Environmental Microbiology

Preface to the Third Edition
Preface to the Second Edition
Preface to the First Edition
Spellings and Abbreviations
Contents
1: Global Environment: Climate and Microorganisms
	1.1 Climate System
		1.1.1 Components of the Climate System
		1.1.2 Interactions Between the Components
		1.1.3 Energy Balance of the Earth
		1.1.4 Climate Change and Its Effects
		1.1.5 Which Substances Have Which Effect on the Climate?
		1.1.6 Projections
	1.2 Global Cycles with Reservoirs and Material Flows
		1.2.1 Global Carbon Cycle
		1.2.2 Global Nitrogen Cycle
		1.2.3 Global Sulfur Cycle
		1.2.4 Global Phosphorus Cycle
		1.2.5 Summary of Global Cycles
	References
		Further Reading
2: Microorganisms, Actors in the Environment
	2.1 Microorganisms, Assignment to Groups
	2.2 Microorganisms, the Advantage of Small Size
	2.3 Microorganisms, Small But Numerous
	2.4 Microorganisms, Do Not Live Alone
	References
		Further Reading
3: Relationship Between Microbial Energy Production and Material Cycles
	3.1 Principles of Energy Production
		3.1.1 Respiratory Chains and ATP Synthase
	3.2 Main Types of Microbial Metabolism
		3.2.1 Phototrophy
		3.2.2 Chemotrophy
			3.2.2.1 Chemotrophy: Electron Donor
			3.2.2.2	 Chemotrophy: Electron Acceptor
		3.2.3 Carbon Source: Heterotrophy and Autotrophy
	Further Reading
4: Carbon Cycle
	4.1 Formation of the Earth’s Atmosphere and Fossil Raw Materials
	4.2 Material Flows in the Carbon Cycle
	4.3 Autotrophic CO2-Fixation
		4.3.1 Calvin Cycle
		4.3.2 Reductive Citrate Cycle
		4.3.3 Reductive Acetyl-CoA Pathway (Acetogenesis)
		4.3.4 CO2-Fixation Cycle in Crenarchaeota
			4.3.4.1	 Dicarboxylate/4-Hydroxybutyrate Cycle
			4.3.4.2	 3-Hydroxypropionate/4-Hydroxybutyrate Cycle
		4.3.5 3-Hydroxypropionate Bi-cycle
		4.3.6 Comparison of the CO2-Fixation Processes
	4.4 Degradation of Natural Substances
		4.4.1 Degradation of Carbohydrates
			4.4.1.1	 Glycolysis
			4.4.1.2	 Oxidative Pyruvate Decarboxylation and Tricarboxylic Acid Cycle
			4.4.1.3	 Balance of Aerobic Respiration and Energy Storage
			4.4.1.4	 Anaerobic Degradation of Carbohydrates
		4.4.2 Degradation of Proteins
		4.4.3 Degradation of Fats
		4.4.4 Degradation of Plant Substances/Lignin and Other Natural Substances/Humus Formation
			4.4.4.1	 Degradation of Starch
			4.4.4.2	 Degradation of Cellulose
			4.4.4.3	 Degradation of Xylan (Hemicellulose)
			4.4.4.4	 Degradation of Pectin
			4.4.4.5	 Degradation of Lignin
			4.4.4.6	 Humification
	4.5 Methane Cycle/Methanogenic Food Chain/Methanotrophy
		4.5.1 Methane Formation
		4.5.2 Methane Degradation
			4.5.2.1	 Aerobic Degradation (Methylotrophy)
			4.5.2.2	 Anaerobic Degradation of Methane
	References
		Further Reading
5: Environmental Chemicals
	5.1 Chemicals in the Environment: Distribution and Concentration
		5.1.1 Transport Processes
			5.1.1.1 Transport in the Water Body
			5.1.1.2	 Atmospheric Transport
		5.1.2 Transfer Processes Between Environmental Media or Compartments
			5.1.2.1	 Volatilisation: Transport from Water and Soil to Air
			5.1.2.2	 Adsorption on Solids: Distribution Between Water and Particles
			5.1.2.3	 Distribution Between Water and Biota: n-Octanol/Water Partition Coefficient
		5.1.3 Transformation Processes
			5.1.3.1	 Abiotic Transformations
			5.1.3.2	 Biotic Transformations
	5.2 Assessment of Chemicals: General Principles and Concepts
		5.2.1 Degradability Tests
			5.2.1.1	 Methods for Tracking Substance Turnover
