Brief Contents UNIT I Chapter 20 Eukaryotic Biology and Eukaryotic Basic of Microbiology Chapter 1 Microorganisms and Microbiology 29 Chapter 2 A World 52 7 Chapter 3 Bacteria and 75 Microorganisms 612 Chapter 2 t Viral Diversity 641 2 Metabolism and Chapter 22 Methods in Microbial Ecology 670 Chapter 23 Major Microbial and Diversity 697 Chapter 24 Nutrient Cycles, Biodegradation, and Chapter 4 Nutrition, Culture, and 726 Microorganisms 113 Chapter 25 Microbial 748 Chapter 5 Microbial Growth 8 Aaents and Molecular Biology Gene Chapter 6 Bacteria 178 Chapter 27 Microbial Interactions with 815 Chapter 7 and Eukaryotic Molecular Biology 219 Chapter 8 Regulation of Gene Expression 237 4 9 Chapter 28 and Host Defense 844 chapter 29 Chapter 9 and 264 Chapter 30 Molecular Immunology 887 Chapter 291 Chapter 11 Genetic Engineering 319 10 chapter 12 Microbial Diseases Chapter 31 Diagnostic Microbiology and 906 Chapter 32 941 11 DiveTsity and Biocatalyses Chapter Phototrophy, and Major Human- and Chapter 14 400 Chapter 15 Products and Biotechnology 439 Chapter 33 Microbial Diseases 972 UNIT 6 Chapter 34 Vectorborne and Soilborne Microbial Microbial Evolution and DiveTsity Chapter 16 Evolution and 474 Chapter 17 503 Chapter 18 Bacteria 545 Chapter 35 Water , and Waterborne Microbial Diseases 1032 Chapter 19 Archaea 584 Chapter 36 Food Preservation and Microbial Diseases 1050 Brock Biology of Microorganisms 2012 digitalisiert durch: IDS Basel Bern
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Brief Contents
UNIT I Chapter 20 Eukaryotic Biology and Eukaryotic
Basic of Microbiology Chapter 1 Microorganisms and Microbiology 29 Chapter 2 A World 52 7
Chapter 3 Bacteria and 75
Microorganisms 612 Chapter 2 t Viral Diversity 641
2
Metabolism and Chapter 22 Methods in Microbial Ecology 670 Chapter 23 Major Microbial and Diversity 697 Chapter 24 Nutrient Cycles, Biodegradation, and
Human- and Chapter 14 400 Chapter 15 Products and Biotechnology 439
Chapter 33 Microbial Diseases 972
UNIT 6 Chapter 34 Vectorborne and Soilborne Microbial
Microbial Evolution and DiveTsity
Chapter 16 Evolution and 474 Chapter 17 503 Chapter 18 Bacteria 545 Chapter 35 Water , and Waterborne Microbial Diseases 1032 Chapter 19 Archaea 584
Chapter 36 Food Preservation and Microbial Diseases 1050
Brock Biology of Microorganisms2012
digitalisiert durch:IDS Basel Bern
Contents
About the Authors 3 2.6 Arrangement of DNA in Microbial 61 Preface 5 2.7 The Evolutionary Tree of Life 62
15 III Microbial Diversity 64
Diversity 64 . . 1 2.9 Bacteria 66 210 Archaea 69
Phylogenetic Analyses of Natural Microbial Chapter 1 Microorganisms and 71
2 9 71
I Introduction to Microbiology 30 Chapter 3 Cell Structure and Function 1.1 30 in Bacteria Archaea 75
Microbial Cells 31 Microorganisms and Their Environments 32 Cell 7 6
1.4 Evolution and the Extent Microbial Life 33 3.1 Cell Morphology 76 The Impact of Microorganisms on 35 3.2 Size and the of Smallness 77
II Pathways of Discovery in II The Cytoplasmic Membrane and Microbiology 38 Transport 79
The Historical Roots of Microbiology: Hooke, 3.3 The Cytoplasmic Membrane 79 van Leeuwenhoek, and Cohn 39 3.4 Functions of the Cytoplasmic Membrane 82
1.7 the Defeat of Spontaneous 3.5 Transport and Transport Systems 83 Generation 40
Koch, Infectious Disease, and Pure Culture III Cell Wal l s P roka ryOteS 8 6
