Prokaryotic Diversity: Mechanisms and Significance

doi:10.1017/CBO9780511754913

The true extent of prokaryote diversity, encompassing the spectrum of variability among bacteria, remains unknown. Current research efforts focus on understanding why prokaryote diversification occurs, its underlying mechanisms, and its likely impact. The dynamic nature of the prokaryotic world, and continuing advances in the technological tools available make this an important area and hence this book will appeal to a wide variety of microbiologists. Its coverage ranges from studies of prokaryotes in specialized environmental niches to broad examinations of prokaryote evolution and diversity, and the mechanisms underlying them. Topics include: bacteria of the gastrointestinal tract, unculturable organisms in the mouth and in the soil, organisms from extreme environments, the diversity of archaea and their phages, comparative genomics and the emergence of pathogens, the spread of genomic islands between clinical and environmental organisms, minimal genomes needed for life, horizontal gene transfer, phenotypic innovation, and patterns and extent of biodiversity.

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Contents

Frontmatter
pp i-iv
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Contents
pp v-vi
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Contributors
pp vii-x
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Editors' Preface
pp xi-xii
- By Niall A. Logan, Hilary M. Lappin-Scott, Petra C. F. Oyston
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Microbial diversity in the era of genomics
pp 1-18
- By Rita R. Colwell, University of Maryland, College Park, MD 20742, USA; Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA
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Patterns in prokaryotic biodiversity
pp 19-38
- By M. Claire Horner-Devine, School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA 98195, USA, Jessica Green, School of Natural Sciences, University of California, Merced, CA 95344, USA, Brendan J. M. Bohannan, Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA
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A putative RNA-interference-based immune system in prokaryotes: the epitome of prokaryotic genomic diversity
pp 39-64
- By Eugene V. Koonin, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Kira S. Makarova, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA, Nick V. Grishin, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA, Yuri I. Wolf, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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The significance of prokaryote diversity in the human gastrointestinal tract
pp 65-90
- By Harry J. Flint, Microbial Ecology Group, Rowett Research Institute, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK
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The genetics of phenotypic innovation
pp 91-104
- By Hubertus J. E. Beaumont, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand, Stefanie M. Gehrig, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK, Rees Kassen, Department of Biology and Centre for Advanced Research in Environmental Genomics, University of Ottawa, 150 Louis Pasteur, Ottawa, ON, K1N 6N5, Canada, Christopher G. Knight, School of Chemistry, University of Manchester, Faraday Building, Box 88, Sackville St, Manchester M60 1QD, UK, Jacob Malone, Division of Molecular Microbiology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland, Andrew J. Spiers, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK, Paul B. Rainey, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
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Minimal genomes required for life
pp 105-122
- By Rosario Gil, Insituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Apartado Postal 22085, 46071 València, Spain, Vicente Pérez-Brocal, Insituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Apartado Postal 22085, 46071 València, Spain, Amparo Latorre, Insituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Apartado Postal 22085, 46071 València, Spain, Andrés Moya, Insituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, Apartado Postal 22085, 46071 València, Spain
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Evolution of the core of genes
pp 123-130
- By Vincent Daubin, Laboratoire de Biométrie et Biologie Evolutive, 43 Bld du 11 Novembre 1918, Université Lyon 1, 69622 Villeurbanne cedex, France, Emmanuelle Lerat, Laboratoire de Biométrie et Biologie Evolutive, 43 Bld du 11 Novembre 1918, Université Lyon 1, 69622 Villeurbanne cedex, France
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Biogeographical diversity of archaeal viruses
pp 131-144
- By Kenneth M. Stedman, Department of Biology, Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA, Adam Clore, Department of Biology, Center for Life in Extreme Environments, Portland State University, PO Box 751, Portland, OR 97207-0751, USA, Yannick Combet-Blanc, Laboratoire de Microbiologie IRD, Université de Provence, CESB/ESIL case 925, 163 avenue de Luminy, F-13288 Marseille Cedex 9, France
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Is there a link between Chlamydia and heart disease?
pp 145-162
- By Lee A. Campbell, Department of Pathobiology, University of Washington, Seattle, WA 98195, USA, Cho-chou Kuo, Department of Pathobiology, University of Washington, Seattle, WA 98195, USA
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Unculturable oral bacteria
pp 163-174
- By William G. Wade, King's College London Dental Institute at Guy's, King's College and St Thomas' Hospitals, Infection Research Group, London SE1 9RT, UK
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Comparative genomics – what do such studies tell us about the emergence and spread of key pathogens?
pp 175-186
- By Richard W. Titball, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK, Melanie Duffield, Defence Science and Technology Laboratory, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
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Spread of genomic islands between clinical and environmental strains
pp 187-200
- By Jens Klockgether, Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany, Oleg N. Reva, Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany, Burkhard Tümmler, Klinische Forschergruppe, OE 6711, Medizinische Hochschule Hannover, D-30625 Hannover, Germany
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Evolving gene clusters in soil bacteria
pp 201-222
- By Alice Morningstar, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK, William H. Gaze, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK, Sahar Tolba, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK, Elizabeth M. H. Wellington, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK
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Unusual micro-organisms from unusual habitats: hypersaline environments
pp 223-254
- By Antonio Ventosa, Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Seville, 41012 Seville, Spain
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Genomic islands and evolution of catabolic pathways
pp 255-274
- By Stéphan Lacour, Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland, Muriel Gaillard, Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland, Jan Roelof van der Meer, Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
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Horizontal gene transfer and its role in the emergence of new phenotypes
pp 275-294
- By A. Mark Osborn, Department of Animal and Plant Sciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, UK
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Index
pp 295-302
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Prokaryotic Diversity

Mechanisms and Significance

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Contents

Frontmatter
pp i-iv

Contents
pp v-vi

Contributors
pp vii-x

Editors' Preface
pp xi-xii

Microbial diversity in the era of genomics
pp 1-18

Patterns in prokaryotic biodiversity
pp 19-38

A putative RNA-interference-based immune system in prokaryotes: the epitome of prokaryotic genomic diversity
pp 39-64

The significance of prokaryote diversity in the human gastrointestinal tract
pp 65-90

The genetics of phenotypic innovation
pp 91-104

Minimal genomes required for life
pp 105-122

Evolution of the core of genes
pp 123-130

Biogeographical diversity of archaeal viruses
pp 131-144

Is there a link between Chlamydia and heart disease?
pp 145-162

Unculturable oral bacteria
pp 163-174

Comparative genomics – what do such studies tell us about the emergence and spread of key pathogens?
pp 175-186

Spread of genomic islands between clinical and environmental strains
pp 187-200

Evolving gene clusters in soil bacteria
pp 201-222

Unusual micro-organisms from unusual habitats: hypersaline environments
pp 223-254

Genomic islands and evolution of catabolic pathways
pp 255-274

Horizontal gene transfer and its role in the emergence of new phenotypes
pp 275-294

Index
pp 295-302

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Mechanisms and Significance

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