than 100 times their mass of palladium metal. Moreover, it reveals the effect of metal coating on metabolism and replication for a wide range of metal loadings, with bacteria unable to reduce sulfate to sulfide beyond a specific threshold. These findings present a foundation for a novel means of modulating the activity of sulfate-reducing bacteria.
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8
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Ueki T, Lovley DR. Desulfovibrio vulgaris as a model microbe for the study of corrosion under sulfate-reducing conditions. MLIFE 2022; 1:13-20. [PMID: 38818327 PMCID: PMC10989807 DOI: 10.1002/mlf2.12018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/01/2024]
Abstract
Corrosion of iron-containing metals under sulfate-reducing conditions is an economically important problem. Microbial strains now known as Desulfovibrio vulgaris served as the model microbes in many of the foundational studies that developed existing models for the corrosion of iron-containing metals under sulfate-reducing conditions. Proposed mechanisms for corrosion by D. vulgaris include: (1) H2 consumption to accelerate the oxidation of Fe0 coupled to the reduction of protons to H2; (2) production of sulfide that combines with ferrous iron to form iron sulfide coatings that promote H2 production; (3) moribund cells release hydrogenases that catalyze Fe0 oxidation with the production of H2; (4) direct electron transfer from Fe0 to cells; and (5) flavins serving as an electron shuttle for electron transfer between Fe0 and cells. The demonstrated possibility of conducting transcriptomic and proteomic analysis of cells growing on metal surfaces suggests that similar studies on D. vulgaris corrosion biofilms can aid in identifying proteins that play an important role in corrosion. Tools for making targeted gene deletions in D. vulgaris are available for functional genetic studies. These approaches, coupled with instrumentation for the detection of low concentrations of H2, and proven techniques for evaluating putative electron shuttle function, are expected to make it possible to determine which of the proposed mechanisms for D. vulgaris corrosion are most important.
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Affiliation(s)
- Toshiyuki Ueki
- Key Laboratory for Anisotropy and Texture of Materials, Ministry of Education, Electrobiomaterials InstituteNortheastern UniversityShenyangChina
| | - Derek R. Lovley
- Key Laboratory for Anisotropy and Texture of Materials, Ministry of Education, Electrobiomaterials InstituteNortheastern UniversityShenyangChina
- Department of Microbiology University of MassachusettsAmherstMAUSA
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9
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Mehrshad M, Lopez-Fernandez M, Sundh J, Bell E, Simone D, Buck M, Bernier-Latmani R, Bertilsson S, Dopson M. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nat Commun 2021; 12:4253. [PMID: 34253732 PMCID: PMC8275790 DOI: 10.1038/s41467-021-24549-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.
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Affiliation(s)
- Maliheh Mehrshad
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Margarita Lopez-Fernandez
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.4489.10000000121678994Present Address: Department of Microbiology, University of Granada, Granada, Spain
| | - John Sundh
- grid.10548.380000 0004 1936 9377Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Emma Bell
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.22072.350000 0004 1936 7697Present Address: Department of Biological Sciences, University of Calgary, Calgary, Alberta Canada
| | - Domenico Simone
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.6341.00000 0000 8578 2742SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rizlan Bernier-Latmani
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefan Bertilsson
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark Dopson
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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10
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Sánchez-Soto MF, Cerqueda-García D, Alcántara-Hernández RJ, Falcón LI, Pech D, Árcega-Cabrera F, Aguirre-Macedo ML, García-Maldonado JQ. Assessing the Diversity of Benthic Sulfate-Reducing Microorganisms in Northwestern Gulf of Mexico by Illumina Sequencing of dsrB Gene. MICROBIAL ECOLOGY 2021; 81:908-921. [PMID: 33196853 DOI: 10.1007/s00248-020-01631-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/21/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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Affiliation(s)
- Ma Fernanda Sánchez-Soto
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | - Daniel Cerqueda-García
- Consorcio de Investigación del Golfo de México (CIGOM), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico
| | | | - Luisa I Falcón
- Instituto de Ecología, Universidad Nacional Autónoma de México, Parque Científico y Tecnológico de Yucatán, Sierra Papacal, Mexico
| | - Daniel Pech
- Laboratorio de Biodiversidad Marina y Cambio Climático, El Colegio de la Frontera Sur, Campeche, Mexico
| | - Flor Árcega-Cabrera
- Unidad de Química en Sisal, Facultad de Química, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico
| | - Ma Leopoldina Aguirre-Macedo
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, Mexico.
| | - José Q García-Maldonado
- CONACYT-Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mérida, Yucatán, México.
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11
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Duarte AG, Barbosa ACC, Ferreira D, Manteigas G, Domingos RM, Pereira IAC. Redox loops in anaerobic respiration - The role of the widespread NrfD protein family and associated dimeric redox module. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148416. [PMID: 33753023 DOI: 10.1016/j.bbabio.2021.148416] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/25/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023]
Abstract
In prokaryotes, the proton or sodium motive force required for ATP synthesis is produced by respiratory complexes that present an ion-pumping mechanism or are involved in redox loops performed by membrane proteins that usually have substrate and quinone-binding sites on opposite sides of the membrane. Some respiratory complexes include a dimeric redox module composed of a quinone-interacting membrane protein of the NrfD family and an iron‑sulfur protein of the NrfC family. The QrcABCD complex of sulfate reducers, which includes the QrcCD module homologous to NrfCD, was recently shown to perform electrogenic quinone reduction providing the first conclusive evidence for energy conservation among this family. Similar redox modules are present in multiple respiratory complexes, which can be associated with electroneutral, energy-driven or electrogenic reactions. This work discusses the presence of the NrfCD/PsrBC dimeric redox module in different bioenergetics contexts and its role in prokaryotic energy conservation mechanisms.
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Affiliation(s)
- Américo G Duarte
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
| | - Ana C C Barbosa
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Gonçalo Manteigas
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Renato M Domingos
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa, Av. da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal.