Microbiology 43 The Cell Wall of Bacteria: Peptidoglycan 86 1.9 Microbial Diversity 46 The Outer Membrane 88 1.10 The Microbiology 48 Cell Archaea 91
Microbial Sidebar Solid Media, Pure Cultures, and the Birth of IV Other Cell Surface Structures Microbial Systematics 45 and Inclusions 92
3.9 Cell Surface Structures 92
Chapter 2 A Brief Journey to the Microbial 3.10 Cell inclusions W o r l d 5 2 96
3.12 Endospores 97
V Microbial 101 I Seeing the Very 53 2.1 Some of Light Microscopy 53 2.2 Microscopy 54 3.13 and 101 2.3 Cells in 57 3.14 Gliding Motility 105 2.4 Electron Microscopy 58 3.15 Microbial Taxes 106
II Cell Structure and Evolutionary History 59 Microbial Sidebar The Cell Wal): A Complex
2.5 Elements of Microbial Structure 59 Upids 99
19
20 Contents
UNIT 2 and Microbial Growth 160 Effect of Temperature on Growth 162
Chapter 4 Nutrition, Culture, and of Microorganisms
Microbial Life in the 162 5.14 Microbial Life at High Temperatures 166
V Other Environmental Factors Nutrition and Culture of Microorganisms 114 Affect.ng Growth 168
5.15 Acidity and Alkalinity 168 5.16 Effects 169 5.17 Microorganisms 171 5.18 Toxic of Oxygen 174
Energetics and Enzymes Microbial Sidebar
4.1 Nutrition and Cell 114 4.2 Culture Media 4.3 Laboratory Culture 118
4.4 Bioenergetics 120 Microbial Growth in Aquatic Systems: 4.5 Catalysis and Enzymes 121 Cyanobacterial Blooms 161
Oxidation-Reduction and Energy-Rich Compounds 122
4.6 Electron Donors and Electron Acceptors 122 4.7 Energy-Rich Compounds and Energy Storage 125
of Catabolism 126
and Gene Expression Chapter 6 Molecular Biology of
DNA Structure and Genetic 4.8 Glycolysis 126 4.9 Respiration and Electron Carriers 129 Information 179 4.10 The Proton Motive Force 131 6.1 Macromolecules and Genes 179 4.11 The Citric Acid 133 6.2 The Double 181 4.12 Catabolic Diversity 134 6.3 Supercoiling 183
6.4 Chromosomes and Other Genetic Elements 184 V Essentials of 136 4.13 and Polysaccharides 136 and Plasmids 185 4.14 Biosynthesis Acids and Nucleotides 137 6.5 Escherichia coli 185 4.15 and Lipids 138 6.6 Plasmids: General 187 4.16 Activity of Enzymes 139 6.7 The Biology of Plasmids 189
Microbial Sidebar DNA Replication 190 Yeast Fermentation, the Pasteur Effect, and the
127 Templates and Enzymes 190 6.9 The Replication Fork 191
_ . 6.10 Bidirectional Replication and the Replisome 193 Chapter 5 Microbial Growth 145 . ,.
The Polymerase Cham (PCR) 197 f Bacterial Cell Division 146 5.1 Cell Growth and Binary Fission 146 5.2 Fts Proteins and Cell Division 146
IV RNA Synthesis: Transcription 198 Overview of Transcription 198
, „ 6.13 Factors and Consensus Sequences 200 5.3 and Cell Morphology 148 • •
, , . • • 201 5.4 149
Population Growth 151 structure and Synthesis 202
Polypeptides, Amino Acids, and the Peptide 202
Translation and the Genetic Code 203
5.5 The Concept of Exponential Growth 151 5.6 The Exponential Growth 152 5.7 The Microbial Growth Cycle 153
5.8 Continuous Culture: The Chemostat 154 T f RNA
III GrOWth 156 Synthesis 208 The Incorporation of Selenocysteine
5.9 156 and Pyrrolysine 211 5.10 157 and Secreting Proteins 211 5.11 159
Contents 21
Chapter 7 and Eukaryotic Molecular Biology 219
I Molecular Biology Archaea 220 7.1 Archaea 220 9 2 6 4 7.2 and Archaea 221 7.3 Archaea 223 Virus 265 7.4 Shared Features Bacteria Archaea 224 9.1 General Properties 265