			5.2.1.2	 OECD Testing Strategy
			5.2.1.3	 Simulation Tests
				5.2.1.3.1 Tests for “Possible Degradability”
				5.2.1.3.2 Screening Tests for Anaerobic Degradability
		5.2.2 Toxicity and Mutagenicity Testing with Microbial Systems
			5.2.2.1	 Toxicity Tests for Aquatic Ecosystems
				5.2.2.1.1 Algae Test
				5.2.2.1.2 Pseudomonas putida Growth Inhibition Test
				5.2.2.1.3 Luminescent Bacteria Test
				5.2.2.1.4 Nitrification Inhibition Test
		5.2.3 Mutagenicity Testing with Bacterial Systems
			5.2.3.1 Ames Test (OECD 471, DIN 38415-4)
			5.2.3.2	 Umu Test (DIN 38415-3)
	References
		Further Reading
6: Microbial Degradation of Pollutants
	6.1 Degradation of Hydrocarbons
		6.1.1 Petroleum: Composition and Properties
		6.1.2 The Process of Oiling in the Sea
		6.1.3 Degradation of Alkanes, Alkenes and Cyclic Alkanes
			6.1.3.1 Alkanes/Alkenes
			6.1.3.2	 Cycloalkanes
		6.1.4 Degradation of Monoaromatic Hydrocarbons
			6.1.4.1	 Aerobic Aromatics Degradation
			6.1.4.2	 Anaerobic Aromatics Degradation
				6.1.4.2.1 Formation of the Central Key Intermediates
					6.1.4.2.1.1 Formation of Benzoyl-CoA
					6.1.4.2.1.2 Formation of 1,3-Diphenols
				6.1.4.2.2 Dearomatisation Reactions
					6.1.4.2.2.1 Degradation of Benzoyl-CoA
					6.1.4.2.2.2 Degradation of Resorcinol, Phloroglucin and Hydroxyhydroquinone
					6.1.4.2.2.3 Hypothesis: Anaerobic Degradation of Naked Aromatic Compounds
			6.1.4.3	 Strategies of an Unorthodox Aerobic Degradation of Aromatics
				6.1.4.3.1 Hybrid Pathway for Benzoate
				6.1.4.3.2 Hybrid Pathway for Phenylacetate
				6.1.4.3.3 Are the Hybrid Degradation Pathways Significant?
		6.1.5 Degradation and Humification of Polynuclear Hydrocarbons
			6.1.5.1	 Bacterial Aerobic Degradation of PAHs
			6.1.5.2	 Degradation of PAHs by Fungi
			6.1.5.3	 Bacterial Anaerobic Degradation of PAHs
		6.1.6 Degradation of Heterocycles
			6.1.6.1	 Sulfur-Containing Heterocycles
			6.1.6.2	 Nitrogen-Containing Heterocycles
			6.1.6.3	 Oxygenated Heterocycles
		6.1.7 Formation of Biosurfactants/Absorption of Mineral Oil Hydrocarbons
			6.1.7.1	 Surface-Active Substances (Biosurfactants)
				6.1.7.1.1 Structure of Biosurfactants
			6.1.7.2	 Sequence of Colonisation of an Oil Droplet
			6.1.7.3	 Use of Biosurfactants
	6.2 Degradation of Chlorinated Pollutants
		6.2.1 Degradation of Chlorinated Aromatics
			6.2.1.1 Chlorinated Aromatics as an Environmental Problem
				6.2.1.1.1 Production and Use
				6.2.1.1.2 Physico-Chemical Properties and Evidence
			6.2.1.2	 Possibilities of Microbial Degradation of Chlorinated Aromatics
				6.2.1.2.1 Cometabolic Degradation
					6.2.1.2.1.1 Cometabolic Conversions by Aerobic Bacteria After Growth on Aromatics
					6.2.1.2.1.2 Cometabolic Degradation by Ligninolytic Fungi
					6.2.1.2.1.3 Cometabolic Dechlorination by Anaerobic Bacterial Populations
				6.2.1.2.2 Chlorinated Aromatic Compounds Beneficial to Microorganisms
					6.2.1.2.2.1 Dehalorespiration, an Anaerobic Respiration
					6.2.1.2.2.2 Chloroaromatics as Carbon and Energy Source of Aerobic Bacteria
		6.2.2 Degradation of Hexachlorocyclohexane
		6.2.3 Degradation of Triazines
		6.2.4 Degradation of Chloroaliphatic Compounds
			6.2.4.1 Environmental Problem Using the Example of Volatile Halogenated Organic Compounds
			6.2.4.2	 Possibilities of Microbial Degradation of Chloroaliphatic Compounds
				6.2.4.2.1 Aerobic Growth with Chloroaliphates
