Microbial Diversity

by Oladele Ogunseitan (University of California, Irvine)

• ISBN13: 9780632047086
• ISBN10: 0632047089
• Format: Paperback
• Copyright: 2004-12-01
• Publisher: Wiley-Blackwell

Summary

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. Beginning with a detailed treatment of key concepts and methods, including the nature of prokaryotic species and the use of microscopic, culture, molecular, and phylogenetic systematic methods, it then focuses on environmental evolution, biogeochemical cycling, species interactions, and the linkage between microbial diversity and global environmental change. The book is accompanied by a dedicated website at www.blackwellpublishing.com/ogunseitan with resources for both instructors and students, including: bull; bull;downloadable artwork (also available to instructors on CD-ROM) bull;instructor tips for each chapter, sample syllabi, and sample chapters bull;animations, interactive exercises, links to web resources and further reading. Combining molecular, genetic, physiological, and ecological knowledge, the book presents recent advances in this growing field and connects microbial diversity with ecology and evolution. Microbial Diversity will be a vital resource, as well as an essential text for classroom use.

Author Biography

Oladele Ogunseitan is professor of Environmental Health, Science, and Policy at the University of California, Irvine. He has been a Global Environmental Assessment Fellow at Harvard University, and a Macy Foundation Fellow at the Marine Biological Laboratory in Woods Hole, Massachusetts.

