Microorganisms Systems Self-Organized Systems Life as Self-Organized Growth of Biomass Cells Organisms and Microorganisms Size of Microorganisms Biology Microbiology Environmental Microbiology Why Are Microbes Used in Environmental Engineering? Organisms of Importance in Environmental Microbiology Viruses Subviral Particles Importance of Viruses in Environmental and Civil Engineering Prokaryotes Bacteria and Archaea Importance of Prokaryotes in Environmental and Civil Engineering Fungi Importance of Fungi in Environmental and Civil Engineering Algae Importance of Algae in Environmental Engineering Protozoa Importance of Protozoa for Environmental Engineering Chapter 1 Quiz Static Biochemistry Static and Dynamic Biochemistry Chemical Features of Life Balance of Elements Covalent Bonds Organic Compounds and Functional Groups Polarity of Chemical Bonds Water pH of Solutions Intermolecular Forces Hydrophobic Substances and Hydrophobic Forces Stereoisomers Biological Monomers and Polymers Monosaccharides Oligosaccharides and Polysaccharides Lipids and Membranes Lipid Membranes Membrane Melting and Freezing Amino Acids and Proteins Structure of a Protein Molecule Globular and Fibrous Proteins Denaturation of Proteins Enzymes Coenzymes Nucleotides Cyclic Nucleotides Oligonucleotides DNA Structure DNA Melting DNA as a Carrier of Genetic Information DNA Sequences and Sequencing RNA mRNA tRNA Genetic Code rRNA and Translation 16S rRNA Functions of rRNA in the Ribosome miRNA Summary of the Functions of Monomers and Polymers in a Cell Chapter 2 Quiz Dynamic Biochemistry Levels of Metabolism Biochemical Reactions Major Features of Enzymes Mechanism of Enzymatic Catalysis Specificity of Enzymes Inactivation of Enzymes Classification of Enzymes Environmental Applications of Microbial Enzymes and Coenzymes Coenzymes Units of Enzymatic Activity Control of Individual Biochemical Reactions Effect of Noncompetitive Inhibitors on Enzymatic Activity Effect of Competitive Inhibitors on Enzymatic Activity Control of a Group of Biochemical Reactions Regulation of Enzymatic Activity in the Sequence of Enzymes Regulation of Enzyme Synthesis and Degradation Metabolic Blocks Control of Metabolic Blocks Cyclic AMP and GMP as Whole-Cell Regulators of Metabolism Temporal Control of Cell Metabolism Nitric Oxide as Controller of Metabolism Quorum Sensing Control of Metabolism in the Biosphere Chapter 3 Quiz Biooxidation and Bioreduction Oxidation¿Reduction Oxidation Numbers Oxidation of Carbon Oxidation¿Reduction during Fermentation Energy Two Sources of Biological Forms of Energy Chemotrophy Chemotrophic Oxidation¿Reduction Reactions Chemotrophy: Fermentation Chemotrophy: Anaerobic (Anoxic) Respiration Chemotrophy: Aerobic Respiration Phototrophy Oxygenic and Anoxygenic Phototrophic Oxidation¿Reduction Reactions Electron-Transfer Chain Proton Motive Force Oxidative Phosphorylation Biological Forms of Energy Production of Biological Energy in Photosynthesis ATP Yield from Oxidative Phosphorylation ATP Production and Yield from Fermentation ATP Yield from Lithotrophy Long-Term Energy Storage in Cells Relation to Oxygen and Generation of Energy Chapter 4 Quiz Biodegradation Biodegradation and biotransformation Biochemical Reactions of Biodegradation Aerobic, Anoxic, and Anaerobic Biodegradation Biodegraded Substances Biodegradation Rates of Natural Substances Biodegradation Rates Correlate with Turnover Rates Degradation of Storage Polysaccharides Biodegradation of Structural Polysaccharides Biodegradation of Hemicellulose and Pectin Biodegradation of Cellulose Biodegradation of Lignin White-Rot Fungi Biodegradation of Chitin Degradation of Proteins Degradation of Amino Acids Degradation of Nucleic Acids Degradation of Lipids Biodegradation of Chemicals Degradation of Aliphatic Hydrocarbons Degradation of Aromatic Hydrocarbons Biodegradation of Benzene, Toluene, Ethylbenzene, and Xylene Bioremediation of Soil and Water Polluted by BTEX Chemicals Xenobiotics Degradative Plasmids Biodegradation of Chlorinated Hydrocarbons Products of Degradation of Aromatic Hydrocarbons Nonbiodegradable and