Brock biology of microorganisms:
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| Previous Title: | Madigan, Michael T. Brock biology of microorganisms |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
San Francisco ; Munich [u.a.]
Pearson, Benjamin Cummings
2009
|
| Edition: | 12. ed., internat. ed. |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | Getr. Zählung zahlr. Ill., graph Darst. |
| ISBN: | 9780321536150 0321536150 |
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| 245 | 1 | 0 | |a Brock biology of microorganisms |c Michael T. Madigan ... |
| 246 | 1 | 3 | |a Biology of microorganisms |
| 250 | |a 12. ed., internat. ed. | ||
| 264 | 1 | |a San Francisco ; Munich [u.a.] |b Pearson, Benjamin Cummings |c 2009 | |
| 300 | |a Getr. Zählung |b zahlr. Ill., graph Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 2 | |a Microbiologie | |
| 650 | 7 | |a Microbiologie |2 ram | |
| 650 | 0 | 7 | |a Mikrobiologe |0 (DE-588)4039199-1 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Mikrobiologie |0 (DE-588)4316357-9 |2 gnd |9 rswk-swf |
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| 650 | 0 | 7 | |a Biologie |0 (DE-588)4006851-1 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4123623-3 |a Lehrbuch |2 gnd-content | |
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| 700 | 1 | |a Madigan, Michael T. |d 1949- |e Sonstige |0 (DE-588)122334507 |4 oth | |
| 700 | 1 | |a Brock, Thomas D. |d 1926-2021 |e Sonstige |0 (DE-588)136686982 |4 oth | |
| 780 | 0 | 0 | |i Bis 11. Auflage |a Madigan, Michael T. |t Brock biology of microorganisms |
| 856 | 4 | 2 | |m Digitalisierung UB Regensburg |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016356594&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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| 883 | 1 | |8 2\p |a cgwrk |d 20201028 |q DE-101 |u https://d-nb.info/provenance/plan#cgwrk | |
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| _version_ | 1805082896728326144 |
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^^^^^В
Principles of Microbiology
Chapter
1
Microorganisms and Microbiology
1
Chapter
2
A Brief Journey to the Microbial World
25
Chapter
3
Chemistry of Cellular Components
50
Chapter
4
Cell Structure and Function in
Bacteria and Archaea
66
Chapter
5
Nutrition, Culture, and Metabolism
of Microorganisms
107
Chapter
6
Microbial Growth
141
Chapter
22
Methods in Microbial Ecology
Chapter
23
Microbial Ecosystems
Chapter
24
Nutrient Cycles, Bioremediation,
and
Symbioses
652
673
694
UNIT
5
Putting Microorganisms to Work
Chapter
25
Industrial Microbiology
Chapter
26
Biotechnology
733
761
Chapter
7
Chapter
8
Chapter
9
Chapter
10
Chapter
11
Chapter
12
Chapter
13
Chapter
14
Chapter
15
Chapter
16
Chapter
17
Chapter
18
Chapter
19
Chapter
20
Chapter
21
Molecular Biology of Microorganisms
Essentials of Molecular Biology
175
Archaeal and Eukaryotic Molecular Biology
207
Regulation of Gene Expression
224
Overview of Viruses and Virology
251
Principles of Bacterial Genetics
278
Genetic Engineering
313
Microbial Genomics
343
Microbial Diversity
Microbial Evolution and Systematics
Bacteria: The Proteobacteria
Bacteria: Gram-Positive
and Other Bacteria
Archaea
Eukaryotic Cell Biology and Eukaryotic
Microorganisms
Viral Diversity
Metabolic Diversity
and Microbial Ecology
Metabolic Diversity: Phototrophy,
Autotrophy, Chemolithotrophy,
and Nitrogen Fixation
Metabolic Diversity: Catabolism
of Organic Compounds
UNIT
6
Antimicrobial Agents
and Pathogenicity
Chapter
27
Microbial Growth Control
Chapter
28
Microbial Interactions with Humans
779
811
UNIT
7
Immunology
Chapter
29
Essentials of Immunology
Chapter
30
Immunology in Host Defense
and Disease
Chapter
31
Molecular Immunology
839
865
881
367
398
I
UNII
8
Diagnosing and tracking
Infectious Diseases
445
487
Chapter
32
Chapter
33
Diagnostic Microbiology
and Immunology
Epidemiology
900
934
516
548
I
UNIT
9
Microbial Diseases
Chapter
34
Person-to-Person Microbial Diseases
964
Chapter
35
Vectorborne and Soilborne Microbial
Diseases
1002
578
Chapter
36
Wastewater Treatment, Water
Purification, and
Waterborne
Microbial Diseases
1025
612
Chapter
37
Food Preservation and Foodborne
Microbial Diseases
1043
XVIII
Preface
UNIT
1
PRINCIPLES OF
MICROBIOLOGY
Chapter
1
Microorganisms and Microbiology
1
I INTRODUCTION TO MICROBIOLOGY
2
1.1
Microbiology
2
1.2
Microorganisms as Cells
3
1.3
Microorganisms and Their
Natural Environments
5
1.4
The Antiquity and Extent
of Microbial Life
6
1.5
The Impact of Microorganisms
on Humans
7
II PATHWAYS OF DISCOVERY
IN MICROBIOLOGY
10
Chapter
3
Chemistry of Cellular Components
50
I CHEMICAL BONDING. MACROMOLECULES,
AND WATER
51
3.1
Strong and Weak Chemical Bonds
51
3.2
An Overview of Macromolecules and Water
as the Solvent of Life
52
II NONINFORMATIONAL
MACROMOLECULES
55
3.3
Polysaccharides
55
3.4
Lipids
56
III INFORMATIONAL MACROMOLECULES
57
3.5
Nucleic Acids
57
3.6
Amino
Acids and the
Peptide
Bond
59
3.7
Proteins: Primary and Secondary Structure
61
3.8
Proteins: Higher Order Structure
and Denaturation
62
1.6
The Historical Roots of Microbiology:
Hooke, van Leeuwenhoek, and Cohn
1.7
Pasteur and the Defeat of
Spontaneous Generation
12
1.8
Koch, Infectious Disease, and Pure
Culture Microbiology
14
1.9
Microbial Diversity and the Rise
of General Microbiology
18
1.10
The Modern Era of Microbiology
20
Microbial Sidebar
Solid Media, the
Petri
Plate,
and Pure Cultures
17
Chapter
2
A Brief Journey to
the Microbial World
10
Chapter
4
Cell Structure and Function
in Bacteria and Archaea
66
25
26
2.1
2.2
2.3
2.4
II
2.5
2.6
2.7
III
2.8
2.9
2.10
2.11
SEEING THE VERY SMALL
Some Principles of Light Microscopy
Improving and Adjusting Contrast
in Light Microscopy
27
Imaging Cells in Three Dimensions
30
Electron Microscopy
31
26
CELL STRUCTURE AND
EVOLUTIONARY HISTORY
33
Elements of Cell and Viral Structure
33
Arrangement of
DNA in
Microbial Cells
35
The Evolutionary Tree of Life
37
MICROBIAL DIVERSITY
38
Physiological Diversity of Microorganisms
Bacteria
40
Archaea
44
Eukaryotic Microorganisms
45
39
I
4.1
4.2
II
4.3
4.4
4.5
III
4.6
4.7
4.8
IV
4.9
4.10
4.11
4.12
V
4.13
4.14
4.15
CELL SHAPE AND SIZE
67
Cell Morphology
67
Cell Size and the Significance of Smallness
THE CYTOPLASMIC MEMBRANE
AND TRANSPORT
70
The Cytoplasmic Membrane in Bacteria
and Archaea
70
The Functions of Cytoplasmic Membranes
Transport and Transport Systems
75
68
73
CELL WALLS OF PROKARYOTES
78
The Cell Wall of Bacteria: Peptidoglycan
78
The Outer Membrane of
Gram-Negative Bacteria
82
Cell Walls of Archaea
84
OTHER CELL SURFACE STRUCTURES
AND INCLUSIONS
86
Cell Surface Layers,
Pili,
and Fimbriae
86
Cell Inclusions
87
Gas Vesicles
89
Endospores
91
MICROBIAL LOCOMOTION
95
Flagella
and Motility
96
Gliding Motility
100
Cell Motion as a Behavioral Response:
Microbial Taxes
102
Microbial
Sidebar
How Long Can an Endospore Survive?
94
xix
XX
Contents
Chapter
5
Nutrition, Culture, and Metabolism
of Microorganisms
107
5.1
5.2
5.3
II
5.4
5.5
III
5.6
5.7
5.8
IV
5.9
5.10
5.11
5.12
5.13
5.14
V
5.15
5.16
5.17
5.18
NUTRITION AND CULTURE
OF MICROORGANISMS
108
Microbial Nutrition
108
Culture Media
111
Laboratory Culture of Microorganisms
ENERGETICS AND ENZYMES
114
Bioenergetics
114
Catalysis and Enzymes
116
113
IV TEMPERATURE AND MICROBIAL GROWTH
157
6.12
Effect of Temperature on Microbial Growth
157
6.13
6.14
V
6.15
6.16
6.17
6.18
OXIDATION-REDUCTION AND
ENERGY-RICH COMPOUNDS
1 18
Microbial Growth at Cold Temperatures
159
Microbial Growth at High Temperatures
162
OTHER ENVIRONMENTAL FACTORS
AFFECTING GROWTH
165
Microbial Growth at Low or High
pH 165
Osmotic Effects on Microbial Growth
166
Oxygen and Microbial Growth
168
Toxic Forms of Oxygen
171
Microbiai Sidebar
Microbial Growth in the Real World:
Biofilms
158
121
122
Oxidation-Reduction: Electron Donors
and Electron Acceptors
118
NAD as
a Redox
Electron Carrier
119
Energy-Rich Compounds and Energy Storage
ESSENTIALS OF CATABOLISM
122
Energy Conservation
122
Glycolysis as an Example of Fermentation
Respiration and Membrane-Associated
Electron Carriers
126
Respiration and the Proton Motive Force
127
Carbon Flow in Respiration:
The Citric Acid Cycle
130
Catabolic Diversity
131
ESSENTIALS OF ANABOLISM
133
Biosynthesis of Sugars and Polysaccharides
133
Biosynthesis of
Amino
Acids and Nucleotides
134
Biosynthesis of Fatty Acids and Lipids
135
Regulation of Activity of Biosynthetic Enzymes
UNIT
2
MOLECULAR BIOLOGY
OF MICROORGANISMS
136
Microbial Sidebar
The Products of Yeast Fermentation
and the Pasteur Effect
125
Chapter
6
Microbial Growth
141
I BACTERIAL CELL DIVISION
142
6.1
Cell Growth and Binary Fission
142
6.2
Fts Proteins and Cell Division
142
6.3
MreB and Determinants of Cell Morphology
144
6.4
Peptidoglycan Synthesis and Cell Division
145
II GROWTH OF BACTERIAL
POPULATIONS
147
6.5
Growth Terminology and the Concept
of Exponential Growth
147
6.6
The Mathematics of Exponential Growth
148
6.7
The Microbial Growth Cycle
149
6.8
Continuous Culture: The Chemostat
151
III MEASURING MICROBIAL GROWTH
152
6.9
Measurements of Total Cell Numbers:
Microscopic Counts
153
6.10
Viable Cell Counting
153
6.11
Measurements of Microbial Mass:
Turbidimetric Methods
156
Chapter
7
Essentials of Molecular Biology
175
I GENES AND GENE EXPRESSION
176
7.1
Macromolecules and Genetic Information
176
II
DNA
STRUCTURE
177
7.2
The Double Helix
177
7.3
Supercoiling
180
7.4
Chromosomes and Other Genetic
Elements
181
III
DNA
REPLICATION
182
7.5
Templates and Enzymes
182
7.6
The Replication Fork
184
7.7
Bidirectional Replication
and the Replisome
186
7.8
Proofreading and Termination
188
IV
RNA
SYNTHESIS: TRANSCRIPTION
189
7.9
Overview of Transcription
189
7.10
Sigma Factors and Consensus Sequences
191
7.11
Termination of Transcription
192
7.12
The Unit of Transcription
193
V PROTEIN SYNTHESIS
194
7.13
The Genetic Code
195
7.14
Transfer
RNA
196
7.15
Translation: The Process
of Protein Synthesis
199
7.16
The Incorporation of
Nonstandard
Amino
Acids
202
7.17
Folding and Secreting Proteins
202
Chapter
8
Archaeal and Eukaryotic
Molecular Biology
207
I MOLECULAR BIOLOGY OF ARCHAEA
208
8.1
Chromosomes and
DNA
Replication
in the Archaea
208
Contents
XXI
8.2
Transcription and
RNA Processing
in Archaea
209
8.3
Protein Synthesis in
Archaea
211
8.4
Shared
Features
of Bacteria and Archaea
211
II
8.5
8.6
8.7
8.8
8.9
8.10
EUKARYOTIC GENETICS AND
MOLECULAR BIOLOGY
213
Genes and Chromosomes in Eukarya
213
Overview of Eukaryotic Cell Division
214
Replication of Linear
DNA 215
RNA
Processing
216
Transcription and Translation in the Eukarya
RNA
Interference (RNAi)
222
Microbial Sidebar
Inteins and Protein Splicing
218
220
10.6
10.7
III
10.8
10.9
10.10
10.11
10.12
IV
10.13
10.14
10.15
Viral Attachment and Penetration
259
Production of Viral Nucleic Acid and Protein
VIRAL DIVERSITY
263
Overview of Bacterial Viruses
263
Virulent Bacteriophages and T4
264
Temperate Bacteriophages, Lambda and PI
Overview of Animal Viruses
270
Retroviruses
271
SUBVIRAL
ENTITIES
273
Defective Viruses
273
Viroids
274
Prions
275
261
267
Microbial Sidebar
Did Viruses Invent
DNA?
