Note: Intro -- Contents -- Part I Introduction -- 1 Organohalide-Respiring Bacteria-An Introduction -- Abstract -- References -- 2 Natural Production of Organohalide Compounds in the Environment -- Abstract -- 2.1 Scope -- 2.2 Evidence -- 2.3 Halogenated Metabolites -- 2.3.1 C1 and C2 Metabolites -- 2.3.2 Phenolic Compounds, Benzoates and Their Methyl Ethers -- 2.3.3 Multi-ring Phenolic Metabolites -- 2.3.4 Chlorinated and Brominated Bipyrroles -- 2.4 Abiotic Formation Chlorinated Compounds in Soil -- 2.5 Biosynthesis of Natural Organohalogens -- 2.6 Biodegradation and Biotransformation of Natural Organohalogens -- 2.7 Conclusions -- References -- 3 Energetic Considerations in Organohalide Respiration -- Abstract -- 3.1 Introduction -- 3.2 Chemistry of Organohalides -- 3.3 Types of Organohalide Respiration -- 3.4 Thermodynamics: The Basics -- 3.5 Gibbs Free Energy of Formation Values -- 3.6 Hydrogenolysis Under Standard Conditions -- 3.7 Dihaloelimination -- 3.8 Change in Gibbs Free Energy Under Environmentally Realistic Conditions -- 3.9 Comparison with Other Electron Acceptors -- 3.10 Co-metabolic Reductive Dehalogenation -- 3.11 Anaerobic Oxidation and Fermentation of Organohalogens -- 3.12 Defluorination -- 3.13 Organohalide Respiration and ATP Generation -- References -- Part II Diversity of Organohalide-Respiring Bacteria -- 4 Discovery of Organohalide-Respiring Processes and the Bacteria Involved -- Abstract -- 4.1 Introduction -- 4.2 Early Studies with Chlorinated Pesticides -- 4.3 Chlorinated Solvent Transformation -- 4.4 Early Work on Reaction Pathways and Organisms Involved -- 4.5 Oxidative Transformation of Chlorinated Solvents -- 4.6 Organohalide Respiration -- 4.7 Reductive Dehalogenation of Vinyl Chloride and the Associated Genus, Dehalococcoides -- 4.8 Summary Statement -- References. , 5 Overview of Known Organohalide-Respiring Bacteria-Phylogenetic Diversity and Environmental Distribution -- Abstract -- 5.1 Introduction -- 5.2 Phylogeny of OHRB -- 5.2.1 Firmicutes -- 5.2.1.1 Dehalobacter -- 5.2.1.2 Desulfitobacterium -- 5.2.2 Chloroflexi -- 5.2.2.1 Dehalococcoides -- 5.2.2.2 Dehalogenimonas -- 5.2.2.3 Dehalobium -- 5.2.3 Deltaproteobacteria -- 5.2.3.1 Anaeromyxobacter -- 5.2.3.2 Desulfuromonas -- 5.2.3.3 Geobacter -- 5.2.3.4 Desulfoluna -- 5.2.3.5 Desulfomonile -- 5.2.3.6 Desulfovibrio -- 5.2.4 Epsilonproteobacteria -- 5.2.4.1 Sulfurospirillum -- 5.2.5 Gammaproteobacteria -- 5.2.5.1 Shewanella -- 5.2.6 Betaproteobacteria -- 5.2.6.1 Comamonas -- 5.3 Environmental Distribution of OHRB -- 5.3.1 Groundwater and Aquifer -- 5.3.2 Marine and Estuarine Environments -- 5.3.3 Riverbed and Lake Sediments -- 5.3.4 Soil -- 5.4 Factors Impacting Environmental Distribution of OHRB -- 5.4.1 Redox Conditions -- 5.4.2 Micronutrients -- 5.4.3 Electron Acceptors -- 5.4.4 Interaction with Chemical Species -- 5.5 Conclusions -- References -- 6 The Genus Dehalococcoides -- Abstract -- Abbreviations -- 6.1 Discovery -- 6.1.1 In the Beginning -- 6.1.2 Success in Ithaca -- 6.1.3 Ramping the Culture up -- 6.1.4 Microbiology Begins -- 6.2 Isolation and Characterization -- 6.2.1 Optimizing Growth -- 6.2.2 Purification and Isolation -- 6.2.3 Initial Characterization: Physiology, MorphologyUltrastructure, and Phylogeny -- 6.3 Diversity and Phylogeny -- 6.3.1 Isolation of Other D. mccartyi Strains -- 6.3.2 Dehalococcoides mccartyi Phylogeny -- 6.4 Genomics and Physiology -- 6.4.1 Streamlined Genomes -- 6.4.2 Multiple RDases -- 6.4.3 Electron Transport -- 6.4.4 Nutrition -- 6.5 Habitat and Ecology -- 6.6 Conclusions -- References -- 7 The Genus Dehalogenimonas -- Abstract -- 7.1 Discovery -- 7.2 Isolation -- 7.3 General Characteristics. , 7.4 Detailed Phylogeny and Diversity -- 7.5 Genomic Features -- 7.5.1 General Genomic Features -- 7.5.2 Reductive Dehalogenases -- References -- 8 The Genus -- Abstract -- 8.1 Enrichment and Isolation of Dehalobacter spp. -- 8.2 Morphology and Cytological Characteristics of Dehalobacter spp. -- 8.3 Habitat of Dehalobacter spp. -- 8.4 Nutritional Requirements and Growth Conditions of Dehalobacter spp. -- 8.5 Physiology and Biochemistry of Dehalobacter spp. -- 8.6 Phylogeny of the Genus Dehalobacter -- 8.7 Metabolic Features Deduced from the Genome of D. restrictus and 'Omics' Studies -- 8.8 Functional Diversity of Reductive Dehalogenases in the Dehalobacter Genus -- 8.9 Corrinoid Metabolism in Dehalobacter spp. -- 8.10 Concluding Remarks -- References -- 9 The Genus -- Abstract -- 9.1 Discovery -- 9.2 Isolation and Habitat -- 9.3 Morphology, Physiology, and Growth Characteristics -- 9.4 Phylogeny -- 9.5 Reductive Dehalogenation Characteristics -- 9.5.1 Dehalogenation of Chloroaliphatic Compounds -- 9.5.2 Dehalogenation of Chloroaromatic Compounds -- 9.5.3 Dehalogenation of Organobromine and Organoiodine Compounds -- 9.6 Bioremediation -- 9.7 Genomic Features -- 9.7.1 Basic Genome Facts -- 9.7.2 Functional Genes and Metabolic Pathways -- 9.7.3 Protein Characterization Based on Genome Data -- References -- 10 The Genus Sulfurospirillum -- Abstract -- 10.1 Discovery -- 10.1.1 A History of the Genus Sulfurospirillum and Its Isolates -- 10.1.2 Isolation -- 10.2 General Characteristics -- 10.2.1 Morphology and Growth Characteristics -- 10.2.2 Habitat -- 10.2.3 General Physiology -- 10.3 Phylogeny and Diversity -- 10.3.1 Phylogeny -- 10.3.2 Diversity -- 10.3.3 Organohalide Respiration and Reductive Dehalogenation Characteristics -- 10.3.4 Genomic Features -- 10.3.4.1 General Genomic Features -- 10.3.5 The OHR Region -- References -- 11 Organohalide-Respiring. , Abstract -- 11.1 Introduction -- 11.2 Characteristics of Studied Organohalide-Respiring Deltaproteobacteria -- 11.2.1 Anaeromyxobacter dehalogenans -- 11.2.2 Desulfoluna spongiiphila Strain AA1 -- 11.2.3 Desulfomonile tiedjei Strain DCB-1 -- 11.2.4 Desulfomonile limimaris Strains DCB-M and DCB-F -- 11.2.5 Strain SF3 -- 11.2.6 sp. Strain TBP-1 -- 11.2.7 Desulfuromonas chloroethenica Strain TT4B -- 11.2.8 Desulfuromonas michiganensis Strains BB1 and BRS1 -- 11.2.9 Geobacter lovleyi Strain SZ -- 11.2.10 Geobacter thiogenes Strain K1 (Formerly "Trichlorobacter thiogenes") -- 11.3 Ecophysiology -- 11.4 Reductive Dehalogenases -- 11.5 Insights