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12
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Wang S, Jiang L, Hu Q, Cui L, Zhu B, Fu X, Lai Q, Shao Z, Yang S. Characterization of Sulfurimonas hydrogeniphila sp. nov., a Novel Bacterium Predominant in Deep-Sea Hydrothermal Vents and Comparative Genomic Analyses of the Genus Sulfurimonas. Front Microbiol 2021; 12:626705. [PMID: 33717015 PMCID: PMC7952632 DOI: 10.3389/fmicb.2021.626705] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteria of the genus Sulfurimonas within the class Campylobacteria are predominant in global deep-sea hydrothermal environments and widespread in global oceans. However, only few bacteria of this group have been isolated, and their adaptations for these extreme environments remain poorly understood. Here, we report a novel mesophilic, hydrogen- and sulfur-oxidizing bacterium, strain NW10T, isolated from a deep-sea sulfide chimney of Northwest Indian Ocean.16S rRNA gene sequence analysis showed that strain NW10T was most closely related to the vent species Sulfurimonas paralvinellae GO25T with 95.8% similarity, but ANI and DDH values between two strains were only 19.20 and 24.70%, respectively, indicating that strain NW10 represents a novel species. Phenotypic characterization showed strain NW10T is an obligate chemolithoautotroph utilizing thiosulfate, sulfide, elemental sulfur, or molecular hydrogen as energy sources, and molecular oxygen, nitrate, or elemental sulfur as electron acceptors. Moreover, hydrogen supported a better growth than reduced sulfur compounds. During thiosulfate oxidation, the strain can produce extracellular sulfur of elemental α-S8 with an unknown mechanism. Polyphasic taxonomy results support that strain NW10T represents a novel species of the genus Sulfurimonas, and named as Sulfurimonas hydrogeniphila sp. nov. Genome analyses revealed its diverse energy metabolisms driving carbon fixation via rTCA cycling, including pathways of sulfur/hydrogen oxidation, coupled oxygen/sulfur respiration and denitrification. Comparative analysis of the 11 available genomes from Sulfurimonas species revealed that vent bacteria, compared to marine non-vent strains, possess unique genes encoding Type V Sqr, Group II, and Coo hydrogenase, and are selectively enriched in genes related to signal transduction and inorganic ion transporters. These phenotypic and genotypic features of vent Sulfurimonas may explain their thriving in hydrothermal environments and help to understand the ecological role of Sulfurimonas bacteria in hydrothermal ecosystems.
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Affiliation(s)
- Shasha Wang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Liang Cui
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Bitong Zhu
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
| | - Xiaoteng Fu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
- Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen, China
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13
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Liu Y, Serrano A, Wyman V, Marcellin E, Southam G, Vaughan J, Villa-Gomez D. Nickel complexation as an innovative approach for nickel-cobalt selective recovery using sulfate-reducing bacteria. JOURNAL OF HAZARDOUS MATERIALS 2021; 402:123506. [PMID: 32712361 DOI: 10.1016/j.jhazmat.2020.123506] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/06/2020] [Accepted: 07/14/2020] [Indexed: 06/11/2023]
Abstract
This study evaluated the differences in nickel (Ni) and cobalt (Co) solubility in the presence of sulfate reducing bacteria (SRB) to evaluate the feasibility of selective recovery of both metals from mine-impacted waters. A series of sulfate reducing activity tests with Ni, Co and both metals showed that up to 99 % Ni remained soluble despite the availability of sulfide for precipitation, while Co sulfide precipitation always occurred (over 84.5 %). The characterization of proteins in the liquid phase of the experiments revealed that some proteins were only produced in the experiments where Ni displayed higher solubility, suggesting their involvement in metal complexation. Some functions of these proteins included maintaining Ni homeostasis, acting as metalloenzymes and containing Ni-binding ligands. Desulfomicrobium baculatum, Stenotrophomonas maltophilia, and Desulfovibrio magneticus, were the main responsible species producing these proteins.
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Affiliation(s)
- Yun Liu
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia.
| | - Antonio Serrano
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia
| | - Valentina Wyman
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 QLD, Australia
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, 4072 QLD, Australia
| | - James Vaughan
- School of Chemical Engineering, The University of Queensland, 4072 QLD, Australia
| | - Denys Villa-Gomez
- School of Civil Engineering, The University of Queensland, 4072 QLD, Australia
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14
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Deng X, Saito J, Kaksonen A, Okamoto A. Enhancement of cell growth by uncoupling extracellular electron uptake and oxidative stress production in sediment sulfate-reducing bacteria. ENVIRONMENT INTERNATIONAL 2020; 144:106006. [PMID: 32795748 DOI: 10.1016/j.envint.2020.106006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/25/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
Microbial extracellular electron uptake (EEU) from solid electron donors has critical implications for microbial energy acquisition in energy-limited environments as well as electrochemical microbial technologies. Although EEU supplies sufficient energy to support cellular growth, additional soluble electron donors are required for most microbes to grow on electrode surfaces. Here, we demonstrated that the minimization of exogenous and endogenous oxidative stress greatly enhanced the growth rate of the sediment EEU-capable sulfate-reducing bacterium Desulfovibrio ferrophilus IS5 on an electrode without the addition of a soluble electron donor. Single-cell activity analysis by nanoscale secondary ion mass spectrometry showed that the metabolic activity of IS5 cells on the electrode was significantly enhanced following incubation in an H-type reactor, which was configured to reduce the exposure of cells to the potential oxidative stress source of the Pt counter electrode (CE). Additionally, the highest metabolic activity was observed at an electrode potential of -0.4 V (versus the standard hydrogen electrode), where electron uptake rate was not at peak. Compared to a single-chamber reactor, incubation in an H-type reactor at -0.4 V shortened the cell doubling time by 50-fold, which resulted in sufficient anabolism for cell replication (15N/Ntotal > 50%). The production of strongly oxidizing species at the CE was confirmed by X-ray photoelectron spectroscopy and inductively coupled plasma mass spectrometry analyses. Transcriptome analysis revealed overexpression of antioxidative genes in cells incubated at a potential with higher current production. These results suggested that higher levels of endogenous oxidative species were produced by a more reduced electron-transport chain from trace amounts of oxygen in the reactor, thereby lowering cell activity. In conclusion, EEU may enable sediment microbes to undergo enhanced cell growth and to find niches on minerals under anaerobic energy-limited conditions, where oxidative stress is much less likely to be present.
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Affiliation(s)
- Xiao Deng
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; Center for Sensor and Actuator Material, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-8656, Japan; CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia
| | - Junki Saito
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-8656, Japan
| | - Anna Kaksonen
- CSIRO Land and Water, 147 Underwood Avenue, Floreat, WA 6014, Australia; School of Biomedical Sciences, University of Western Australia, 35 Stirling Highway, Nedlands, WA 6009, Australia
| | - Akihiro Okamoto
- International Center for Materials Nanoarchitectonics, National Institute for Materials Science, 1-1 Namiki, Tsukuba 305-0044, Japan; Center for Sensor and Actuator Material, National Institute for Materials Science, 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan; Graduate School of Chemical Sciences and Engineering, Hokkaido University, North 13 West 8, Kita-ku, Sapporo, Hokkaido 060-8628, Japan.
