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Marbehan X, Roger M, Fournier F, Infossi P, Guedon E, Delecourt L, Lebrun R, Giudici-Orticoni MT, Delaunay S. Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough. Front Microbiol 2024; 15:1336360. [PMID: 38463485 PMCID: PMC10920352 DOI: 10.3389/fmicb.2024.1336360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/24/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction Desulfovibrio vulgaris Hildenborough is a gram-negative anaerobic bacterium belonging to the sulfate-reducing bacteria that exhibits highly versatile metabolism. By switching from one energy mode to another depending on nutrients availability in the environments" it plays a central role in shaping ecosystems. Despite intensive efforts to study D. vulgaris energy metabolism at the genomic, biochemical and ecological level, bioenergetics in this microorganism remain far from being fully understood. Alternatively, metabolic modeling is a powerful tool to understand bioenergetics. However, all the current models for D. vulgaris appeared to be not easily adaptable to various environmental conditions. Methods To lift off these limitations, here we constructed a novel transparent and robust metabolic model to explain D. vulgaris bioenergetics by combining whole-cell proteomic analysis with modeling approaches (Flux Balance Analysis). Results The iDvu71 model showed over 0.95 correlation with experimental data. Further simulations allowed a detailed description of D. vulgaris metabolism in various conditions of growth. Altogether, the simulations run in this study highlighted the sulfate-to-lactate consumption ratio as a pivotal factor in D. vulgaris energy metabolism. Discussion In particular, the impact on the hydrogen/formate balance and biomass synthesis is discussed. Overall, this study provides a novel insight into D. vulgaris metabolic flexibility.
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Affiliation(s)
| | - Magali Roger
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Pascale Infossi
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
| | | | - Louis Delecourt
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
- LISM-UMR 7255, Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Aix-Marseille Université, CNRS, Marseille, France
| | - Régine Lebrun
- IMM-FR3479, Marseille Protéomique, Aix-Marseille Université, CNRS, Marseille, France
| | - Marie-Thérèse Giudici-Orticoni
- BIP-UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, Aix-Marseille Université, CNRS, Marseille, France
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Bährle R, Böhnke S, Englhard J, Bachmann J, Perner M. Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications. BIORESOUR BIOPROCESS 2023; 10:84. [PMID: 38647803 PMCID: PMC10992861 DOI: 10.1186/s40643-023-00705-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/16/2023] [Indexed: 04/25/2024] Open
Abstract
Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.
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Affiliation(s)
- Rebecca Bährle
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Stefanie Böhnke
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany
| | - Jonas Englhard
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Julien Bachmann
- Chemistry of Thin Film Materials, IZNF, Friedrich-Alexander-Universität Erlangen-Nürnberg, Cauerstr. 3, 91058, Erlangen, Germany
| | - Mirjam Perner
- Department of Marine Geomicrobiology, Faculty of Marine Biogeochemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Wischhofstr. 1-3, 24148, Kiel, Germany.
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3
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Wynne JJ, Titus TN, Agha‐Mohammadi A, Azua‐Bustos A, Boston PJ, de León P, Demirel‐Floyd C, De Waele J, Jones H, Malaska MJ, Miller AZ, Sapers HM, Sauro F, Sonderegger DL, Uckert K, Wong UY, Alexander EC, Chiao L, Cushing GE, DeDecker J, Fairén AG, Frumkin A, Harris GL, Kearney ML, Kerber L, Léveillé RJ, Manyapu K, Massironi M, Mylroie JE, Onac BP, Parazynski SE, Phillips‐Lander CM, Prettyman TH, Schulze‐Makuch D, Wagner RV, Whittaker WL, Williams KE. Fundamental Science and Engineering Questions in Planetary Cave Exploration. JOURNAL OF GEOPHYSICAL RESEARCH. PLANETS 2022; 127:e2022JE007194. [PMID: 36582809 PMCID: PMC9787064 DOI: 10.1029/2022je007194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 06/17/2023]
Abstract
Nearly half a century ago, two papers postulated the likelihood of lunar lava tube caves using mathematical models. Today, armed with an array of orbiting and fly-by satellites and survey instrumentation, we have now acquired cave data across our solar system-including the identification of potential cave entrances on the Moon, Mars, and at least nine other planetary bodies. These discoveries gave rise to the study of planetary caves. To help advance this field, we leveraged the expertise of an interdisciplinary group to identify a strategy to explore caves beyond Earth. Focusing primarily on astrobiology, the cave environment, geology, robotics, instrumentation, and human exploration, our goal was to produce a framework to guide this subdiscipline through at least the next decade. To do this, we first assembled a list of 198 science and engineering questions. Then, through a series of social surveys, 114 scientists and engineers winnowed down the list to the top 53 highest priority questions. This exercise resulted in identifying emerging and crucial research areas that require robust development to ultimately support a robotic mission to a planetary cave-principally the Moon and/or Mars. With the necessary financial investment and institutional support, the research and technological development required to achieve these necessary advancements over the next decade are attainable. Subsequently, we will be positioned to robotically examine lunar caves and search for evidence of life within Martian caves; in turn, this will set the stage for human exploration and potential habitation of both the lunar and Martian subsurface.
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Affiliation(s)
- J. Judson Wynne
- Department of Biological Sciences and Center for Adaptable Western LandscapesNorthern Arizona UniversityFlagstaffAZUSA
| | | | | | - Armando Azua‐Bustos
- Centro de AstrobiologíaCSIC‐INTAUnidad María de MaeztuInstituto Nacional de Técnica Aeroespacial Ctra de Torrejón a AjalvirMadridSpain
- Instituto de Ciencias BiomédicasFacultad de Ciencias de la SaludUniversidad Autónoma de ChileSantiagoChile
| | | | - Pablo de León
- Human Spaceflight LaboratoryDepartment of Space StudiesUniversity of North DakotaGrand ForksNDUSA
| | | | - Jo De Waele
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Heather Jones
- Robotics InstituteCarnegie Mellon UniversityPittsburghPAUSA
| | - Michael J. Malaska
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Ana Z. Miller
- Laboratório HERCULESUniversity of ÉvoraÉvoraPortugal
- Instituto de Recursos Naturales y AgrobiologíaConsejo Superior de Investigaciones CientíficasSevilleSpain
| | - Haley M. Sapers
- Department of Earth and Space Science and EngineeringYork UniversityTorontoONCanada
| | - Francesco Sauro
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Derek L. Sonderegger
- Department of Mathematics and StatisticsNorthern Arizona UniversityFlagstaffAZUSA
| | - Kyle Uckert
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | | | - E. Calvin Alexander
- Earth and Environmental Sciences DepartmentUniversity of MinnesotaMinneapolisMNUSA
| | - Leroy Chiao
- Department of Mechanical EngineeringRice UniversityHoustonTXUSA
| | - Glen E. Cushing
- U.S. Geological SurveyAstrogeology Science CenterFlagstaffAZUSA
| | - John DeDecker
- Center for Mineral Resources ScienceColorado School of MinesGoldenCOUSA
| | - Alberto G. Fairén
- Centro de AstrobiologíaCSIC‐INTAUnidad María de MaeztuInstituto Nacional de Técnica Aeroespacial Ctra de Torrejón a AjalvirMadridSpain
- Department of AstronomyCornell UniversityIthacaNYUSA
| | - Amos Frumkin
- Institute of Earth SciencesThe Hebrew UniversityJerusalemIsrael
| | - Gary L. Harris
- Human Spaceflight LaboratoryDepartment of Space StudiesUniversity of North DakotaGrand ForksNDUSA
| | - Michelle L. Kearney
- Department of Astronomy and Planetary SciencesNorthern Arizona UniversityFlagstaffAZUSA
| | - Laura Kerber
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Richard J. Léveillé
- Department of Earth and Planetary SciencesMcGill UniversityMontrealQCCanada
- Geosciences DepartmentJohn Abbott CollegeSte‐Anne‐de‐BellevueQCCanada
| | | | - Matteo Massironi
- Dipartimento di GeoscienzeUniversità degli Studi di PadovaPadovaItaly
| | - John E. Mylroie
- Department of GeosciencesMississippi State UniversityStarkvilleMSUSA
| | - Bogdan P. Onac
- School of GeosciencesUniversity of South FloridaTampaFLUSA
- Emil G. Racoviță InstituteBabeș‐Bolyai UniversityCluj‐NapocaRomania
| | | | | | | | - Dirk Schulze‐Makuch
- Astrobiology GroupCenter of Astronomy and AstrophysicsTechnische Universität BerlinBerlinGermany