9.2 the Virion 266 II Eukaryotic Molecular Biology 225 9.3 The Virus Host 269 7.5 Genes and Chromosomes Eukarya 225 ofViruses 269 7.6 Overview of Eukaryotic Cell Division 226 7.7 Linear DNA 227 Viral Repl icat ion 2 7 1 7.8 RNA Processing 228 9.5 General Virus Replication 271 7.9 Transcription and Translation in Eukarya 231 9.6 Viral Attachment and Penetration 271 7.10 RNA Interference (RNAi) 233 9.7 Production of Viral Nucleic Acid and Protein 273
Regulation by MicroRNA 234
Microbial Sidebar Inteins and Protein Splicing 231
Viral Diversity 275 9.8 Overview of Bacterial Viruses 275 9.9 Virulent Bacteriophages and T4 278
. . . . . Temperate Bacteriophages, and 279 Chapter 8 Regulation of Gene Expression 237 ft11
9.12 Retroviruses 283 I Overview of Regulation 238 8.1 Regulation 238 Subviral 2 8 5
Repression Induction 240 Did Viruses Invent DNA? 276
8.4 Positive Control of Transcription 242 8.5 Operon 244 C h a p t e r 0 G e n e t l C S 8.6 Control Transcription Archaea 245 2 9 1
III Sensing Transduction 246 Mutation 292 8.7 Regulatory Systems 246 10.1 Mutations and Mutants 292 8.8 Chemotaxis 248 10.2 Molecular Basis of Mutation 294 8.9 Quorum Sensing 249 10.3 Mutation Rates 296 8.10 The Stringent Response 251 10.4 Mutagenesis 297 8.11 Other Global Control Networks 252 10.5 Mutagenesis and Carcinogenesis: The Arnes Test 300
IV Regulation of Development Gene Transfer 301 in Mode l 2 5 3 10.6 Genetic Recombination 301
10.9 Conjugation: Essential Features 307 V Regulat ion 2 5 6 10.10 The and 8.14 RNA Regulation and Antisense RNA 256 Mobilization 309 8.15 Riboswitches 258 10.11 312 8.16 259 10.12 Gene Transfer in Archaea 313
10.13 Elements 314 Microbial Sidebar The Antiviral Defense System 257
2 2 Contents
Genetic Engineering 319 II 381 13.6 The Energetics of Chemolithotrophy 381
Methods DNA 320 382 11.1 Restriction and Enzymes 320 13.8 Oxidation of Reduced Sulfur Compounds 382 11.2 Nucleic Acid Hybridization 322 13.9 Oxidation 384 11.3 Essentials of Molecular Cloning 323 13.10 Nitrification 386
Molecular Methods for Mutagenesis 325 Anammox 387 Gene Fusions and Reporter Genes 327
Major Biosyntheses: Autotrophy Gene Cloning 328 and Nitrogen Fixation 389
11.6 Plasmids as Cloning Vectors 328 The Calvin Cycle 389
Hosts for Cloning Vectors 330 Other Autotrophic Pathways in Phototrophs 390 11.8 Shuttle Vectors and Expression Vectors 332 Nitrogen Fixation and Nitrogenase 391 11.9 Bacteriophage as Vector 335 Genetics and Regulation of Nitrogen Fixation 395
Vectors for Genomic Cloning and Sequencing 336
Microbial Chapter Catabolism of Organic Fluorescence Labeling 329 Compounds 400
Microbial 341 401 14.1 Energetic and Redox Considerations 401
a n d GenomiCS 3 4 2 14.2 and Mixed-Acid Fermentations 402
12.1 to Genomics 342 14.3 Clostridial and Propionic Acid Fermentations 405 12.2 Sequencing and Annotating Genomes 342 14.4 Fermentations Lacking Substrate-Level 12.3 Bioinformatic Analyses and Gene Distributions 346 Phosphorylation 407 12.4 The 351 14.5 Syntrophy 409
The Genomes of Eukaryotic Microorganisms 353 12.6 Metagenomics 355 Anaerobic Respiration 411
14.6 Anaerobic Respiration: General 411
Genome Function and Regulation 355 14.7 Nitrate Reduction and 412 12.7 Microarrays and the 355 14.8 Sulfate and Sulfur Reduction 414
12.8 Proteomics and the 357 14.9 Acetogenesis 416 12.9 Metabolomics 359 14.10 Methanogenesis 418