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15
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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16
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Greening C, Boyd E. Editorial: Microbial Hydrogen Metabolism. Front Microbiol 2020; 11:56. [PMID: 32082284 PMCID: PMC7002543 DOI: 10.3389/fmicb.2020.00056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/13/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Eric Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
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17
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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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18
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Zacarias S, Vélez M, Pita M, De Lacey AL, Matias PM, Pereira IAC. Characterization of the [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough. Methods Enzymol 2018; 613:169-201. [PMID: 30509465 DOI: 10.1016/bs.mie.2018.10.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The [NiFeSe] hydrogenases are a subgroup of the well-characterized family of [NiFe] hydrogenases, in which a selenocysteine is a ligand to the nickel atom in the binuclear NiFe active site instead of cysteine. These enzymes display very interesting catalytic properties for biological hydrogen production and bioelectrochemical applications: high H2 production activity, bias for H2 evolution, low H2 inhibition, and some degree of O2 tolerance. Here we describe the methodologies employed to study the [NiFeSe] hydrogenase isolated from the sulfate-reducing bacteria D. vulgaris Hildenborough and the creation of a homologous expression system for production of variant forms of the enzyme.
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Affiliation(s)
- Sónia Zacarias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | - Marcos Pita
- Instituto de Catálisis y Petroleoquímica, CSIC, Madrid, Spain
| | | | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal; iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal.
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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19
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Efficiency of cationic surfactant as microbial corrosion inhibitor for carbon steel in oilfield saline water. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.02.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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20
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Nies F, Wörner S, Wunsch N, Armant O, Sharma V, Hesselschwerdt A, Falk F, Weber N, Weiß J, Trautmann A, Posten C, Prakash T, Lamparter T. Characterization of Phormidium lacuna strains from the North Sea and the Mediterranean Sea for biotechnological applications. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.05.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Mourato C, Martins M, da Silva SM, Pereira IAC. A continuous system for biocatalytic hydrogenation of CO 2 to formate. BIORESOURCE TECHNOLOGY 2017; 235:149-156. [PMID: 28365342 DOI: 10.1016/j.biortech.2017.03.091] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 05/20/2023]
Abstract
In this work a novel bioprocess for hydrogenation of CO2 to formate was developed, using whole cell catalysis by a sulfate-reducing bacterium. Three Desulfovibrio species were tested (D. vulgaris Hildenborough, D. alaskensis G20, and D. desulfuricans ATCC 27774), of which D. desulfuricans showed the highest activity, producing 12mM of formate in batch, with a production rate of 0.09mMh-1. Gene expression analysis indicated that among the three formate dehydrogenases and five hydrogenases, the cytoplasmic FdhAB and the periplasmic [FeFe] HydAB are the main enzymes expressed in D. desulfuricans in these conditions. The new bioprocess for continuous formate production by D. desulfuricans had a maximum specific formate production rate of 14mMgdcw-1h-1, and more than 45mM of formate were obtained with a production rate of 0.40mMh-1. This is the first report of a continuous process for biocatalytic formate production.
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Affiliation(s)
- Cláudia Mourato
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa (ITQB NOVA), Av. da Republica-EAN, 2780-157 Oeiras, Portugal
| | - Mónica Martins
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa (ITQB NOVA), Av. da Republica-EAN, 2780-157 Oeiras, Portugal
| | - Sofia M da Silva
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa (ITQB NOVA), Av. da Republica-EAN, 2780-157 Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier/Universidade Nova de Lisboa (ITQB NOVA), Av. da Republica-EAN, 2780-157 Oeiras, Portugal.
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22
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Sapojnikova N, Asatiani N, Kartvelishvili T, Asanishvili L, Zinkevich V, Bogdarina I, Mitchell J, Al-Humam A. A comparison of DNA fragmentation methods - Applications for the biochip technology. J Biotechnol 2017; 256:1-5. [PMID: 28666852 DOI: 10.1016/j.jbiotec.2017.06.1202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/12/2017] [Accepted: 06/26/2017] [Indexed: 11/28/2022]
Abstract
The efficiency of hybridization signal detection in a biochip is affected by the method used for test DNA preparation, such as fragmentation, amplification and fluorescent labelling. DNA fragmentation is the commonest methods used and it is recognised as a critical step in biochip analysis. Currently methods used for DNA fragmentation are based either on sonication or on the enzymatic digestion. In this study, we compared the effect of different types of enzymatic DNA fragmentations, using DNase I to generate ssDNA breaks, NEBNext dsDNA fragmentase and SaqAI restrictase, on DNA labelling. DNA from different Desulfovibrio species was used as a substrate for these enzymes. Of the methods used, DNA fragmented by NEBNext dsDNA Fragmentase digestion was subsequently labelled with the greatest efficiency. As a result of this, the use of this enzyme to fragment target DNA increases the sensitivity of biochip-based detection significantly, and this is an important consideration when determining the presence of targeted DNA in ecological and medical samples.
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Affiliation(s)
- Nelly Sapojnikova
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia.
| | - Nino Asatiani
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia
| | - Tamar Kartvelishvili
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia
| | - Lali Asanishvili
- Andronikashvili Institute of Physics, I. Javakhishvili Tbilisi State University,6 Tamarashvili Street, 0177 Tbilisi, Georgia
| | - Vitaly Zinkevich
- School of Pharmacy and Biomedical Sciences, University of Portsmouth,St. Michael's Building, White Swan Road, PO1 2DT, UK
| | - Irina Bogdarina
- School of Pharmacy and Biomedical Sciences, University of Portsmouth,St. Michael's Building, White Swan Road, PO1 2DT, UK
| | - Julian Mitchell
- School of Biological Sciences, University of Portsmouth,King Henry Building, King Henry I Street, PO1 2DY, UK
| | - Abdulmohsen Al-Humam
- Applied Microbiology Unit, Research & Development Center Saudi Aramco, P.O. Box. 00865, 31311 Dhahran, Saudi Arabia, Saudi Arabia
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23
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Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B. Genome-Guided Analysis and Whole Transcriptome Profiling of the Mesophilic Syntrophic Acetate Oxidising Bacterium Syntrophaceticus schinkii. PLoS One 2016; 11:e0166520. [PMID: 27851830 PMCID: PMC5113046 DOI: 10.1371/journal.pone.0166520] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/31/2016] [Indexed: 01/29/2023] Open
Abstract
Syntrophaceticus schinkii is a mesophilic, anaerobic bacterium capable of oxidising acetate to CO2 and H2 in intimate association with a methanogenic partner, a syntrophic relationship which operates close to the energetic limits of microbial life. Syntrophaceticus schinkii has been identified as a key organism in engineered methane-producing processes relying on syntrophic acetate oxidation as the main methane-producing pathway. However, due to strict cultivation requirements and difficulties in reconstituting the thermodynamically unfavourable acetate oxidation, the physiology of this functional group is poorly understood. Genome-guided and whole transcriptome analyses performed in the present study provide new insights into habitat adaptation, syntrophic acetate oxidation and energy conservation. The working draft genome of Syntrophaceticus schinkii indicates limited metabolic capacities, with lack of organic nutrient uptake systems, chemotactic machineries, carbon catabolite repression and incomplete biosynthesis pathways. Ech hydrogenase, [FeFe] hydrogenases, [NiFe] hydrogenases, F1F0-ATP synthase and membrane-bound and cytoplasmic formate dehydrogenases were found clearly expressed, whereas Rnf and a predicted oxidoreductase/heterodisulphide reductase complex, both found encoded in the genome, were not expressed under syntrophic growth condition. A transporter sharing similarities to the high-affinity acetate transporters of aceticlastic methanogens was also found expressed, suggesting that Syntrophaceticus schinkii can potentially compete with methanogens for acetate. Acetate oxidation seems to proceed via the Wood-Ljungdahl pathway as all genes involved in this pathway were highly expressed. This study shows that Syntrophaceticus schinkii is a highly specialised, habitat-adapted organism relying on syntrophic acetate oxidation rather than metabolic versatility. By expanding its complement of respiratory complexes, it might overcome limiting bioenergetic barriers, and drive efficient energy conservation from reactions operating close to the thermodynamic equilibrium, which might enable S. schinkii to occupy the same niche as the aceticlastic methanogens. The knowledge gained here will help specify process conditions supporting efficient and robust biogas production and will help identify mechanisms important for the syntrophic lifestyle.