- Section GeomicrobiologyGFZ German Research Centre for GeosciencesPotsdamGermany
- Department of Experimental LimnologyLeibniz‐Institute of Freshwater Ecology and Inland Fisheries (IGB)StechlinGermany
| | - Robert V. Wagner
- School of Earth and Space ExplorationArizona State UniversityTempeAZUSA
| | - William L. Whittaker
- Department of Biological, Geological and Environmental SciencesUniversity of BolognaBolognaItaly
| | - Kaj E. Williams
- U.S. Geological SurveyAstrogeology Science CenterFlagstaffAZUSA
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Park MJ, Kim YJ, Park M, Yu J, Namirimu T, Roh YR, Kwon KK. Establishment of Genome Based Criteria for Classification of the Family Desulfovibrionaceae and Proposal of Two Novel Genera, Alkalidesulfovibrio gen. nov. and Salidesulfovibrio gen. nov. Front Microbiol 2022; 13:738205. [PMID: 35694308 PMCID: PMC9174804 DOI: 10.3389/fmicb.2022.738205] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
Bacteria in the Desulfovibrionaceae family, which contribute to S element turnover as sulfate-reducing bacteria (SRB) and disproportionation of partially oxidized sulfoxy anions, have been extensively investigated since the importance of the sulfur cycle emerged. Novel species belonging to this taxon are frequently reported, because they exist in various environments and are easy to culture using established methods. Due to the rapid expansion of the taxon, correction and reclassification have been conducted. The development of high-throughput sequencing facilitated rapid expansion of genome sequence database. Genome-based criteria, based on these databases, proved to be potential classification standard by overcoming the limitations of 16S rRNA-based phylogeny. Although standards methods for taxogenomics are being established, the addition of a novel genus requires extensive calculations with taxa, including many species, such as Desulfovibrionaceae. Thus, the genome-based criteria for classification of Desulfovibrionaceae were established and validated in this study. The average amino-acid identity (AAI) cut-off value, 63.43 ± 0.01, was calculated to be an appropriate criterion for genus delineation of the family Desulfovibrionaceae. By applying the AAI cut-off value, 88 genomes of the Desulfovibrionaceae were divided into 27 genera, which follows the core gene phylogeny results. In this process, two novel genera (Alkalidesulfovibrio and Salidesulfovibrio) and one former invalid genus (“Psychrodesulfovibrio”) were officially proposed. Further, by applying the 95–96% average nucleotide identity (ANI) standard and the 70% digital DNA–DNA hybridization standard values for species delineation of strains that were classified as the same species, five strains have the potential to be newly classified. After verifying that the classification was appropriately performed through relative synonymous codon usage analysis, common characteristics were listed by group. In addition, by detecting metal resistance related genes via in silico analysis, it was confirmed that most strains display metal tolerance.
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Affiliation(s)
- Mi-Jeong Park
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yun Jae Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
| | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Jihyun Yu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Teddy Namirimu
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Yoo-Rim Roh
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
| | - Kae Kyoung Kwon
- Marine Biotechnology Research Center, Korea Institute of Ocean Science & Technology, Busan, South Korea
- Department of Applied Ocean Science, University of Science and Technology, Daejeon, South Korea
- *Correspondence: Kae Kyoung Kwon,
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5
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Stegenta-Dąbrowska S, Randerson PF, Białowiec A. Aerobic Biostabilization of the Organic Fraction of Municipal Solid Waste-Monitoring Hot and Cold Spots in the Reactor as a Novel Tool for Process Optimization. MATERIALS 2022; 15:ma15093300. [PMID: 35591634 PMCID: PMC9104568 DOI: 10.3390/ma15093300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/30/2022] [Accepted: 05/02/2022] [Indexed: 12/04/2022]
Abstract
The process of aerobic biostabilization (AB) has been adopted for treatment of the organic fraction of municipal solid waste (OFMSW). However, thermal gradients and some side effects in the bioreactors present difficulties in optimization of AB. Forced aeration is more effective than natural ventilation of waste piles, but “hot and cold spots” exist due to inhomogeneous distribution of air and heat. This study identified the occurrence of hot and cold spots during the OFMSW biostabilization process at full technical scale. It was shown that the number of hot and cold spots depended on the size of the pile and aeration rate. When the mass of stabilized waste was significantly lower and the aeration rate was two-fold higher the number of anaerobic hot spots decreased, while cold spots increased. In addition, the results indicated that pile construction with sidewalls decreased the number of hot spots. However, channelizing the airflow under similar conditions increased the number of cold spots. Knowledge of the spatial and temporal distribution of process gases can enable optimization and adoption of the OFMSW flow aeration regime. Temperature monitoring within the waste pile enables the operator to eliminate undesirable “hot spots” by modifying the aeration regime and hence improve the overall treatment efficiency.
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Affiliation(s)
- Sylwia Stegenta-Dąbrowska
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, 37a, Chełmońskiego Str., 51-630 Wrocław, Poland;
| | - Peter F. Randerson
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK;
| | - Andrzej Białowiec
- Department of Applied Bioeconomy, Wrocław University of Environmental and Life Sciences, 37a, Chełmońskiego Str., 51-630 Wrocław, Poland;
- Correspondence:
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Tripathi AK, Thakur P, Saxena P, Rauniyar S, Gopalakrishnan V, Singh RN, Gadhamshetty V, Gnimpieba EZ, Jasthi BK, Sani RK. Gene Sets and Mechanisms of Sulfate-Reducing Bacteria Biofilm Formation and Quorum Sensing With Impact on Corrosion. Front Microbiol 2021; 12:754140. [PMID: 34777309 PMCID: PMC8586430 DOI: 10.3389/fmicb.2021.754140] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/24/2021] [Indexed: 01/02/2023] Open
Abstract
Sulfate-reducing bacteria (SRB) have a unique ability to respire under anaerobic conditions using sulfate as a terminal electron acceptor, reducing it to hydrogen sulfide. SRB thrives in many natural environments (freshwater sediments and salty marshes), deep subsurface environments (oil wells and hydrothermal vents), and processing facilities in an industrial setting. Owing to their ability to alter the physicochemical properties of underlying metals, SRB can induce fouling, corrosion, and pipeline clogging challenges. Indigenous SRB causes oil souring and associated product loss and, subsequently, the abandonment of impacted oil wells. The sessile cells in biofilms are 1,000 times more resistant to biocides and induce 100-fold greater corrosion than their planktonic counterparts. To effectively combat the challenges posed by SRB, it is essential to understand their molecular mechanisms of biofilm formation and corrosion. Here, we examine the critical genes involved in biofilm formation and microbiologically influenced corrosion and categorize them into various functional categories. The current effort also discusses chemical and biological methods for controlling the SRB biofilms. Finally, we highlight the importance of surface engineering approaches for controlling biofilm formation on underlying metal surfaces.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkataramana Gadhamshetty
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Civil and Environmental Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Etienne Z Gnimpieba
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Biomedical Engineering Program, University of South Dakota, Sioux Falls, SD, United States
| | - Bharat K Jasthi
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Department of Materials and Metallurgical Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States.,2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD, United States.,BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD, United States.,Composite and Nanocomposite Advanced Manufacturing Centre-Biomaterials, Rapid City, SD, United States
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7
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Kuroda K, Narihiro T, Nobu MK, Tobo A, Yamauchi M, Yamada M. Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater. Microbes Environ 2021; 36. [PMID: 34588388 PMCID: PMC8674449 DOI: 10.1264/jsme2.me21045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.
