Microbe

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Format: Paperback
Pub. Date: 2005-11-30
Publisher(s): Amer Society for Microbiology
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Summary

Microbe, a brand-new, general microbiology textbook intended for upper-division undergraduate courses, is an exciting introduction to the world of microbes. With a distinct ecological and evolutionary orientation, Microbe invites readers to partake of the most current advances in the field. Written by prominent scientists with practical teaching, textbook writing, and research experience, this new textbook will engage students in the learning process with its clear, reader-friendly style and unique perspective of the field. Microbe is paradigm-driven rather than fact-driven. Key concepts are illustrated by inspiring examples that convey the excitement of the field. This is not a compendium of facts, but rather a textbook in the older, traditional sense: a book that can be used for studying rather than for looking up factual information. The book is divided into seven sections covering the most pertinent information related to the study of microbes, including microbial

Author Biography

Moselio Schaechter, San Diego State University and University of California, San Diego John L. Ingraham, University of California, Davis Frederick C. Neidhardt, University of Michigan, Ann Arbor

Table of Contents

Preface xix
About the Authors xxi
Study Aids xxiii
section I microbial activity
1(16)
the world of microbes
2(15)
Introduction
3(1)
What is a microbe?
3(2)
Having a long past
5(1)
Being small
6(2)
Being many
8(1)
Growing and persisting
8(1)
Colonizing every niche and making Earth inhabitable
9(2)
Shaping the planet
11(1)
Making a living
12(1)
Cooperating for complex endeavors
13(2)
Conclusions
15(1)
Study questions
15(2)
section II structure and function
17(32)
prokaryotic cell structure and function: envelopes and appendages
18(20)
Prokaryotic cells
19(1)
Microscopes
20(2)
Newer microscopes
21(1)
Scanned-proximity probe microscopes
21(1)
Molecular stains
21(1)
Prokaryotes have complex envelopes and appendages
22(1)
The cell membrane
22(1)
How the cell membrane is protected
23(8)
The gram-positive solution
23(3)
The gram-negative solution
26(2)
The acid-fast solution
28(1)
Crystalline surface layers
29(1)
Bacteria without cell walls: the mycoplasmas
30(1)
Cell envelopes of the Archaea
30(1)
Capsules, flagella, and pili: how prokaryotes cope in certain environments
31(6)
Capsules and slime layers
31(1)
Flagella
32(3)
Pili
35(2)
Study questions
37(1)
prokaryotic cell structure and function: the cell interior
38(11)
General observations
39(1)
The nucleoid
39(5)
The cytoplasm
44(1)
Inclusions and vesicles
45(2)
Gas vesicles
45(1)
Organelles for photosynthesis and chemosynthesis
46(1)
Carboxysomes
46(1)
Enterosomes
47(1)
Storage granules and others
47(1)
Conclusions
47(1)
Study questions
48(1)
section III growth
49(134)
growth of microbial populations
50(20)
Introduction
51(2)
How to measure growth of a bacterial culture
53(1)
When should the growth rate be determined?
54(1)
The law of growth
55(2)
Balanced growth
57(1)
Continuous culture
58(1)
How is the physiology of the cells affected by the growth rate?
59(2)
Effects of temperature, hydrostatic pressure, osmotic strength, and pH
61(7)
Temperature
62(1)
Effect on growth rate
62(1)
Classifying the temperature responses of microbes
63(1)
Growth limits at temperature extremes
63(3)
Lethal effects
66(1)
Hydrostatic pressure
67(1)
Osmotic pressure
67(1)
pH
68(1)
Conclusions
68(1)
Study questions
69(1)
making a cell
70(12)
Introduction
71(1)
Growth metabolism: making life from nonlife
71(2)
Framework of growth metabolism
73(7)
Making two from one
74(1)
Assembling cell structures
75(1)
Making macromolecules
76(1)
Synthesizing building blocks
76(1)
Fueling
77(3)
Global effects of growth metabolism
80(1)
Earth's chemical cycles
80(1)
Bioremediation
80(1)
Summary and plan
81(1)
Study questions
81(1)
fueling