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Affiliation(s)
- Shahid Manzoor
- Department of Information Technology, University of the Punjab, Lahore, Pakistan
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, SE 750 07, Sweden
| | - Anna Schnürer
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07, Sweden
| | - Bettina Müller
- Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, SE 750 07, Sweden
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Unification of [FeFe]-hydrogenases into three structural and functional groups. Biochim Biophys Acta Gen Subj 2016; 1860:1910-21. [DOI: 10.1016/j.bbagen.2016.05.034] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/20/2016] [Accepted: 05/26/2016] [Indexed: 11/22/2022]
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25
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Electron transfer pathways of formate-driven H2 production in Desulfovibrio. Appl Microbiol Biotechnol 2016; 100:8135-46. [DOI: 10.1007/s00253-016-7649-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/12/2016] [Accepted: 05/25/2016] [Indexed: 10/21/2022]
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Wolf PG, Biswas A, Morales SE, Greening C, Gaskins HR. H2 metabolism is widespread and diverse among human colonic microbes. Gut Microbes 2016; 7:235-45. [PMID: 27123663 PMCID: PMC4939926 DOI: 10.1080/19490976.2016.1182288] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Microbial molecular hydrogen (H2) cycling is central to metabolic homeostasis and microbial composition in the human gastrointestinal tract. Molecular H2 is produced as an endproduct of carbohydrate fermentation and is reoxidised primarily by sulfate-reduction, acetogenesis, and methanogenesis. However, the enzymatic basis for these processes is incompletely understood and the hydrogenases responsible have not been investigated. In this work, we surveyed the genomic and metagenomic distribution of hydrogenase-encoding genes in the human colon to infer dominant mechanisms of H2 cycling. The data demonstrate that 70% of gastrointestinal microbial species listed in the Human Microbiome Project encode the genetic capacity to metabolise H2. A wide variety of anaerobically-adapted hydrogenases were present, with [FeFe]-hydrogenases predominant. We subsequently analyzed the hydrogenase gene content of stools from 20 healthy human subjects. The hydrogenase gene content of all samples was overwhelmingly dominated by fermentative and electron-bifurcating [FeFe]-hydrogenases emerging from the Bacteroidetes and Firmicutes. This study supports that H2 metabolism in the human gut is driven by fermentative H2 production and interspecies H2 transfer. However, it suggests that electron-bifurcation rather than respiration is the dominant mechanism of H2 reoxidation in the human colon, generating reduced ferredoxin to sustain carbon-fixation (e.g. acetogenesis) and respiration (via the Rnf complex). This work provides the first comprehensive bioinformatic insight into the mechanisms of H2 metabolism in the human colon.
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Affiliation(s)
- Patricia G. Wolf
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Sergio E. Morales
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Chris Greening
- CSIRO Land and Water, Ecosystem Sciences Building, Acton, Australia
| | - H. Rex Gaskins
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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27
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An D, Dong X, An A, Park HS, Strous M, Voordouw G. Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite. Front Microbiol 2016; 7:28. [PMID: 26858705 PMCID: PMC4729907 DOI: 10.3389/fmicb.2016.00028] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/11/2016] [Indexed: 11/29/2022] Open
Abstract
Sodium bisulfite (SBS) is used as an oxygen scavenger to decrease corrosion in pipelines transporting brackish subsurface water used in the production of bitumen by steam-assisted gravity drainage. Sequencing 16S rRNA gene amplicons has indicated that SBS addition increased the fraction of the sulfate-reducing bacteria (SRB) Desulfomicrobium, as well as of Desulfocapsa, which can also grow by disproportionating sulfite into sulfide, sulfur, and sulfate. SRB use cathodic H2, formed by reduction of aqueous protons at the iron surface, or use low potential electrons from iron and aqueous protons directly for sulfate reduction. In order to reveal the effects of SBS treatment in more detail, metagenomic analysis was performed with pipe-associated solids (PAS) scraped from a pipe section upstream (PAS-616P) and downstream (PAS-821TP) of the SBS injection point. A major SBS-induced change in microbial community composition and in affiliated hynL genes for the large subunit of [NiFe] hydrogenase was the appearance of sulfur-metabolizing Epsilonproteobacteria of the genera Sulfuricurvum and Sulfurovum. These are chemolithotrophs, which oxidize sulfide or sulfur with O2 or reduce sulfur with H2. Because O2 was absent, this class likely catalyzed reduction of sulfur (S0) originating from the metabolism of bisulfite with cathodic H2 (or low potential electrons and aqueous protons) originating from the corrosion of steel (Fe0). Overall this accelerates reaction of of S0 and Fe0 to form FeS, making this class a potentially powerful contributor to microbial corrosion. The PAS-821TP metagenome also had increased fractions of Deltaproteobacteria including the SRB Desulfomicrobium and Desulfocapsa. Altogether, SBS increased the fraction of hydrogen-utilizing Delta- and Epsilonproteobacteria in brackish-water-transporting pipelines, potentially stimulating anaerobic pipeline corrosion if dosed in excess of the intended oxygen scavenger function.