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Affiliation(s)
- Kyohei Kuroda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Takashi Narihiro
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Masaru K Nobu
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Atsushi Tobo
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masahito Yamauchi
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
| | - Masayoshi Yamada
- Department of Urban Environmental Design and Engineering, National Institute of Technology, Kagoshima College
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Tang WT, Hao TW, Chen GH. Comparative metabolic modeling of multiple sulfate-reducing prokaryotes reveals versatile energy conservation mechanisms. Biotechnol Bioeng 2021; 118:2676-2693. [PMID: 33844295 DOI: 10.1002/bit.27787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/21/2021] [Accepted: 03/11/2021] [Indexed: 11/07/2022]
Abstract
Sulfate-reducing prokaryotes (SRPs) are crucial participants in the cycling of sulfur, carbon, and various metals in the natural environment and in engineered systems. Despite recent advances in genetics and molecular biology bringing a huge amount of information about the energy metabolism of SRPs, little effort has been made to link this important information with their biotechnological studies. This study aims to construct multiple metabolic models of SRPs that systematically compile genomic, genetic, biochemical, and molecular information about SRPs to study their energy metabolism. Pan-genome analysis was conducted to compare the genomes of SRPs, from which a list of orthologous genes related to central and energy metabolism was obtained. Twenty-four SRP metabolic models via the inference of pan-genome analysis were efficiently constructed. The metabolic model of the well-studied model SRP Desulfovibrio vulgaris Hildenborough (DvH) was validated via flux balance analysis (FBA). The DvH model predictions matched reported experimental growth and energy yields, which demonstrated that the core metabolic model worked successfully. Further, steady-state simulation of SRP metabolic models under different growth conditions showed how the use of different electron transfer pathways leads to energy generation. Three energy conservation mechanisms were identified, including menaquinone-based redox loop, hydrogen cycling, and proton pumping. Flavin-based electron bifurcation (FBEB) was also demonstrated to be an essential mechanism for supporting energy conservation. The developed models can be easily extended to other species of SRPs not examined in this study. More importantly, the present work develops an accurate and efficient approach for constructing metabolic models of multiple organisms, which can be applied to other critical microbes in environmental and industrial systems, thereby enabling the quantitative prediction of their metabolic behaviors to benefit relevant applications.
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Affiliation(s)
- Wen-Tao Tang
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tian-Wei Hao
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,Department of Civil and Environmental Engineering, Faculty of Science and Technology, University of Macau, Macau, China
| | - Guang-Hao Chen
- Department of Civil and Environmental Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
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9
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Picard A, Gartman A, Girguis PR. Interactions Between Iron Sulfide Minerals and Organic Carbon: Implications for Biosignature Preservation and Detection. ASTROBIOLOGY 2021; 21:587-604. [PMID: 33780638 DOI: 10.1089/ast.2020.2276] [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] [Indexed: 06/12/2023]
Abstract
Microbe-mineral interactions can produce unique composite materials, which can preserve biosignatures. Geological evidence suggests that iron sulfide (Fe-S) minerals are abundant in the subsurface of Mars. On Earth, the formation of Fe-S minerals is driven by sulfate-reducing microorganisms (SRM) that produce reactive sulfide. Moreover, SRM metabolites, as well as intact cells, can influence the morphology, particle size, aggregation, and composition of biogenic Fe-S minerals. In this work, we evaluated how simple and complex organic molecules-hexoses and amino acid/peptide mixtures, respectively-influence the formation of Fe-S minerals (simulated prebiotic conditions), and whether the observed patterns mimic the biological influence of SRM. To this end, organo-mineral aggregates were characterized with X-ray diffraction, scanning electron microscopy, and scanning transmission X-ray microscopy coupled to near-edge X-ray absorption fine structure spectroscopy. Overall, Fe-S minerals were found to have a strong affinity for proteinaceous organic matter. Fe-S minerals precipitated at simulated prebiotic conditions yielded organic carbon distributions that were more homogeneous than treatments with whole SRM cells. In prebiotic experiments, spectroscopy detected potential organic transformations during Fe-S mineral formation, including conversion of hexoses to sugar acids and polymerization of amino acids/peptides into larger peptides/proteins. In addition, prebiotic mineral-carbon assemblages produced nanometer-scaled filamentous aggregated morphologies. On the contrary, in biotic treatments with cells, organic carbon in minerals displayed a more heterogeneous distribution. Notably, "hot spots" of organic carbon and oxygen-containing functional groups, with the size, shape, and composition of microbial cells, were preserved in mineral aggregates. We propose a list of characteristics that could be used to help distinguish biogenic from prebiotic/abiotic Fe-S minerals and help refine the search of extant or extinct microbial life in the martian subsurface.
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Affiliation(s)
- Aude Picard
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, Nevada, USA
| | - Amy Gartman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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Hopper CP, De La Cruz LK, Lyles KV, Wareham LK, Gilbert JA, Eichenbaum Z, Magierowski M, Poole RK, Wollborn J, Wang B. Role of Carbon Monoxide in Host-Gut Microbiome Communication. Chem Rev 2020; 120:13273-13311. [PMID: 33089988 DOI: 10.1021/acs.chemrev.0c00586] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nature is full of examples of symbiotic relationships. The critical symbiotic relation between host and mutualistic bacteria is attracting increasing attention to the degree that the gut microbiome is proposed by some as a new organ system. The microbiome exerts its systemic effect through a diverse range of metabolites, which include gaseous molecules such as H2, CO2, NH3, CH4, NO, H2S, and CO. In turn, the human host can influence the microbiome through these gaseous molecules as well in a reciprocal manner. Among these gaseous molecules, NO, H2S, and CO occupy a special place because of their widely known physiological functions in the host and their overlap and similarity in both targets and functions. The roles that NO and H2S play have been extensively examined by others. Herein, the roles of CO in host-gut microbiome communication are examined through a discussion of (1) host production and function of CO, (2) available CO donors as research tools, (3) CO production from diet and bacterial sources, (4) effect of CO on bacteria including CO sensing, and (5) gut microbiome production of CO. There is a large amount of literature suggesting the "messenger" role of CO in host-gut microbiome communication. However, much more work is needed to begin achieving a systematic understanding of this issue.
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Affiliation(s)
- Christopher P Hopper
- Institute for Experimental Biomedicine, University Hospital Wuerzburg, Wuerzburg, Bavaria DE 97080, Germany.,Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, Florida 32611, United States
| | - Ladie Kimberly De La Cruz
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kristin V Lyles
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lauren K Wareham
- The Vanderbilt Eye Institute and Department of Ophthalmology & Visual Sciences, The Vanderbilt University Medical Center and School of Medicine, Nashville, Tennessee 37232, United States
| | - Jack A Gilbert
- Department of Pediatrics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Zehava Eichenbaum
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Marcin Magierowski
- Cellular Engineering and Isotope Diagnostics Laboratory, Department of Physiology, Jagiellonian University Medical College, Cracow PL 31-531, Poland
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Sheffield S10 2TN, U.K
| | - Jakob Wollborn
- Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg DE 79085, Germany.,Department of Anesthesiology, Perioperative and Pain Management, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Binghe Wang
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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11
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Bachochin MJ, Venegas JC, Singh G, Zhang L, Barber RD. Characterization of a butyrate kinase from Desulfovibrio vulgaris str. Hildenborough. FEMS Microbiol Lett 2020; 367:5804727. [PMID: 32166312 DOI: 10.1093/femsle/fnaa047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/10/2020] [Indexed: 11/13/2022] Open
Abstract
Short and branched chain fatty acid kinases participate in both bacterial anabolic and catabolic processes, including fermentation, through the reversible, ATP-dependent synthesis of acyl phosphates. This study reports biochemical properties of a predicted butyrate kinase from Desulfovibrio vulgaris str. Hildenborough (DvBuk) expressed heterologously and purified from Escherichia coli. Gel filtration chromatography indicates purified DvBuk is active as a dimer. The optimum temperature and pH for DvBuk activity is 44°C and 7.5, respectively. The enzyme displays enhanced thermal stability in the presence of substrates as observed for similar enzymes. Measurement of kcat and KM for various substrates reveals DvBuk exhibits the highest catalytic efficiencies for butyrate, valerate and isobutyrate. In particular, these measurements reveal this enzyme's apparent high affinity for C4 fatty acids relative to other butyrate kinases. These results have implications on structure and function relationships within the ASKHA superfamily of phosphotransferases, particularly regarding the acyl binding pocket, as well as potential physiological roles for this enzyme in Desulfovibrio vulgaris str. Hildenborough.
