Introduction to Bacteria and Their Ecobiology

The purpose of this book is to illustrate a selection of biological prop­ erties of bacteria that reveal them as important living beings. We have primarily addressed readers who have had some previous educa­ tion in the natural sciences, and we have assumed a modest under­ standing of elementary chemical and biological principles. Our aim is to provide abrief survey of bacterial forms and structures, placing special emphasis on the activities of bacteria in their environment and some important interrelations within it. Bacterial ecobiology is the study of those aspects of bacteria that influence, and are in­ fluenced by, environmental phenomena. Some material traditionally covered in standard texts-such as medi­ cal bacteriology and immunology, applied bacteriology, and bacterial classification-will not be found here, because it is our opinion that these are peripheral to the idea of ecobiology and because numerous excellent treatments of this material are readily available. There is also no formal presentation ofbacterial genetics or of molecular biology per se in this book. However, mention of phenomena involved in these subjects is made where considered appropriate.

one Bacteria in Nature.- 1.1 The Origin of Bacteria.- 1.2 The Uncertainty of Knowledge Concerning Bacteria.- 1.3 Some Methods for Studying Bacteria in Natural Habitats.- 1.4 Functions of Bacteria in Nature.- References.- two Some General Structural Features of Bacteria.- 2.1 Bacteria as Prokaryotic Forms.- 2.2 Bacterial Shapes and Some Consequences of Their Being Very Small.- 2.3 Capsules.- 2.4 Pili.- 2.5 Flagella and Bacterial Behavior.- 2.6 Cell Walls.- 2.7 The Cytoplasmic Membrane and Its Ramifications.- 2.8 The Nucleus.- 2.9 Ribosomes.- 2.10 Endospores, Cysts, Conidia, and Myxospores..- 2.11 Cytoplasmic Inclusions.- 2.12 Rhapidosomes.- 2.13 Colony Formation.- 2.14 Gross Chemical Composition of Bacteria.- References.- three Heterogeneity of Form and Function.- 3.1 Budding Bacteria.- 3.2 Stalked Bacteria.- 3.3 Ribbon-Forming Bacteria.- 3.4 Fruiting Bacteria.- 3.5 Net-Forming Bacteria.- 3.6 Thiothrix, Leucothrix, and Some “Gliders”.- 3.7 Sphaerotilus and Leptothrix.- 3.8 Filamentous Branching Bacteria.- 3.9 Cell Wall-less Bacteria.- 3.10 Flexible, Helical Bacteria.- 3.11 Blue-Green Algae.- 3.12 Hydrogen Oxidation.- 3.13 Carbon Monoxide Oxidation.- 3.14 Methane Oxidation.- 3.15 Nonsymbiotic Nitrogen Fixation.- 3.16 Sulftir Oxidation.- 3.17 Sulfate Reduction.- 3.18 Luminescent Bacteria.- 3.19 Photosynthetic Bacteria.- 3.20 Extreme Halophiles.- References.- four Populations and Habitats.- 4.1 Bacteria as Open Systems.- 4.2 Multiplication and Growth.- 4.3 Estimating Bacterial Numbers.- 4.4 The Rise and Decline of Bacterial Populations.- 4.5 Biological Aspects of Dormancy in Bacteria.- 4.6 The L-Phase of Bacteria.- 4.7 Bacterial Distribution.- 4.8 Extrinsic and Intrinsic Influences.- 4.9 Temperature Effects.- 4.10 Pressure Effects.- 4.11 Radiant Energy Effects.- 4.12 pH Effects.- 4.13 Oxygen Relationships.- 4.14 Currents and Surfaces.- 4.15 Extrinsic Biological Factors.- 4.16 Habitats.- 4.17 Ecological Aspects of Chemolithotrophy.- 4.18 Bacterial Interactions.- 4.19 Some Exobiological Problems.- 4.20 Gnotobiosis.- References.- five Bacterial Energetics.- 5.1 Enzyme Localization.- 5.2 Energy Sources and Carbon Compounds Used by Bacteria.- 5.3 Energy Metabolism in Bacteria.- Respiration and fermentation.- Bacterial respiration and tricarboxylic acid cycle.- Bacterial electron transport systems.- Electron transport components in obligate anaerobes.- Function of the glyoxylate cycle during growth on acetate.- 5.4 Characteristic Bacterial Fermentations of Carbohydrates.- Pathways of carbohydrate dissimilation.- 5.5 Fermentation of Noncarbohydrate Materials.- 5.6 Pathways for the Dissimilation of Aromatic Compounds by Bacteria.- 5.7 The Role of Inorganic Compounds in Bacterial Energy Metabolism.- 5.8 Inorganic Compounds as Terminal Electron Acceptors.- Nitrate reduction.- Assimilatory sulfate reduction.- Dissimilatory sulfate reduction.- Methanogenesis.- Reduction of other inorganic compounds.- 5.9 Some Aspects of the Biochemistry of Chemolithotrophy.- Nitrification and the nitrifying bacteria.- Oxidation of reduced sulfur compounds by thiobacilli.- Metabolism of molecular hydrogen.- Energy coupling and CO2 fixation in chemolithotrophs.- The biochemical basis of obligate chemolithotrophy.- 5.10 Energy Transduction in Bacterial Systems.- 5.11 Bacterial Luminescence.- 5.12 Bacterial Photosynthesis.- Photophosphorylation.- Photosynthetic electron transport systems.- Utilization of CO2 in photosynthesis.- References.- six Bacteria as Environmental Determinants.- 6.1 The Age of the Earth and the Beginning of Life.- 6.2 Nonbiological Geochemical Processes.- Radioactive decay.- Formation of igneous rocks.- Sedimentation.- 6.3 Participation of Bacteria in Cyclic Geochemical Transformations of the Elements.- 6.4 The Carbon Cycle.- Photosynthesis.- Mineralization.- 6.5 The Nitrogen Cycle.- 6.6 The Sulfur Cycle.- 6.7 Phosphorus Transformations.- 6.8 Bacterial Degradation of Plant Materials.- Cellulose degradation.- Attack on pectin.- Starch hydrolysis.- Lignin degradation and humification.- 6.9 Chitin Degradation.- 6.10 Bacteria in Relation to Fossil Fuels.- Origin of fossil fuels.- Utilization of fossil fuels.- 6.11 Formation of Mineral Deposits by Bacterial Activities.- Deposition of calcite.- Deposition of elemental sulfur.- Bacterial fractionation of isotopes in epigenetic sulfur deposits.- Formation of iron and manganese minerals.- 6.12 Bacterial Attack on Minerals.- Thiobacilli and leaching of metallic ores.- References.- seven Epilogue.