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Affiliation(s)
- Dongshan An
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Xiaoli Dong
- Department of Geosciences, University of Calgary Calgary, AB, Canada
| | - Annie An
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Hyung S Park
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Marc Strous
- Department of Geosciences, University of Calgary Calgary, AB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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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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Ramos AR, Grein F, Oliveira GP, Venceslau SS, Keller KL, Wall JD, Pereira IAC. The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 2015; 17:2288-305. [PMID: 25367508 DOI: 10.1111/1462-2920.12689] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/23/2014] [Indexed: 11/29/2022]
Abstract
Flavin-based electron bifurcation (FBEB) is an important mechanism for the energy metabolism of anaerobes. A new family of NADH dehydrogenases, the flavin oxidoreductase (FlxABCD, previously called FloxABCD), was proposed to perform FBEB in sulphate-reducing organisms coupled with heterodisulfide reductase (HdrABC). We found that the hdrABC-flxABCD gene cluster is widespread among anaerobic bacteria, pointing to a general and important role in their bioenergetics. In this work, we studied FlxABCD of Desulfovibrio vulgaris Hildenborough. The hdr-flx genes are part of the same transcriptional unit and are increased in transcription during growth in ethanol-sulfate, and to a less extent during pyruvate fermentation. Two mutant strains were generated: one where expression of the hdr-flx genes was interrupted and another lacking the flxA gene. Both strains were unable to grow with ethanol-sulfate, whereas growth was restored in a flxA-complemented strain. The mutant strains also produced very reduced amounts of ethanol compared with the wild type during pyruvate fermentation. Our results show that in D. vulgaris, the FlxABCD-HdrABC proteins are essential for NADH oxidation during growth on ethanol, probably involving a FBEB mechanism that leads to reduction of ferredoxin and the small protein DsrC, while in fermentation they operate in reverse, reducing NAD(+) for ethanol production.
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Affiliation(s)
- Ana Raquel Ramos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Fabian Grein
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Gonçalo P Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
| | - Kimberly L Keller
- Biochemistry Department, University of Missouri, Columbia, MO, USA.,ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Berkeley, CA, USA
| | - Judy D Wall
- Biochemistry Department, University of Missouri, Columbia, MO, USA.,ENIGMA (Ecosystems and Networks Integrated with Genes and Molecular Assemblies), Berkeley, CA, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, 2780-157, Portugal
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Syntrophic growth of Desulfovibrio alaskensis requires genes for H2 and formate metabolism as well as those for flagellum and biofilm formation. Appl Environ Microbiol 2015; 81:2339-48. [PMID: 25616787 DOI: 10.1128/aem.03358-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In anaerobic environments, mutually beneficial metabolic interactions between microorganisms (syntrophy) are essential for oxidation of organic matter to carbon dioxide and methane. Syntrophic interactions typically involve a microorganism degrading an organic compound to primary fermentation by-products and sources of electrons (i.e., formate, hydrogen, or nanowires) and a partner producing methane or respiring the electrons via alternative electron accepting processes. Using a transposon gene mutant library of the sulfate-reducing Desulfovibrio alaskensis G20, we screened for mutants incapable of serving as the electron-accepting partner of the butyrate-oxidizing bacterium, Syntrophomonas wolfei. A total of 17 gene mutants of D. alaskensis were identified as incapable of serving as the electron-accepting partner. The genes identified predominantly fell into three categories: membrane surface assembly, flagellum-pilus synthesis, and energy metabolism. Among these genes required to serve as the electron-accepting partner, the glycosyltransferase, pilus assembly protein (tadC), and flagellar biosynthesis protein showed reduced biofilm formation, suggesting that each of these components is involved in cell-to-cell interactions. Energy metabolism genes encoded proteins primarily involved in H2 uptake and electron cycling, including a rhodanese-containing complex that is phylogenetically conserved among sulfate-reducing Deltaproteobacteria. Utilizing an mRNA sequencing approach, analysis of transcript abundance in wild-type axenic and cocultures confirmed that genes identified as important for serving as the electron-accepting partner were more highly expressed under syntrophic conditions. The results imply that sulfate-reducing microorganisms require flagellar and outer membrane components to effectively couple to their syntrophic partners; furthermore, H2 metabolism is essential for syntrophic growth of D. alaskensis G20.
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31
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Biswas R, Zheng T, Olson DG, Lynd LR, Guss AM. Elimination of hydrogenase active site assembly blocks H2 production and increases ethanol yield in Clostridium thermocellum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:20. [PMID: 25763101 PMCID: PMC4355364 DOI: 10.1186/s13068-015-0204-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/13/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND The native ability of Clostridium thermocellum to rapidly consume cellulose and produce ethanol makes it a leading candidate for a consolidated bioprocessing (CBP) biofuel production strategy. C. thermocellum also synthesizes lactate, formate, acetate, H2, and amino acids that compete with ethanol production for carbon and electrons. Elimination of H2 production could redirect carbon flux towards ethanol production by making more electrons available for acetyl coenzyme A reduction to ethanol. RESULTS H2 production in C. thermocellum is encoded by four hydrogenases. Rather than delete each individually, we targeted hydrogenase maturase gene hydG, involved in converting the three [FeFe] hydrogenase apoenzymes into holoenzymes. Further deletion of the [NiFe] hydrogenase (ech) resulted in a mutant that functionally lacks all four hydrogenases. H2 production in ∆hydG∆ech was undetectable, and the ethanol yield nearly doubled to 64% of the maximum theoretical yield. Genomic analysis of ∆hydG revealed a mutation in adhE, resulting in a strain with both NADH- and NADPH-dependent alcohol dehydrogenase activities. While this same adhE mutation was found in ethanol-tolerant C. thermocellum strain E50C, ∆hydG and ∆hydG∆ech are not more ethanol tolerant than the wild type, illustrating the complicated interactions between redox balancing and ethanol tolerance in C. thermocellum. CONCLUSIONS The dramatic increase in ethanol production suggests that targeting protein post-translational modification is a promising new approach for simultaneous inactivation of multiple enzymes.
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Affiliation(s)
- Ranjita Biswas
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Current address: Centre for Rural Development and Technology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016 India
| | - Tianyong Zheng
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Thayer School of Engineering at Dartmouth College, Hanover, NH 03755 USA
| | - Daniel G Olson
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Thayer School of Engineering at Dartmouth College, Hanover, NH 03755 USA
| | - Lee R Lynd
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />Thayer School of Engineering at Dartmouth College, Hanover, NH 03755 USA
| | - Adam M Guss
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37830 USA
- />One Bethel Valley Road, Oak Ridge, TN 37831-6038 USA
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Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri. Sci Rep 2014; 4:7478. [PMID: 25504148 PMCID: PMC4265775 DOI: 10.1038/srep07478] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/25/2014] [Indexed: 01/09/2023] Open
Abstract
Microbial syntrophic metabolism has been well accepted as the heart of how methanogenic and other anaerobic microbial communities function. In this work, we applied a single-cell RT-qPCR approach to reveal gene-expression heterogeneity in a model syntrophic system of Desulfovibrio vulgaris and Methanosarcina barkeri, as compared with the D. vulgaris monoculture. Using the optimized primers and single-cell analytical protocol, we quantitatively determine gene-expression levels of 6 selected target genes in each of the 120 single cells of D. vulgaris isolated from its monoculture and dual-culture with M. barkeri. The results demonstrated very significant cell-to-cell gene-expression heterogeneity for the selected D. vulgaris genes in both the monoculture and the syntrophic dual-culture. Interestingly, no obvious increase in gene-expression heterogeneity for the selected genes was observed for the syntrophic dual-culture when compared with its monoculture, although the community structure and cell-cell interactions have become more complicated in the syntrophic dual-culture. In addition, the single-cell RT-qPCR analysis also provided further evidence that the gene cluster (DVU0148-DVU0150) may be involved syntrophic metabolism between D. vulgaris and M. barkeri. Finally, the study validated that single-cell RT-qPCR analysis could be a valuable tool in deciphering gene functions and metabolism in mixed-cultured microbial communities.