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Affiliation(s)
- Maxwell J Bachochin
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Jessica Castillo Venegas
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Gundeep Singh
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Liyang Zhang
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
| | - Robert D Barber
- Department of Biological Sciences, College of Natural and Health Sciences, University of Wisconsin-Parkside, Room 355 Greenquist Hall; 900 Wood Rd., Kenosha, WI 53141-2000, USA
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12
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Study on the Effectiveness of Sulfate-Reducing Bacteria Combined with Coal Gangue in Repairing Acid Mine Drainage Containing Fe and Mn. ENERGIES 2020. [DOI: 10.3390/en13040995] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
In view of the characteristics of the high content of SO42−, Fe2+ and Mn2+ in acid mine drainage (AMD) and low pH value, based on adsorption and biological methods, coal gangue was combined with sulfate-reducing bacteria (SRB). On this basis, four dynamic columns, including Column 1 (SRB combined with spontaneous combustion gangue from the Gaode coal mine), Column 2 (SRB combined with spontaneous combustion gangue from Haizhou), Column 3 (SRB combined with gangue from Haizhou), and Column 4 (SRB combined with gangue from Shanxi), were constructed. The efficacy of four columns was compared by the inflow of AMD with different pollution load. Results showed that the repair effect of four columns was: Column 3 > Column 2 > Column 1 > Column 4. In the second stage of the experiment, the repair effect of Column 3 was the best. The average effluent pH value and oxidation reduction potential (ORP) value were 9.09 and –262.83 mV, the highest removal percentages of chemical oxygen demand (COD) and SO42− were 84.41% and 72.73%, and the average removal percentages of Fe2+, Mn2+ were 98.70% and 79.97%, respectively. At the end of the experiment, when deionized water was injected, the fixed effect of AMD in the four columns was stable and no secondary release appeared.
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13
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Zhu L, Gong T, Wood TL, Yamasaki R, Wood TK. σ 54 -Dependent regulator DVU2956 switches Desulfovibrio vulgaris from biofilm formation to planktonic growth and regulates hydrogen sulfide production. Environ Microbiol 2019; 21:3564-3576. [PMID: 31087603 DOI: 10.1111/1462-2920.14679] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/11/2019] [Indexed: 11/30/2022]
Abstract
Microbiologically influenced corrosion causes $100 billion in damage per year, and biofilms formed by sulfate-reducing bacteria (SRB) are the major culprit. However, little is known about the regulation of SRB biofilm formation. Using Desulfovibrio vulgaris as a model SRB organism, we compared the transcriptomes of biofilm and planktonic cells and identified that the gene for σ54 -dependent regulator DVU2956 is repressed in biofilms. Utilizing a novel promoter that is primarily transcribed in biofilms (Pdvu0304 ), we found production of DVU2956 inhibits biofilm formation by 70%. Corroborating this result, deleting dvu2956 increased biofilm formation, and this biofilm phenotype could be complemented. By producing proteins in biofilms from genes controlled by DVU2956 (dvu2960 and dvu2962), biofilm formation was inhibited almost completely. A second round of RNA-seq for the production of DVU2956 revealed DVU2956 influences electron transport via an Hmc complex (high-molecular-weight cytochrome c encoded by dvu0531-dvu0536) and the Fe-only hydrogenase (encoded by dvu1769, hydA and dvu1770, hydB) to control H2 S production. Corroborating these results, producing DVU2956 in biofilms decreased H2 S production by half, deleting dvu2956 increased H2 S production by 131 ± 5%, and producing DVU2956 in the dvu2956 strain reduced H2 S production. Therefore, DVU2956 maintains SRB in the planktonic state and reduces H2 S formation.
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Affiliation(s)
- Lei Zhu
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ting Gong
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thammajun L Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Ryota Yamasaki
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Thomas K Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, State College, PA, 16802, USA
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Abstract
Microbial adaptation to extreme conditions takes many forms, including specialized metabolism which may be crucial to survival in adverse conditions. Here, we analyze the diversity and environmental importance of systems allowing microbial carbon monoxide (CO) metabolism. CO is a toxic gas that can poison most organisms because of its tight binding to metalloproteins. Microbial CO uptake was first noted by Kluyver and Schnellen in 1947, and since then many microbes using CO via oxidation have emerged. Many strains use molecular oxygen as the electron acceptor for aerobic oxidation of CO using Mo-containing CO oxidoreductase enzymes named CO dehydrogenase. Anaerobic carboxydotrophs oxidize CO using CooS enzymes that contain Ni/Fe catalytic centers and are unrelated to CO dehydrogenase. Though rare on Earth in free form, CO is an important intermediate compound in anaerobic carbon cycling, as it can be coupled to acetogenesis, methanogenesis, hydrogenogenesis, and metal reduction. Many microbial species—both bacteria and archaea—have been shown to use CO to conserve energy or fix cell carbon or both. Microbial CO formation is also very common. Carboxydotrophs thus glean energy and fix carbon from a “metabolic leftover” that is not consumed by, and is toxic to, most microorganisms. Surprisingly, many species are able to thrive under culture headspaces sometimes exceeding 1 atmosphere of CO. It appears that carboxydotrophs are adapted to provide a metabolic “currency exchange” system in microbial communities in which CO arising either abiotically or biogenically is converted to CO
2 and H
2 that feed major metabolic pathways for energy conservation or carbon fixation. Solventogenic CO metabolism has been exploited to construct very large gas fermentation plants converting CO-rich industrial flue emissions into biofuels and chemical feedstocks, creating renewable energy while mitigating global warming. The use of thermostable CO dehydrogenase enzymes to construct sensitive CO gas sensors is also in progress.
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Affiliation(s)
- Frank T Robb
- Department of Microbiology and Immunology, and Inst of Marine and Environmental Technology, University of Maryland, Baltimore, Baltimore, MD, 21202, USA
| | - Stephen M Techtmann
- Department of Biological Sciences, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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15
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Schoeffler M, Gaudin AL, Ramel F, Valette O, Denis Y, Hania WB, Hirschler-Réa A, Dolla A. Growth of an anaerobic sulfate-reducing bacterium sustained by oxygen respiratory energy conservation after O 2 -driven experimental evolution. Environ Microbiol 2018; 21:360-373. [PMID: 30394641 DOI: 10.1111/1462-2920.14466] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 11/30/2022]
Abstract
Desulfovibrio species are representatives of microorganisms at the boundary between anaerobic and aerobic lifestyles, since they contain the enzymatic systems required for both sulfate and oxygen reduction. However, the latter has been shown to be solely a protective mechanism. By implementing the oxygen-driven experimental evolution of Desulfovibrio vulgaris Hildenborough, we have obtained strains that have evolved to grow with energy derived from oxidative phosphorylation linked to oxygen reduction. We show that a few mutations are sufficient for the emergence of this phenotype and reveal two routes of evolution primarily involving either inactivation or overexpression of the gene encoding heterodisulfide reductase. We propose that the oxygen respiration for energy conservation that sustains the growth of the O2 -evolved strains is associated with a rearrangement of metabolite fluxes, especially NAD+ /NADH, leading to an optimized O2 reduction. These evolved strains are the first sulfate-reducing bacteria that exhibit a demonstrated oxygen respiratory process that enables growth.
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Affiliation(s)
- Marine Schoeffler
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Anne-Laure Gaudin
- Aix Marseille Université, CNRS, LCB, Marseille, France.,GERME SA, Technopôle de Château Gombert, Marseille, France
| | - Fanny Ramel
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Odile Valette
- Aix Marseille Université, CNRS, LCB, Marseille, France
| | - Yann Denis
- Aix Marseille Université, CNRS, IMM, Marseille, France
| | - Wagdi Ben Hania
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Agnès Hirschler-Réa
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Alain Dolla
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
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16
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Kováč J, Vítězová M, Kushkevych I. Metabolic Activity of Sulfate-Reducing Bacteria from Rodents with Colitis. Open Med (Wars) 2018; 13:344-349. [PMID: 30191181 DOI: 10.1515/med-2018-0052] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/26/2018] [Indexed: 12/25/2022] Open
Abstract
Sulfate-reducing bacteria (SRB) are anaerobic microorganisms, which use sulfate as an electron acceptor in the process of dissimilatory sulfate reduction. The final metabolic product of these anaerobic microorganisms is hydrogen sulfide, which is known as toxic and can lead to damage to epithelial cells of the large intestine at high concentrations. Different genera of SRB are detected in the large intestine of healthy human and animals, and with diseases like Crohn's disease and ulcerative colitis. SRB isolated from rodents with ulcerative colitis have produced 1.14 (mice) and 1.03 (rats) times more sulfide ions than healthy rodents. The species of Desulfovibrio genus are the most widespread among all SRB in the intestine. The object of our research was to observe and compare the difference of production of sulfide and reduction of sulfate in intestinal SRB isolated from healthy rodents and rodents with ulcerative colitis.