				6.2.4.2.2 Cometabolic Degradation
				6.2.4.2.3 Chloroaliphates Beneficial to Anaerobic Microorganisms
		6.2.5 Organohalogens from Nature/Natural Sources
	6.3 Degradation and Humification of Nitroaromatics
		6.3.1 Environmental Problem Caused by Nitroaromatics
		6.3.2 Possibility of Microbial Degradation of Nitroaromatics
		6.3.3 Elimination of Trinitrotoluene by Sequestration on Soil
	6.4 Degradation of Aromatic Sulfonic Acids and Azo Dyes
		6.4.1 Aromatic Sulfonic Acids
			6.4.1.1 Use and Environmental Relevance
			6.4.1.2	 Degradation of Aromatic Sulfonic Acids
		6.4.2 Degradation of Azo Dyes
	6.5 Plastics, Bioplastics
		6.5.1 Degradability of Plastics
		6.5.2 Bioplastics
			6.5.2.1	 Biopol: A Degradable Thermoplastic Resin
			6.5.2.2	 Degradable Plastics: Not Only from Renewable Raw Materials
		6.5.3 An Assessment of the Environmental Impact of Plastics and Bioplastics
	6.6 Complexing Agents: Aminopolycarboxylic Acids
	6.7 Endocrine Active Compounds
		6.7.1 Tributyltin Compounds
		6.7.2 Alkylphenols
		6.7.3 Bisphenol A
	6.8 Methyl Tert-Butyl Ether
	6.9 Glyphosate
	References
		Further Reading
7: The Microbial Nitrogen Cycle
	7.1 Nitrogen Fixation
	7.2 Ammonification
	7.3 Nitrification
	7.4 ANAMMOX
	7.5 Nitrate Reduction
		7.5.1 Denitrification
		7.5.2 Dissimilatory Nitrate Reduction to Ammonium
	References
		Further Reading
8: Cycles of Sulfur, Iron and Manganese
	8.1 Sulfur Cycle
		8.1.1 Sulfate Reduction
		8.1.2 Reduction of Elemental Sulfur
		8.1.3 Sulfur Disproportionation
		8.1.4 Oxidation of Sulfide and Elemental Sulfur
		8.1.5 Organic Sulfur Compounds
	8.2 The Iron Cycle
		8.2.1 Oxidation of Divalent Iron
			8.2.1.1	 Oxidative Leaching of Pyrite and Other Sulfides at Low pH
		8.2.2 Reduction of Trivalent Iron
	8.3 The Manganese Cycle
		8.3.1 Oxidation of Divalent Manganese
		8.3.2 Reduction of Tetravalent Manganese (Mn4+): Anaerobic Respiration
	References
		Further Reading
9: Heavy Metals and Other Toxic Inorganic Ions
	9.1 Toxicity
	9.2 Environmental Quality Standards
	9.3 Natural and Anthropogenic Occurrences
	9.4 Resistance of Microorganisms
	9.5 Mercury
	9.6 Arsenic
		9.6.1 Arsenite Oxidation
		9.6.2 Arsenate Reduction
		9.6.3 Arsenate Methylation
	9.7 Selenium
	9.8 Uranium
	References
		Further Reading
10: Microorganisms at Different Sites: Living Conditions and Adaptation Strategies
	10.1 Microbial Competition and Cooperation
		10.1.1 Growth Rates and Nutrient Concentrations
		10.1.2 Adaptation
			10.1.2.1	 Adaptation to the Presence of High Salt Concentration
			10.1.2.2	 Adaptation to the Presence of Solvents
		10.1.3 Mixed Substrates
		10.1.4 Limit Concentrations
		10.1.5 Microbial Cooperation
	10.2 Attachment to Surfaces and Biofilms
		10.2.1 Surfaces
		10.2.2 Biofilms
	10.3 Soil as Microbial Habitat
	10.4 Aquatic Biotopes
		10.4.1 Freshwater Environment
			10.4.1.1 The Free Water
			10.4.1.2	 The Sediment
		10.4.2 Marine Environments
			10.4.2.1 Coastal and Intertidal Areas
			10.4.2.2	 The Pelagic Zone
				10.4.2.2.1 Epipelagic Zone/Euphotic Zone
				10.4.2.2.2 The Deep Sea
					10.4.2.2.2.1 Meso- and Bathypelagic Zones
					10.4.2.2.2.2 Oxygen Minimum Zones and Oxic-Anoxic Interfaces
					10.4.2.2.2.3 Hydrothermal Vents of the Deep Sea
					10.4.2.2.2.4 Cold Gas Leaks/Cold Seeps
					10.4.2.2.2.5 Sediment
					10.4.2.2.2.6 Mountain Sides
	References
		Further Reading
11: Microbial Communities: Structural and Functional Analyses with Classical Approach