264
Chapter
9
Regulation of Gene Expression
224
I
9.1
II
9.2
9.3
9.4
III
9.5
9.6
9.7
9.8
IV
9.9
9.10
9.11
9.12
9.13
VI
9.14
9.15
9.16
OVERVIEW OF REGULATION
225
Major Modes of Regulation
225
DNA-BINDING PROTEINS AND REGULATION
OF TRANSCRIPTION
225
DNA-Binding Proteins
226
Negative Control of Transcription: Repression
and Induction
228
Positive Control of Transcription
230
SENSING AND SIGNAL TRANSDUCTION
231
Two-Component Regulatory Systems
231
Quorum Sensing
233
Regulation of Chemotaxis
235
Control of Transcription in Archaea
236
GLOBAL REGULATORY MECHANISMS
Global Control and the lac Operon
237
The Stringent Response
239
Other Global Control Networks
240
REGULATION OF DEVELOPMENT
IN MODEL BACTERIA
242
Sporulation
in Bacillus
242
Caidobacter Differentiation
243
RNA-BASED REGULATION
244
RNA
Regulation and Antisense
RNA
244
Riboswitches
245
Attenuation
246
237
Chapter
11
Principles of Bacterial Genetics
278
I BACTERIAL CHROMOSOMES
AND PLASMIDS
279
11.1
Genetic Map of the Escherichia
coli
Chromosome
279
11.2
Plasmids: General Principles
282
11.3
Types of Plasmids and Their
Biological Significance
283
II MUTATION
285
11.4
Mutations and Mutants
285
11.5
Molecular Basis of Mutation
287
11.6
Mutation Rates
290
11.7
Mutagenesis
290
11.8
Mutagenesis and Carcinogenesis:
The Ames Test
293
III GENETIC EXCHANGE IN PROKARYOTES
294
11.9
Genetic Recombination
295
11.10
Transformation
297
11.11
Transduction
299
11.12
Conjugation: Essential Features
301
11.13
The Formation of Hfr Strains
and Chromosome Mobilization
303
11.14
Complementation
306
11.15
Gene Transfer in Archaea
308
11.16
Mobile
DNA:
Transposable Elements
309
Chapter
12
Genetic Engineering
313
Chapter
10
Overview of Viruses and Virology
251
I VIRUS STRUCTURE AND GROWTH
252
10.1
General Properties of Viruses
252
10.2
Nature of the Virion
253
10.3
The
Viras
Host
256
10.4
Quantification of Viruses
257
II VIRAL REPLICATION
258
10.5
General Features of Virus Replication
258
I
12.1
12.2
12.3
12.4
TOOLS AND TECHNIQUES
OF GENETIC ENGINEERING
314
Restriction and Modification Enzymes
Nucleic Acid Hybridization
and the Southern Blot
316
Essentials of Molecular Cloning
316
Plasmids as Cloning Vectors
318
314
II SEQUENCING. SYNTHESIS.
AND AMPLIFICATION OF
DNA
12.5
Sequencing
DNA 320
320
xxü Contents
Chapter^ (continued)
12.6
Sequencing and Annotating Entire Genomes
322
12.7
Synthesizing
DNA 323
12.8
Amplifying
DNA:
The Polymerase
Chain Reaction
324
III BACTERIAL GENE MANIPULATION
327
12.9
Molecular Methods for Mutagenesis
327
12.10
Gene Fusions and Reporter Genes
329
IV ADVANCED CLONING TECHNIQUES
330
12.11
Hosts for Cloning Vectors
330
12.12
Finding the Right Clone
332
12.13
Shuttle Vectors and Expression Vectors
334
12.14
Bacteriophage Lambda as a Cloning Vector
337
12.15
Vectors for Genomic Cloning and Sequencing
338
Microbiaf Sidebar
DNA
Fingerprinting
326
14.3
Microbial Diversification: Consequences
for Earth's Biosphere
373
14.4
Endosymbiotic Origin of Eukaryotes
374
II MICROBIAL EVOLUTION
377
14.5
The Evolutionary Process
377
14.6
Evolutionary Analysis: Theoretical Aspects
14.7
Evolutionary Analysis: Analytical Methods
14.8
Microbial Phylogeny
381
14.9
Applications of
SSU rRNA
Phylogenetic Methods
384
HI MICROBIAL SYSTEMATICS
385
14.10
Phenotypic Analysis
385
14.11
Genotypie
Analysis
387
14.12
Phylogenetic Analysis
389
14.13
The Species Concept in Microbiology
390
14.14
Classification and Nomenclature
393
377
379
Chapter
13
Microbial Genomics
343
Chapter
15
Bacteria: The Proteobacteria
398
I
13.1
13.2
13.3
13.4
13.5
II
13.6
13.7
13.8
III
13.9
13.10
13.11
13.12
IV
13.13
13.14
344
344
355
UNIT
3
MICROBIAL GENOMES
A Short History of Genomics
344
Prokaryotic Genomes: Sizes and
ORF
Contents
Prokaryotic Genomes: Bioinformatic
Analyses and Gene Distributions
347
The Genomes of Eukaryotic
Organelies
350
Eukaryotic Microbial Genomes
353
GENOME FUNCTION AND REGULATION
Microarrays and the
Transcriptome
355
Proteomics
357
Metabolomics
358
THE EVOLUTION OF GENOMES
359
Gene Families, Duplications, and Deletions
359
Mobile
DNA:
Transposons
and
Insertion Sequences
360
Horizontal Gene Transfer and
Genome Stability
361
Evolution of Virulence: Pathogenicity Islands
362
ENVIRONMENTAL GENOMICS
364
Detecting Uncultured Microorganisms
364
Viral Genomes in Nature
364
Microbial Sidebar
RNA
Editing
352
MiCROBIAL DIVERSITY
Chapter
14
Microbial Evolution
and Systematics
I EARLY EARTH AND THE ORIGIN
AND DIVERSIFICATION OF LIFE
368
14.1
Formation and Early History of Earth
368
14.2
Origin of Cellular Life
369
367
I THE PHYLOGENY OF BACTERIA
399
15.1
Phylogenetic Overview of Bacteria
399
II PHOTOTROPHIC, CHEMOLITHOTROPHIC,
AND METHANOTROPHIC
PROTEOBACTERIA
400
15.2
Purple Phototrophic Bacteria
401
15.3
The Nitrifying Bacteria
403
15.4
Sulfur- and Iron-Oxidizing Bacteria
405
15.5
Hydrogen-Oxidizing Bacteria
408
15.6
Methanotrophs and Methylotrophs
410
III AEROBIC AND FACULTATIVELY AEROBIC
CHEMOORGANOTROPHIC
PROTEOBACTERIA
413
15.7
Pseudomonas and the Pseudomonads
413
15.8
Acetic Acid Bacteria
415
15.9
Free-Living Aerobic, Nitrogen-Fixing Bacteria
416
15.10
Neisseria, Chromobacterium, and Relatives
418
15.11
Enteric Bacteria
419
15.12
Vibrio
,
Aliivibrio
,
and Photobacterium
423
15.13
Rickettsias
425
IV MORPHOLOGICALLY
UNUSUAL PROTEOBACTERIA
427
15.14
Spirilla
427
15.15
Sheathed Proteobacteria: Sphaerotilus
and Leptothrix
430
15.16
Budding and Prosthecate/Stalked Bacteria
431
V DELTA- AND EPSILONPROTEOBACTERIA
436
15.17
Gliding Myxobacteria
436
15.18
Sulfate-
and Sulfur-Reducing Proteobacteria
438
15.19
The Epsilonproteobacteria
441
Chapter
16
Bacteria: Gram-Positive
and Other Bacteria
I OVERVIEW OF GRAM-POSITIVE
AND OTHER BACTERIA
446
445
Contents xxüi
II
GRAM-POSITIVE BACTERIA
AND ACTINOBACTERIA
446
16.1
Nonsporulating, Gram-Positive Bacteria
446
16.2
Endospore-Forming Gram-Positive Bacteria
450
16.3
Cell Wall-Less Gram-Positive Bacteria:
The Mycoplasmas
451
16.4
Actinobacteria: Coryneform and Propionic
Acid Bacteria
456
16.5
Actinobacteria: Mycobacterium
457
16.6
Filamentous Actinobacteria: Streptomyces
and Relatives
459
III CYANOBACTERIA
AND PROCHLOROPHYTES
463
16.7
Cyanobacteria
463
16.8
Prochlorophytes
467
IV CHLAMYDIA
468
16.9
TheChlamydia
468
V PLANCTOMYCES/PIRELLULA
16.10
Planctomyces: A Phylogenetically Unique
Stalked Bacterium
470
VI THE VERRUCOMICROBIA
471
16.11
Verrucomicrobium and Prosthecobacter
471
VII
THE FLAVOBACTERIA
472
16.12
Bacteroides and Flavobacterium
472
16.13
Acidobacteria
473
VIII
THE CYTOPHAGA GROUP
473
16.14
Cytophaga and Relatives
473
IX GREEN SULFUR BACTERIA
474
16.15
Chlorobium and Other Green Sulfur Bacteria
474
X THE SPIROCHETES
477
16.16
Spirochetes
477
XI DEINOCOCCI
480
16.17
Deinococcus and Thermus
480
XII
THE GREEN NONSULFUR BACTERIA
481
16.18
Chloroflexus and Relatives
481
XIII
HYPERTHERMOPHILIC BACTERIA
483
16.19
Thennotoga and Thennodesulfobacterium
483
16.20
Aquifex, Thermocrinis, and Relatives
484
XIV
NITROSPIRA AND DEFERRIBACTER
485
16.21
Nitrospira, Deferribacter, and Relatives
485
Chapter
17
Archaea
I PHYLOGENY AND GENERAL METABOLISM
17.1
Phylogenetic Overview of Archaea
488
17.2
Energy Conservation and Autotrophy
in Archaea
489
II EURYARCHAEOTA
49O
17.3
Extremely Halophilic Archaea
490
487
488
17.4
Methane-Producing Archaea:
Methanogens
494
17.5
Thermoplasmatales
498
17.6
Thermococcales and Methanopyrus
499
17.7
Archaeoglobales
500
17.8
Nanoarchaeum and Aciduliprofundum
501
III CRENARCHAEOTA
503
17.9
Habitats and Energy Metabolism
of Crenarchaeota
503
17.10
Hyperthermophiles from Terrestrial
Volcanic Habitats
504
17.11
Hyperthermophiles from Submarine
Volcanic Habitats
506
17.12
Nonthermophilic Crenarchaeota
509
IV EVOLUTION AND LIFE AT
HIGH TEMPERATURES
510
17.13
An Upper Temperature Limit for
Microbial Life
510
17.14
Adaptations to Life at High Temperature
511
17.15
Hyperthermophilic Archaea, H2, and
Microbial Evolution
513
Chapter
18
Eukaryotic Cell Biology and
Eukaryotic Microorganisms
516
I
18.1
18.2
18.3
18.4
18.5
II
18.6
III
18.7
18.8
18.9
18.10
18.11
18.12
IV
18.13
18.14
18.15
18.16
18.17
18.18
18.19
V
18.20
18.21
EUKARYOTIC CELL
STRUCTURE AND FUNCTION
517
517
Eukaryotic Cell Structure and the Nucleus
Respiratory and Fermentative
Organelies:
The Mitochondrion and the Hydrogenosome
518
Photosynthetic
Organelle:
The
Chloroplast
519
Endosymbiosis: Relationships of Mitochondria
and
Chloroplaste
to Bacteria
520
Other
Organelies
and Eukaryotic
Cell Structures
522
EUKARYOTIC MICROBIAL DIVERSITY
524
Phylogeny of the Eukarya
524
PROTISTS
526
Diplomonads and Parabasalids
526
Euglenozoans
527
Alveolates
528
Stramenopiles
530
Cercozoans and Radiolarians
531
Amoebozoa
532
FUNGI
535
Fungal Physiology, Structure, and Associations
with Other Organisms
535
Fungal Reproduction and Phylogeny
537
Chytridiomycetes
539
Zygomycetes
539
Glomeromycetes
540
Ascomycetes
540
Basidiomycetes
542
UNICELLULAR RED AND GREEN ALGAE
Unicellular Red Algae
543
Unicellular Green Algae
544
543
xxiv Contents
Chapter
19
Viral Diversity
548
t
19.1
19.2
19.3
19.4
И
19.5
III
19.6
19.7
19.8
19.9
IV
19.10
19.11
19.12
19.13
19.14
VIRUSES OF BACTERIA
549
RNA Bacteriophages
549
Single-Stranded
DNA
Bacteriophages
550
Double-Stranded
DNA
Bacteriophages
553
Mu: A
Double-Stranded Transposable
DNA
Bacteriophage
555
20.12
Nitrification
602
20.13
Anammox
603
■••IVF;;.