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33
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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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Mand J, Park HS, Jack TR, Voordouw G. The role of acetogens in microbially influenced corrosion of steel. Front Microbiol 2014; 5:268. [PMID: 24917861 PMCID: PMC4043135 DOI: 10.3389/fmicb.2014.00268] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/15/2014] [Indexed: 11/13/2022] Open
Abstract
Microbially influenced corrosion (MIC) of iron (Fe(0)) by sulfate-reducing bacteria (SRB) has been studied extensively. Through a mechanism, that is still poorly understood, electrons or hydrogen (H2) molecules are removed from the metal surface and used as electron donor for sulfate reduction. The resulting ferrous ions precipitate in part with the sulfide produced, forming characteristic black iron sulfide. Hydrogenotrophic methanogens can also contribute to MIC. Incubation of pipeline water samples, containing bicarbonate and some sulfate, in serum bottles with steel coupons and a headspace of 10% (vol/vol) CO2 and 90% N2, indicated formation of acetate and methane. Incubation of these samples in serum bottles, containing medium with coupons and bicarbonate but no sulfate, also indicated that formation of acetate preceded the formation of methane. Microbial community analyses of these enrichments indicated the presence of Acetobacterium, as well as of hydrogenotrophic and acetotrophic methanogens. The formation of acetate by homoacetogens, such as Acetobacterium woodii from H2 (or Fe(0)) and CO2, is potentially important, because acetate is a required carbon source for many SRB growing with H2 and sulfate. A consortium of the SRB Desulfovibrio vulgaris Hildenborough and A. woodii was able to grow in defined medium with H2, CO2, and sulfate, because A. woodii provides the acetate, needed by D. vulgaris under these conditions. Likewise, general corrosion rates of metal coupons incubated with D. vulgaris in the presence of acetate or in the presence of A. woodii were higher than in the absence of acetate or A. woodii, respectively. An extended MIC model capturing these results is presented.
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Affiliation(s)
- Jaspreet Mand
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Hyung Soo Park
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Thomas R Jack
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Gerrit Voordouw
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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35
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Venceslau SS, Stockdreher Y, Dahl C, Pereira IAC. The "bacterial heterodisulfide" DsrC is a key protein in dissimilatory sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1148-64. [PMID: 24662917 DOI: 10.1016/j.bbabio.2014.03.007] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 03/07/2014] [Accepted: 03/13/2014] [Indexed: 12/16/2022]
Abstract
DsrC is a small protein present in organisms that dissimilate sulfur compounds, working as a physiological partner of the DsrAB sulfite reductase. DsrC contains two redox active cysteines in a flexible carboxy-terminal arm that are involved in the process of sulfite reduction or sulfur(1) compound oxidation in sulfur-reducing(2) or sulfur-oxidizing(3) organisms, respectively. In both processes, a disulfide formed between the two cysteines is believed to serve as the substrate of several proteins present in these organisms that are related to heterodisulfide reductases of methanogens. Here, we review the information on DsrC and its possible physiological partners, and discuss the idea that this protein may serve as a redox hub linking oxidation of several substrates to dissimilative sulfur metabolism. In addition, we analyze the distribution of proteins of the DsrC superfamily, including TusE that only requires the last Cys of the C-terminus for its role in the biosynthesis of 2-thiouridine, and a new protein that we name RspA (for regulatory sulfur-related protein) that is possibly involved in the regulation of gene expression and does not need the conserved Cys for its function. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- S S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Y Stockdreher
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - C Dahl
- Institut für Mikrobiologie & Biotechnologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany
| | - I A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal.
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36
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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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37
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Meyer B, Kuehl JV, Deutschbauer AM, Arkin AP, Stahl DA. Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. J Bacteriol 2013; 195:4900-14. [PMID: 23974031 PMCID: PMC3807489 DOI: 10.1128/jb.00504-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 08/20/2013] [Indexed: 12/31/2022] Open
Abstract
The mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers obligately linked by interspecies metabolite exchange in syntrophic consortia that may include sulfate reducing species such as Desulfovibrio. To evaluate the metabolic flexibility of syntrophic Desulfovibrio to adapt to naturally fluctuating methanogenic environments, we studied Desulfovibrio alaskensis strain G20 grown in chemostats under respiratory and syntrophic conditions with alternative methanogenic partners, Methanococcus maripaludis and Methanospirillum hungatei, at different growth rates. Comparative whole-genome transcriptional analyses, complemented by G20 mutant strain growth experiments and physiological data, revealed a significant influence of both energy source availability (as controlled by dilution rate) and methanogen on the electron transfer systems, ratios of interspecies electron carriers, energy generating systems, and interspecies physical associations. A total of 68 genes were commonly differentially expressed under syntrophic versus respiratory lifestyle. Under low-energy (low-growth-rate) conditions, strain G20 further had the capacity to adapt to the metabolism of its methanogenic partners, as shown by its differing gene expression of enzymes involved in the direct metabolic interactions (e.g., periplasmic hydrogenases) and the ratio shift in electron carriers used for interspecies metabolite exchange (hydrogen/formate). A putative monomeric [Fe-Fe] hydrogenase and Hmc (high-molecular-weight-cytochrome c3) complex-linked reverse menaquinone (MQ) redox loop become increasingly important for the reoxidation of the lactate-/pyruvate oxidation-derived redox pair, DsrC(red) and Fd(red), relative to the Qmo-MQ-Qrc (quinone-interacting membrane-bound oxidoreductase; quinone-reducing complex) loop. Together, these data underscore the high enzymatic and metabolic adaptive flexibility that likely sustains Desulfovibrio in naturally fluctuating methanogenic environments.
