Sulfate-Reducing Bacteria and Archaea

The abundance of sulfate-reducing bacteria and archaea (SRBA) is impressive and new isolates are being reported continuously. A few decades ago, only two genera of sulfate-reducing bacteria (SRB) had been identified. As of 2018, 92 genera containing more than 420 species of SRB have been isolated and characterized and there are several species of archaea. This book addresses the development of the research with SRBA and includes historical background of this field. Biochemical characterization of the enzymes, cytochromes and electron carriers involved with dissimilatory sulfate reduction are reviewed and the presence of relevant genes in cultured and uncultured SRBA are assessed using genome analysis. The contributions of transmembrane electron transport complexes as related to cell energetics are discussed. This book highlights the unique cellular and molecular features of the SRBA and discusses the biochemical interactions behind their metabolic capabilities which enable SRBA to grow in extreme environments. Examples are provided to detoxify and alleviate pollution situations, to evaluate mechanisms proposed for corrosion of ferrous metals and to examine the effects of SRB on human and animal hosts. Contents Chapter 1: Sulfate-Reducing Prokaryotes: Changing Paradigms 1.1 Introduction 1.2 Nutrients for Growth: Initial Discovery Followed by an Exploration to Assess Diversity 1.2.1 Broadening the Scope of Electron Donors 1.2.1.1 From Acetate to Complex Organic Molecules 1.2.1.2 Growth Coupled to CO Oxidation 1.2.1.3 Hydrogen as an Electron Donor 1.2.1.4 Inorganic Sulfur Compounds as Electron Donors 1.2.1.5 Phosphite as an Electron Donor 1.2.1.6 Extracellular Electron Transport Donors 1.2.2 Diverse Electron Acceptors 1.2.2.1 Sulfur Oxyanions 1.2.2.2 Elemental Sulfur 1.2.2.3 Nitrogen Compounds 1.2.2.4 Fumarate 1.2.2.5 Dismutation of Organic Compounds 1.2.2.6 Oxygen 1.2.2.7 Carbon Dioxide 1.2.2.8 Acrylate 1.2.2.9 Sulfonates 1.2.2.10 Dissimilatory Metal Reduction 1.2.2.11 Growth by Dehalorespiration 1.2.2.12 Growth with DMSO 1.2.3 Disproportionation of Thiosulfate, Sulfite, and Sulfur 1.2.4 Fermentation of Organic Substrates 1.2.5 Sulfide/Sulfur Oxidation Coupled to Nitrate, Mn(IV), and O2 Reduction 1.3 Syntrophic Growth 1.4 Autotrophic Growth 1.5 Geographic Distribution 1.6 Perspective References Chapter 2: Characteristics and Taxonomy 2.1 Introduction 2.2 Phenotypic Characteristics 2.2.1 Cell Anatomy and Morphology 2.2.2 Cell Architecture 2.2.2.1 Surfaceome and Outer Membrane Protein Complexes 2.2.2.2 Nanowires 2.2.3 Cytoplasmic Structures 2.2.3.1 Polyglucose as a Storage Polymer 2.2.3.2 Polyhydroxyalkanoate 2.2.3.3 Iron Inclusions and Magnetosomes 2.2.3.4 Phosphorus Inclusions 2.2.3.5 Gas Vacuoles 2.3 Endospores 2.4 Chemotaxonomy 2.4.1 Biomarkers 2.4.2 FISH Technologies, PhyloChip, and GeoChip 2.4.3 Cytochromes 2.4.4 Quinones and Lipids 2.4.5 DNA G + C Content 2.5 Taxonomic Placement 2.5.1 Classification 2.5.1.1 Archaea 2.5.1.2 Endospore-Producing SRB 2.5.1.3 Deltaproteobacteria and Non-sporing Bacteria 2.5.2 Insights from Gene and Genome Analysis 2.5.2.1 Archaea Domain 2.5.2.2 Bacteria Domain: Class Deltaproteobacteria 2.5.2.3 Plasmids 2.5.2.4 Uncultured Bacteria 2.6 Filamentous or Cable Bacteria 2.7 DSR, APS, and Lateral Gene Transfer 2.8 Development of Genetic Manipulations 2.9 Perspective References