NITROGEN FIXATION
604
20.14
Nitrogenase and Nitrogen Fixation
604
20.15
Genetics and Regulation of N2 Fixation
608
Microbial Sidebar
Winogradsky and Chemolithoautotrophy
597
VIRUSES OF ARCHAEA
Viruses of Archaea
557
557
Chapter
21
Metabolic Diversity: Catabolism
of Organic Compounds
612
RNA
VIRUSES OF EUKARYOTES
558
Plant
RNA
Viruses
558
Positive-Strand RNA
Viruses of Animals:
Poliovirus
and Coronaviruses
559
Negative-Strand RNA
Viruses of Animals:
Rabies, Influenza, and Related Viruses
562
Double-Stranded
RNA
Viruses: Reoviruses
564
DNA
VIRUSES OF EUKARYOTES
565
Plant
DNA
Viruses
565
Replication of Double-Stranded
DNA
Viruses of Animals
568
Double-Stranded
DNA
Viruses: Herpesviruses
569
Double-Stranded
DNA
Viruses: Pox Viruses
571
Double-Stranded
DNA
Viruses: Adenoviruses
572
V VIRUSES THAT EMPLOY REVERSE
TRANSCRIPTASE
573
19.15
Retroviruses and Hepadnavirus
573
Microbial Sidebar
Mimivirus
and Viral Evolution
566
UNIT
4
METABOLIC DIVERSITY
AND MICROBIAL ECOLOGY
Chapter
20
Metabolic Diversity: Phototrophy,
Autotrophy, Chemolithotrophy,
and Nitrogen Fixation
578
I THE PHOTOTROPHIC WAY OF LIFE
579
20.1
Photosynthesis
579
20.2
Chlorophylls and Bacteriochlorophylls
579
20.3
Carotenoids and Phycobilins
582
20.4
Anoxygenic Photosynthesis
585
20.5
Oxygenic Photosynthesis
589
If AUTOTROPHY
591
20.6
The Calvin Cycle
591
20.7
Other Autotrophic Pathways in Phototrophs
593
III CHEMOLITHOTROPHY
595
20.8
The Energetics of Chemolithotrophy
595
20.9
Hydrogen Oxidation
595
20.10
Oxidation of Reduced Sulfur Compounds
596
20.11
Iron Oxidation
599
flip FERMENTATIONS
613
21.1
Fermentations: Energetic and
Redox
Considerations
613
21.2
Fermentative Diversity: Lactic and Mixed-Acid
Fermentations
615
21.3
Fermentative Diversity: Clostridial and Propionic
Acid Fermentations
618
21.4
Fermentations without Substrate-Level
Phosphorylation
620
21.5
Syntrophy
622
fl|fr ANAEROBIC RESPIRATION
624
21.6
Anaerobic Respiration: General Principles
624
21.7
Nitrate Reduction and Denitrification
625
21.8
Sulfate
and Sulfur Reduction
627
21.9
Acetogenesis
630
21.10
Methanogenesis
631
21.11
Proton Reduction
635
21.12
Other Electron Acceptors
636
21.13
Anoxic Hydrocarbon Oxidation Linked to
Anaerobic Respiration
639
"Ш!
AEROBIC CHEMOORGANOTROPHIC
PROCESSES
641
21.14
Molecular Oxygen as a Reactant in Biochemical
Processes
641
21.15
Aerobic Hydrocarbon Oxidation
642
21.16
Methylotrophy and Methanotrophy
643
21.17
Hexose, Pentose, and Polysaccharide
Metabolism
645
21.18
Organic Acid Metabolism
647
21.19
Lipid
Metabolism
648
Chapter
22
Methods in Microbial Ecology
652
./*!,'.;
CULTURE-DEPENDENT ANALYSES
OF MICROBIAL COMMUNITIES
653
22.1
Enrichment and Isolation
653
22.2
Isolation in Pure Culture
657
II CULTURE-INDEPENDENT ANALYSES
OF MICROBIAL COMMUNITIES
658
22.3
General Staining Methods
659
22.4
FISH
661
22.5
Linking Specific Genes to Specific
Organisms Using PCR
662
22.6
Environmental Genomics
665
Contents xxv
IM
MEASURING
MICROBIAL
ACTIVITIES IN NATURE
666
22.7 Chemical
Assays, Radioisotopic Methods,
and Microelectrodes
666
22.8
Stable Isotopes
669
Chapter
23
Microbial Ecosystems
UNIT
5
673
I PRINCIPLES OF MICROBIAL ECOLOGY
674
23.1
Ecological Concepts
674
23.2
Microbial Ecosystems and
Biogeochemical Cycling
675
•víľ:·
THE MICROBIAL HABITAT
676
23.3
Environments and
Microenvironments 676
23.4
Biofilms:
Microbial Growth on Surfaces
677
23.5
Biofilms:
Advantages and Control
679
III FRESHWATER, SOIL, AND PLANT
MICROBIAL ECOSYSTEMS
680
23.6
Freshwater Environments
680
23.7
Terrestrial Environments
682
23.8
Plants as Microbial Habitats
686
ÍV
MARINE MICROBIAL ECOSYSTEMS
687
23.9
Open Oceans
687
23.10
The Deep Sea and Barophilism
690
Microbial Sidebar
Microbial Life Deep Underground
685
Chapter
24
Nutrient Cycles, Bioremediation,
and
Symbioses
I THE CARBON AND OXYGEN CYCLES
695
24.1
The Carbon Cycle
695
24.2
Syntrophy and Methanogenesis
697
'11.
NITROGEN, SULFUR,
AND IRON CYCLES
699
24.3
The Nitrogen Cycle
700
24.4
The Sulfur Cycle
701
24.5
The Iron Cycle
703
III MICROBIAL BIOREMEDIATION
705
24.6
Microbial Leaching of Ores
705
24.7
Mercury and Heavy Metal
Transformations
708
24.8
Petroleum
Biodegradation 709
24.9 Biodegradation
of Xenobiotics
711
IV ANIMAL-MICROBIAL
SYMBIOSES
714
24.10
The Rumen and Ruminant Animals
714
24.11 Hydrothermal
Vent Microbial Ecosystems
717
24.12
Squia-Aliivibrio Symbiosis
720
V PLANT-MICROBIAL
SYMBIOSES
721
24.13
Lichens and Mycorrhizae
722
24.14
Agrobacterium and Crown Gall Disease
724
24.15
The Legume-Root Nodule Symbiosis
725
PUTTING MICROORGANISMS
TO WORK
Chapter
25
Industrial Microbiology
733
Ж
INDUSTRIAL MICROOGANISMS
AND PRODUCT FORMATION
734
25.1
Industrial Microorganisms and Their Products
734
25.2
Primary and Secondary Metabolites
735
25.3
Characteristics of Large-Scale Fermentations
736
25.4
Scale-Up of Industrial Fermentations
738
Jfjft PRODUCTS FOR THE HEALTH INDUSTRY
739
25.5
Antibiotics: Isolation and Characterization
739
25.6
Industrial Production of Penicillins
and Tetracyclines
742
25.7
Vitamins and
Amino
Acids
744
25.8
Steroids and Other
Biotransformations
745
25.9
Enzymes as Industrial Products
747
ІІЦ!