Proton Reduction 422 The Evolution Of Genomes 360 14.12 Acceptors 423
12.10 Gene Duplications, and Deletions 360 14.13 Anoxic Hydrocarbon Oxidation Linked 12.11 Horizontal Gene Transfer and Genome Stability 361 to Anaerobic Respiration 425
12.12 Transposons and Insertion Sequences 362 . 12.13 of Virulence: Islands 363 AeroblC
Processes 428
Details 348
14.15 Methylotrophy and Methanotrophy 429 UNITS 431
Chapter 13 Phototrophy, Chemolithotrophy, commercial Products and Major Biosyntheses 368 and Biotechnology 439
I Phototrophy 369 Microorganisms to Work 440
, , , Industrial Products and the Microorganisms 13.2 Chlorophylls and 370 440 13.3 373 13.4 Photosynthesis 374 Photosynthesis 378
Contents 23
II Drugs, Other Chemicals, and III Microbial Systematics 491 4 4 3 16.10 Phenotypic Analysis: Acid
15.3 Antibiotics: Isolation, and 443 Methyl Esters (FAME) 491 15.4 Industrial Production Penicillins 16.11 Genotypic Analysis 493
and Tetracyclines 445 16.12 The Species Concept in Microbiology 495 15.5 Vitamins and Amino Acids 447 16.13 Classification and Nomenclature 498 15.6 Enzymes as Industrial Products 448
Chapter 17 Bacteria: The Proteobacteria 503 III Alcoholic Beverages and Biofuels 451 15.7 451 I The Phylogeny of Bacteria 504 15.8 Brewing and Distilling 453 17.1 Phylogenetic Overview Bacteria 504 15.9 Biofuels 455
II Phototrophic, and IV Products from Genetically Engineered Methanotrophic Proteobacteria 505
II Cyanobacteria and Prochlorophytes 560 III Crenarchaeota 598 18.7 Cyanobacteria 560 19.8 Habitats and Energy Metabolism 598
Prochlorophytes 564 Crenarchaeota from Volcanic Habitats 599 Crenarchaeota from Submarine Volcanic Habitats 602
III C h l a m y d i a 5 6 5 Crenarchaeota Nonthermal Habitats and 18.9 The Chlamydia 565 Nitrification Archaea 604
IV The 567 IV Evolution and Life at High 18.10 A Phylogenetically TemperatureS 6 0 5
Unique Stalked Bacterium 567 19.12 An Upper Temperature Limit for Microbial Life 605
Molecular Adaptations to Life at High Temperature 606 V T h e VerrUCOmicrobia 5 6 8 19.14 Archaea, Microbial
and Prosthecobacter 568 Evolution 608
VI Flavobacteria Acidobacteria 569 Chapter 20 Eukaryotic Cell Biology and 18.12 Bacteroides 569 6 1 2 18.13 Acidobacteria 569
I Eukaryotic Cell Structure and VII The Cytophaga Group 570 Function 613 18.14 Cytophaga Relatives 570 20.1 Eukaryotic Cell Structure and the Nucleus 613
. 20.2 The Mitochondrion and the 614
VIII Green Sulfur Bacteria 571 and Other Green Sulfur Bacteria 571 20.4 Relationships of Mitochondria and
Chloroplasts to Bacteria 616 IX T h e SpirOCheteS 5 7 3 20.5 Other Organelles and Eukaryotic Cell Structures 617
Spirochetes 573 II Eukaryotic Microbial Diversity 619
X T h e DeinoCOCCi 5 7 6 20.6 Eukarya 619 18.17 Deinococcus and Thermus 576
III Protists 621 XI T h e NonSUlfur Bacteria: 20.7 Parabasalids 621
ChlOrOflexi 5 7 7 20.8 Euglenozoans 622
18.18 Chloroflexus and Relatives 577 20.9 Alveolates 622 624
XII Hyperthermophi l i c Bacter ia 5 7 8 20.11 Cercozoans and Radiolarians 626 18.19 and 578 20.12 Amoebozoa 626
V Red and Green 635 II Euryarchaeota 586 20.19 Red Algae 636 19.2 Extremely Archaea 586 Green Algae 636 19.3 Methanogenic Archaea 590 19.4 593 Chapter 21 Viral Diversity 641 19.5 Thermococcales 595