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Affiliation(s)
- Jozef Kováč
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Monika Vítězová
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
| | - Ivan Kushkevych
- Department of Experimental Biology (Section of Microbiology), Faculty of Science, Masaryk University, Kamenice 753/5, 62500 Brno, Czech Republic
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17
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Li X, Lan SM, Zhu ZP, Zhang C, Zeng GM, Liu YG, Cao WC, Song B, Yang H, Wang SF, Wu SH. The bioenergetics mechanisms and applications of sulfate-reducing bacteria in remediation of pollutants in drainage: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2018; 158:162-170. [PMID: 29684746 DOI: 10.1016/j.ecoenv.2018.04.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/30/2018] [Accepted: 04/12/2018] [Indexed: 06/08/2023]
Abstract
Sulfate-reducing bacteria (SRB), a group of anaerobic prokaryotes, can use sulfur species as a terminal electron acceptor for the oxidation of organic compounds. They not only have significant ecological functions, but also play an important role in bioremediation of contaminated sites. Although numerous studies on metabolism and applications of SRB have been conducted, they still remain incompletely understood and even controversial. Fully understanding the metabolism of SRB paves the way for allowing the microorganisms to provide more beneficial services in bioremediation. Here we review progress in bioenergetics mechanisms and application of SRB including: (1) electron acceptors and donors for SRB; (2) pathway for sulfate reduction; (3) electron transfer in sulfate reduction; (4) application of SRB for economical and concomitant treatment of heavy metal, organic contaminants and sulfates. Moreover, current knowledge gaps and further research needs are identified.
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Affiliation(s)
- Xin Li
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China.
| | - Shi-Ming Lan
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Zhong-Ping Zhu
- School of Minerals processing and Bioengineering, Central South University, No. 932 South Lushan road, Changsha, Hunan 410083, PR China
| | - Chang Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Guang-Ming Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Yun-Guo Liu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Wei-Cheng Cao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Biao Song
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Hong Yang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Sheng-Fan Wang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
| | - Shao-Hua Wu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, PR China; Key Laboratory of Environmental Biology and Pollution Control (Hunan University), Ministry of Education, Changsha 410082, PR China
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18
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Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. ISME JOURNAL 2018; 12:2039-2050. [PMID: 29849169 PMCID: PMC6052044 DOI: 10.1038/s41396-018-0148-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 11/08/2022]
Abstract
Spirochaetes are frequently detected in anoxic hydrocarbon- and organohalide-polluted groundwater, but their role in such ecosystems has remained unclear. To address this, we studied a sulfate-reducing, naphthalene-degrading enrichment culture, mainly comprising the sulfate reducer Desulfobacterium N47 and the rod-shaped Spirochete Rectinema cohabitans HM. Genome sequencing and proteome analysis suggested that the Spirochete is an obligate fermenter that catabolizes proteins and carbohydrates, resulting in acetate, ethanol, and molecular hydrogen (H2) production. Physiological experiments inferred that hydrogen is an important link between the two bacteria in the enrichment culture, with H2 derived from fermentation by R. cohabitans used as reductant for sulfate reduction by Desulfobacterium N47. Differential proteomics and physiological experiments showed that R. cohabitans utilizes biomass (proteins and carbohydrates) released from dead cells of Desulfobacterium N47. Further comparative and community genome analyses indicated that other Rectinema phylotypes are widespread in contaminated environments and may perform a hydrogenogenic fermentative lifestyle similar to R. cohabitans. Together, these findings indicate that environmental Spirochaetes scavenge detrital biomass and in turn drive necromass recycling at anoxic hydrocarbon-contaminated sites and potentially other habitats.
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19
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Pellerin A, Wenk CB, Halevy I, Wing BA. Sulfur Isotope Fractionation by Sulfate-Reducing Microbes Can Reflect Past Physiology. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:4013-4022. [PMID: 29505248 DOI: 10.1021/acs.est.7b05119] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sulfur (S) isotope fractionation by sulfate-reducing microorganisms is a direct manifestation of their respiratory metabolism. This fractionation is apparent in the substrate (sulfate) and waste (sulfide) produced. The sulfate-reducing metabolism responds to variability in the local environment, with the response determined by the underlying genotype, resulting in the expression of an "isotope phenotype". Sulfur isotope phenotypes have been used as a diagnostic tool for the metabolic activity of sulfate-reducing microorganisms in the environment. Our experiments with Desulfovibrio vulgaris Hildenborough (DvH) grown in batch culture suggest that the S isotope phenotype of sulfate respiring microbes may lag environmental changes on time scales that are longer than generational. When inocula from different phases of growth are assayed under the same environmental conditions, we observed that DvH exhibited different net apparent fractionations of up to -9‰. The magnitude of fractionation was weakly correlated with physiological parameters but was strongly correlated to the age of the initial inoculum. The S isotope fractionation observed between sulfate and sulfide showed a positive correlation with respiration rate, contradicting the well-described negative dependence of fractionation on respiration rate. Quantitative modeling of S isotope fractionation shows that either a large increase (≈50×) in the abundance of sulfate adenylyl transferase (Sat) or a smaller increase in sulfate transport proteins (≈2×) is sufficient to account for the change in fractionation associated with past physiology. Temporal transcriptomic studies with DvH imply that expression of sulfate permeases doubles over the transition from early exponential to early stationary phase, lending support to the transport hypothesis proposed here. As it is apparently maintained for multiple generations (≈1-6) of subsequent growth in the assay environment, we suggest that this fractionation effect acts as a sort of isotopic "memory" of a previous physiological and environmental state. Whatever its root cause, this physiological hysteresis effect can explain variations in fractionations observed in many environments. It may also enable new insights into life at energetic limits, especially if its historical footprint extends deeper than generational.
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Affiliation(s)
- André Pellerin
- Center for Geomicrobiology, Department of Bioscience , Aarhus University , Ny Munkegade 114 , Aarhus C 8000 , Denmark
| | - Christine B Wenk
- Department of Earth and Planetary Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Itay Halevy
- Department of Earth and Planetary Sciences , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Boswell A Wing
- Geological Sciences , University of Colorado Boulder , UCB 399, Boulder , Colorado 80309-0399 , United States
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20
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21
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Seo Y, Kang H, Chang S, Lee YY, Cho KS. Effects of nitrate and sulfate on the performance and bacterial community structure of membrane-less single-chamber air-cathode microbial fuel cells. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2018; 53:13-24. [PMID: 29035628 DOI: 10.1080/10934529.2017.1366242] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Membrane-less, single-chamber, air-cathode, microbial fuel cells (ML-SC MFCs) have attracted attention as being suitable for wastewater treatment. In this study, the effects of nitrate and sulfate on the performance of ML-SC MFCs and their bacterial structures were evaluated. The maximum power density increased after nitrate addition from 8.6 mW·m-2 to 14.0 mW·m-2, while it decreased after sulfate addition from 11.5 mW·m-2 to 7.7 mW·m-2. The chemical oxygen demand removal efficiencies remained at more than 90% regardless of the nitrate or sulfate additions. The nitrate was removed completely (93.0%) in the ML-SC MFC, while the sulfate removal efficiency was relatively low (17.6%). Clostridium (23.1%), Petrimonas (20.0%), and unclassified Rhodocyclaceae (6.2%) were dominant on the anode before the addition of nitrate or sulfate. After the addition of nitrate, Clostridium was still the most dominant on the anode (23.6%), but Petrimonas significantly decreased (6.0%) and unclassified Rhodocyclaceae increased (17.1%). After the addition of sulfate, the amount of Clostridium almost doubled in the composition on the anode (43.2%), while Petrimonas decreased (5.5%). The bacterial community on the cathode was similar to that on the anode after the addition of nitrate. However, Desulfovibrio was remarkably dominant on the cathode (32.9%) after the addition of sulfate. These results promote a deeper understanding of the effects of nitrate or sulfate on the ML-SC MFCs' performance and their bacterial community.