PRODUCTS FOR THE FOOD INDUSTRY
749
25.10
Wine
749
25.11
Brewing, Distilling, and Commodity Alcohol
751
25.12
Vinegar
755
25.13
Citric Acid and Other Organic Compounds
756
25.14
Yeast as a Food and Food Supplement
757
25.15
Mushrooms as a Food Source
758
Microbial Sidebar
Home Brew
753
694
Chapter
26
Biotechnology
761
■its
26.1
26.2
26.3
26.4
26.5
26.6
26.7
26.8
26.9
26.10
PRODUCTS FROM GENETIC ENGINEERING
762
Overview of Biotechnology
762
Expression of Mammalian Genes in Bacteria
762
Production of Hormones
765
Other Mammalian Proteins and Products
766
Genetically Engineered Vaccines
767
Mining Genomes
769
TRANSGENIC ORGANISMS
770
Engineering Metabolic Pathways in Bacteria
Genetic Engineering of Animals
772
Gene Therapy in Humans
774
Transgenic Plants in Agriculture
775
Microbial Sidebar
Synthetic Biology and Bacterial Photography
770
777
UNIT
6
ANTIMICROBIAL AGENTS
AND PATHOGENICITY
Chapter
27
Microbial Growth Control
779
/■■
W
r
PHYSICAL ANTIMICROBIAL CONTROL
780
27.1
Heat Sterilization
780
xxvi Contents
Chapter
27
(continued)
27.2
Radiation Sterilization
783
27.3
Filter Sterilization
784
II CHEMICAL ANTIMICROBIAL CONTROL
27.4
Chemical Growth Control
786
27.5
Chemical Antimicrobial Agents
for External Use
788
III ANTIMICROBIAL AGENTS USED
IN VIVO
791
27.6
Synthetic Antimicrobial Drugs
793
27.7
Naturally Occurring Antimicrobial Drugs:
Antibiotics
794
27.8 ß-Lactam
Antibiotics: Penicillins
and Cephalosporins
795
27.9
Antibiotics from Prokaryotes
797
IV CONTROL OF VIRUSES AND
EUKARYOTIC PATHOGENS
799
27.10
Antiviral Drugs
799
27.11
Antifungal Drugs
801
V ANTIMICROBIAL DRUG RESISTANCE
AND DRUG DISCOVERY
802
27.12
Antimicrobial Drug Resistance
802
27.13
The Search for New Antimicrobial Drugs
Microbial Sidebar
Preventing Antimicrobial Drug Resistance
Chapter
28
Microbial Interactions
with Humans
786
806
790
811
I
28.1
28.2
28.3
28.4
28.5
II
28.6
28.7
28.8
III
28.9
28.10
28.11
28.12
IV
28.13
28.14
BENEFICIAL MICROBIAL INTERACTIONS
WITH HUMANS
812
Overview of Human-Microbial
Interactions
812
Normal Microbial Flora of the Skin
813
Normal Microbial Flora of the
Oral Cavity
814
Normal Microbial Flora of the
Gastrointestinal Tract
817
Normal Microbial Flora of Other
Body Regions
819
HARMFUL MICROBIAL INTERACTIONS
WITH HUMANS
822
Entry of the Pathogen into the Host
Colonization and Growth
824
Virulence
825
822
VIRULENCE FACTORS AND TOXINS
828
Virulence Factors
828
Exotoxins
828
Enterotoxins
831
Endotoxins
833
HOST FACTORS IN INFECTION
834
Host Risk Factors for Infection
834
Innate Resistance to Infection
836
UNIT
7
Microbial Sidebar
Probiotics
820
IMMUNOLOGY
Chapter
29
Essentials of Immunology
839
I
29.1
29.2
29.3
29.4
II
29.5
29.6
III
29.7
29.8
IV
29.9
29.10
29.11
OVERVIEW OF IMMUNITY
84O
Cells and Organs of the Immune System
840
The Innate Immune Response
843
Inflammation, Fever, and Septic Shock
846
The Adaptive Immune Response
848
ANTIGENS AND ANTIGEN
PRESENTATION
849
Immunogens and Antigens
849
Antigen Presentation to
Τ
Lymphocytes
850
Τ
LYMPHOCYTES
853
T-Cytotoxic Cells and Natural
Killer Cells
853
Т
-Helper
Cells: Activating the Immune
Response
854
ANTIBODIES
855
Antibodies
855
Antibody Production
858
Complement, Antibodies, and Pathogen
Destruction
860
Chapter
30
Immunology in Host Defense
and Disease
865
I
30.1
30.2
30.3
II
30.4
30.5
30.6
III
30.7
30.8
IMMUNITY AND HOST DEFENSE
866
Innate Immunity
866
Adaptive Immunity and
Τ
Cells
867
Adaptive Immunity and Antibodies
868
IMMUNITY AND PREVENTION
OF INFECTIOUS DISEASES
869
Natural Immunity
869
Artificial Immunity and Immunization
870
New Immunization Strategies
872
IMMUNE RESPONSE DISEASES
873
Allergy, Hypersensitivity, and Autoimmunity
873
Superantigens
878
Microbial
Sidebar
The Promise of New Vaccines
875
Chapter
31
Molecular Immunology
881
882
I RECEPTORS AND IMMUNITY
31.1
Innate Immunity and Pattern Recognition
882
31.2
Adaptive Immunity and the Immunoglobulin
Superfamily
885
Contents xxvii
II
31.3
31.4
III
31.5
31.6
IV
31.7
V
31.8
31.9
31.10
UNIT
8
THE MAJOR HISTOCOMPATIBILITY
COMPLEX (MHC)
886
MHC Protein Structure
886
MHC Polymorphism and Antigen Binding
887
ANTIBODIES
888
Antibody Proteins and Antigen Binding
888
Antibody Genes and Diversity
889
Τ
CELL RECEPTORS
891
Τ
Cell Receptors: Proteins, Genes, and Diversity
891
MOLECULAR SIGNALS IN IMMUNITY
893
Clonal Selection and Tolerance
893
Τ
Cell and
В
Cell Activation
895
Cytokines and Chemokines
896
Microbial Sidebar
Drosophila
Toll Receptors
—
An Ancient Response
to Infections
883
DIAGNOSING AND TRACKING
INFECTIOUS DISEASES
II CURRENT EPIDEMICS
944
33.6
The AIDS Pandemic
944
33.7
Healthcare-Associated Infections
945
III
33.8
33.9
33.10
33.11
33.12
UNIT
9
EPIDEMIOLOGY AND PUBLIC HEALTH
947
Public Health Measures for the Control
of Disease
947
Global Health Considerations
950
Emerging and Reemerging Infectious Diseases
951
Biological Warfare and Biological Weapons
957
Anthrax as a Biological Weapon
960
Microbial Sidebar
SARS as a Model of Epidemiological Success
958
MICROBIAL DISEASES
Chapter
34
Person-to-Person Microbial
Diseases
964
Chapter
32
Diagnostic Microbiology
and Immunology
900
I GROWTH-DEPENDENT DIAGNOSTIC
METHODS
901
32.1
Isolation of Pathogens from Clinical
Specimens
901
32.2
Growth-Dependent Identification Methods
906
32.3
Antimicrobial Drug Susceptibility Testing
908
32.4
Safety in the Microbiology Laboratory
911
II IMMUNOLOGY AND DIAGNOSTIC
METHODS
913
32.5
Immunoassays for Infectious Disease
913
32.6
Polyclonal and Monoclonal Antibodies
914
32.7
In Vitro Antigen-Antibody Reactions: Serology
917
32.8
Agglutination
919
32.9
Fluorescent Antibodies
920
32.10
Enzyme-Linked Immunosorbent Assay
and Radioimmunoassay
922
32.11
Immunoblot Procedures
927
III NUCLEIC ACID-BASED DIAGNOSTIC
METHODS
929
32.12
Nucleic Acid Probes and PCR
929
I AIRBORNE TRANSMISSION OF DISEASES
965
34.1
Airborne Pathogens
965
34.2
Streptococcal Diseases
966
34.3
Corynebacterium and Diphtheria
969
34.4
Bordetella and Pertussis
970
34.5
Mycobacterium
,
Tuberculosis, and
Hansens
Disease
971
34.6
Neisseria meningitidis
,
Meningitis,
and Meningococcemia
974
34.7
Viruses and Respiratory Infections
975
34.8
Colds
977
34.9
Influenza
979
II DIRECT CONTACT TRANSMISSION
OF DISEASES
982
34.10
Staphylococcus
982
34.11
Helicobacter pylori and Gastric Ulcers
983
34.12
Hepatitis Viruses
984
III SEXUALLY TRANSMITTED INFECTIONS
986
34.13
Gonorrhea and Syphilis
987
34.14
Chlamydia, Herpes, Trichomoniasis,
and Human Papillomavirus
990
34.15
Acquired Immunodeficiency Syndrome:
AIDS and
HIV 992
Chapter
33
Epidemiology
I PRINCIPLES OF EPIDEMIOLOGY
935
33.1
The Science of Epidemiology
935
33.2
The Vocabulary of Epidemiology
935
33.3
Disease Reservoirs and Epidemics
937
33.4
Infectious Disease Transmission
940
33.5
The Host Community
942
Chapter
35
Vectorborne and Soilborne
Microbial Diseases
1002
934
1003
I ANIMAL-TRANSMITTED DISEASES
35.1
Rabies
1003
35.2
Hantavirus Syndromes
1005
II ARTHROPOD-TRANSMITTED DISEASES
35.3
Rickettsial Diseases
1007
35.4
Lyme Disease
1010
1ОО7
xxviii Contents
Chapter
35
(continued)
35.5
35.6
35.7
III
35.8
35.9
Malaria
1012
West Nile Virus
Plague
1017
1015
SOILBORNE DISEASES
1019
Pathogenic Fungi
1019
Tetanus
1022
Microbial Sidebar
Special Pathogens and Viral Hemorrhagic
Fevers
1006
Chapter
36
Wastewater Treatment, Water
Purification, and
Waterborne
Microbial Diseases
I WASTEWATER MICROBIOLOGY
AND WATER PURIFICATION
1026
36.1
Public Health and Water Quality
1026
36.2
Wastewater and Sewage Treatment
1028
36.3
Drinking Water Purification
1031
II
WATERBORNE
MICROBIAL DISEASES
36.4
Sources of
Waterborne
Infection
1033
36.5
Cholera
1035
36.6
Giardiasis and Cryptosporidiosis
1036
36.7
Legionellosis (Legionnaires' Disease)
1038
36.8
Typhoid Fever and Other
Waterborne
Diseases
1039
1025
1033
Chapter
37
Food Preservation and Foodborne
Microbial Diseases
1043
I FOOD PRESERVATION AND MICROBIAL
GROWTH
1044
37.1
Microbial Growth and Food Spoilage
1044
37.2
Food Preservation
1045
37.3
Fermented Foods
1048
II MICROBIAL SAMPLING AND FOOD
POISONING
1049
37.4
Foodborne Diseases and Microbial Sampling
1050
37.5
Staphylococcal Food Poisoning
1051
37.6
Clostridial Food Poisoning
1052
III FOOD INFECTION
1054
37.7
Salmonellosis
1054
37.8
Pathogenic Escherichia
coli
1055
37.9
Campylobacter
1057
37.10
Listeriosis
1058
37.11
Other Foodborne Infectious Diseases
1058
Microbial Sidebar
Spinach and Escherichia
coli
O157:H7
1056
Appendix
1
Energy Calculations in
Microbial
Bioenergetics A-1
Appendix
2
Bergey's Manual of Systematic Bacteriology,
Second Edition A-5
Glossary G-1
Photo Credits
Index
1-1
P-1 |
| adam_txt |
^^^^^В
Principles of Microbiology
Chapter
1
Microorganisms and Microbiology
1
Chapter
2
A Brief Journey to the Microbial World
25
Chapter
3
Chemistry of Cellular Components
50
Chapter
4
Cell Structure and Function in
Bacteria and Archaea