Chapter 3: Reduction of Sulfur and Nitrogen Compounds 3.1 Introduction 3.2 Sulfate Activation and Bisulfite Production 3.2.1 ATP Sulfurylase 3.2.2 Inorganic Pyrophosphatase 3.2.3 APS Reductase 3.3 Assimilatory Sulfate Reduction 3.4 Dissimilatory Sulfate Reduction 3.4.1 Dissimilatory Bisulfite Reductase 3.4.2 Thiosulfate Reductase 3.4.3 Trithionate Metabolism 3.4.4 Mechanism of Bisulfite Reduction 3.5 Sulfate Transport 3.6 Elemental Sulfur Reduction 3.7 Contributions of SRP to Sulfur Cycling 3.8 Enzymology of Nitrogen Respiration 3.8.1 Nitrate Reduction 3.8.2 Nitrite Reduction 3.9 Nitrogen Fixation 3.10 Role of SRP in Nitrogen Cycling 3.11 Summary and Perspective References Chapter 4: Electron Transport Proteins and Cytochromes 4.1 Introduction 4.2 Hydrogenases 4.2.1 [FeFe] Hydrogenases 4.2.1.1 Electron-Bifurcating Hydrogenases 4.2.1.2 H2-Sensing Hydrogenase 4.2.1.3 Hydrogenase Maturation and Architecture 4.2.2 [NiFe] Hydrogenases 4.2.2.1 Maturation 4.2.3 [FeNiSe] Hydrogenases 4.3 Formate Dehydrogenase 4.3.1 Periplasmic and Membrane 4.3.2 Cytoplasmic 4.4 Cytoplasmic Proteins with Low Redox Potentials 4.4.1 Ferredoxin 4.4.2 Flavodoxin 4.5 Cytoplasmic Proteins with High Redox Potentials 4.5.1 Rubredoxin 4.5.2 Rubrerythrin 4.5.3 Desulfoferrodoxin 4.5.4 Desulforedoxin 4.5.5 Neelaredoxin 4.5.6 Nigerythrin 4.6 Cytochromes 4.6.1 C-Type Cytochromes 4.6.1.1 Monoheme Cytochrome c553 4.6.1.2 Homodimeric Diheme Split-Soret Cytochrome c 4.6.1.3 Tetraheme Cytochrome c3 (TpI-c3/TpII-c3) 4.6.1.4 Octaheme Cytochrome c3 (Mr 26,000) 4.6.1.5 Nonaheme Cytochrome c3: NhcA 4.6.1.6 Hexadecaheme Cytochrome c3: HmcA 4.6.1.7 Molecular Docking, Bohr Effect, Proton Thrustor 4.6.2 B-Type Cytochromes 4.6.2.1 Heme b Distribution in Sulfate Reducers 4.6.2.2 Presence in Electron Transport Complexes 4.7 Heme-Containing Enzymes 4.7.1 Nitrite Reductase 4.7.2 Nitrate Reductase 4.7.3 Sulfite Reductase: Sirohemes 4.7.4 Oxygen Reductases 4.7.4.1 Quinol bd-Type Oxidase 4.7.4.2 Cytochrome cc(b/o)o3 Oxidase 4.7.5 Quinol:Fumarate Oxidoreductase 4.7.6 Molybdopterin Oxidoreductase 4.7.7 Catalase 4.8 Synthesis of Heme 4.9 Conclusion and Perspective References Chapter 5: Systems Contributing to the Energetics of SRBP 5.1 Introduction 5.2 Growth and Yield Coefficients 5.3 Energetic Considerations with Organic Acids and Ethanol 5.3.1 Lactate Oxidation 5.3.2 Pyruvate Oxidation 5.3.3 Formate Dehydrogenases 5.3.4 Alcohol Dehydrogenase 5.4 Location of Soluble Hydrogenases, Formate Dehydrogenases and Cytochromes 5.4.1 Periplasmic Activity 5.4.2 Cytoplasmic Activity 5.5 Protons and Energetic Considerations 5.5.1 Proton Motive Force 5.5.2 Proton Translocation Experiments Using Cells 5.5.3 Proton-Translocating Pyrophosphatase: HppA Complex 5.6 Transmembrane Electron Transport Complexes 5.6.1 Quinone Oxidoreductase Complex: Qmo 5.6.2 Sulfite Reduction Complex: Dsr 5.6.3 Redox Complexes: Hmc, Tmc, Nhc, Ohc 5.6.4 Quinone Reductase Complex: Qrc 5.6.5 Ion-Translocating NADH Dehydrogenase Complexes: Rnf, Nqr, Nuo 5.7 Cytoplasmic Electron Transport Complexes 5.7.1 NADH-Ferredoxin Complex: Nfn 5.7.2 Heterodisulfide Reductase: Hdr/flox 5.8 ATPase (F-Type and V-Type) 5.9 Direct Measurement of ATP Production via Anaerobic Oxidative Phosphorylation 5.9.1 Phosphorylation Coupled to Dissimilatory Sulfate Reduction: Bisulfite and Associated Reactions 5.9.2 Elemental Sulfur Reduction 5.9.3 Fumarate as an