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Affiliation(s)
- Birte Meyer
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
| | - Jennifer V. Kuehl
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M. Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam P. Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David A. Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, Washington, USA
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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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da Silva SM, Voordouw J, Leitão C, Martins M, Voordouw G, Pereira IAC. Function of formate dehydrogenases in Desulfovibrio vulgaris Hildenborough energy metabolism. Microbiology (Reading) 2013; 159:1760-1769. [DOI: 10.1099/mic.0.067868-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sofia M. da Silva
- Instituto de Tecnologia Quimica e Biologica, António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Johanna Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Cristina Leitão
- Instituto de Tecnologia Quimica e Biologica, António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mónica Martins
- Instituto de Tecnologia Quimica e Biologica, António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Gerrit Voordouw
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Inês A. C. Pereira
- Instituto de Tecnologia Quimica e Biologica, António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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40
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Abstract
Sulfate-reducing bacteria (SRB) colonize the guts of ∼50% of humans. We used genome-wide transposon mutagenesis and insertion-site sequencing, RNA-Seq, plus mass spectrometry to characterize genetic and environmental factors that impact the niche of Desulfovibrio piger, the most common SRB in a surveyed cohort of healthy US adults. Gnotobiotic mice were colonized with an assemblage of sequenced human gut bacterial species with or without D. piger and fed diets with different levels and types of carbohydrates and sulfur sources. Diet was a major determinant of functions expressed by this artificial nine-member community and of the genes that impact D. piger fitness; the latter includes high- and low-affinity systems for using ammonia, a limiting resource for D. piger in mice consuming a polysaccharide-rich diet. Although genes involved in hydrogen consumption and sulfate reduction are necessary for its colonization, varying dietary-free sulfate levels did not significantly alter levels of D. piger, which can obtain sulfate from the host in part via cross-feeding mediated by Bacteroides-encoded sulfatases. Chondroitin sulfate, a common dietary supplement, increased D. piger and H2S levels without compromising gut barrier integrity. A chondroitin sulfate-supplemented diet together with D. piger impacted the assemblage's substrate utilization preferences, allowing consumption of more reduced carbon sources and increasing the abundance of the H2-producing Actinobacterium, Collinsella aerofaciens. Our findings provide genetic and metabolic details of how this H2-consuming SRB shapes the responses of a microbiota to diet ingredients and a framework for examining how individuals lacking D. piger differ from those who harbor it.
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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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Nonaka K, Nguyen NT, Yoon KS, Ogo S. Novel H2-oxidizing [NiFeSe]hydrogenase from Desulfovibrio vulgaris Miyazaki F. J Biosci Bioeng 2013. [DOI: 10.1016/j.jbiosc.2012.10.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J Bacteriol 2012; 195:990-1004. [PMID: 23264581 DOI: 10.1128/jb.01959-12] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mineralization of organic matter in anoxic environments relies on the cooperative activities of hydrogen producers and consumers linked by interspecies electron transfer in syntrophic consortia that may include sulfate-reducing species (e.g., Desulfovibrio). Physiological differences and various gene repertoires implicated in syntrophic metabolism among Desulfovibrio species suggest considerable variation in the biochemical basis of syntrophy. In this study, comparative transcriptional and mutant analyses of Desulfovibrio alaskensis strain G20 and Desulfovibrio vulgaris strain Hildenborough growing syntrophically with Methanococcus maripaludis on lactate were used to develop new and revised models for their alternative electron transfer and energy conservation systems. Lactate oxidation by strain G20 generates a reduced thiol-disulfide redox pair(s) and ferredoxin that are energetically coupled to H(+)/CO(2) reduction by periplasmic formate dehydrogenase and hydrogenase via a flavin-based reverse electron bifurcation process (electron confurcation) and a menaquinone (MQ) redox loop-mediated reverse electron flow involving the membrane-bound Qmo and Qrc complexes. In contrast, strain Hildenborough uses a larger number of cytoplasmic and periplasmic proteins linked in three intertwining pathways to couple H(+) reduction to lactate oxidation. The faster growth of strain G20 in coculture is associated with a kinetic advantage conferred by the Qmo-MQ-Qrc loop as an electron transfer system that permits higher lactate oxidation rates under elevated hydrogen levels (thereby enhancing methanogenic growth) and use of formate as the main electron-exchange mediator (>70% electron flux), as opposed to the primarily hydrogen-based exchange by strain Hildenborough. This study further demonstrates the absence of a conserved gene core in Desulfovibrio that would determine the ability for a syntrophic lifestyle.
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Walian PJ, Allen S, Shatsky M, Zeng L, Szakal ED, Liu H, Hall SC, Fisher SJ, Lam BR, Singer ME, Geller JT, Brenner SE, Chandonia JM, Hazen TC, Witkowska HE, Biggin MD, Jap BK. High-throughput isolation and characterization of untagged membrane protein complexes: outer membrane complexes of Desulfovibrio vulgaris. J Proteome Res 2012; 11:5720-35. [PMID: 23098413 PMCID: PMC3516867 DOI: 10.1021/pr300548d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Cell membranes represent the “front line”
of cellular defense and the interface between a cell and its environment.
To determine the range of proteins and protein complexes that are
present in the cell membranes of a target organism, we have utilized
a “tagless” process for the system-wide isolation and
identification of native membrane protein complexes. As an initial
subject for study, we have chosen the Gram-negative sulfate-reducing
bacterium Desulfovibrio vulgaris. With this tagless
methodology, we have identified about two-thirds of the outer membrane-
associated proteins anticipated. Approximately three-fourths of these
appear to form homomeric complexes. Statistical and machine-learning
methods used to analyze data compiled over multiple experiments revealed
networks of additional protein–protein interactions providing
insight into heteromeric contacts made between proteins across this
region of the cell. Taken together, these results establish a D. vulgaris outer membrane protein data set that will be
essential for the detection and characterization of environment-driven
changes in the outer membrane proteome and in the modeling of stress
response pathways. The workflow utilized here should be effective
for the global characterization of membrane protein complexes in a
wide range of organisms.
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Affiliation(s)
- Peter J Walian
- Lawrence Berkeley National Laboratory, Berkeley, California, United States.
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Grein F, Ramos AR, Venceslau SS, Pereira IAC. Unifying concepts in anaerobic respiration: insights from dissimilatory sulfur metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1827:145-60. [PMID: 22982583 DOI: 10.1016/j.bbabio.2012.09.001] [Citation(s) in RCA: 125] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 10/27/2022]
Abstract
Behind the versatile nature of prokaryotic energy metabolism is a set of redox proteins having a highly modular character. It has become increasingly recognized that a limited number of redox modules or building blocks appear grouped in different arrangements, giving rise to different proteins and functionalities. This modularity most likely reveals a common and ancient origin for these redox modules, and is obviously reflected in similar energy conservation mechanisms. The dissimilation of sulfur compounds was probably one of the earliest biological strategies used by primitive organisms to obtain energy. Here, we review some of the redox proteins involved in dissimilatory sulfur metabolism, focusing on sulfate reducing organisms, and highlight links between these proteins and others involved in different processes of anaerobic respiration. Noteworthy are links to the complex iron-sulfur molybdoenzyme family, and heterodisulfide reductases of methanogenic archaea. We discuss how chemiosmotic and electron bifurcation/confurcation may be involved in energy conservation during sulfate reduction, and how introduction of an additional module, multiheme cytochromes c, opens an alternative bioenergetic strategy that seems to increase metabolic versatility. Finally, we highlight new families of heterodisulfide reductase-related proteins from non-methanogenic organisms, which indicate a widespread distribution for these protein modules and may indicate a more general involvement of thiol/disulfide conversions in energy metabolism. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.