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Affiliation(s)
- Yoonjoo Seo
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , Republic of Korea
| | - Hyemin Kang
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , Republic of Korea
| | - Sumin Chang
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , Republic of Korea
| | - Yun-Yeong Lee
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , Republic of Korea
| | - Kyung-Suk Cho
- a Department of Environmental Science and Engineering , Ewha Womans University , Seoul , Republic of Korea
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22
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Zhou C, Zhou Y, Rittmann BE. Reductive precipitation of sulfate and soluble Fe(III) by Desulfovibrio vulgaris: Electron donor regulates intracellular electron flow and nano-FeS crystallization. WATER RESEARCH 2017; 119:91-101. [PMID: 28436827 DOI: 10.1016/j.watres.2017.04.044] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/15/2017] [Accepted: 04/17/2017] [Indexed: 06/07/2023]
Abstract
Fully understanding the metabolism of SRB provides fundamental guidelines for allowing the microorganisms to provide more beneficial services in water treatment and resource recovery. The electron-transfer pathway of sulfate respiration by Desulfovibrio vulgaris is well studied, but still partly unresolved. Here we provide deeper insight by comprehensively monitoring metabolite changes during D. vulgaris metabolism with two electron donors, lactate and pyruvate, in presence or absence of citrate-chelated soluble FeIII as an additional competing electron acceptor. H2 was produced from lactate oxidation to pyruvate, but pyruvate oxidation produced mostly formate. Accumulation of lactate-originated H2 during lag phases inhibited pyruvate transformation to acetate. Sulfate reduction was initiated by lactate-originated H2, but MQ-mediated e- flow initiated sulfate reduction without delay when pyruvate was the donor. When H2-induced electron flow gave priority to FeIII reduction over sulfate reduction, the long lag phase before sulfate reduction shortened the time for iron-sulfide crystallite growth and led to smaller mackinawite (Fe1+xS) nanocrystallites. Synthesizing all the results, we propose that electron flow from lactate or pyruvate towards SO42- reduction to H2S are through at least three routes that are regulated by the e- donor (lactate or pyruvate) and the presence or absence of another e- acceptor (FeIII here). These routes are not competing, but complementary: e.g., H2 or formate production and oxidation were necessary for sulfite and disulfide/trisulfide reduction to sulfide. Our study suggests that the e- donor provides a practical tool to regulate and optimize SRB-predominant bioremediation systems.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA.
| | - Yun Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA; College of Environmental Science and Engineering, Tongji University, China
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
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23
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Amrani A, van Helden J, Bergon A, Aouane A, Ben Hania W, Tamburini C, Loriod B, Imbert J, Ollivier B, Pradel N, Dolla A. Deciphering the adaptation strategies of Desulfovibrio piezophilus to hydrostatic pressure through metabolic and transcriptional analyses. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:520-526. [PMID: 27264199 DOI: 10.1111/1758-2229.12427] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/10/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
Desulfovibrio piezophilus strain C1TLV30(T) is a mesophilic piezophilic sulfate-reducer isolated from Wood Falls at 1700 m depth in the Mediterranean Sea. In this study, we analysed the effect of the hydrostatic pressure on this deep-sea living bacterium at the physiologic and transcriptomic levels. Our results showed that lactate oxidation and energy metabolism were affected by the hydrostatic pressure. Especially, acetyl-CoA oxidation pathway and energy conservation through hydrogen and formate recycling would be more important when the hydrostatic pressure is above (26 MPa) than below (0.1 MPa) the optimal one (10 MPa). This work underlines also the role of the amino acid glutamate as a piezolyte for the Desulfovibrio genus. The transcriptomic analysis revealed 146 differentially expressed genes emphasizing energy production and conversion, amino acid transport and metabolism and cell motility and signal transduction mechanisms as hydrostatic pressure responding processes. This dataset allowed us to identify a sequence motif upstream of a subset of differentially expressed genes as putative pressure-dependent regulatory element.
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Affiliation(s)
- Amira Amrani
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
| | - Jacques van Helden
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Aurélie Bergon
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Aicha Aouane
- Service de Microscopie Electronique, IBDML, Marseille, Cedex 09, 13288, France
| | - Wajdi Ben Hania
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Christian Tamburini
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Béatrice Loriod
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Jean Imbert
- Inserm, U1090; TGML/TAGC, Marseille, F-13009, France
- Aix-Marseille Université, UMR_S 1090; TGML/TAGC, Marseille, F-13007, France
| | - Bernard Ollivier
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Nathalie Pradel
- Aix-Marseille Université, Université du Sud Toulon-Var, IRD, CNRS/INSU, MIO, UM110, Marseille, Cedex 09, 13288, France
| | - Alain Dolla
- Aix-Marseille Université, CNRS, LCB-UMR7283, Marseille, France
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24
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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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25
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Martins M, Mourato C, Pereira IAC. Desulfovibrio vulgaris Growth Coupled to Formate-Driven H2 Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:14655-14662. [PMID: 26579558 DOI: 10.1021/acs.est.5b02251] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Formate is recognized as a superior substrate for biological H2 production by several bacteria. However, the growth of a single organism coupled to this energetic pathway has not been shown in mesophilic conditions. In the present study, a bioreactor with gas sparging was used, where we observed for the first time that H2 production from formate can be coupled with growth of the model sulfate-reducing bacterium Desulfovibrio vulgaris in the absence of sulfate or a syntrophic partner. In these conditions, D. vulgaris had a maximum growth rate of 0.078 h(-1) and a doubling time of 9 h, and the ΔG of the reaction ranged between -21 and -18 kJ mol(-1). This is the first report of a single mesophilic organism that can grow while catalyzing the oxidation of formate to H2 and bicarbonate. Furthermore, high volumetric and specific H2 production rates (125 mL L(-1) h(-1) and 2500 mL gdcw(-1) h(-1)) were achieved in a new bioreactor designed and optimized for H2 production. This high H2 production demonstrates that the nonconventional H2-producing organism D. vulgaris is a good biocatalyst for converting formate to H2.
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Affiliation(s)
- Mónica Martins
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa , EAN 2780-157, Oeiras, Portugal
| | - Cláudia Mourato
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa , EAN 2780-157, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa , EAN 2780-157, Oeiras, Portugal
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26
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The Carbon Monoxide Dehydrogenase from Desulfovibrio vulgaris. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1574-83. [DOI: 10.1016/j.bbabio.2015.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/29/2015] [Accepted: 08/04/2015] [Indexed: 11/21/2022]
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27
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Brady AL, Sharp CE, Grasby SE, Dunfield PF. Anaerobic carboxydotrophic bacteria in geothermal springs identified using stable isotope probing. Front Microbiol 2015; 6:897. [PMID: 26388850 PMCID: PMC4555085 DOI: 10.3389/fmicb.2015.00897] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 08/17/2015] [Indexed: 12/25/2022] Open
Abstract
Carbon monoxide (CO) is a potential energy and carbon source for thermophilic bacteria in geothermal environments. Geothermal sites ranging in temperature from 45 to 65°C were investigated for the presence and activity of anaerobic CO-oxidizing bacteria. Anaerobic CO oxidation potentials were measured at up to 48.9 μmoles CO g−1 (wet weight) day−1 within five selected sites. Active anaerobic carboxydotrophic bacteria were identified using 13CO DNA stable isotope probing (SIP) combined with pyrosequencing of 16S rRNA genes amplified from labeled DNA. Bacterial communities identified in heavy DNA fractions were predominated by Firmicutes, which comprised up to 95% of all sequences in 13CO incubations. The predominant bacteria that assimilated 13C derived from CO were closely related (>98% 16S rRNA gene sequence identity) to genera of known carboxydotrophs including Thermincola, Desulfotomaculum, Thermolithobacter, and Carboxydocella, although a few species with lower similarity to known bacteria were also found that may represent previously unconfirmed CO-oxidizers. While the distribution was variable, many of the same OTUs were identified across sample sites from different temperature regimes. These results show that bacteria capable of using CO as a carbon source are common in geothermal springs, and that thermophilic carboxydotrophs are probably already quite well known from cultivation studies.
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Affiliation(s)
- Allyson L Brady
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | - Christine E Sharp
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
| | | | - Peter F Dunfield
- Department of Biological Sciences, University of Calgary Calgary, AB, Canada
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28
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Assessment of the Carbon Monoxide Metabolism of the Hyperthermophilic Sulfate-Reducing Archaeon Archaeoglobus fulgidus VC-16 by Comparative Transcriptome Analyses. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2015; 2015:235384. [PMID: 26345487 PMCID: PMC4543118 DOI: 10.1155/2015/235384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/09/2015] [Accepted: 06/14/2015] [Indexed: 11/23/2022]
Abstract
The hyperthermophilic, sulfate-reducing archaeon, Archaeoglobus fulgidus, utilizes CO as an energy source and it is resistant to the toxic effects of high CO concentrations. Herein, transcription profiles were obtained from A. fulgidus during growth with CO and sulfate or thiosulfate, or without an electron acceptor. This provided a basis for a model of the CO metabolism of A. fulgidus. The model suggests proton translocation by “Mitchell-type” loops facilitated by Fqo catalyzing a Fdred:menaquinone oxidoreductase reaction, as the major mode of energy conservation, rather than formate or H2 cycling during respiratory growth. The bifunctional CODH (cdhAB-2) is predicted to play an ubiquitous role in the metabolism of CO, and a novel nitrate reductase-associated respiratory complex was induced specifically in the presence of sulfate. A potential role of this complex in relation to Fdred and APS reduction is discussed. Multiple membrane-bound heterodisulfide reductase (DsrMK) could promote both energy-conserving and non-energy-conserving menaquinol oxidation. Finally, the FqoF subunit may catalyze a Fdred:F420 oxidoreductase reaction. In the absence of electron acceptor, downregulation of F420H2 dependent steps of the acetyl-CoA pathway is linked to transient formate generation. Overall, carboxidotrophic growth seems as an intrinsic capacity of A. fulgidus with little need for novel resistance or respiratory complexes.