82(30)
Overview of fueling reactions
83(1)
Getting energy and reducing power
84(14)
Driving force and its generation
84(3)
Substrate level phosphorylation and fermentation
87(3)
Transmembrane ion gradients
90(1)
Respiration
90(4)
Photosynthesis
94(2)
Enzyme pumps
96(1)
Scalar reactions
96(2)
Oxygen and life
98(1)
Making precursor metabolites: heterotrophy
98(11)
Acquiring nutrients
98(1)
Transport through the OM of gram-negative bacteria
99(1)
Transport through the cell membrane
100(3)
Feeder pathways
103(1)
Central metabolism
104(1)
Common pathways of central metabolism
104(2)
Auxiliary pathways of central metabolism
106(1)
Diversity and flexibility of central metabolism
107(2)
Making precursor metabolites: autotrophy
109(1)
The Calvin cycle
109(1)
Other CO2-fixing cycles
109(1)
Summary
110(1)
Study questions
111(1)
biosynthesis
112(18)
Some general observations
113(5)
Biosynthesis and nutrition
113(1)
Bacterial studies and biosynthetic pathways
113(1)
The concept of a biosynthetic pathway
114(4)
Assimilation of nitrogen
118(4)
Central actors: glutamate and glutamine
118(2)
Synthesis of glutamate and glutamine
120(1)
Getting ammonia
121(1)
Ammonia from dinitrogen
122(1)
Assimilation of sulfur
122(2)
Assimilation of phosphorus
124(1)
Pathways to building blocks
124(3)
Amino acids
124(1)
Nucleotides
125(1)
Sugars and sugar-like derivatives
126(1)
Fatty acids and lipids
126(1)
Summary
127(1)
Study questions
127(3)
building macromolecules
130(38)
Introduction
131(1)
DNA
132(9)
Overview of replication
132(1)
Initiation of replication
133(2)
DNA strand elongation
135(1)
Repair of errors in replication
136(2)
Termination of replication
138(1)
Protecting the DNA
139(1)
Assembly of the nucleoid
140(1)
RNA
141(8)
Overview of transcription
141(1)
RNA-P and its function
141(1)
Products of transcription
142(1)
Initiation of transcription
142(1)
The promoter
143(2)
Starting the transcript
145(1)
RNA chain elongation
145(1)
Termination of transcription
146(1)
Fate of transcripts
146(1)
Life and death of mRNA
147(1)
Modification and assembly of stable RNA
147(1)
Polymerase collision and genome organization
148(1)
Protein
149(13)
Special tempo and mode of protein synthesis
149(2)
Translation
151(1)
Initiation of protein synthesis
151(2)
Polypeptide chain elongation
153(2)
Termination of translation
155(1)
Processing of proteins
156(1)
Covalent modification
156(1)
Protein folding
157(1)
Translocation of proteins
158(4)
Envelope formation
162(4)
Challenges of envelope formation
162(1)
The cell membrane
163(1)
The cell wall
164(1)
The outer membrane
165(1)
Appendages
165(1)
Capsules
166(1)
Concluding remarks
166(1)
Study questions
166(2)
the cell division cycle
168(15)
Introduction
169(1)
Strategies for studying the bacterial cell cycle
169(2)
DNA replication during the cell cycle
171(1)
How is DNA replication regulated?
172(2)
Cell division
174(4)
Morphological considerations
174(1)
How is the septum formed?
175(2)
How does a bacterium find its middle?
177(1)
The connection between cell division and DNA replication
178(2)
Cell division and plasmid replication
180(1)
The prokaryotic equivalent of mitosis
181(1)
Study questions
182(1)
section IV inheritance
183(36)
genetics
184(20)
Introduction
185(1)
Exchange of DNA among prokaryotes
185(10)
Transformation
186(1)
Artificial transformation
187(1)
Natural transformation
187(2)
Transduction
189(1)
Generalized transduction
190(1)
Abortive transduction
191(1)
Specialized transduction
192(1)
Conjugation
193(1)
Conjugation among gram-negative bacteria
193(2)
Conjugation among gram-positive bacteria
195(1)
Mutation and sources of genetic variation among prokaryotes
195(5)
Kinds of mutations
196(1)
Sources of mutations
197(1)
Mutagens
198(2)
Site-directed mutagenesis
200(1)
Genomics
200(2)
Annotation
201(1)
Relatedness
202(1)
Conclusions
202(1)
Study questions
203(1)
evolution
204(15)
Overview
205(1)
Sequence of bases in macromolecules
206(4)
Small-subunit ribosomal RNA
206(2)
Proteins as markers of evolution
208(2)