23.9 Coastal and Ocean Waters: Phototrophic III DNA Viruses of Eukaryotes 661 Microorganisms 713 21.12 Plant DNA Viruses 661 23.10 Bacteria, Archaea, Viruses 715 21.13 SV40 663 23.11 The Deep Sea and Deep-Sea Sediments 718 21.14 Herpesviruses 664 23.12 Hydrothermal Vents 721 21.15 Viruses 665
21.16 Chapter 24 Cycles, Biodegradation, Microbial and Bioremediation 726
and Viral Evolution 662
Microbial Ecology I Nutrient Cycles 727 24.1 The Carbon Cycle 727 24.2 Syntrophy and Methanogenesis 729
Chapter 22 Methods in Microbial Ecology 670
I
6 7 1 The Calcium, and Silica Cycles 737
22.1 Enrichment 671 Biodegradation and Bioremediation 739 22.2 Isolation 675
II Transformations . . . . . . 24.9 Petroleum Biodegradation and Bioremediation 742
of Microbial Communities 677 ,. . . . . . 24.10 Biodegradation and Bioremediation 743
22.3 General Staining Methods 677 22.4 Situ (FISH) 679 Microbial Sidebar 22.5 PCR Microbial Community Analysis 680 735 22.6 Microarrays and Microbial Diversity: Phylochips 683 22.7 Environmental and Related Methods 684 C h a p t e r 2 5 S y m b l O S e S 7 4 8
III Measur ing Activities between Microorganisms 749 in Nature 686 25.1 Lichens 749
22.8 Assays, Methods, 750
and Microelectrodes 686
22.9 688 Plants as Habitats 751 22.10 Linking Specific Genes and Functions 25.3 The Nodule 751
to Specific 690 25.4 and Crown Disease 757 25.5 Mycorrhizae 758
Chapter 23 Major Microbial Habitats III Mammals as Microbial Habitats 760
and Diversity 697 25.6 The Mammalian Gut 760
I Microbial ECOlogy 6 9 8 Rumen and Ruminant Animals 762
23.1 Concepts 698 The Human 766
23.2 Service: and Nutrient 699
26 Contents
IV InsectS Microbial 769 27.1 816
25.9 Heritable Insects 769 Normal Microflora of the Skin 818 25.10 Termites 772 Normal Microflora Cavity 819
27.4 Normal Microflora the Gastrointestinal Tract 821 V AquatiC Microbial 27.5 Normal Other Body Regions 825
Chapter 32 941 I Receptors and Immunity 888 30.1 Innate Immunity and 888 Of 942 30.2 Adaptive Immunity and the Immunoglobulin 32.1 The Epidemiology 942
Superfamily 890 32.2 The Epidemiology 942 32.3 Disease Reservoirs and Epidemics 944
II T h e Major HistOCOmpatibility 32.4 Infectious Disease Transmission 947 Complex (MHC) 892 32.5 The Host Community 949
30.3 MHC Protein Structure 892 30.4 and Binding 894 Current 950
32.6 The 950 III Antibodies 894 32.7 Infections 953
Epidemiology and Public Health 954 30.6 Antibody Genes and Diversity 895
32.8 Public Health Measures for the Control of Disease 954 IV T Cell Receptors 897 Health Considerations 957 30.7 Cell Receptors: Proteins, Genes and Diversity 897 and Infectious Diseases 959
Biological Warfare and Biological 964 V Switches in Immunity 899 Weapon 967 30.8 Tolerance 899 Microbial Sidebar 30.9 T Cell and B Cell Activation 901 Swine 2009 Influenza 951 30.10 902 Microbial Sidebar
Microbial Sidebar SARS as a Model of Epidemiological Success 966 Leucine-Rich Repeats and the Immune
Microbial Sidebar 36.12 Other Foodborne Infectious Diseases 1068 Special Pathogens and Viral Hemorrhagic Fevers 1013 Appendix 1 Energy Calculations in Microbial
Bioenergetics 1073 Common-SouTce
Appendix 2 Bacteriology, Second Edition:
Chapter 35 Water of Genera and Higher-Order
and Waterborne
Microbial Diseases 1032 Glossary 1087
I Wastewater Microbiology and Water Purification 1033 Photo Credits 1105
35.1 Public Health and Water Quality 1033 35.2 Wastewater and Sewage Treatment 1035 35.3 Water Purification 1038