66
Chapter
5
Nutrition, Culture, and Metabolism
of Microorganisms
107
Chapter
6
Microbial Growth
141
Chapter
22
Methods in Microbial Ecology
Chapter
23
Microbial Ecosystems
Chapter
24
Nutrient Cycles, Bioremediation,
and
Symbioses
652
673
694
UNIT
5
Putting Microorganisms to Work
Chapter
25
Industrial Microbiology
Chapter
26
Biotechnology
733
761
Chapter
7
Chapter
8
Chapter
9
Chapter
10
Chapter
11
Chapter
12
Chapter
13
Chapter
14
Chapter
15
Chapter
16
Chapter
17
Chapter
18
Chapter
19
Chapter
20
Chapter
21
Molecular Biology of Microorganisms
Essentials of Molecular Biology
175
Archaeal and Eukaryotic Molecular Biology
207
Regulation of Gene Expression
224
Overview of Viruses and Virology
251
Principles of Bacterial Genetics
278
Genetic Engineering
313
Microbial Genomics
343
Microbial Diversity
Microbial Evolution and Systematics
Bacteria: The Proteobacteria
Bacteria: Gram-Positive
and Other Bacteria
Archaea
Eukaryotic Cell Biology and Eukaryotic
Microorganisms
Viral Diversity
Metabolic Diversity
and Microbial Ecology
Metabolic Diversity: Phototrophy,
Autotrophy, Chemolithotrophy,
and Nitrogen Fixation
Metabolic Diversity: Catabolism
of Organic Compounds
UNIT
6
Antimicrobial Agents
and Pathogenicity
Chapter
27
Microbial Growth Control
Chapter
28
Microbial Interactions with Humans
779
811
UNIT
7
Immunology
Chapter
29
Essentials of Immunology
Chapter
30
Immunology in Host Defense
and Disease
Chapter
31
Molecular Immunology
839
865
881
367
398
I
UNII
8
Diagnosing and tracking
Infectious Diseases
445
487
Chapter
32
Chapter
33
Diagnostic Microbiology
and Immunology
Epidemiology
900
934
516
548
I
UNIT
9
Microbial Diseases
Chapter
34
Person-to-Person Microbial Diseases
964
Chapter
35
Vectorborne and Soilborne Microbial
Diseases
1002
578
Chapter
36
Wastewater Treatment, Water
Purification, and
Waterborne
Microbial Diseases
1025
612
Chapter
37
Food Preservation and Foodborne
Microbial Diseases
1043
XVIII
Preface
UNIT
1
PRINCIPLES OF
MICROBIOLOGY
Chapter
1
Microorganisms and Microbiology
1
I INTRODUCTION TO MICROBIOLOGY
2
1.1
Microbiology
2
1.2
Microorganisms as Cells
3
1.3
Microorganisms and Their
Natural Environments
5
1.4
The Antiquity and Extent
of Microbial Life
6
1.5
The Impact of Microorganisms
on Humans
7
II PATHWAYS OF DISCOVERY
IN MICROBIOLOGY
10
Chapter
3
Chemistry of Cellular Components
50
I CHEMICAL BONDING. MACROMOLECULES,
AND WATER
51
3.1
Strong and Weak Chemical Bonds
51
3.2
An Overview of Macromolecules and Water
as the Solvent of Life
52
II NONINFORMATIONAL
MACROMOLECULES
55
3.3
Polysaccharides
55
3.4
Lipids
56
III INFORMATIONAL MACROMOLECULES
57
3.5
Nucleic Acids
57
3.6
Amino
Acids and the
Peptide
Bond
59
3.7
Proteins: Primary and Secondary Structure
61
3.8
Proteins: Higher Order Structure
and Denaturation
62
1.6
The Historical Roots of Microbiology:
Hooke, van Leeuwenhoek, and Cohn
1.7
Pasteur and the Defeat of
Spontaneous Generation
12
1.8
Koch, Infectious Disease, and Pure
Culture Microbiology
14
1.9
Microbial Diversity and the Rise
of General Microbiology
18
1.10
The Modern Era of Microbiology
20
Microbial Sidebar
Solid Media, the
Petri
Plate,
and Pure Cultures
17
Chapter
2
A Brief Journey to
the Microbial World
10
Chapter
4
Cell Structure and Function
in Bacteria and Archaea
66
25
26
2.1
2.2
2.3
2.4
II
2.5
2.6
2.7
III
2.8
2.9
2.10
2.11
SEEING THE VERY SMALL
Some Principles of Light Microscopy
Improving and Adjusting Contrast
in Light Microscopy
27
Imaging Cells in Three Dimensions
30
Electron Microscopy
31
26
CELL STRUCTURE AND
EVOLUTIONARY HISTORY
33
Elements of Cell and Viral Structure
33
Arrangement of
DNA in
Microbial Cells
35
The Evolutionary Tree of Life
37
MICROBIAL DIVERSITY
38
Physiological Diversity of Microorganisms
Bacteria
40
Archaea
44
Eukaryotic Microorganisms
45
39
I
4.1
4.2
II
4.3
4.4
4.5
III
4.6
4.7
4.8
IV
4.9
4.10
4.11
4.12
V
4.13
4.14
4.15
CELL SHAPE AND SIZE
67
Cell Morphology
67
Cell Size and the Significance of Smallness
THE CYTOPLASMIC MEMBRANE
AND TRANSPORT
70
The Cytoplasmic Membrane in Bacteria
and Archaea
70
The Functions of Cytoplasmic Membranes
Transport and Transport Systems
75
68
73
CELL WALLS OF PROKARYOTES
78
The Cell Wall of Bacteria: Peptidoglycan
78
The Outer Membrane of
Gram-Negative Bacteria
82
Cell Walls of Archaea
84
OTHER CELL SURFACE STRUCTURES
AND INCLUSIONS
86
Cell Surface Layers,
Pili,
and Fimbriae
86
Cell Inclusions
87
Gas Vesicles
89
Endospores
91
MICROBIAL LOCOMOTION
95
Flagella
and Motility
96
Gliding Motility
100
Cell Motion as a Behavioral Response:
Microbial Taxes
102
Microbial
Sidebar
How Long Can an Endospore Survive?
94
xix
XX
Contents
Chapter
5
Nutrition, Culture, and Metabolism
of Microorganisms
107
5.1
5.2
5.3
II
5.4
5.5
III
5.6
5.7
5.8
IV
5.9
5.10
5.11
5.12
5.13
5.14
V
5.15
5.16
5.17
5.18
NUTRITION AND CULTURE
OF MICROORGANISMS
108
Microbial Nutrition
108
Culture Media
111
Laboratory Culture of Microorganisms
ENERGETICS AND ENZYMES
114
Bioenergetics
114
Catalysis and Enzymes
116
113
IV TEMPERATURE AND MICROBIAL GROWTH
157
6.12
Effect of Temperature on Microbial Growth
157
6.13
6.14
V
6.15
6.16
6.17
6.18
OXIDATION-REDUCTION AND
ENERGY-RICH COMPOUNDS
1 18
Microbial Growth at Cold Temperatures
159
Microbial Growth at High Temperatures
162
OTHER ENVIRONMENTAL FACTORS
AFFECTING GROWTH
165
Microbial Growth at Low or High
pH 165
Osmotic Effects on Microbial Growth
166
Oxygen and Microbial Growth
168
Toxic Forms of Oxygen
171
Microbiai Sidebar
Microbial Growth in the Real World:
Biofilms
158
121
122
Oxidation-Reduction: Electron Donors
and Electron Acceptors
118
NAD as
a Redox
Electron Carrier
119
Energy-Rich Compounds and Energy Storage
ESSENTIALS OF CATABOLISM
122
Energy Conservation
122
Glycolysis as an Example of Fermentation
Respiration and Membrane-Associated
Electron Carriers
126
Respiration and the Proton Motive Force
127
Carbon Flow in Respiration:
The Citric Acid Cycle
130
Catabolic Diversity
131
ESSENTIALS OF ANABOLISM
133
Biosynthesis of Sugars and Polysaccharides
133
Biosynthesis of
Amino
Acids and Nucleotides
134
Biosynthesis of Fatty Acids and Lipids
135
Regulation of Activity of Biosynthetic Enzymes
UNIT
2
MOLECULAR BIOLOGY
OF MICROORGANISMS
136
Microbial Sidebar
The Products of Yeast Fermentation
and the Pasteur Effect
125
Chapter
6
Microbial Growth
141
I BACTERIAL CELL DIVISION
142
6.1
Cell Growth and Binary Fission
142
6.2
Fts Proteins and Cell Division
142
6.3
MreB and Determinants of Cell Morphology
144
6.4
Peptidoglycan Synthesis and Cell Division
145
II GROWTH OF BACTERIAL
POPULATIONS
147
6.5
Growth Terminology and the Concept
of Exponential Growth
147
6.6
The Mathematics of Exponential Growth
148
6.7
The Microbial Growth Cycle
149
6.8
Continuous Culture: The Chemostat
151
III MEASURING MICROBIAL GROWTH
152
6.9
Measurements of Total Cell Numbers:
Microscopic Counts
153
6.10
Viable Cell Counting
153
6.11
Measurements of Microbial Mass:
Turbidimetric Methods
156
Chapter
7
Essentials of Molecular Biology
175
I GENES AND GENE EXPRESSION
176
7.1
Macromolecules and Genetic Information
176
II
DNA
STRUCTURE
177
7.2
The Double Helix
177
7.3
Supercoiling
180
7.4
Chromosomes and Other Genetic
Elements
181
III
DNA
REPLICATION
182
7.5
Templates and Enzymes
182
7.6
The Replication Fork
184
7.7
Bidirectional Replication
and the Replisome
186
7.8
Proofreading and Termination
188
IV
RNA
SYNTHESIS: TRANSCRIPTION
189
7.9
Overview of Transcription
189
7.10
Sigma Factors and Consensus Sequences
191
7.11
Termination of Transcription
192
7.12
The Unit of Transcription
193
V PROTEIN SYNTHESIS
194
7.13
The Genetic Code
195
7.14
Transfer
RNA
196
7.15
Translation: The Process
of Protein Synthesis
199
7.16
The Incorporation of
Nonstandard
Amino
Acids
202
7.17
Folding and Secreting Proteins
202
Chapter
8
Archaeal and Eukaryotic
Molecular Biology
207
I MOLECULAR BIOLOGY OF ARCHAEA
208
8.1
Chromosomes and
DNA
Replication
in the Archaea
208
Contents
XXI
8.2
Transcription and
RNA Processing
in Archaea
209
8.3
Protein Synthesis in
Archaea
211
8.4
Shared
Features
of Bacteria and Archaea
211
II
8.5
8.6
8.7
8.8
8.9
8.10
EUKARYOTIC GENETICS AND
MOLECULAR BIOLOGY
213
Genes and Chromosomes in Eukarya
213
Overview of Eukaryotic Cell Division
214
Replication of Linear
DNA 215
RNA
Processing
216
Transcription and Translation in the Eukarya
RNA
Interference (RNAi)
222
Microbial Sidebar
Inteins and Protein Splicing
218
220
10.6
10.7
III
10.8
10.9
10.10
10.11
10.12
IV
10.13
10.14
10.15
Viral Attachment and Penetration
259
Production of Viral Nucleic Acid and Protein
VIRAL DIVERSITY
263
Overview of Bacterial Viruses
263
Virulent Bacteriophages and T4
264
Temperate Bacteriophages, Lambda and PI
Overview of Animal Viruses
270
Retroviruses
271
SUBVIRAL
ENTITIES
273
Defective Viruses
273
Viroids
274
Prions
275
261
267
Microbial Sidebar
Did Viruses Invent
DNA?