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29
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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: 173] [Impact Index Per Article: 19.2] [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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30
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Vita N, Valette O, Brasseur G, Lignon S, Denis Y, Ansaldi M, Dolla A, Pieulle L. The primary pathway for lactate oxidation in Desulfovibrio vulgaris. Front Microbiol 2015; 6:606. [PMID: 26167158 PMCID: PMC4481167 DOI: 10.3389/fmicb.2015.00606] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/02/2015] [Indexed: 12/16/2022] Open
Abstract
The ability to respire sulfate linked to lactate oxidation is a key metabolic signature of the Desulfovibrio genus. Lactate oxidation by these incomplete oxidizers generates reductants through lactate dehydrogenase (LDH) and pyruvate-ferredoxin oxidoreductase (PFOR), with the latter catalyzing pyruvate conversion into acetyl-CoA. Acetyl-CoA is the source of substrate-level phosphorylation through the production of ATP. Here, we show that these crucial steps are performed by enzymes encoded by a nonacistronic transcriptional unit named now as operon luo (for lactate utilization operon). Using a combination of genetic and biochemical techniques, we assigned a physiological role to the operon genes DVU3027-28 and DVU3032-33. The growth of mutant Δ26-28 was highly disrupted on D-lactate, whereas the growth of mutant Δ32-33 was slower on L-lactate, which could be related to a decrease in the activity of D-lactate or L-lactate oxidase in the corresponding mutants. The DVU3027-28 and DVU3032-33 genes thus encode functional D-LDH and L-LDH enzymes, respectively. Scanning of the genome for lactate utilization revealed several lactate permease and dehydrogenase homologs. However, transcriptional compensation was not observed in any of the mutants except for lactate permease. Although there is a high degree of redundancy for lactate oxidase, it is not functionally efficient in LDH mutants. This result could be related to the identification of several operon enzymes, including LDHs, in the PFOR activity bands, suggesting the occurrence of a lactate-oxidizing supermolecular structure that can optimize the performance of lactate utilization in Desulfovibrio species.
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Affiliation(s)
- Nicolas Vita
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Odile Valette
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Gaël Brasseur
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Sabrina Lignon
- CNRS, IMM-FR3479, Plate-forme Protéomique-IBISA Marseille-Protéomique Marseille, France
| | - Yann Denis
- IMM-FR3479, Plate-forme Transcriptomique Marseille, France
| | | | - Alain Dolla
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France
| | - Laetitia Pieulle
- CNRS, LCB-UMR7283, Aix-Marseille Université Marseille, France ; Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université Marseille, France
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31
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Zhou A, Hillesland KL, He Z, Schackwitz W, Tu Q, Zane GM, Ma Q, Qu Y, Stahl DA, Wall JD, Hazen TC, Fields MW, Arkin AP, Zhou J. Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris. ISME JOURNAL 2015; 9:2360-72. [PMID: 25848870 DOI: 10.1038/ismej.2015.45] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/07/2015] [Accepted: 02/26/2015] [Indexed: 01/19/2023]
Abstract
To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.
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Affiliation(s)
- Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | | | - Zhili He
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Wendy Schackwitz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Qichao Tu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Grant M Zane
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Qiao Ma
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - Yuanyuan Qu
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian, China
| | - David A Stahl
- Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
| | - Judy D Wall
- Departments of Biochemistry and Molecular Microbiology and Immunology, University of Missouri-Columbia, Columbia, MO, USA
| | - Terry C Hazen
- Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA.,Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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32
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Benomar S, Ranava D, Cárdenas ML, Trably E, Rafrafi Y, Ducret A, Hamelin J, Lojou E, Steyer JP, Giudici-Orticoni MT. Nutritional stress induces exchange of cell material and energetic coupling between bacterial species. Nat Commun 2015; 6:6283. [PMID: 25704114 DOI: 10.1038/ncomms7283] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/12/2015] [Indexed: 12/24/2022] Open
Abstract
Knowledge of the behaviour of bacterial communities is crucial for understanding biogeochemical cycles and developing environmental biotechnology. Here we demonstrate the formation of an artificial consortium between two anaerobic bacteria, Clostridium acetobutylicum (Gram-positive) and Desulfovibrio vulgaris Hildenborough (Gram-negative, sulfate-reducing) in which physical interactions between the two partners induce emergent properties. Molecular and cellular approaches show that tight cell-cell interactions are associated with an exchange of molecules, including proteins, which allows the growth of one partner (D. vulgaris) in spite of the shortage of nutrients. This physical interaction induces changes in expression of two genes encoding enzymes at the pyruvate crossroads, with concomitant changes in the distribution of metabolic fluxes, and allows a substantial increase in hydrogen production without requiring genetic engineering. The stress induced by the shortage of nutrients of D. vulgaris appears to trigger the interaction.
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Affiliation(s)
- Saida Benomar
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - David Ranava
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - María Luz Cárdenas
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Eric Trably
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Yan Rafrafi
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Adrien Ducret
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 13009 Marseille, France
| | - Jérôme Hamelin
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Elisabeth Lojou
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
| | - Jean-Philippe Steyer
- INRA, UR050, Laboratoire de Biotechnologie de l'Environnement, Avenue des Etangs, F-11100 Narbonne, France
| | - Marie-Thérèse Giudici-Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille Université, 31 Chemin Joseph Aiguier, 13009 Marseille, France
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33
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Zhou C, Liu Z, Pataranutaporn P, Vannela R, Hayes KF, Rittmann BE. Biogenic nano-particulate iron-sulfide produced through sulfate and Fe(iii)-(hydr)oxide reductions was enhanced by pyruvate as the electron donor. RSC Adv 2015. [DOI: 10.1039/c5ra20556e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In nature, the formation of iron sulfide solids is mainly attributed to reductions of sulfate and ferric minerals by microorganisms such asDesulfovibrio vulgaris.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Zhuolin Liu
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Pat Pataranutaporn
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Raveender Vannela
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
| | - Kim F. Hayes
- Department of Civil and Environmental Engineering
- University of Michigan
- USA
| | - Bruce E. Rittmann
- Swette Center for Environmental Biotechnology
- Biodesign Institute
- Arizona State University
- Tempe
- USA
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34
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Genomic, proteomic, and biochemical analysis of the organohalide respiratory pathway in Desulfitobacterium dehalogenans. J Bacteriol 2014; 197:893-904. [PMID: 25512312 DOI: 10.1128/jb.02370-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Desulfitobacterium dehalogenans is able to grow by organohalide respiration using 3-chloro-4-hydroxyphenyl acetate (Cl-OHPA) as an electron acceptor. We used a combination of genome sequencing, biochemical analysis of redox active components, and shotgun proteomics to study elements of the organohalide respiratory electron transport chain. The genome of Desulfitobacterium dehalogenans JW/IU-DC1(T) consists of a single circular chromosome of 4,321,753 bp with a GC content of 44.97%. The genome contains 4,252 genes, including six rRNA operons and six predicted reductive dehalogenases. One of the reductive dehalogenases, CprA, is encoded by a well-characterized cprTKZEBACD gene cluster. Redox active components were identified in concentrated suspensions of cells grown on formate and Cl-OHPA or formate and fumarate, using electron paramagnetic resonance (EPR), visible spectroscopy, and high-performance liquid chromatography (HPLC) analysis of membrane extracts. In cell suspensions, these components were reduced upon addition of formate and oxidized after addition of Cl-OHPA, indicating involvement in organohalide respiration. Genome analysis revealed genes that likely encode the identified components of the electron transport chain from formate to fumarate or Cl-OHPA. Data presented here suggest that the first part of the electron transport chain from formate to fumarate or Cl-OHPA is shared. Electrons are channeled from an outward-facing formate dehydrogenase via menaquinones to a fumarate reductase located at the cytoplasmic face of the membrane. When Cl-OHPA is the terminal electron acceptor, electrons are transferred from menaquinones to outward-facing CprA, via an as-yet-unidentified membrane complex, and potentially an extracellular flavoprotein acting as an electron shuttle between the quinol dehydrogenase membrane complex and CprA.