Biodegradable Polymers Polylactic Acid and Polyhydroxyalkanoates Chapter 5 Quiz Molecular Biology and Genetics Metabolic Blocks of Biosynthesis Energy for Biosynthesis Balance of Energy Excess of Biological Energy Number of Enzymes Genes Noncoding RNA Genes Chromosomes Genomes Genomes of Chloroplasts and Mitochondria The Genome in Comparison with a Book Flow of Genetic Information Genetics, Molecular Biology, Bioinformatics, and Epigenetics Collection of DNA Sequences Nucleus and Nucleoid Plasmids Transposons DNA Replication Speed of DNA Replication Transcription Translation Genetic Code Genome Changes Natural Genetic Recombination in Prokaryotes Conjugation Transformation Transduction Horizontal Gene Transfer DNA Reparation and Mutations Chemical Mutagens Physical Mutagens Biological Mutagens Genetic Adaptation of Microbial Population to Changed Environment Chapter 6 Quiz Bioagents of Environmental and Engineering Bioprocesses Hierarchy of Life Cell Aggregates Microbial Communities and Ecosystems Shapes of Individual and Connected Prokaryotic Cells Prokaryotic Cell Shapes as Evolutionary Adaptation to Environment Inner Structure of Prokaryotic Cells Intracellular Inclusions in Prokaryotic Cells Outer Components of Prokaryotic Cells Cytoplasmic Membrane Vulnerability of the Cytoplasmic Membrane Prokaryotic Cell Walls Origin of Gram-Negative Cells Origin of Gram-Positive Cells Flagella, Fimbriae, and Pili Outer Membrane, Lipopolysaccharides, and S-Layer Glycocalyx and Capsule Anabiotic Prokaryotic Cells Structure of Eukaryotic Cells Organelles Chapter 7 Quiz Reproduction, Proliferation, and Growth Reproduction of Viruses Reproduction of Prokaryotes Vegetative Reproduction of Microscopic Eukaryotes Asexual and Sexual Reproduction of Microscopic Eukaryotes Cell Growth and the Cell Division Cycle Coordination of Cell Cycle Events Periods of Exotrophy and Endotrophy in the Cell Cycle Cell Differentiation Growth and Proliferation of Cell Populations Generation Time and Number of Generations Specific Growth Rate Stoichiometry of Microbial Growth Cell Age and Cell Trophic State Distributions in Microbial Populations Quantification of Microbial Biomass Microscopic Enumeration Flow Cytometry Enumeration Physical Methods of Microbial Biomass Measurement Chemical Methods of Microbial Biomass Measurement Physiological Methods of Microbial Biomass Measurement Biological Methods of Cell Enumeration: Plate Count Biological Methods of Cell Enumeration: Most Probable Number Count Enumeration of Cells and Viral Particles at Low Concentrations Molecular-Biological Methods of Microbial Biomass Quantification Chapter 8 Quiz Microbial Ecology Ecosystems Levels of Ecosystems Ecosystem Boundaries Boundaries of Unicellular Organisms Boundaries of Multicellular Aggregates Boundaries of Microbial Communities in Environmental Engineering Systems Diversity of a Microbial Ecosystem Quantification of Ecosystem Diversity Diversity in an Anaerobic Digester Types of Interactions in Microbial Ecosystems Population Density Determines Interaction Type Commensalism Mutualism Interactions of Microorganisms in Cellular Aggregates Positive Interactions between Animals and Microorganisms Symbiotic Mutualism Positive Interactions between Plants and Microorganisms Symbiosis of Plants and Microorganisms Neutral Competition Amensalism Antagonism Predation Parasitism Microbial Parasites of Plants Microbial Parasites of Human and Animals Effects of Nutrients on Biotic Elements Effects of Nutrients on Yield Effect of Starvation on Microorganisms Effect of Oxygen on Biotic Elements Anoxic Microorganisms Effect of Temperature on Growth Effect of pH on Growth Effect of Osmotic Pressure on Growth Natural Death of Microorganisms Fate of Microorganisms Released into the Environment Chapter 9 Quiz Classification of Viruses and Microorganisms Biological Classification Units of Biological Classification Names of Species Classification of Viruses Groups of Viruses Importance of Viruses for Environmental Engineering Isolation and Collection of Microbial Strains Microbial Collections Classification of Microorgani.