The universal ancestor
210(1)
Origin of life
211(1)
Mechanisms of bacterial evolution
212(2)
Darwinism
212(1)
Neo-Lamarckism
213(1)
Early eukaryotes and endosymbiosis
214(2)
Evolution of molecules
216(1)
Conclusions
217(1)
Study questions
217(2)
section V physiology
219(70)
coordination and regulation
220(28)
Introduction
221(1)
Evidence for coordination of metabolic reactions
221(2)
Coordination in biosynthesis
221(1)
Coordination in fueling
222(1)
Coordination in polymerization
223(1)
Two modes of regulation
223(2)
Controlling enzyme activity
224(1)
Controlling enzyme amounts
224(1)
Why two modes of regulation?
224(1)
Modulation of protein activity
225(3)
Allosteric interactions
225(1)
Allostery in biosynthesis
226(1)
Allostery in fueling
227(1)
Covalent modification
228(1)
Modulation of protein amounts
228(17)
Regulation of operon expression
229(3)
Mechanisms at site 1: promoter recognition
232(1)
Mechanisms at sites 2, 3, and 4: transcriptional repression, activation, and enhancement
232(1)
Mechanisms at site 5: targeting by sRNAs
233(1)
Mechanisms at site 6: DNA supercoiling
233(1)
Mechanisms at site 7: translational repression
234(1)
Mechanisms at site 8: attenuation
234(4)
Mechanisms at site 9: mRNA stability
238(1)
Mechanisms at site 10: proteolysis
238(1)
Regulation beyond the operon
238(1)
Regulatory units above the operon
239(3)
Examples of global regulatory systems
242(3)
Cooperative interaction of regulatory devices
245(1)
Summary and conclusions: networks for coordination and response
245(1)
Study questions
246(2)
succeeding in the environment
248(26)
Microbes in their habitat
249(1)
Coping with stress as individual cells
250(18)
Nature of stress
250(1)
Overview of stress responses
251(1)
Sensing the environment
251(1)
Complex circuitry for complex responses
252(1)
Monitoring stimulons
253(4)
Major stress response networks
257(1)
Global response networks
257(2)
The ultimate stress response: stationary phase
259(3)
Stress responses and microbial diversity
262(1)
Stress responses and safety in numbers
263(1)
Coping with stress by escaping
263(1)
Flagellar motility
264(3)
Swarming motility
267(1)
Gliding motility
267(1)
Twitching motility
268(1)
Coping with stress by community effort
268(3)
Sensing the population
268(2)
Formation of organized communities
270(1)
Quorum sensing, motility, and biofilm formation
271(1)
Conclusions
271(1)
Study questions
272(2)
differentiation and development
274(15)
Overview
275(2)
Endospores
277(5)
Properties
277(1)
Phylogenetic distribution
277(1)
Formation
278(2)
Programming and regulation
280(1)
Activation of Spo0A
280(1)
Activity of Spo0A~P
281(1)
Sporulation: a group activity
281(1)
Development of Caulobacter crescentus
282(2)
The cell cycle
282(1)
Genetic control of development
283(1)
Development of myxobacteria
284(2)
Regulation of development
285(1)
Other bacteria that undergo differentiation and development
286(1)
Summary
287(1)
Study questions
287(2)
section VI diversity
289(64)
prokaryotic microbes
290(22)
Introduction
291(1)
Making order of prokaryotic diversity
291(2)
Prokaryotic species
293(1)
Extent of prokaryotic diversity
294(3)
Higher taxa of prokaryotes
297(1)
Archaea
297(5)
Crenarchaeota
299(1)
Euryarchaeota
299(1)
Methanogens
300(1)
Extreme halophiles
301(1)
Bacteria
302(8)
Phylum B4: Deinococcus-Thermus
303(3)
Phylum B10: Cyanobacteria
306(1)
Phylum B12: Proteobacteria
307(1)
Alphaproteobacteria
307(2)
Betaproteobacteria and Gammaproteobacteria
309(1)
Phylum B14: Actinobacteria
309(1)
Conclusions
310(1)
Study questions
310(2)
eukaryotic microbes
312(18)
Introduction
313(1)
Fungi
314(5)
The yeasts
315(1)
The fungal lifestyle
316(2)
Why is yeast such a popular genetic tool?
318(1)
Protists
319(9)
Paramecium
319(3)
Plasmodium, the parasite that causes malaria
322(3)
Diatoms and others
325(3)
Conclusions
328(1)
Study questions
328(2)
viruses, viroids, and prions
330(23)
Introduction
331(1)
Size and shape
331(3)
Ecology and classification
334(1)
Viral replication
335(6)
Attachment and penetration