264
Chapter
9
Regulation of Gene Expression
224
I
9.1
II
9.2
9.3
9.4
III
9.5
9.6
9.7
9.8
IV
9.9
9.10
9.11
9.12
9.13
VI
9.14
9.15
9.16
OVERVIEW OF REGULATION
225
Major Modes of Regulation
225
DNA-BINDING PROTEINS AND REGULATION
OF TRANSCRIPTION
225
DNA-Binding Proteins
226
Negative Control of Transcription: Repression
and Induction
228
Positive Control of Transcription
230
SENSING AND SIGNAL TRANSDUCTION
231
Two-Component Regulatory Systems
231
Quorum Sensing
233
Regulation of Chemotaxis
235
Control of Transcription in Archaea
236
GLOBAL REGULATORY MECHANISMS
Global Control and the lac Operon
237
The Stringent Response
239
Other Global Control Networks
240
REGULATION OF DEVELOPMENT
IN MODEL BACTERIA
242
Sporulation
in Bacillus
242
Caidobacter Differentiation
243
RNA-BASED REGULATION
244
RNA
Regulation and Antisense
RNA
244
Riboswitches
245
Attenuation
246
237
Chapter
11
Principles of Bacterial Genetics
278
I BACTERIAL CHROMOSOMES
AND PLASMIDS
279
11.1
Genetic Map of the Escherichia
coli
Chromosome
279
11.2
Plasmids: General Principles
282
11.3
Types of Plasmids and Their
Biological Significance
283
II MUTATION
285
11.4
Mutations and Mutants
285
11.5
Molecular Basis of Mutation
287
11.6
Mutation Rates
290
11.7
Mutagenesis
290
11.8
Mutagenesis and Carcinogenesis:
The Ames Test
293
III GENETIC EXCHANGE IN PROKARYOTES
294
11.9
Genetic Recombination
295
11.10
Transformation
297
11.11
Transduction
299
11.12
Conjugation: Essential Features
301
11.13
The Formation of Hfr Strains
and Chromosome Mobilization
303
11.14
Complementation
306
11.15
Gene Transfer in Archaea
308
11.16
Mobile
DNA:
Transposable Elements
309
Chapter
12
Genetic Engineering
313
Chapter
10
Overview of Viruses and Virology
251
I VIRUS STRUCTURE AND GROWTH
252
10.1
General Properties of Viruses
252
10.2
Nature of the Virion
253
10.3
The
Viras
Host
256
10.4
Quantification of Viruses
257
II VIRAL REPLICATION
258
10.5
General Features of Virus Replication
258
I
12.1
12.2
12.3
12.4
TOOLS AND TECHNIQUES
OF GENETIC ENGINEERING
314
Restriction and Modification Enzymes
Nucleic Acid Hybridization
and the Southern Blot
316
Essentials of Molecular Cloning
316
Plasmids as Cloning Vectors
318
314
II SEQUENCING. SYNTHESIS.
AND AMPLIFICATION OF
DNA
12.5
Sequencing
DNA 320
320
xxü Contents
Chapter^ (continued)
12.6
Sequencing and Annotating Entire Genomes
322
12.7
Synthesizing
DNA 323
12.8
Amplifying
DNA:
The Polymerase
Chain Reaction
324
III BACTERIAL GENE MANIPULATION
327
12.9
Molecular Methods for Mutagenesis
327
12.10
Gene Fusions and Reporter Genes
329
IV ADVANCED CLONING TECHNIQUES
330
12.11
Hosts for Cloning Vectors
330
12.12
Finding the Right Clone
332
12.13
Shuttle Vectors and Expression Vectors
334
12.14
Bacteriophage Lambda as a Cloning Vector
337
12.15
Vectors for Genomic Cloning and Sequencing
338
Microbiaf Sidebar
DNA
Fingerprinting
326
14.3
Microbial Diversification: Consequences
for Earth's Biosphere
373
14.4
Endosymbiotic Origin of Eukaryotes
374
II MICROBIAL EVOLUTION
377
14.5
The Evolutionary Process
377
14.6
Evolutionary Analysis: Theoretical Aspects
14.7
Evolutionary Analysis: Analytical Methods
14.8
Microbial Phylogeny
381
14.9
Applications of
SSU rRNA
Phylogenetic Methods
384
HI MICROBIAL SYSTEMATICS
385
14.10
Phenotypic Analysis
385
14.11
Genotypie
Analysis
387
14.12
Phylogenetic Analysis
389
14.13
The Species Concept in Microbiology
390
14.14
Classification and Nomenclature
393
377
379
Chapter
13
Microbial Genomics
343
Chapter
15
Bacteria: The Proteobacteria
398
I
13.1
13.2
13.3
13.4
13.5
II
13.6
13.7
13.8
III
13.9
13.10
13.11
13.12
IV
13.13
13.14
344
344
355
UNIT
3
MICROBIAL GENOMES
A Short History of Genomics
344
Prokaryotic Genomes: Sizes and
ORF
Contents
Prokaryotic Genomes: Bioinformatic
Analyses and Gene Distributions
347
The Genomes of Eukaryotic
Organelies
350
Eukaryotic Microbial Genomes
353
GENOME FUNCTION AND REGULATION
Microarrays and the
Transcriptome
355
Proteomics
357
Metabolomics
358
THE EVOLUTION OF GENOMES
359
Gene Families, Duplications, and Deletions
359
Mobile
DNA:
Transposons
and
Insertion Sequences
360
Horizontal Gene Transfer and
Genome Stability
361
Evolution of Virulence: Pathogenicity Islands
362
ENVIRONMENTAL GENOMICS
364
Detecting Uncultured Microorganisms
364
Viral Genomes in Nature
364
Microbial Sidebar
RNA
Editing
352
MiCROBIAL DIVERSITY
Chapter
14
Microbial Evolution
and Systematics
I EARLY EARTH AND THE ORIGIN
AND DIVERSIFICATION OF LIFE
368
14.1
Formation and Early History of Earth
368
14.2
Origin of Cellular Life
369
367
I THE PHYLOGENY OF BACTERIA
399
15.1
Phylogenetic Overview of Bacteria
399
II PHOTOTROPHIC, CHEMOLITHOTROPHIC,
AND METHANOTROPHIC
PROTEOBACTERIA
400
15.2
Purple Phototrophic Bacteria
401
15.3
The Nitrifying Bacteria
403
15.4
Sulfur- and Iron-Oxidizing Bacteria
405
15.5
Hydrogen-Oxidizing Bacteria
408
15.6
Methanotrophs and Methylotrophs
410
III AEROBIC AND FACULTATIVELY AEROBIC
CHEMOORGANOTROPHIC
PROTEOBACTERIA
413
15.7
Pseudomonas and the Pseudomonads
413
15.8
Acetic Acid Bacteria
415
15.9
Free-Living Aerobic, Nitrogen-Fixing Bacteria
416
15.10
Neisseria, Chromobacterium, and Relatives
418
15.11
Enteric Bacteria
419
15.12
Vibrio
,
Aliivibrio
,
and Photobacterium
423
15.13
Rickettsias
425
IV MORPHOLOGICALLY
UNUSUAL PROTEOBACTERIA
427
15.14
Spirilla
427
15.15
Sheathed Proteobacteria: Sphaerotilus
and Leptothrix
430
15.16
Budding and Prosthecate/Stalked Bacteria
431
V DELTA- AND EPSILONPROTEOBACTERIA
436
15.17
Gliding Myxobacteria
436
15.18
Sulfate-
and Sulfur-Reducing Proteobacteria
438
15.19
The Epsilonproteobacteria
441
Chapter
16
Bacteria: Gram-Positive
and Other Bacteria
I OVERVIEW OF GRAM-POSITIVE
AND OTHER BACTERIA
446
445
Contents xxüi
II
GRAM-POSITIVE BACTERIA
AND ACTINOBACTERIA
446
16.1
Nonsporulating, Gram-Positive Bacteria
446
16.2
Endospore-Forming Gram-Positive Bacteria
450
16.3
Cell Wall-Less Gram-Positive Bacteria:
The Mycoplasmas
451
16.4
Actinobacteria: Coryneform and Propionic
Acid Bacteria
456
16.5
Actinobacteria: Mycobacterium
457
16.6
Filamentous Actinobacteria: Streptomyces
and Relatives
459
III CYANOBACTERIA
AND PROCHLOROPHYTES
463
16.7
Cyanobacteria
463
16.8
Prochlorophytes
467
IV CHLAMYDIA
468
16.9
TheChlamydia
468
V PLANCTOMYCES/PIRELLULA
16.10
Planctomyces: A Phylogenetically Unique
Stalked Bacterium
470
VI THE VERRUCOMICROBIA
471
16.11
Verrucomicrobium and Prosthecobacter
471
VII
THE FLAVOBACTERIA
472
16.12
Bacteroides and Flavobacterium
472
16.13
Acidobacteria
473
VIII
THE CYTOPHAGA GROUP
473
16.14
Cytophaga and Relatives
473
IX GREEN SULFUR BACTERIA
474
16.15
Chlorobium and Other Green Sulfur Bacteria
474
X THE SPIROCHETES
477
16.16
Spirochetes
477
XI DEINOCOCCI
480
16.17
Deinococcus and Thermus
480
XII
THE GREEN NONSULFUR BACTERIA
481
16.18
Chloroflexus and Relatives
481
XIII
HYPERTHERMOPHILIC BACTERIA
483
16.19
Thennotoga and Thennodesulfobacterium
483
16.20
Aquifex, Thermocrinis, and Relatives
484
XIV
NITROSPIRA AND DEFERRIBACTER
485
16.21
Nitrospira, Deferribacter, and Relatives
485
Chapter
17
Archaea
I PHYLOGENY AND GENERAL METABOLISM
17.1
Phylogenetic Overview of Archaea
488
17.2
Energy Conservation and Autotrophy
in Archaea
489
II EURYARCHAEOTA
49O
17.3
Extremely Halophilic Archaea
490
487
488
17.4
Methane-Producing Archaea:
Methanogens
494
17.5
Thermoplasmatales
498
17.6
Thermococcales and Methanopyrus
499
17.7
Archaeoglobales
500
17.8
Nanoarchaeum and Aciduliprofundum
501
III CRENARCHAEOTA
503
17.9
Habitats and Energy Metabolism
of Crenarchaeota
503
17.10
Hyperthermophiles from Terrestrial
Volcanic Habitats
504
17.11
Hyperthermophiles from Submarine
Volcanic Habitats
506
17.12
Nonthermophilic Crenarchaeota
509
IV EVOLUTION AND LIFE AT
HIGH TEMPERATURES
510
17.13
An Upper Temperature Limit for
Microbial Life
510
17.14
Adaptations to Life at High Temperature
511
17.15
Hyperthermophilic Archaea, H2, and
Microbial Evolution
513
Chapter
18
Eukaryotic Cell Biology and
Eukaryotic Microorganisms
516
I
18.1
18.2
18.3
18.4
18.5
II
18.6
III
18.7
18.8
18.9
18.10
18.11
18.12
IV
18.13
18.14
18.15
18.16
18.17
18.18
18.19
V
18.20
18.21
EUKARYOTIC CELL
STRUCTURE AND FUNCTION
517
517
Eukaryotic Cell Structure and the Nucleus
Respiratory and Fermentative
Organelies:
The Mitochondrion and the Hydrogenosome
518
Photosynthetic
Organelle:
The
Chloroplast
519
Endosymbiosis: Relationships of Mitochondria
and
Chloroplaste
to Bacteria
520
Other
Organelies
and Eukaryotic
Cell Structures
522
EUKARYOTIC MICROBIAL DIVERSITY
524
Phylogeny of the Eukarya
524
PROTISTS
526
Diplomonads and Parabasalids
526
Euglenozoans
527
Alveolates
528
Stramenopiles
530
Cercozoans and Radiolarians
531
Amoebozoa
532
FUNGI
535
Fungal Physiology, Structure, and Associations
with Other Organisms
535
Fungal Reproduction and Phylogeny
537
Chytridiomycetes
539
Zygomycetes
539
Glomeromycetes
540
Ascomycetes
540
Basidiomycetes
542
UNICELLULAR RED AND GREEN ALGAE
Unicellular Red Algae
543
Unicellular Green Algae
544
543
xxiv Contents
Chapter
19
Viral Diversity
548
t
19.1
19.2
19.3
19.4
И
19.5
III
19.6
19.7
19.8
19.9
IV
19.10
19.11
19.12
19.13
19.14
VIRUSES OF BACTERIA
549
RNA Bacteriophages
549
Single-Stranded
DNA
Bacteriophages
550
Double-Stranded
DNA
Bacteriophages
553
Mu: A
Double-Stranded Transposable
DNA
Bacteriophage
555
20.12
Nitrification
602
20.13
Anammox
603
■••IVF;;.
