Principles of microbial diversity:
Saved in:
| Main Author: | |
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| Format: | Book |
| Language: | English |
| Published: |
Washington, D.C.
ASM Press
2015
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XVI, 390 S. Ill. |
| ISBN: | 9781555814427 |
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Record in the Search Index
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| adam_text | PRINCIPLES OF
Microbial
Diversity
JAMES W BROWN
Department of Biological Sciences
North Carolina State University
Raleigh, North Carolina
A
ASM
PRESS
Washington, DC
Contents
Preface xi
Acknowledgments xiii
About the Author xv
SECTIONI
Introduction to Microbial Diversity 3
1 What Is Microbial Diversity? 5
Facets of microbial diversity 5
The fundamental similarity of all living things 11
2 Context and Historical Baggage 15
The evolution of evolutionary thought 15
Taxonomy and phylogeny 21
The false eukaryote-prokaryote dichotomy 22
3 Phylogenetic Information 25
Deciding which organisms and sequences to use in the analysis 26
Obtaining the required sequence data 29
Assembling sequences in a multiple-sequence alignment 32
4 Constructing a Phylogenetic Tree 41
Tree construction: the neighbor-joining method 42
How to read a phylogenetic tree 51
Example analysis 57
vii
5 Tree Construction Complexities 63
Substitution models 63
Treeing algorithms 67
Bootstrapping 69
6 Alternatives to Small-Subunit rRNA Analysis 73
SSU rRNA cannot be used to distinguish closely related organisms
Alternative sequences 74
Alternatives to sequence-based method^ 78
7 The Tree of Life 85
Major lessons of the Big Tree of Life 85
Rooting the Tree of Life 88
The caveat of horizontal transfer 90
SECTIONII
The Microbial Zoo 95
8 Primitive Thermophilic Bacteria 97
Phylum Aquificae (Aquifex and relatives) 98
Phylum Thermotogae (Thermotoga and relatives) 102
Other primitive thermophiles 104
Thermophilic ancestry of Bacteria 105
Life at high temperatures 105
9 Green Phototrophic Bacteria 111
Phylum Chloroflexi (green nonsulfur bacteria) 112
Phylum Chlorobi (green sulfur bacteria) 117
Phylum Cyanobacteria (blue-green algae) 120
Other green phototrophs 128
Bacterial photosynthesis 128
Carbon fixation 131
10 Proteobacteria 135
Phylum Proteobacteria (purple bacteria and relatives) 135
Class Alphaproteobacteria 137
Class Betaproteobacteria 143
Class Gammaproteobacteria 148
Class Deltaproteobacteria 154
Class Epsilonproteobacteria , 158
The concept of proteobacteria 161
viii Contents
11 Gram-Positive Bacteria 165
What does being gram positive mean? 166
An alternative view of gram-positive bacteria 167
Phylum Firmicutes (low G+C gram-positive bacteria) 167
Phylum Actinobacteria (high G+C gram-positive bacteria) 176
Bacterial development 183
Bacterial multicellularity 184
12 Spirochetes and Bacteroids 187
Phylum Spirochaetae 188
Phylum Bacteroidetes (sphingobacteria or
BacteroideslFlavobacteriumlCytophaga group) 193
Bacterial motility 197
13 Deinococci, Chlamydiae, and Planctomycetes 203
Phylum Deinococcus-Thermus 204
Phylum Chlamydiae (Chlamydia and relatives) 209
Phylum Planctomycetes (Planctomyces and relatives) 213
Reductive evolution in parasites 219
14 Bacterial Phyla with Few or No Cultivated Species 221
How do we know about these organisms? 223
Phyla with few cultivated species 225
Phyla with no cultivated species 232
Phylogenetic groups at all levels are dominated
by uncultivated sequences 234
How much of the microbial world do we know about? 234
15 Archaea 237
General properties of the Archaea 237
Phylum Crenarchaeota 240
Phylum Euryarchaeota 245
Phylum Korarchaeota 256
Phylum Nanoarchaeota 257
Archaea as 258
16 Eukaryotes 261
General properties of the eukaryotes 262
Unikonta 264
Plantae 267
Chromalveolata 270
Rhizaria 274
Excavata 279
Contents i x
17 Viruses and Prions 285
Viruses 285
Prions 292
SECTIONIII
Microbial Populations 297
18 Identification of Uncultivatec^ Organisms 299
19 Sequence-Based Microbial Surveys 307
20 Fluorescent In Situ Hybridization Surveys 323
Fluorescent in situ hybridization 323
Confocal laser scanning microscopy 324
21 Molecular Fingerprinting of Microbial Populations 329
Denaturing gradient gel electrophoresis 330
Terminal restriction fragment length polymorphism 333
22 Linking Phenotype and Phylotype 339
The genomic or metagenomic approach 340
The stable-isotope probing approach 343
SECTIONIV
Conclusion: The Phylogenetic Perspective 351
23 Genomics, Comparative Genomics, and Metagenomics
Genomics 353
Comparative genomics 360
Metagenomics 363
24 Origins and Early Evolution 367
The timescale 367
Ancient microbial fossils 370
The last common ancestor 372
The RNA world hypothesis 373
The emergence of life 376
Index 381
x Contents
|
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| spelling | Brown, James W. Verfasser aut Principles of microbial diversity James W. Brown Washington, D.C. ASM Press 2015 XVI, 390 S. Ill. txt rdacontent n rdamedia nc rdacarrier Mikroorganismus (DE-588)4039226-0 gnd rswk-swf Vielfalt (DE-588)4312811-7 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 s Vielfalt (DE-588)4312811-7 s DE-604 HEBIS Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026934390&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Brown, James W. Principles of microbial diversity Mikroorganismus (DE-588)4039226-0 gnd Vielfalt (DE-588)4312811-7 gnd |
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| title | Principles of microbial diversity |
| title_auth | Principles of microbial diversity |
| title_exact_search | Principles of microbial diversity |
| title_full | Principles of microbial diversity James W. Brown |
| title_fullStr | Principles of microbial diversity James W. Brown |
| title_full_unstemmed | Principles of microbial diversity James W. Brown |
| title_short | Principles of microbial diversity |
| title_sort | principles of microbial diversity |
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