335(2)
Viral nucleic acid synthesis: a theme with variations
337(1)
Making viral proteins
338(2)
Virion assembly and release from the host cell
340(1)
Visualizing and quantitating viral growth
341(1)
Lysogeny and integration into the host genome
341(6)
Introduction
341(2)
How does the genome of a temperate phage become integrated into that of a host cell?
343(1)
How does the integrated viral genome remain quiescent?
344(1)
What causes viral induction?
345(1)
Deciding between lysogeny and lysis
345(1)
What are the genetic consequences of lysogeny?
346(1)
What is the effect of lysogeny in evolution?
347(1)
Viroids and prions
347(3)
Viroids
348(1)
Prions
349(1)
Conclusions
350(1)
Study questions
351(2)
section VII interactions
353(120)
ecology
354(22)
Overview
355(2)
Methods of microbial ecology
357(4)
Enrichment culture
358(1)
Studying microbes in the laboratory and in their natural environments
358(3)
Biogeochemical cycles
361(8)
Carbon and oxygen cycles
361(3)
The nitrogen cycle
364(3)
The sulfur cycle
367(1)
The phosphorus cycle
368(1)
Solid substrates
369(1)
Microbial ecosystems
370(3)
Soil
370(1)
Oceans
370(2)
Microbes, climates, and weather
372(1)
The future of microbial ecology
373(1)
Conclusions
374(1)
Study questions
374(2)
symbiosis, predation, and antibiosis
376(26)
Symbiosis
377(16)
Introduction
377(1)
Mitochondria, chloroplasts, and the origin of eukaryotic cells
378(3)
Bacterial endosymbionts of insects: organelles in the making?
381(4)
Nitrogen-fixing bacteria and the legumes
385(3)
The rumen and its microbes
388(2)
Feeding via a murderous partnership: bacteria and nematodes
390(1)
Leaf-cutting ants, fungi, and bacteria
391(2)
Behavioral changes due to parasitism
393(2)
Reckless rats and fatal attraction
393(1)
The urge to climb
394(1)
When is a flower not a flower?
394(1)
Predation
395(3)
Antibiotics and bacteriocins
398(1)
Conclusions
399(1)
Study questions
400(2)
infection: the vertebrate host
402(22)
Introduction
403(4)
Encounter
404(1)
Entry
405(1)
Becoming established
405(1)
Causing damage
406(1)
Host defenses
407(15)
Innate defenses
408(1)
External barriers
408(1)
In tissues
408(6)
How do microbes evade the innate defenses?
414(2)
Intracellular life
416(1)
Adaptive defenses
416(1)
Antibodies
416(2)
Cell-mediated immunity
418(2)
Immunological memory
420(1)
How do microbes defend themselves against adaptive immunity?
421(1)
Integration of the defense mechanisms
422(1)
Conclusions
422(1)
Study questions
422(2)
infection: the microbe
424(20)
Introduction
425(1)
Case reports
426(16)
Tetanus, a relatively ``simple'' infectious disease
426(2)
An outbreak of hemorrhagic colitis, a complicated infection caused by E. coli strain O157:H7
428(4)
TB, a disease caused mainly by the host response
432(3)
Infectious mononucleosis: the ``kissing disease''
435(2)
How does EBV cause infectious mono?
437(1)
How does EBV persist in the body?
437(1)
How does EBV contribute to cancer?
438(1)
HIV infection and AIDS
438(4)
Conclusions
442(1)
Study questions
442(2)
microbes and human history
444(12)
Introduction
445(2)
How infectious diseases change
447(2)
Microbial agents of warfare
449(4)
Smallpox
449(1)
Anthrax
450(2)
Anthrax as a weapon
452(1)
A microbiological ruse
452(1)
Coping with danger in a microbial world
453(1)
Sanitation
453(1)
Vaccination
453(1)
Antimicrobial drugs
454(1)
Conclusion
454(1)
Suggested reading
455(1)
Study questions
455(1)
putting microbes to work
456(17)
Introduction
457(1)
Various uses of microbes
457(1)
Making better wines: the malolactic fermentation
458(2)
Protecting plants and making snow: ice-minus bacteria
460(2)
Using microbes to make protein drugs: insulin and human growth hormone (hGH)
462(2)
Microbial enzymes: sweeteners from corn
464(3)
Biological insecticides: Bt
467(1)
Undoing pollution: bioremediation
468(3)
Conclusion
471(1)
Study questions
471(2)
Coda 473(2)
Glossary 475(20)
Answers to Study Questions 495(14)
Figure and Table Credits 509(4)
Index 513

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