	11.1 Summary Methods
		11.1.1 Determination of Bacterial Counts and Biomasses
		11.1.2 Determination of Activities
	11.2 Detection of Certain Microorganisms
	11.3 Microorganisms, from Nature to the Laboratory, the Isolation of Pure Cultures
		11.3.1 Organisms That Cannot Be Cultivated?
		11.3.2 Isolation and Problems
		11.3.3 Enrichment System
		11.3.4 Analogue Enrichment: Sense or Nonsense?
		11.3.5 Inoculum for Enrichment Culture
	References
		Further Reading
12: Microbial Communities: Structural and Functional Analyses with Molecular Biological Approach
	12.1 Basic Molecular Genetic Methods for Classification and Identification of Pure Cultures
	12.2 Molecular Genetic Methods for Community Characterization
	12.3 Metagenomics
		12.3.1 Community of an Acid Mine Drainage System
		12.3.2 Community of the Sargasso Sea
		12.3.3 The Global Ocean Sampling Expedition
		12.3.4 Sequence Data and Functionality: A Critical View
	References
		Further Reading
13: Damage to Inorganic Materials Due to Microbial Activities, Biocorrosion
	13.1 Iron Corrosion
	13.2 Concrete Corrosion
	13.3 Building Corrosion/Damage to Stone
	Reference
		Further Reading
14: Biological Waste Water Treatment
	14.1 Formation and Composition of Waste Water
	14.2 Waste Water Treatment in Mechanical-Biological Treatment Plants with Aerobic Stage
	14.3 Biological Phosphate Elimination
	14.4 Nitrogen Elimination During Waste Water Treatment
	14.5 Anaerobic Sludge Treatment, Direct Anaerobic Wastewater Treatment and Biogas Production
	14.6 Treatment of Industrial Waste Water
	14.7 Near-Natural Wastewater Treatment Processes
	References
		Further Reading
15: Biological Exhaust Air Treatment
	15.1 Problems with Exhaust Air Flows
	15.2 Microbial Exhaust Air Purification, General Principles
	15.3 Exhaust Air Purification Systems: Biofilter
	15.4 Exhaust Air Purification Systems: Bioscrubbers
	15.5 Exhaust Air Purification Systems: Trickling Filter Scrubbers
	15.6 Exhaust Air Purification Systems: Membrane Reactors
	15.7 Selection Criteria for Procedure Selection
	References
		Further Reading
		Technical Rules
16: Biological Soil Remediation
	16.1 Contaminated Site Issues
	16.2 Methods of Biological Soil Remediation
		16.2.1 Ex Situ Procedure
			16.2.1.1	 Rental Technique
			16.2.1.2	 Landfarming
			16.2.1.3	 Reactor Process
		16.2.2 In Situ Soil Remediation
			16.2.2.1	 Phytoremediation
			16.2.2.2	 Infiltration Method (“Pump and Treat” Technology)
			16.2.2.3	 Aeration Process
	Further Reading
17: Biological Waste Treatment
	17.1 Waste Issues
	17.2 Biological Waste Treatment Processes
		17.2.1 The Composting Process
		17.2.2 Composting Processes
		17.2.3 Anaerobic Waste Treatment by Digestion
	References
		Further Reading
18: Biotechnology and Environmental Protection
	18.1 Biological Pest Control
		18.1.1 Bioinsecticides
			18.1.1.1 Bacillus thuringiensis and B. sphaericus
			18.1.1.2 Bioinsecticides from Actinomycetes
			18.1.1.3 Mushroom Preparations
			18.1.1.4 Virus Preparations
		18.1.2 Biofungicides and Herbicides
	18.2 Design of New Chemicals
		18.2.1 Structure-Activity Relationship/Predictability of Degradation
		18.2.2 Degradable Alternatives to Current Chemicals
	18.3 Product-Integrated Environmental Protection Through Biotechnology
		18.3.1 Process Comparison: Biotechnical and Chemical-Technical Processes
			18.3.1.1 Biotechnological and Chemical-Technical Production of Vitamin B2
			18.3.1.2 Biotechnological and Chemical-Technical Production of Leather
		18.3.2 Environmental Relief Effects Through Product Substitution
			18.3.2.1 Product Comparison: Enzyme Use in Heavy-Duty Detergents
		18.3.3 Summary PIUS
	18.4 Biofuels
		18.4.1 Bioethanol
		18.4.2 Biodiesel
		18.4.3 Biomass-to-Liquid Fuel
	18.5 Electricity from Microorganisms
		18.5.1 Hydrogen Production in Bioreactors for Conventional Fuel Cells
		18.5.2 Microbial Production of Fuel in the Anode Compartment of the Fuel Cell
		18.5.3 Direct Electron Transport from the Cell to the Electrode
		18.5.4 Mediators for Electron Transport
	References
		Further Reading
19: Food for Thought
	19.1 Sustainability, the Concept
	19.2 Sustainability, Environmental Microbiology a Contribution
	19.3 Environment and Environmental Microbiology, Reflection
	References
		Further Reading