Microbial Diversity: Form and Function in Prokaryotes
by Oladele Ogunseitan (Author)
Product Details
Paperback: 312 pages
Publisher: Wiley-Blackwell (December 7, 2004)
Language: English
ISBN-10: 0632047089
Book Description
This book offers the first comprehensive, in-depth treatment of microbial diversity for undergraduate and graduate students. Using a global approach, Microbial Diversity illustrates the impact of microorganisms on ecological and Earth system phenomena.
Accompanied by a devoted website with resources for both instructors and students: www.blackwellpublishing.com/ogunseitan
Uses key ecological and global phenomena to show the continuity of microbial contribution.
Illustrates the importance of microbial diversity for the understanding of global physiochemical and biological processes.
Presents analyses of microscopic, culture, molecular, and phylogenetic systematic methods.
Shows the relevance of microbial diversity to global environmental problems, such as climate change and ozone depletion.
Features numerous illustrations, including over 60 4-color photographs of microbes.
CONTENTS
Foreword ix
Preface xiii
PART I CONCEPTS AND
METHODS 1
1 The concept of microbial species 3
Old and new challenges for assessing microbial
diversity 4
Traditional concepts of species 6
Typological species concept 6
Morphological species concept 7
Biological species concept 7
Evolutionary species concept 8
Other concepts 8
Species concepts for prokaryotes 10
Theoretical mechanisms of speciation 12
Anagenesis 12
Cladogenesis 13
Macroevolution theories 13
Species fusion theory 14
Gradual speciation 17
Microbial speciation 18
Conclusion: Emerging concepts and applications of
microbial diversity 19
Questions for further investigation 21
Suggested readings 21
2 Microscopic methods for assessing
microbial diversity 23
Advances in instrumentation and methodology 23
Basic light microscopy 24
Electron microscopy 24
Specialized light microscopy 26
Microscopic video image analysis 27
Objectives for microscopic analysis in microbial
diversity assessment 27
Microbial cell morphological types 28
Multicellular organization in microbial colonies 29
Relative abundance of species in a community 29
Cell–cell interactions 30
Viability and metabolic activities 32
Cell components 33
Predation and parasitism that regulate
populations 33
Differentiation and life cycles 36
Fossil microorganisms 36
Conclusion 38
Questions for further investigation 41
Suggested readings 41
3 Culture methods 43
Cultivation and diversity assessment 43
Axenic cultures 47
Modeling microbial nutrition 47
Microbial trophic systems 48
Aeration 48
Carbon and energy sources 49
Selective growth conditions 50
Microcosm cultures 50
Somnicells and microbial diversity assessment 51
Conclusion 56
Questions for further investigation 56
Suggested readings 56
4 Molecular and genomic methods 58
The molecular context of microbial diversity 58
Interpretation of molecular diversity 59
Nucleic acid sequence comparisons 60
Specific nucleic acid-based methods 61
Signature lipid biomarkers 66
Protein profiles 69
Molecular microarray systems 70
Conclusion 71
Questions for further investigation 71
Suggested readings 71
5 Phylogenetic analysis 73
The rationale for phylogenetic trees 73
Multiple sequence alignments 75
Constructing phylogenetic trees from aligned
sequences 75
Interpreting phylogenetic trees 76
Case study of phylogenetic relationships and
niche diversity 77
Conclusion 82
Questions for further investigation 84
Suggested readings 84
PART II PRINCIPLES AND
APPLICATIONS 85
6 Environmental evolution 87
Biogenesis 87
The case for panspermia 89
The history of microbial diversity in stromatolites
(microbialites) 94
Contemporary microbial mats 96
Microbial life and evolution in extreme
environments 101
The emergence of multicellularity and eukaryosis,
and their consequences for environmental
evolution 104
Endosymbiosis 104
Biotic effects on the evolution of Earth’s
atmosphere 106
Practical aspects of microbial diversity and
environmental evolution 107
Hydrogenesis 107
Methanogenesis 108
Carbon sequestration 109
Conclusion 109
Questions for further investigation 110
Suggested readings 110
7 Biogeochemical cycling of carbon
and nitrogen 112
The Earth as an integrated biogeochemical system 113
Integrative research on biogeochemical cycling 116
The carbon cycle 119
Photosynthesis 122
Methanogenesis 125
Methanotrophy 131
Heterotrophy 134
Biochemical and phylogenetic range of
heterotrophy 139
The nitrogen cycle 141
Nitrogen fixation 143
Evolutionary history of biological nitrogen
fixation 144
Nitrogen fixation and environmental change 149
Ammonification and nitrification 151
Ammonification 151
Nitrification 151
Denitrification 154
The global dimension of the nitrogen cycle:
Prospects and challenges 156
Conclusion 157
Questions for further investigation 157
Suggested readings 157
8 Biogeochemical cycling of
phosphorus, sulfur, metals, and trace
elements 159
The phosphorus cycle 160
Phosphine cycling 164
The sulfur cycle 165
Desulfuration 165
Sulfur oxidation 169
Sulfur reduction 170
Prospects and challenges of the sulfur cycle 170
Metals and trace element cycles 172
Conclusion 176
Questions for further investigation 177
Suggested readings 177
9 Cross-species interactions among
prokaryotes 178
Quorum sensing 179
Interactions with viruses 183
Aquatic viruses 184
Soil viruses 187
Prokaryotic interactions and genetic exchange 189
Microbial consortia and the crisis of isolation 191
Natural antibiosis and microbial diversity 193
Conclusion 196
Questions for further investigation 197
Suggested readings 197
10 Interactions between microorganisms
and large eukaryotes 198
Microbial diversity and geography 198
Plant diseases 199
Impacts of global environmental change on
microbial pathogens and plant diseases 205
Animal diseases 209
Mad cow disease 210
Foot and mouth disease 212
Human diseases 213
Tuberculosis 213
Cholera 216
Diseases of marine organisms 218
The beneficial effects of microbe–eukaryote
interactions 220 Conclusion 222
Questions for further investigation 223
Suggested readings 223
11 Microbial diversity and global
environmental issues 225
Microbial diversity and indexes of environmental
change 226
Quantitative measures of species diversity 227
Global climate change 233
Stratospheric ozone depletion 235
Toxic chemical pollution 237
Conservation of global biodiversity 238
Conclusion 241
Questions for further investigation 242
Suggested readings 242
Appendix 1 Partial list of sequenced microbial
genomes 243
Glossary 251
References 258
Index 287
