Bacteria in Nature

Any branch of biology depends for its progress on the development of new concepts and to a lesser, but sometimes crucial, extent on the elimination of erroneous notions. Understanding the roles of bacteria required first the observation that such minute creatures existed, and subsequently the exper­ imental demonstrations that their presence was necessary for the occurrence of particular phenomena. In this first volume, the authors review the development of scientific understanding of the role of microbes as agents of diverse natural processes. Notably absent is a separate review of the history of microbes as agents of disease, a his tory available in many other publications. Regrettably absent is a review of the his tory of microbes as agents of inorganic transformations, a serious omission that resulted from the illness of the prospective author late in the preparation of this volume. The topic will of course be treated in later volumes, although not predominantly in a historical manner. Otherwise, the emphasis in this volume is on the history of understanding interrelationships between modes of bacterial existence and the inanimate environment. These relationships were established long be fore multicellular, differentiated or­ ganisms appeared as potential microbial habitats, and their recognition and elucidation contributed greatly to the widened appreciation of bacterial di­ versity and the importance of these simpler creatures to the physiochemical conditions of the biosphere.

1 The Scientific Study of Bacteria, 1780–1980.- How Were the Activities of Bacteria Recognized?.- Steps toward a Science of Bacteriology.- Constancy of Form.- Spontaneous Generation.- The Process of Fermentation.- Pasteur and Fermentation.- Ferments and Enzymes.- The Growth of Medical Bacteriology.- Bacteria and Disease.- Pure Cultures and Mixed Cultures.- Public Health Aspects.- Bacteria and the Natural Cycles.- Isolates from Nature.- Nitrifiers.- Nitrogen Fixation.- Autotrophic Sulfur Bacteria.- Photosynthetic Bacteria.- Chemical Transformations Carried Out by Bacteria.- Oxidations.- Anaerobic Fermentations.- Bacterial Metabolism and the Unity of Biochemistry.- Biochemical Variation.- Genetic Variation.- Levels of Understanding.- From Nature to the Laboratory.- What about Bacterial Species?.- The Impact of Genetics.- Adaptation―Genotype or Phenotype?.- Molecular Biology.- Bacterial Growth.- Present and Future.- References.- 2 Anaerobic Biotransformations of Organic Matter.- Abiotic Transformations.- Synthesis.- Evolution of Metabolism.- The Advent of Dioxygen.- Human Appreciation of Anaerobiosis.- Pasteur’s Great Contributions.- Development of Biochemistry in Relation to Anaerobic Transformations.- Hydration and Dehydrogenation.- Types of Fermentation of Carbohydrates.- Lactacidigenesis.- Ethanolic Fermentation.- Acetigenic Fermentation.- Succinigenic and Propionigenic Fermentations.- Butyrigenic Fermentation.- Mixed Product Fermentations.- Development of Anaerobic Methods.- Ecological Considerations.- The Liquid Enrichment Method.- The Solid Medium Enrichment Method.- Gradients in Anaerobiosis―the Redox Potential.- Factors Influencing Redox Potential.- Redox Potentials in the Organism.- Categories of Organismic Relationships to Dioxygen.- Methanogenic Fermentations.- Modern Anaerobic Habitats: The Alimentary Tracts of Animals.- The Competition Model.- The Cooperation Model.- The Combined Competition―Cooperation Model.- Continuous Fermentation.- The Rumen.- Modern Nonalimentary Anaerobic Habitats.- Aquatic Habitats.- Soils and Sediments.- Anaerobic Digestors.- Digestion of Plant Cell Walls.- Transformations of Nitrogenous Materials.- Ultimate Events in Anaerobic Transformations.- Soluble Nutrients in Anaerobic Transformations.- Leakage of Metabolites from Anaerobic Digesters of Wall Materials.- Conclusion.- References.- 3 The Mineralization of Organic Materials under Aerobic Conditions.- History.- Chemistry.- Regulation.- The Bacteria.- Stages of Mineralization.- Pathway Structure.- Genetic Organization.- The Chromosome.- Plasmids.- Prospects and Trends in Research.- Pathways.- Xenobiotic Compounds as Pollutants.- Mixed Cultures.- Conclusions.- References.- 4 Stages in the Recognition of Bacteria Using Light as a Source of Energy.- The Studies of Engelmann on the Responses of Green Algae and of Purple Bacteria to Light.- Winogradsky’s Work on the Sulfur Bacteria.- The Contribution of Molisch to the Knowledge of the Purple Bacteria.- Progress in the Study of the Sulfur Bacteria.- The Work of Buder with Purple Sulfur Bacteria.- Van Niel’s Broadened Concept of Photosynthesis.- Oxygenic and Anoxygenic Photosynthesis: Solutions to Classical Problems.- Structure of the Photosynthetic Apparatus in Purple and Green Bacteria.- Purple Bacteria.- Green Bacteria.- Conclusion.- References.- 5 Oxygenic Photosynthesis in Prokaryotes.- From Blue-Green Algae to Cyanobacteria.- History of the Relationship between Blue-Green Algae and Bacteria.- Modern Methods for Establishment of Affinities among Organisms.- Recognition as Prokaryotae.- Discovery of the Role of Photosynthetic Pigments and Electron Carriers in Cyanobacteria.- Accessory Pigments.- Mechanisms of Energy Transfer.- Existence of Two Photosystems.- Other Components of Cyanobacterial Photosynthesis.- Fractionation of Photosynthetic Function.- Photosynthetic Mutants of Cyanobacteria.- Path of Carbon in Photosynthesis.- Photosynthetic Structures in Cyanobacteria.- Thylakoids.- Phycobilisomes.- Nutritional Adaptations in the Photosynthetic Apparatus.- Light Quality and Quantity.- Temperature Effects.- Other Nutritional Adaptations.- Facultative Anoxygenic Photosynthesis.- Conclusions.- References.- 6 Consumption of Atmospheric Nitrogen.- Early Observations.- The Ancient Roots.- Beginnings of Scientific Agriculture.- Early Controversies Regarding the Sources of Plant Nitrogen.- Advances Prior to 1940.- Methodological Problems.- Development of an Ecological Understanding.- Advent of Isotopic Techniques.- Discovery of New N2-fixing Organisms.- Expansion of Ecological Understanding.- Development of a Biochemical Understanding.- Advent of the Acetylene Reduction Technique.- Further Advances in Ecological Understanding.- Current Perspectives and Future Prospects.- References.- 7 The Position of Bacteria and Their Products in Food Webs.- Concepts.- Bacterial Interactions in Food Webs.- Primary Producers.- Decomposers.- Bacteria as Predators and Prey.- Bacteria as Mutualistic, Commensal, or Parasitic Symbionts.- Syntrophy.- Antibiosis.- Conclusion.- References.- 8 A Comparison of the Roles of Bacteria and Fungi.- Significance of Growth Habit.- Unicellular and Filamentous Forms.- Translocation.- Growth Pattern of Mycelial Colonies.- Complex Structures.- Attachment and Penetration.- Physiological Aspects.- General.- Maximal Activity Rates.- Copiotrophs and Oligotrophs.- Temperature.- Hydrogen Ion Concentration.- Water Stress.- Genetics.- Some Important Microbial Ecosystems.- Soil.- Lichens.- Associations between Microbes and Higher Organisms.- Conclusions.- References.