Microbial diversity

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 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 vi Contents 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