Electron Acceptor 5.9.4 Nitrite as an Electron Acceptor 5.9.5 Energy Generated by Heme Biosynthesis 5.10 Energy Conservation by Metabolite Cycling 5.10.1 Hydrogen Cycling 5.10.2 CO Cycling 5.10.3 Formate Cycling 5.11 Substrate-Level Phosphorylation 5.11.1 Fermentation 5.11.2 Pyruvate Phosphoroclastic Reaction 5.11.3 Succinate-Fumarate Reactions 5.12 Summary and Perspective References Chapter 6: Cell Biology and Metabolism 6.1 Introduction 6.2 Using Genomic, Proteomic, and Biochemical Analysis 6.2.1 Cell Surface 6.2.1.1 Outer Membrane, Porins, and Vesicles 6.2.1.2 Cell Size of Desulfovibrio Gigas 6.2.2 Metabolism of Carbon Compounds 6.2.2.1 Lactate Oxidation 6.2.2.2 Pyruvate Oxidation 6.2.2.3 Phosphotransacetylase 6.2.2.4 Acetate Kinase 6.2.2.5 Fumarate Respiration 6.2.2.6 Intermediary Metabolism 6.2.2.7 Sugars and Amino Acids as Energy Substrates 6.2.2.8 Acetate, Butyrate, and Propionate Oxidation 6.2.2.9 Oxidation of Alcohols 6.2.2.10 CO as an Electron Donor 6.2.2.11 Formate Oxidation 6.2.3 Transition to Stationary Phase 6.2.3.1 Sigma Factors 6.2.3.2 Rex Regulon 6.2.3.3 SahR Regulon 6.2.3.4 Fur Regulon 6.2.3.5 TunR Regulon 6.2.4 Genomic Islands 6.3 Stress Response 6.3.1 Oxidative Stress 6.3.2 Starvation Response and CO2 Stress 6.3.3 Extreme Temperatures 6.3.3.1 Heat Shock 6.3.3.2 Cold Shock 6.3.4 Salt Adaptation 6.3.5 Nitrogen Stress 6.3.5.1 Nitrate Stress 6.3.5.2 Nitrite Stress 6.3.5.3 Nitric Oxide Stress 6.3.6 pH Extremes 6.3.6.1 Acid Stress 6.3.6.2 Alkaline Stress 6.4 Biofilm 6.5 CRISPR-Cas Systems, Proviruses, and Viruses 6.6 Perspective References Chapter 7: Geomicrobiology, Biotechnology, and Industrial Applications 7.1 Introduction 7.2 Contributions of SRB to Major Nutrient Cycles 7.2.1 Sulfur and Nitrogen Cycling 7.2.2 Carbon Cycling 7.2.2.1 Decomposition of Organic Matter 7.2.2.2 Anaerobic Methane Oxidation 7.3 H2S Pollution: Agricultural and Commercial Impact 7.4 Oil Technology and SRB 7.5 Metabolism of Hydrocarbons 7.5.1 Oxidation of Environmentally Relevant Organic Compounds 7.5.2 Reductive Dehalogenation 7.6 Magnetosomes and Iron Mineralization 7.7 Mercury Methylation 7.8 Biologically Induced Minerals 7.8.1 Iron Sulfide Mineral Precipitation 7.8.2 Cu Sulfide Deposits 7.8.3 Zn Sulfide Deposits 7.8.4 Ni Sulfide Formations 7.8.5 Mo Sulfide Minerals 7.8.6 Co Sulfides 7.8.7 Carbonate Minerals and Dolomite 7.9 Reduction of Redox Active Metals and Metalloids Including U and Radionucleotides 7.9.1 Reduction of Metal(loid)s: Cr, Mo, Se, and As 7.9.1.1 Chromium 7.9.1.2 Molybdenum 7.9.1.3 Selenium 7.9.1.4 Arsenic 7.10 Pollutants and Bioremediation Processes 7.10.1 Biogenic Hydrogen Sulfide Production 7.10.2 Acid Mine and Acid Rock Drainage Bioremediation 7.10.3 Uranium Remediation 7.10.4 Perchlorate Reduction and Use as an Inhibitor 7.10.5 Bioremediation of Petroleum Hydrocarbons 7.11 Industrial Applications 7.11.1 Production of Metallic Nanoparticles 7.11.2 Energy Technology 7.11.3 Dye Decolorization 7.12 Perspective References Chapter 8: Biocorrosion 8.1 Destructive Effects of Biocorrosion 8.1.1 Activities of SRB Leading to Corrosion of Non-metallic Surfaces 8.1.1.1 Biocorrosion of Concrete and Stone 8.1.1.2 Remediation of Artistic Stoneworks 8.1.2 Association of SRB with Metal Corrosion 8.1.3 Mechanisms for Corrosion of Ferrous Metals 8.1.4 Biocorrosion of Different Types of Steel Alloys 8.1.5 SRB-Metal Interface 8.1.5.1 SRB Biofilms 