Table of Contents

Foreword	ix
Preface	xiii
PART I CONCEPTS AND METHODS	1	(84)
The concept of microbial species	3	(20)
Old and new challenges for assessing microbial diversity	4	(2)
Traditional concepts of species	6	(4)
Typological species concept	6	(1)
Morphological species concept	7	(1)
Biological species concept	7	(1)
Evolutionary species concept	8	(1)
Other concepts	8	(2)
Species concepts for prokaryotes	10	(2)
Theoretical mechanisms of speciation	12	(6)
Anagenesis	12	(1)
Cladogenesis	13	(1)
Macroevolution theories	13	(1)
Species fusion theory	14	(3)
Gradual speciation	17	(1)
Microbial speciation	18	(1)
Conclusion: Emerging concepts and applications of microbial diversity	19	(2)
Questions for further investigation	21	(1)
Suggested readings	21	(2)
Microscopic methods for assessing microbial diversity	23	(20)
Advances in instrumentation and methodology	23	(4)
Basic light microscopy	24	(1)
Electron microscopy	24	(2)
Specialized light microscopy	26	(1)
Microscopic video image analysis	27	(1)
Objectives for microscopic analysis in microbial diversity assessment	27	(11)
Microbial cell morphological types	28	(1)
Multicellular organization in microbial colonies	29	(1)
Relative abundance of species in a community	29	(1)
Cell--cell interactions	30	(2)
Viability and metabolic activities	32	(1)
Cell components	33	(1)
Predation and parasitism that regulate populations	33	(3)
Differentiation and life cycles	36	(1)
Fossil microorganisms	36	(2)
Conclusion	38	(3)
Questions for further investigation	41	(1)
Suggested readings	41	(2)
Culture methods	43	(15)
Cultivation and diversity assessment	43	(4)
Axenic cultures	47	(3)
Modeling microbial nutrition	47	(1)
Microbial trophic systems	48	(1)
Aeration	48	(1)
Carbon and energy sources	49	(1)
Selective growth conditions	50	(1)
Microcosm cultures	50	(1)
Somnicells and microbial diversity assessment	51	(5)
Conclusion	56	(1)
Questions for further investigation	56	(1)
Suggested readings	56	(2)
Molecular and genomic methods	58	(15)
The molecular context of microbial diversity	58	(2)
Interpretation of molecular diversity	59	(1)
Nucleic acid sequence comparisons	60	(6)
Specific nucleic acid-based methods	61	(5)
Signature lipid biomarkers	66	(3)
Protein profiles	69	(1)
Molecular microarray systems	70	(1)
Conclusion	71	(1)
Questions for further investigation	71	(1)
Suggested readings	71	(2)
Phylogenetic analysis	73	(12)
The rationale for phylogenetic trees	73	(2)
Multiple sequence alignments	75	(1)
Constructing phylogenetic trees from aligned sequences	75	(1)
Interpreting phylogenetic trees	76	(6)
Case study of phylogenetic relationships and niche diversity	77	(5)
Conclusion	82	(2)
Questions for further investigation	84	(1)
Suggested readings	84	(1)
PART II PRINCIPLES AND APPLICATIONS	85	(158)
Environmental evolution	87	(25)
Biogenesis	87	(7)
The case for panspermia	89	(5)
The history of microbial diversity in stromatolites (microbialites)	94	(2)
Contemporary microbial mats	96	(5)
Microbial life and evolution in extreme environments	101	(3)
The emergence of multicellularity and eukaryosis, and their consequences for environmental evolution	104	(3)
Endosymbiosis	104	(2)
Biotic effects on the evolution of Earth's atmosphere	106	(1)
Practical aspects of microbial diversity and environmental evolution	107	(2)
Hydrogenesis	107	(1)
Methanogenesis	108	(1)
Carbon sequestration	109	(1)
Conclusion	109	(1)
Questions for further investigation	110	(1)
Suggested readings	110	(2)
Biogeochemical cycling of carbon and nitrogen	112	(47)
The Earth as an integrated biogeochemical system	113	(6)
Integrative research on biogeochemical cycling	116	(3)
The carbon cycle	119	(22)
Photosynthesis	122	(3)
Methanogenesis	125	(6)
Methanotrophy	131	(3)
Heterotrophy	134	(5)
Biochemical and phylogenetic range of heterotrophy	139	(2)
The nitrogen cycle	141	(16)
Nitrogen fixation	143	(1)
Evolutionary history of biological nitrogen fixation	144	(5)
Nitrogen fixation and environmental change	149	(2)
Ammonification and nitrification	151	(1)
Ammonification	151	(1)
Nitrification	151	(3)
Denitrification	154	(2)
The global dimension of the nitrogen cycle: Prospects and challenges	156	(1)
Conclusion	157	(1)
Questions for further investigation	157	(1)
Suggested readings	157	(2)
Biogeochemical cycling of phosphorus, sulfur, metals, and trace elements	159	(19)
The phosphorus cycle	160	(5)
Phosphine cycling	164	(1)
The sulfur cycle	165	(7)
Desulfuration	165	(4)
Sulfur oxidation	169	(1)
Sulfur reduction	170	(1)
Prospects and challenges of the sulfur cycle	170	(2)
Metals and trace element cycles	172	(4)
Conclusion	176	(1)
Questions for further investigation	177	(1)
Suggested readings	177	(1)
Cross-species interactions among prokaryotes	178	(20)
Quorum sensing	179	(4)
Interactions with viruses	183	(6)
Aquatic viruses	184	(3)
Soil viruses	187	(2)
Prokaryotic interactions and genetic exchange	189	(2)
Microbial consortia and the crisis of isolation	191	(2)
Natural antibiosis and microbial diversity	193	(3)
Conclusion	196	(1)
Questions for further investigation	197	(1)
Suggested readings	197	(1)
Interactions between microorganisms and large eukaryotes	198	(27)
Microbial diversity and geography	198	(1)
Plant diseases	199	(10)
Impacts of global environmental change on microbial pathogens and plant diseases	205	(4)
Animal diseases	209	(4)
Mad cow disease	210	(2)
Foot and mouth disease	212	(1)
Human diseases	213	(5)
Tuberculosis	213	(3)
Cholera	216	(2)
Diseases of marine organisms	218	(2)
The beneficial effects of microbe--eukaryote interactions	220	(2)
Conclusion	222	(1)
Questions for further investigation	223	(1)
Suggested readings	223	(2)
Microbial diversity and global environmental issues	225	(18)
Microbial diversity and indexes of environmental change	226	(7)
Quantitative measures of species diversity	227	(6)
Global climate change	233	(2)
Stratospheric ozone depletion	235	(2)
Toxic chemical pollution	237	(1)
Conservation of global biodiversity	238	(3)
Conclusion	241	(1)
Questions for further investigation	242	(1)
Suggested readings	242	(1)
Appendix 1 Partial list of sequenced microbial genomes	243	(8)
Glossary	251	(7)
References	258	(29)
Index	287