NITROGEN FIXATION
604
20.14
Nitrogenase and Nitrogen Fixation
604
20.15
Genetics and Regulation of N2 Fixation
608
Microbial Sidebar
Winogradsky and Chemolithoautotrophy
597
VIRUSES OF ARCHAEA
Viruses of Archaea
557
557
Chapter
21
Metabolic Diversity: Catabolism
of Organic Compounds
612
RNA
VIRUSES OF EUKARYOTES
558
Plant
RNA
Viruses
558
Positive-Strand RNA
Viruses of Animals:
Poliovirus
and Coronaviruses
559
Negative-Strand RNA
Viruses of Animals:
Rabies, Influenza, and Related Viruses
562
Double-Stranded
RNA
Viruses: Reoviruses
564
DNA
VIRUSES OF EUKARYOTES
565
Plant
DNA
Viruses
565
Replication of Double-Stranded
DNA
Viruses of Animals
568
Double-Stranded
DNA
Viruses: Herpesviruses
569
Double-Stranded
DNA
Viruses: Pox Viruses
571
Double-Stranded
DNA
Viruses: Adenoviruses
572
V VIRUSES THAT EMPLOY REVERSE
TRANSCRIPTASE
573
19.15
Retroviruses and Hepadnavirus
573
Microbial Sidebar
Mimivirus
and Viral Evolution
566
UNIT
4
METABOLIC DIVERSITY
AND MICROBIAL ECOLOGY
Chapter
20
Metabolic Diversity: Phototrophy,
Autotrophy, Chemolithotrophy,
and Nitrogen Fixation
578
I THE PHOTOTROPHIC WAY OF LIFE
579
20.1
Photosynthesis
579
20.2
Chlorophylls and Bacteriochlorophylls
579
20.3
Carotenoids and Phycobilins
582
20.4
Anoxygenic Photosynthesis
585
20.5
Oxygenic Photosynthesis
589
If AUTOTROPHY
591
20.6
The Calvin Cycle
591
20.7
Other Autotrophic Pathways in Phototrophs
593
III CHEMOLITHOTROPHY
595
20.8
The Energetics of Chemolithotrophy
595
20.9
Hydrogen Oxidation
595
20.10
Oxidation of Reduced Sulfur Compounds
596
20.11
Iron Oxidation
599
flip FERMENTATIONS
613
21.1
Fermentations: Energetic and
Redox
Considerations
613
21.2
Fermentative Diversity: Lactic and Mixed-Acid
Fermentations
615
21.3
Fermentative Diversity: Clostridial and Propionic
Acid Fermentations
618
21.4
Fermentations without Substrate-Level
Phosphorylation
620
21.5
Syntrophy
622
fl|fr ANAEROBIC RESPIRATION
624
21.6
Anaerobic Respiration: General Principles
624
21.7
Nitrate Reduction and Denitrification
625
21.8
Sulfate
and Sulfur Reduction
627
21.9
Acetogenesis
630
21.10
Methanogenesis
631
21.11
Proton Reduction
635
21.12
Other Electron Acceptors
636
21.13
Anoxic Hydrocarbon Oxidation Linked to
Anaerobic Respiration
639
"Ш!
AEROBIC CHEMOORGANOTROPHIC
PROCESSES
641
21.14
Molecular Oxygen as a Reactant in Biochemical
Processes
641
21.15
Aerobic Hydrocarbon Oxidation
642
21.16
Methylotrophy and Methanotrophy
643
21.17
Hexose, Pentose, and Polysaccharide
Metabolism
645
21.18
Organic Acid Metabolism
647
21.19
Lipid
Metabolism
648
Chapter
22
Methods in Microbial Ecology
652
./*!,'.;
CULTURE-DEPENDENT ANALYSES
OF MICROBIAL COMMUNITIES
653
22.1
Enrichment and Isolation
653
22.2
Isolation in Pure Culture
657
II CULTURE-INDEPENDENT ANALYSES
OF MICROBIAL COMMUNITIES
658
22.3
General Staining Methods
659
22.4
FISH
661
22.5
Linking Specific Genes to Specific
Organisms Using PCR
662
22.6
Environmental Genomics
665
Contents xxv
IM
MEASURING
MICROBIAL
ACTIVITIES IN NATURE
666
22.7 Chemical
Assays, Radioisotopic Methods,
and Microelectrodes
666
22.8
Stable Isotopes
669
Chapter
23
Microbial Ecosystems
UNIT
5
673
I PRINCIPLES OF MICROBIAL ECOLOGY
674
23.1
Ecological Concepts
674
23.2
Microbial Ecosystems and
Biogeochemical Cycling
675
•víľ:·
THE MICROBIAL HABITAT
676
23.3
Environments and
Microenvironments 676
23.4
Biofilms:
Microbial Growth on Surfaces
677
23.5
Biofilms:
Advantages and Control
679
III FRESHWATER, SOIL, AND PLANT
MICROBIAL ECOSYSTEMS
680
23.6
Freshwater Environments
680
23.7
Terrestrial Environments
682
23.8
Plants as Microbial Habitats
686
ÍV
MARINE MICROBIAL ECOSYSTEMS
687
23.9
Open Oceans
687
23.10
The Deep Sea and Barophilism
690
Microbial Sidebar
Microbial Life Deep Underground
685
Chapter
24
Nutrient Cycles, Bioremediation,
and
Symbioses
I THE CARBON AND OXYGEN CYCLES
695
24.1
The Carbon Cycle
695
24.2
Syntrophy and Methanogenesis
697
'11.
NITROGEN, SULFUR,
AND IRON CYCLES
699
24.3
The Nitrogen Cycle
700
24.4
The Sulfur Cycle
701
24.5
The Iron Cycle
703
III MICROBIAL BIOREMEDIATION
705
24.6
Microbial Leaching of Ores
705
24.7
Mercury and Heavy Metal
Transformations
708
24.8
Petroleum
Biodegradation 709
24.9 Biodegradation
of Xenobiotics
711
IV ANIMAL-MICROBIAL
SYMBIOSES
714
24.10
The Rumen and Ruminant Animals
714
24.11 Hydrothermal
Vent Microbial Ecosystems
717
24.12
Squia-Aliivibrio Symbiosis
720
V PLANT-MICROBIAL
SYMBIOSES
721
24.13
Lichens and Mycorrhizae
722
24.14
Agrobacterium and Crown Gall Disease
724
24.15
The Legume-Root Nodule Symbiosis
725
PUTTING MICROORGANISMS
TO WORK
Chapter
25
Industrial Microbiology
733
Ж
INDUSTRIAL MICROOGANISMS
AND PRODUCT FORMATION
734
25.1
Industrial Microorganisms and Their Products
734
25.2
Primary and Secondary Metabolites
735
25.3
Characteristics of Large-Scale Fermentations
736
25.4
Scale-Up of Industrial Fermentations
738
Jfjft PRODUCTS FOR THE HEALTH INDUSTRY
739
25.5
Antibiotics: Isolation and Characterization
739
25.6
Industrial Production of Penicillins
and Tetracyclines
742
25.7
Vitamins and
Amino
Acids
744
25.8
Steroids and Other
Biotransformations
745
25.9
Enzymes as Industrial Products
747
ІІЦ!
PRODUCTS FOR THE FOOD INDUSTRY
749
25.10
Wine
749
25.11
Brewing, Distilling, and Commodity Alcohol
751
25.12
Vinegar
755
25.13
Citric Acid and Other Organic Compounds
756
25.14
Yeast as a Food and Food Supplement
757
25.15
Mushrooms as a Food Source
758
Microbial Sidebar
Home Brew
753
694
Chapter
26
Biotechnology
761
■its
26.1
26.2
26.3
26.4
26.5
26.6
26.7
26.8
26.9
26.10
PRODUCTS FROM GENETIC ENGINEERING
762
Overview of Biotechnology
762
Expression of Mammalian Genes in Bacteria
762
Production of Hormones
765
Other Mammalian Proteins and Products
766
Genetically Engineered Vaccines
767
Mining Genomes
769
TRANSGENIC ORGANISMS
770
Engineering Metabolic Pathways in Bacteria
Genetic Engineering of Animals
772
Gene Therapy in Humans
774
Transgenic Plants in Agriculture
775
Microbial Sidebar
Synthetic Biology and Bacterial Photography
770
777
UNIT
6
ANTIMICROBIAL AGENTS
AND PATHOGENICITY
Chapter
27
Microbial Growth Control
779
/■■
W
r
PHYSICAL ANTIMICROBIAL CONTROL
780
27.1
Heat Sterilization
780
xxvi Contents
Chapter
27
(continued)
27.2
Radiation Sterilization
783
27.3
Filter Sterilization
784
II CHEMICAL ANTIMICROBIAL CONTROL
27.4
Chemical Growth Control
786
27.5
Chemical Antimicrobial Agents
for External Use
788
III ANTIMICROBIAL AGENTS USED
IN VIVO
791
27.6
Synthetic Antimicrobial Drugs
793
27.7
Naturally Occurring Antimicrobial Drugs:
Antibiotics
794
27.8 ß-Lactam
Antibiotics: Penicillins
and Cephalosporins
795
27.9
Antibiotics from Prokaryotes
797
IV CONTROL OF VIRUSES AND
EUKARYOTIC PATHOGENS
799
27.10
Antiviral Drugs
799
27.11
Antifungal Drugs
801
V ANTIMICROBIAL DRUG RESISTANCE
AND DRUG DISCOVERY
802
27.12
Antimicrobial Drug Resistance
802
27.13
The Search for New Antimicrobial Drugs
Microbial Sidebar
Preventing Antimicrobial Drug Resistance
Chapter
28
Microbial Interactions
with Humans
786
806
790
811
I
28.1
28.2
28.3
28.4
28.5
II
28.6
28.7
28.8
III
28.9
28.10
28.11
28.12
IV
28.13
28.14
BENEFICIAL MICROBIAL INTERACTIONS
WITH HUMANS
812
Overview of Human-Microbial
Interactions
812
Normal Microbial Flora of the Skin
813
Normal Microbial Flora of the
Oral Cavity
814
Normal Microbial Flora of the
Gastrointestinal Tract
817
Normal Microbial Flora of Other
Body Regions
819
HARMFUL MICROBIAL INTERACTIONS
WITH HUMANS
822
Entry of the Pathogen into the Host
Colonization and Growth
824
Virulence
825
822
VIRULENCE FACTORS AND TOXINS
828
Virulence Factors
828
Exotoxins
828
Enterotoxins
831
Endotoxins
833
HOST FACTORS IN INFECTION
834
Host Risk Factors for Infection
834
Innate Resistance to Infection
836
UNIT
7
Microbial Sidebar
Probiotics
820
IMMUNOLOGY
Chapter
29
Essentials of Immunology
839
I
29.1
29.2
29.3
29.4
II
29.5
29.6
III
29.7
29.8
IV
29.9
29.10
29.11
OVERVIEW OF IMMUNITY
84O
Cells and Organs of the Immune System
840
The Innate Immune Response
843
Inflammation, Fever, and Septic Shock
846
The Adaptive Immune Response
848
ANTIGENS AND ANTIGEN
PRESENTATION
849
Immunogens and Antigens
849
Antigen Presentation to
Τ
Lymphocytes
850
Τ
LYMPHOCYTES
853
T-Cytotoxic Cells and Natural
Killer Cells
853
Т
-Helper
Cells: Activating the Immune
Response
854
ANTIBODIES
855
Antibodies
855
Antibody Production
858
Complement, Antibodies, and Pathogen
Destruction
860
Chapter
30
Immunology in Host Defense
and Disease
865
I
30.1
30.2
30.3
II
30.4
30.5
30.6
III
30.7
30.8
IMMUNITY AND HOST DEFENSE
866
Innate Immunity
866
Adaptive Immunity and
Τ
Cells
867
Adaptive Immunity and Antibodies
868
IMMUNITY AND PREVENTION
OF INFECTIOUS DISEASES
869
Natural Immunity
869
Artificial Immunity and Immunization
870
New Immunization Strategies
872
IMMUNE RESPONSE DISEASES
873
Allergy, Hypersensitivity, and Autoimmunity
873
Superantigens
878
Microbial
Sidebar
The Promise of New Vaccines