8.1.5.2 Accelerated Low Water Corrosion 8.1.5.3 Case Studies Oil Facility in the Gulf of Mexico Steel Plates Immersed in Seawater 8.1.5.4 Nanowires and Outer Membrane Cytochromes 8.1.5.5 Shuttle Molecules 8.1.6 Control of SRB-Based Corrosion 8.1.6.1 Physical Methods to Control Biocorrosion 8.1.6.2 Chemical Control of Iron Biocorrosion 8.1.6.3 Green Strategies to Control Biocorrosion 8.1.6.4 Impact of O2 on Anaerobic Biocorrosion 8.1.6.5 Biocompetitive Exclusion with Nitrate 8.1.6.6 Bacteria to Inhibit SRB in Biofilms 8.1.6.7 Inhibition by Disruption of Quorum Sensing 8.2 Perspective References Chapter 9: Ecology of Dissimilatory Sulfate Reducers: Life in Extreme Conditions and Activities of SRB 9.1 Introduction 9.2 Microbes in Extreme Environments 9.2.1 Hyperthermophiles 9.2.2 Thermophiles: Extreme and Moderate 9.2.3 Psychrophiles 9.2.4 Halophiles 9.2.5 Alkaliphiles 9.2.6 Acidophiles 9.2.7 Piezophiles 9.3 Activities and Communities in Extreme, Unique, or Isolated Environments 9.3.1 Adaptations to the Environment 9.3.1.1 Impact of Temperature 9.3.1.2 Extremely Acidic Environments 9.3.2 Soda Lakes and Other Alkaline Environments 9.3.3 SRB Growing on Surfaces 9.3.3.1 Environmental Mats 9.3.3.2 Lithification of Mats 9.3.3.3 Dolomite Bioformation 9.3.3.4 Biofilms 9.3.4 Hydrothermal Vent Sediments 9.3.5 Deep Subsurface and Mines 9.3.6 Floodplains and Estuaries 9.3.7 Low Nutrient Environment 9.4 Summary and Perspective References Chapter 10: Interactions of SRB with Animals and Plants 10.1 Introduction 10.2 Symbiosis with Termites and a Gut-Residing Protist 10.3 Symbiosis with Root-Feeding Larvae 10.4 Symbiosis with Invertebrates 10.4.1 Gutless Marine Worm 10.4.2 Polychaete Serpulid Worm 10.4.3 Sea Cucumber 10.5 SRB Presence/Activity in Mice 10.6 SRB Present in Rats 10.7 SRB in Pigs 10.8 SRB Associated with Ruminates 10.9 Interactions of SRB with Humans 10.9.1 SRB as Flora of the Human Gastrointestinal Tract 10.9.2 Oral SRB 10.9.3 Are Desulfovibrio Human Pathogens? 10.9.4 Antibiotic Susceptibility and Resistance 10.9.5 Do SRB Have Virulence Factors? 10.10 SRB Interactions with Plants 10.11 SRB on Surfaces of Living Marine Organisms 10.12 SRB with Other Animals 10.13 Summary and Perspective References Index The abundance of sulfate-reducing bacteria and archaea (SRBA) is impressive and new isolates are being reported continuously. A few decades ago, only two genera of dissimilatory sulfate reducers had been identified and as of 2018, 92 genera containing more than 420 species of SRB and several species of archaea have been isolated. This book addresses the historical background of SRBA research and reviews the current status of research examining the growth of these anaerobic microorganisms. Additionally, this book covers metabolic and genomic diversity, enzymatic processes, response to stress, biocorrosion of ferrous metals, biogeochemical processes and interactions with other microorganisms in the anaerobic biosphere. It highlights the unique cellular and molecular features of these microorganisms, discusses the production and consumption of gases and reviews genomic content influencing their metabolic capabilities. Examples are provided of detoxification reactions to alleviate pollution situations, growth in in hostile environments including low nutrient availability, and the effects of sulfate-reducing bacteria (SRB) on human and animal hosts