from Genome Analyses -- 11.6 Enrichment and Isolation of Organohalide-Respiring Deltaproteobacteria -- References -- 12 Comparative Physiology of Organohalide-Respiring Bacteria -- Abstract -- 12.1 Physiological Differences Between Obligate and Facultative Organohalide-Respiring Bacteria -- 12.1.1 Function of Reductive Dehalogenases in Energy Metabolism -- 12.1.2 Are Menaquinones Universal Electron Carriers in Organohalide Respiration? -- 12.2 Comparative Genomics and Evolution of Obligate Organohalide-Respiring Bacteria -- 12.2.1 The High Plasticity Region Concept in Dehalococcoides mccartyi -- 12.2.2 Comparative Genomics Between Dehalococcoides mccartyi and Dehalogenimonas lykanthroporepellens -- 12.2.3 Comparative Genomics Between Dehalococcoides mccartyi and Dehalobacter spp. -- 12.3 Conclusion -- Literature -- Part III Ecology of Organohalide-Respiring Bacteria -- 13 Electron Acceptor Interactions Between Organohalide-Respiring Bacteria: Cross-Feeding, Competition, and Inhibition -- Abstract -- 13.1 Introduction -- 13.2 Lessons from Field Observations and Enrichment Cultures -- 13.2.1 Simulations of Field and Laboratory Observations. , 13.2.2 Microbial Diversity, Competition, Inhibition, and Reductive Dehalogenases -- 13.3 Experimental Approaches to Quantify Inhibition in Microbial Communities -- 13.3.1 Deconvoluting the Mechanisms of Inhibition -- 13.3.2 Challenges in Experimental Design to Deconvolute Inhibitory Effects -- 13.4 Inhibition of Reductive Dehalogenases (Enzyme Level) -- 13.4.1 Inhibition of Chloroalkene Reductive Dehalogenases by Chlorinated Alkanes -- 13.4.2 Inhibition of Chloroalkane Reductive Dehalogenases by Chlorinated Alkenes -- 13.5 Inhibition in Whole Cell Assays -- 13.5.1 Cross-Inhibitory Effects Examined in Whole Cell Suspension Assays -- 13.5.2 Inhibition Model Type and Fit and Underlying Mechanisms -- 13.6 Inhibition in Actively Growing Microbial Cultures and Communities -- 13.7 Cross-Feeding and Competition in Anaerobic Dehalogenating Microbial Communities -- 13.8 Summary -- References -- 14 Organohalide-Respiring Bacteria as Members of Microbial Communities: Catabolic Food Webs and Biochemical Interactions -- Abstract -- Abbreviations -- 14.1 Introduction -- 14.2 Catabolic Food Webs in Organohalide-Respiring Microbial Communities -- 14.2.1 Organohalide Food webs -- 14.2.2 Electron Donor and Carbon Flow -- 14.2.3 Commonly Observed Groups of Non-OHRB Involved in Metabolic Food Webs -- 14.3 Other Biochemical Interactions in OHRB Communities -- 14.3.1 Cofactors and Nutrients -- 14.3.2 Toxins and Inhibitors -- 14.4 Variations in Community Ecology and Composition -- 14.4.1 Electron Donor and Electron AcceptorElectron Donor Ratio -- 14.4.2 Organohalide Class -- 14.5 Case Studies in Community Ecology: Simple Mixed Communities -- 14.6 Organohalide Respiration Rates in OHRB Communities and Modeling of Community Food Webs -- 14.7 Community Structure in Contaminated AquiferSediment Environments -- 14.8 Roles of OHRB in Natural Systems -- 14.9 Summary -- References. , Part IV Genomics and Regulation of Organohalide-Respiring Bacteria.