The Sulfate-Reducing Bacteria: Contemporary Perspectives

1 The Sulfate-Reducing Bacteria: An Overview.- 1.1 Introduction.- 1.2 Metabolic Considerations.- General Patterns of Metabolism.- Metabolic Processes in Sulfate-Reducing Bacteria: Electron Donors.- Metabolic Processes in Sulfate-Reducing Bacteria: Electron Acceptors and Bioenergetics.- 1.3 Laboratory Manipulations of Sulfate-Reducing Bacteria.- 1.4 Taxonomic Considerations.- 1.5 Importance of Sulfate-Reducing Bacteria.- Economic Importance.- Environmental Importance.- Evolutionary Importance.- 1.6 Summary.- 2 Carbon Metabolism of Sulfate-Reducing Bacteria.- 2.1 Introduction.- 2.2 Energy Substrates of Sulfate-Reducing Bacteria.- 2.3 Degradation of Various Organic Compounds in the Presence of Sulfate.- Complete or Incomplete Oxidation.- Utilization of Lactate.- Oxidation of Primary Alcohols, Secondary Alcohols, Diols, and Glycerol.- Utilization of Formate, Acetate, and Longer Straight and Branched Alkanoic Acids.- Utilization of Sugars.- Utilization of Aromatic Compounds.- Utilization of Dicarboxylic Acids.- Utilization of Amino Acids.- Miscellaneous Compounds.- 2.4 Fermentative Capacities of Sulfate-Reducing Bacteria.- Fermentations at Low Hydrogen Partial Pressure.- Fermentations Not Dependent on a Low Hydrogen Partial Pressure.- 2.5 Storage Polymers.- 2.6 Some Aspects of Carbon Assimilation.- Carbon Nutrition.- C2 Assimilation Involving C2 + C1.- Autotrophic Growth.- 2.7 Summary and Concluding Remarks.- 3 Bioenergetic Strategies of the Sulfate-Reducing Bacteria.- 3.1 Introduction.- Evolutionary Considerations of Bioenergetic Mechanisms.- Sulfate Reduction and Bioenergetic Mechanisms.- 3.2 General Bioenergetic Considerations.- 3.3 Unique Biochemical and Physiological Aspects of the Sulfate-Reducing Bacteria.- 3.4 Enzymes and Proteins Involved in Respiratory Sulfate Reduction.- APS Reductase.- Bisulfite Reductase.- Terminal Electron Acceptors.- Cytochrome b.- c-Type Cytochromes.- Hydrogenase.- 3.5 Hydrogen Utilization.- Historical Development.- Enzymology of Sulfate Respiration.- Energetics of Respiration of Sulfate and Related Compounds.- Energetics of Nitrate/Nitrite Respiration.- 3.6 Fermentation of Inorganic Sulfur Compounds.- 3.7 Hydrogen Production by Sulfate-Reducing Bacteria.- 3.8 Intracellular H2 Transfer or H2 Cycling.- 3.9 Conclusions.- 4 Genetics of the Sulfate-Reducing Bacteria.- 4.1 Introduction.- 4.2 Considerations for Development of a Genetic System.- Metabolic Properties.- Plating Efficiencies.- Genome Structure.- Plasmids.- Antibiotic Sensitivities.- Restriction Systems.- 4.3 Desulfovibrio Bacteriophages.- 4.4 Conjugation of Desulfovibrio.- 4.5 Electroporation of Desulfovibrio.- 4.6 Summary.- 5 Molecular Biology of the Sulfate-Reducing Bacteria.- 5.1 Introduction.- 5.2 Cloning, Sequencing, and Expression of Desulfovibrio Genes.- and Survey.- 5.3 Hydrogenase Genes.- [Fe] Hydrogenase Genes.- [NiFe] and [NiFeSe] Hydrogenase Genes.- Export and Localization of Hydrogenases.- Distribution of Hydrogenase Genes.- 5.4 Genes for c-Type Cytochromes.- Cloning, Sequencing, and Expression of Cytochrome c3 Gene.- Cloning, Sequencing, and Expression of the Cytochrome c553 Gene.- Cloning, Sequencing, and Expression of the Gene for High-Molecular-Weight Cytochrome.- Summary of c-Type Cytochromes.- 5.5 Construction of a Gene Library for Dv. vulgaris Hildenborough for Rapid Gene Cloning and Genome Mapping.- 5.6 Genes for Cytoplasmic Electron Carriers.- The rbo-rub Operon from Dv. vulgaris Hildenborough.- The dsr Gene from Dv. gigas.- The fla Gene from Dv. vulgaris Hildenborough.- 5.7 Nitrogen Fixation by Desulfovibrio.- 5.8 Summary and Future Perspectives.- 6 Phylogeny of Sulfate-Reducing Bacteria and a Perspective for Analyzing Their Natural Communities.- 6.1 Introduction.- 6.2 16S Ribosomal RNA Sequence Comparisons.- Why Ribosomal RNA?.- Phylogenetic Trees.- 6.3 Sulfate-Reducing Archaea.- 6.4 Phylogenetic Relationships among Sulfate-Reducing Bacteria.- Gram-Positive, Sulfate-Reducing Bacteria.- Gram-Negative, Mesophilic, Sulfate-Reducing Bacteria.- Desulfovibrio Species.- Remaining Genera.- 6.5 Application of 16S rRNA Sequences to Determinative and Ecological Studies.- Characterization of Microbial Populations by rRNA Sequence Comparisons.- rRNA-Targeted Hybridization Probes.- Use of Fluorescent DNA Probes for Single-Cell Identification.- Fluorescent Probe Length and Mismatch Discrimination.- 6.6 Summary.- 7 Ecological Actions of Sulfate-Reducing Bacteria.- 7.1 Introduction.- 7.2 Experimental Approaches to Microbial Ecology.- 7.3 Balanced Metabolic and Ecological Processes.- 7.4 Metabolic Diversity of Sulfate-Reducing Bacteria.- 7.5 Methodology.- Measurement of SRA.- Isotope Discrimination Effects.- Sampling Techniques.- Use of Inhibitors.- 7.6 Substrates for SRA in situ.- Environments Used for SRA Study.- Organic Electron Donors.- H2 as Electron Donor.- Sulfite and Thiosulfate as Electron Donors.- 7.7 Interactions with Methane-Producing Bacteria.- Competition.- Coexistence.- Synergism.- 7.8 Aerobic SRA.- Aerobic/Anaerobic Interface.- Cyanobacterial Mats.- 7.9 Conclusion.- 8 Industrial and Environmental Activities of Sulfate-Reducing Bacteria.- 8.1 Introduction.- 8.2 Historical Perspective.- 8.3 The Oil and Gas Industry.- 8.4 Detection and Identification of Sulfate-Reducing Bacteria.- Standard Industrial Practices.- Taxonomic Markers.- Genetic Approaches and Chemical Markers.- Immunological Approaches to Detection.- 8.5 Corrosion of Iron and Steel: Mechanisms.- General Considerations.- Mechanisms Involving Sulfate-Reducing Bacteria.- Cathodic Depolarization and Methanogenic Bacteria.- 8.6 Anaerobic Corrosion and Sulfate Reducers: Commercial Cures.- 8.7 Environmental Activities: The Sulfur Cycle.- 8.8 Sulfur Cycling and Sewage Treatment.- Concrete Corrosion.- 8.9 Anaerobic Transformations of Mercury.- 8.10 Transformation of Other Industrial Pollutants.- 8.11 Conclusions.- References.