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Affiliation(s)
- Fabian Grein
- Instituto de Tecnologia Quimica e Biologica, Universidade Nova de Lisboa, Oeiras, Portugal
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Metaproteomics of a gutless marine worm and its symbiotic microbial community reveal unusual pathways for carbon and energy use. Proc Natl Acad Sci U S A 2012; 109:E1173-82. [PMID: 22517752 DOI: 10.1073/pnas.1121198109] [Citation(s) in RCA: 150] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Low nutrient and energy availability has led to the evolution of numerous strategies for overcoming these limitations, of which symbiotic associations represent a key mechanism. Particularly striking are the associations between chemosynthetic bacteria and marine animals that thrive in nutrient-poor environments such as the deep sea because the symbionts allow their hosts to grow on inorganic energy and carbon sources such as sulfide and CO(2). Remarkably little is known about the physiological strategies that enable chemosynthetic symbioses to colonize oligotrophic environments. In this study, we used metaproteomics and metabolomics to investigate the intricate network of metabolic interactions in the chemosynthetic association between Olavius algarvensis, a gutless marine worm, and its bacterial symbionts. We propose previously undescribed pathways for coping with energy and nutrient limitation, some of which may be widespread in both free-living and symbiotic bacteria. These pathways include (i) a pathway for symbiont assimilation of the host waste products acetate, propionate, succinate and malate; (ii) the potential use of carbon monoxide as an energy source, a substrate previously not known to play a role in marine invertebrate symbioses; (iii) the potential use of hydrogen as an energy source; (iv) the strong expression of high-affinity uptake transporters; and (v) as yet undescribed energy-efficient steps in CO(2) fixation and sulfate reduction. The high expression of proteins involved in pathways for energy and carbon uptake and conservation in the O. algarvensis symbiosis indicates that the oligotrophic nature of its environment exerted a strong selective pressure in shaping these associations.
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47
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Oxygen exposure increases resistance of Desulfovibrio vulgaris Hildenborough to killing by hydrogen peroxide. Antonie van Leeuwenhoek 2011; 101:303-11. [DOI: 10.1007/s10482-011-9634-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 08/22/2011] [Indexed: 11/30/2022]
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Li X, McInerney MJ, Stahl DA, Krumholz LR. Metabolism of H2 by Desulfovibrio alaskensis G20 during syntrophic growth on lactate. MICROBIOLOGY-SGM 2011; 157:2912-2921. [PMID: 21798981 DOI: 10.1099/mic.0.051284-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Syntrophic growth involves the oxidation of organic compounds and subsequent transfer of electrons to an H(2)- or formate-consuming micro-organism. In order to identify genes involved specifically in syntrophic growth, a mutant library of Desulfovibrio alaskensis G20 was screened for loss of the ability to grow syntrophically with Methanospirillum hungatei JF-1. A collection of 20 mutants with an impaired ability to grow syntrophically was obtained. All 20 mutants grew in pure culture on lactate under sulfidogenic conditions at a rate and to a maximum OD(600) similar to those of the parental strain. The largest number of mutations that affected syntrophic growth with lactate was in genes encoding proteins involved in H(2) oxidation, electron transfer, hydrogenase post-translational modification, pyruvate degradation and signal transduction. The qrcB gene, encoding a quinone reductase complex (Qrc), and cycA, encoding the periplasmic tetrahaem cytochrome c(3) (TpIc(3)), were required by G20 to grow syntrophically with lactate. A mutant in the hydA gene, encoding an Fe-only hydrogenase (Hyd), is also impaired in syntrophic growth with lactate. The other mutants grew more slowly than the parental strain in syntrophic culture with M. hungatei JF-1. qrcB and cycA were shown previously to be required for growth of G20 pure cultures with H(2) and sulfate. Washed cells of the parental strain produced H(2) from either lactate or pyruvate, but washed cells of qrcB, cycA and hydA mutants produced H(2) at rates similar to the parental strain from pyruvate and did not produce significant amounts of H(2) from lactate. Real-time quantitative PCR assays showed increases in expression of the above three genes during syntrophic growth compared with pure-culture growth with lactate and sulfate. Our work shows that Hyd, Qrc and TpIc(3) are involved in H(2) production during syntrophic lactate metabolism by D. alaskensis G20 and emphasizes the importance of H(2) production for syntrophic lactate metabolism in this strain.
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Affiliation(s)
- Xiangzhen Li
- Department of Botany and Microbiology, The University of Oklahoma, Norman, OK 73019, USA
| | - Michael J McInerney
- Department of Botany and Microbiology, The University of Oklahoma, Norman, OK 73019, USA
| | - David A Stahl
- Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195, USA
| | - Lee R Krumholz
- Institute for Energy and the Environment, The University of Oklahoma, Norman, OK 73019, USA.,Department of Botany and Microbiology, The University of Oklahoma, Norman, OK 73019, USA
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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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50
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Pereira IAC, Ramos AR, Grein F, Marques MC, da Silva SM, Venceslau SS. A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol 2011; 2:69. [PMID: 21747791 PMCID: PMC3119410 DOI: 10.3389/fmicb.2011.00069] [Citation(s) in RCA: 215] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/25/2011] [Indexed: 11/13/2022] Open
Abstract
The number of sequenced genomes of sulfate reducing organisms (SRO) has increased significantly in the recent years, providing an opportunity for a broader perspective into their energy metabolism. In this work we carried out a comparative survey of energy metabolism genes found in 25 available genomes of SRO. This analysis revealed a higher diversity of possible energy conserving pathways than classically considered to be present in these organisms, and permitted the identification of new proteins not known to be present in this group. The Deltaproteobacteria (and Thermodesulfovibrio yellowstonii) are characterized by a large number of cytochromes c and cytochrome c-associated membrane redox complexes, indicating that periplasmic electron transfer pathways are important in these bacteria. The Archaea and Clostridia groups contain practically no cytochromes c or associated membrane complexes. However, despite the absence of a periplasmic space, a few extracytoplasmic membrane redox proteins were detected in the Gram-positive bacteria. Several ion-translocating complexes were detected in SRO including H(+)-pyrophosphatases, complex I homologs, Rnf, and Ech/Coo hydrogenases. Furthermore, we found evidence that cytoplasmic electron bifurcating mechanisms, recently described for other anaerobes, are also likely to play an important role in energy metabolism of SRO. A number of cytoplasmic [NiFe] and [FeFe] hydrogenases, formate dehydrogenases, and heterodisulfide reductase-related proteins are likely candidates to be involved in energy coupling through electron bifurcation, from diverse electron donors such as H(2), formate, pyruvate, NAD(P)H, β-oxidation, and others. In conclusion, this analysis indicates that energy metabolism of SRO is far more versatile than previously considered, and that both chemiosmotic and flavin-based electron bifurcating mechanisms provide alternative strategies for energy conservation.
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Affiliation(s)
- Inês A Cardoso Pereira
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa Oeiras, Portugal
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