875
Chapter
31
Molecular Immunology
881
882
I RECEPTORS AND IMMUNITY
31.1
Innate Immunity and Pattern Recognition
882
31.2
Adaptive Immunity and the Immunoglobulin
Superfamily
885
Contents xxvii
II
31.3
31.4
III
31.5
31.6
IV
31.7
V
31.8
31.9
31.10
UNIT
8
THE MAJOR HISTOCOMPATIBILITY
COMPLEX (MHC)
886
MHC Protein Structure
886
MHC Polymorphism and Antigen Binding
887
ANTIBODIES
888
Antibody Proteins and Antigen Binding
888
Antibody Genes and Diversity
889
Τ
CELL RECEPTORS
891
Τ
Cell Receptors: Proteins, Genes, and Diversity
891
MOLECULAR SIGNALS IN IMMUNITY
893
Clonal Selection and Tolerance
893
Τ
Cell and
В
Cell Activation
895
Cytokines and Chemokines
896
Microbial Sidebar
Drosophila
Toll Receptors
—
An Ancient Response
to Infections
883
DIAGNOSING AND TRACKING
INFECTIOUS DISEASES
II CURRENT EPIDEMICS
944
33.6
The AIDS Pandemic
944
33.7
Healthcare-Associated Infections
945
III
33.8
33.9
33.10
33.11
33.12
UNIT
9
EPIDEMIOLOGY AND PUBLIC HEALTH
947
Public Health Measures for the Control
of Disease
947
Global Health Considerations
950
Emerging and Reemerging Infectious Diseases
951
Biological Warfare and Biological Weapons
957
Anthrax as a Biological Weapon
960
Microbial Sidebar
SARS as a Model of Epidemiological Success
958
MICROBIAL DISEASES
Chapter
34
Person-to-Person Microbial
Diseases
964
Chapter
32
Diagnostic Microbiology
and Immunology
900
I GROWTH-DEPENDENT DIAGNOSTIC
METHODS
901
32.1
Isolation of Pathogens from Clinical
Specimens
901
32.2
Growth-Dependent Identification Methods
906
32.3
Antimicrobial Drug Susceptibility Testing
908
32.4
Safety in the Microbiology Laboratory
911
II IMMUNOLOGY AND DIAGNOSTIC
METHODS
913
32.5
Immunoassays for Infectious Disease
913
32.6
Polyclonal and Monoclonal Antibodies
914
32.7
In Vitro Antigen-Antibody Reactions: Serology
917
32.8
Agglutination
919
32.9
Fluorescent Antibodies
920
32.10
Enzyme-Linked Immunosorbent Assay
and Radioimmunoassay
922
32.11
Immunoblot Procedures
927
III NUCLEIC ACID-BASED DIAGNOSTIC
METHODS
929
32.12
Nucleic Acid Probes and PCR
929
I AIRBORNE TRANSMISSION OF DISEASES
965
34.1
Airborne Pathogens
965
34.2
Streptococcal Diseases
966
34.3
Corynebacterium and Diphtheria
969
34.4
Bordetella and Pertussis
970
34.5
Mycobacterium
,
Tuberculosis, and
Hansens
Disease
971
34.6
Neisseria meningitidis
,
Meningitis,
and Meningococcemia
974
34.7
Viruses and Respiratory Infections
975
34.8
Colds
977
34.9
Influenza
979
II DIRECT CONTACT TRANSMISSION
OF DISEASES
982
34.10
Staphylococcus
982
34.11
Helicobacter pylori and Gastric Ulcers
983
34.12
Hepatitis Viruses
984
III SEXUALLY TRANSMITTED INFECTIONS
986
34.13
Gonorrhea and Syphilis
987
34.14
Chlamydia, Herpes, Trichomoniasis,
and Human Papillomavirus
990
34.15
Acquired Immunodeficiency Syndrome:
AIDS and
HIV 992
Chapter
33
Epidemiology
I PRINCIPLES OF EPIDEMIOLOGY
935
33.1
The Science of Epidemiology
935
33.2
The Vocabulary of Epidemiology
935
33.3
Disease Reservoirs and Epidemics
937
33.4
Infectious Disease Transmission
940
33.5
The Host Community
942
Chapter
35
Vectorborne and Soilborne
Microbial Diseases
1002
934
1003
I ANIMAL-TRANSMITTED DISEASES
35.1
Rabies
1003
35.2
Hantavirus Syndromes
1005
II ARTHROPOD-TRANSMITTED DISEASES
35.3
Rickettsial Diseases
1007
35.4
Lyme Disease
1010
1ОО7
xxviii Contents
Chapter
35
(continued)
35.5
35.6
35.7
III
35.8
35.9
Malaria
1012
West Nile Virus
Plague
1017
1015
SOILBORNE DISEASES
1019
Pathogenic Fungi
1019
Tetanus
1022
Microbial Sidebar
Special Pathogens and Viral Hemorrhagic
Fevers
1006
Chapter
36
Wastewater Treatment, Water
Purification, and
Waterborne
Microbial Diseases
I WASTEWATER MICROBIOLOGY
AND WATER PURIFICATION
1026
36.1
Public Health and Water Quality
1026
36.2
Wastewater and Sewage Treatment
1028
36.3
Drinking Water Purification
1031
II
WATERBORNE
MICROBIAL DISEASES
36.4
Sources of
Waterborne
Infection
1033
36.5
Cholera
1035
36.6
Giardiasis and Cryptosporidiosis
1036
36.7
Legionellosis (Legionnaires' Disease)
1038
36.8
Typhoid Fever and Other
Waterborne
Diseases
1039
1025
1033
Chapter
37
Food Preservation and Foodborne
Microbial Diseases
1043
I FOOD PRESERVATION AND MICROBIAL
GROWTH
1044
37.1
Microbial Growth and Food Spoilage
1044
37.2
Food Preservation
1045
37.3
Fermented Foods
1048
II MICROBIAL SAMPLING AND FOOD
POISONING
1049
37.4
Foodborne Diseases and Microbial Sampling
1050
37.5
Staphylococcal Food Poisoning
1051
37.6
Clostridial Food Poisoning
1052
III FOOD INFECTION
1054
37.7
Salmonellosis
1054
37.8
Pathogenic Escherichia
coli
1055
37.9
Campylobacter
1057
37.10
Listeriosis
1058
37.11
Other Foodborne Infectious Diseases
1058
Microbial Sidebar
Spinach and Escherichia
coli
O157:H7
1056
Appendix
1
Energy Calculations in
Microbial
Bioenergetics A-1
Appendix
2
Bergey's Manual of Systematic Bacteriology,
Second Edition A-5
Glossary G-1
Photo Credits
Index
1-1
P-1 |
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| any_adam_object_boolean | 1 |
| author_GND | (DE-588)122334507 (DE-588)136686982 |
| building | Verbundindex |
| bvnumber | BV023169914 |
| classification_rvk | WF 1000 WF 2000 |
| classification_tum | BIO 250f |
| ctrlnum | (OCoLC)836726849 (DE-599)BVBBV023169914 |
| dewey-full | 579 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 579 - Microorganisms, fungi & algae |
| dewey-raw | 579 |
| dewey-search | 579 |
| dewey-sort | 3579 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| discipline_str_mv | Biologie |
| edition | 12. ed., internat. ed. |
| format | Book |
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| genre | (DE-588)4123623-3 Lehrbuch gnd-content |
| genre_facet | Lehrbuch |
| id | DE-604.BV023169914 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:57:13Z |
| indexdate | 2024-07-20T07:39:56Z |
| institution | BVB |
| isbn | 9780321536150 0321536150 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-016356594 |
| oclc_num | 836726849 |
| open_access_boolean | |
| owner | DE-703 DE-20 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-M49 DE-BY-TUM DE-858 DE-634 |
| owner_facet | DE-703 DE-20 DE-355 DE-BY-UBR DE-19 DE-BY-UBM DE-M49 DE-BY-TUM DE-858 DE-634 |
| physical | Getr. Zählung zahlr. Ill., graph Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Pearson, Benjamin Cummings |
| record_format | marc |
| spelling | Brock biology of microorganisms Michael T. Madigan ... Biology of microorganisms 12. ed., internat. ed. San Francisco ; Munich [u.a.] Pearson, Benjamin Cummings 2009 Getr. Zählung zahlr. Ill., graph Darst. txt rdacontent n rdamedia nc rdacarrier Microbiologie Microbiologie ram Mikrobiologe (DE-588)4039199-1 gnd rswk-swf Mikrobiologie (DE-588)4316357-9 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 gnd rswk-swf Biologie (DE-588)4006851-1 gnd rswk-swf (DE-588)4123623-3 Lehrbuch gnd-content Mikrobiologie (DE-588)4316357-9 s DE-604 Mikroorganismus (DE-588)4039226-0 s Biologie (DE-588)4006851-1 s 1\p DE-604 Mikrobiologe (DE-588)4039199-1 s 2\p DE-604 Madigan, Michael T. 1949- Sonstige (DE-588)122334507 oth Brock, Thomas D. 1926-2021 Sonstige (DE-588)136686982 oth Bis 11. Auflage Madigan, Michael T. Brock biology of microorganisms Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016356594&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk 2\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Brock biology of microorganisms Microbiologie Microbiologie ram Mikrobiologe (DE-588)4039199-1 gnd Mikrobiologie (DE-588)4316357-9 gnd Mikroorganismus (DE-588)4039226-0 gnd Biologie (DE-588)4006851-1 gnd |
| subject_GND | (DE-588)4039199-1 (DE-588)4316357-9 (DE-588)4039226-0 (DE-588)4006851-1 (DE-588)4123623-3 |
| title | Brock biology of microorganisms |
| title_alt | Biology of microorganisms |
| title_auth | Brock biology of microorganisms |
| title_exact_search | Brock biology of microorganisms |
| title_exact_search_txtP | Brock biology of microorganisms |
| title_full | Brock biology of microorganisms Michael T. Madigan ... |
| title_fullStr | Brock biology of microorganisms Michael T. Madigan ... |
| title_full_unstemmed | Brock biology of microorganisms Michael T. Madigan ... |
| title_old | Madigan, Michael T. Brock biology of microorganisms |
| title_short | Brock biology of microorganisms |
| title_sort | brock biology of microorganisms |
| topic | Microbiologie Microbiologie ram Mikrobiologe (DE-588)4039199-1 gnd Mikrobiologie (DE-588)4316357-9 gnd Mikroorganismus (DE-588)4039226-0 gnd Biologie (DE-588)4006851-1 gnd |
| topic_facet | Microbiologie Mikrobiologe Mikrobiologie Mikroorganismus Biologie Lehrbuch |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016356594&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT madiganmichaelt brockbiologyofmicroorganisms AT brockthomasd brockbiologyofmicroorganisms AT madiganmichaelt biologyofmicroorganisms AT brockthomasd biologyofmicroorganisms |