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Changes in metabolic pathways of Desulfovibrio alaskensis G20 cells induced by molybdate excess. J Biol Inorg Chem 2014; 20:311-22. [PMID: 25488518 DOI: 10.1007/s00775-014-1224-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/25/2014] [Indexed: 01/06/2023]
Abstract
The activity of sulfate-reducing bacteria (SRB) intensifies the problems associated to corrosion of metals and the solution entails significant economic costs. Although molybdate can be used to control the negative effects of these organisms, the mechanisms triggered in the cells exposed to Mo-excess are poorly understood. In this work, the effects of molybdate ions on the growth and morphology of the SRB Desulfovibrio alaskensis G20 (DaG20) were investigated. In addition, the cellular localization, ion uptake and regulation of protein expression were studied. We found that molybdate concentrations ranging between 50 and 150 µM produce a twofold increase in the doubling time with this effect being more significant at 200 µM molybdate (five times increase in the doubling time). It was also observed that 500 µM molybdate completely inhibits the cellular growth. On the context of protein regulation, we found that several enzymes involved in energy metabolism, cellular division and metal uptake processes were particularly influenced under the conditions tested. An overall description of some of the mechanisms involved in the DaG20 adaptation to molybdate-stress conditions is discussed.
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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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Morais-Silva FO, Rezende AM, Pimentel C, Santos CI, Clemente C, Varela-Raposo A, Resende DM, da Silva SM, de Oliveira LM, Matos M, Costa DA, Flores O, Ruiz JC, Rodrigues-Pousada C. Genome sequence of the model sulfate reducer Desulfovibrio gigas: a comparative analysis within the Desulfovibrio genus. Microbiologyopen 2014; 3:513-30. [PMID: 25055974 PMCID: PMC4287179 DOI: 10.1002/mbo3.184] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/30/2014] [Accepted: 05/15/2014] [Indexed: 11/20/2022] Open
Abstract
Desulfovibrio gigas is a model organism of sulfate-reducing bacteria of which energy metabolism and stress response have been extensively studied. The complete genomic context of this organism was however, not yet available. The sequencing of the D. gigas genome provides insights into the integrated network of energy conserving complexes and structures present in this bacterium. Comparison with genomes of other Desulfovibrio spp. reveals the presence of two different CRISPR/Cas systems in D. gigas. Phylogenetic analysis using conserved protein sequences (encoded by rpoB and gyrB) indicates two main groups of Desulfovibrio spp, being D. gigas more closely related to D. vulgaris and D. desulfuricans strains. Gene duplications were found such as those encoding fumarate reductase, formate dehydrogenase, and superoxide dismutase. Complexes not yet described within Desulfovibrio genus were identified: Mnh complex, a v-type ATP-synthase as well as genes encoding the MinCDE system that could be responsible for the larger size of D. gigas when compared to other members of the genus. A low number of hydrogenases and the absence of the codh/acs and pfl genes, both present in D. vulgaris strains, indicate that intermediate cycling mechanisms may contribute substantially less to the energy gain in D. gigas compared to other Desulfovibrio spp. This might be compensated by the presence of other unique genomic arrangements of complexes such as the Rnf and the Hdr/Flox, or by the presence of NAD(P)H related complexes, like the Nuo, NfnAB or Mnh.
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Affiliation(s)
- Fabio O Morais-Silva
- Instituto de Tecnologia Quómica e Biológica - Antonio Xavier, Universidade Nova de Lisboa (ITQB-UNL), Av. da República - Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
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Zhou C, Vannela R, Hayes KF, Rittmann BE. Effect of growth conditions on microbial activity and iron-sulfide production by Desulfovibrio vulgaris. JOURNAL OF HAZARDOUS MATERIALS 2014; 272:28-35. [PMID: 24675611 DOI: 10.1016/j.jhazmat.2014.02.046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/21/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
Sulfate-reducing bacteria (SRB) can produce iron sulfide (FeS) solids with mineralogical characteristics that may be beneficial for a variety of biogeochemical applications, such as long-term immobilization of uranium. In this study, the growth and metabolism of Desulfovibrio vulgaris, one of the best-studied SRB species, were comprehensively monitored in batch studies, and the biogenic FeS solids were characterized by X-ray diffraction. Controlling the pH by varying the initial pH, the iron-to-sulfate ratio, or the electron donor - affected the growth of D. vulgaris and strongly influenced the formation and growth of FeS solids. In particular, lower pH (from initial conditions or a decrease caused by less sulfate reduction, FeS precipitation, or using pyruvate as the electron donor) produced larger-sized mackinawite (Fe1+xS). Greater accumulation of free sulfide, from more sulfate reduction by D. vulgaris, also led to larger-sized mackinawite and particularly stimulated mackinawite transformation to greigite (Fe3S4) when the free sulfide concentration was 29.3mM. Furthermore, sufficient free Fe(2+) led to the additional formation of vivianite [Fe3(PO4)2·8(H2O)]. Thus, microbially relevant conditions (initial pH, choice of electron donor, and excess or deficiency of sulfide) are tools to generate biogenic FeS solids of different characteristics.
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Affiliation(s)
- Chen Zhou
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA.
| | - Raveender Vannela
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
| | - Kim F Hayes
- Department of Civil and Environmental Engineering, University of Michigan, USA
| | - Bruce E Rittmann
- Swette Center for Environmental Biotechnology, Biodesign Institute, Arizona State University, USA
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Molecular mechanisms of heme based sensors from sediment organisms capable of extracellular electron transfer. J Inorg Biochem 2014; 133:104-9. [DOI: 10.1016/j.jinorgbio.2013.10.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2013] [Revised: 10/15/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022]
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40
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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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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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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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Desulfovibrio vulgaris Hildenborough prefers lactate over hydrogen as electron donor. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0675-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Aono S. The Dos family of globin-related sensors using PAS domains to accommodate haem acting as the active site for sensing external signals. Adv Microb Physiol 2013; 63:273-327. [PMID: 24054799 DOI: 10.1016/b978-0-12-407693-8.00007-8] [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: 10/26/2022]
Abstract
Sensor proteins play crucial roles in maintaining homeostasis of cells by sensing changes in extra- and intracellular chemical and physical conditions to trigger biological responses. It has recently become clear that gas molecules function as signalling molecules in these biological regulatory systems responsible for transcription, chemotaxis, synthesis/hydrolysis of nucleotide second messengers, and other complex physiological processes. Haem-containing sensor proteins are widely used to sense gas molecules because haem can bind gas molecules reversibly. Ligand binding to the haem in the sensor proteins triggers conformational changes around the haem, which results in their functional regulation. Spectroscopic and crystallographic studies are essential to understand how these sensor proteins function in these biological regulatory systems. In this chapter, I discuss structural and functional relationships of haem-containing PAS and PAS-related families of the sensor proteins.
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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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Spring S, Visser M, Lu M, Copeland A, Lapidus A, Lucas S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Ivanova N, Land M, Hauser L, Larimer F, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T, Schaap PJ, Plugge CM, Muyzer G, Kuever J, Pereira IAC, Parshina SN, Bernier-Latmani R, Stams AJM, Klenk HP. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)). Stand Genomic Sci 2012; 7:304-19. [PMID: 23408247 PMCID: PMC3569383 DOI: 10.4056/sigs.3226659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.
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Affiliation(s)
- Stefan Spring
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Aklujkar M, Haveman SA, DiDonato R, Chertkov O, Han CS, Land ML, Brown P, Lovley DR. The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features. BMC Genomics 2012; 13:690. [PMID: 23227809 PMCID: PMC3543383 DOI: 10.1186/1471-2164-13-690] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 11/22/2012] [Indexed: 11/24/2022] Open
Abstract
Background The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. Conclusions Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.
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Affiliation(s)
- Muktak Aklujkar
- University of Massachusetts Amherst, Amherst, MA 01003, USA.
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Santana MM, Portillo MC, Gonzalez JM. Mutualistic growth of the sulfate-reducer Desulfovibrio vulgaris Hildenborough with different carbohydrates. Microbiology (Reading) 2012. [DOI: 10.1134/s002626171206015x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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