Thermophiles - Springer978-1-4615-1197-7/1.pdf · Thermophiles Biodiversity, Ecology, and Evolution Edited Ьу Anna-Louise Reysenbach Portland State University Portland, Oregon Mary

Thermophiles Biodiversity, Ecology, and Evolution


Edited Ьу

Anna-Louise Reysenbach Portland State University Portland, Oregon

Mary Voytek United States Geological Survey Reston, Virginia

and

Rocco Mancinelli NASAlAтes Research Ceпter Moffett Field, California

Springer Science+Business Media, LLC

Library of Congress Cataloging-in-Publication Data

Reysenbach, Anna-Louise; Voytek, Mary; Mancinelli, Rocco Тherrnophiles: Biodiversity, Ecology, and Evolution!Anna-Lоuisе Reysenbach, Mary Voytek,

Rocco Mancinelli р. ст.

Includes bibliographical references and index. ISBN 978-1-4613-5436-9 ISBN 978-1-4615-1197-7 (eBook) DOI 10.1007/978-1-4615-1197-7 1. 2.

ISBN 978-1-4613-5436-9

©2ОО1 Springer Science+ Business Media N ew York Originally published Ьу Юuwег Academic/Plenum Publishers, New York in 2001 Softcover reprint of the hardcover 1 Б! edition 2001

ю 9 8 7 6 5 4 3 2 1

А C.I.P. record for this book is available from the Library of Congress

АН rights reserved

No part of this book тау Ье reproduced, stored in а retrieval system, or transmitted in any [оrrn or Ьу any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher.

In memory of Rick Hutchinson and chocolate

There are only meters in this book, and it took more than 365 days

to put the book together.

Contributors

Kai S. Anderson, Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305-2115

Mary M. Bateson, Department of Microbiology, Montana State University, Bozeman, Montana 59717

Deborah A. Body, School of Biological Sciences, University of Wales, Bangor; LL572uw, Wales

Deena Braunstein, Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305-2115

Toni A. M. Bridge, School of Biological Sciences, University of Wales, Bangor; LL572uw, Wales

Thomas D. Brock, E. B. Fred Professor of Natural Sciences Emeritus, University of Wisconsin-Madison, Madison, Wisconsin 53705

C. K. Browning, Ransom Hill Bioscience, Inc., Ramona, California 92065

Debby F. Bruhn, Lockheed Martin Idaho Technologies Co., Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho 83415-2203

D. K. Bulmer, Biotechnologies Department, Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho 83415-2203

Siegfried Burggraf, Lehrstuhl flir Mikrobiologie and Archaeenzentrum, Universitiit Regensburg, 93053 Regensburg, Germany

Charles C. Chester, World Foundation for Environment and Development, Washington, D.C. 20036

Joan Combie, Montana Biotech, Belgrade, Montana 59714

M. J. Ferris, Department of Microbiology, Montana State University, Bozeman, Montana 59717

vii

viii Contributors

Joseph R. Graber, Department of Microbiology and Biochemistry, Cook College, Rutgers University, New Brunswick, New Jersey 08903

Robert Huber, Lehrstuhl for Mikrobiologie and Archaeenzentrum, Universitiit Regensburg, 93053 Regensburg, Germany

Christian Jeanthon, CNRS, UPR 9042 and UPMC, Station Biologique, Roscoff and Universite de Bretagne Occidentale, Brest, France

D. Barrie Johnson, School of Biological Sciences, University of Wales, Bangor, LL572uw, Wales

Julie Kirshtein, Department of Microbiology and Biochemistry, Cook College, Rutgers University, New Brunswick, New Jersey 08903

Jan W. de Leeuw, Division of Marine Biochemistry, Netherlands Institute for Sea Research (NIOZ), 1790 AB Den Burg, Texel, Netherlands

Robert F. Lindstrom, Yellowstone Center for Resources, Yellowstone National Park, lVYoming 82190

Donald R. Lowe, Department of Geological and Environmental Sciences, Stanford University, Stanford, California 94305-2115

M. T. MacDonell, Ransom Hill Bioscience, Inc., Ramona, California 92065

Michael T. Madigan, Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901

Thomas Mayer, Lehrstuhl for Mikrobiologie and Archaeenzentrum, Universitiit Regensburg, 93053 Regensburg, Germany

S. C. Nold, Montana State University, Department of Microbiology, Bozeman, Montana 59717

William D. O'Dell, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center and Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68198-4525

Daniel Prieur, CNRS, UPR 9042 and UPMC, Station Biologique, Roscoff and Universite de Bretagne Occidentale, Brest, France

Reinhard Rachel, Lehrstuhl for Mikrobiologie and Archaeenzentrum, Universitiit Regensburg, 93053 Regensburg, Germany

Robert F. Ramaley, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center and Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68198-4525

Anna-Louise Reysenbach, Department of Environmental Biology, Portland State University, Portland, Oregon 97201

Francisco F. Roberto, Biotechnologies Department, Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho 83415-2203

Contributors ix

Petra Rossnagel, Lehrstuhl for Mikrobiologie and Archaeenzentrum, Universitiit Regensburg, 93053 Regensburg, Germany

Lynn J. Rothschild, Ecosystem Science and Technology Branch, NASNAmes Research Center, Moffet Field, California 94035-1000

Kenneth Runnion, Montana Biotech, Belgrade, Montana 59714

C. M. Santegoeds, Montana State University, Department of Microbiology, Bozeman, Montana 59717

Pamela L. Scanlan, Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center and Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska 68198-4525

Mark Speck. Department of Microbiology and Biochemistry, Cook College, Rutgers University, New Brunswick, New Jersey 08903

D. L. Stoner, Biotechnologies Department, Idaho National Engineering and Environmental Laboratory, Lockheed Martin Idaho Technologies Co., Idaho Falls, Idaho 83415-2203

John D. Varley, Yellowstone Center for Resources, Yellowstone National Park, lVYoming 82190

Mary Voytek, United States Geological Survey, MS430, Reston, Virginia 20192

David M. Ward, Department of Microbiology, Montana State University, Bozeman, Montana 59717

T. E. Ward, Biotechnologies Department, Idaho National Engineering and Environmental Laboratory, Idaho Falls, Idaho 83415-2203

Preface

These are indeed exciting times to be a microbiologist. With one of the buzzwords of the past decade-"Biodiversity," and microbes are reveling in the attention as they represent by far most of the biodiversity on Earth. Microbes can thrive in almost any environment where there is an exploitable energy source, and, as a result, the possible existence of microbial life elsewhere in the solar system has stimulated the imaginations of many. Extremophiles have taken center stage in these investigations, and thermophiles have taken on the lead roles. Consequently, in the past decade there has been a surge of interest and research in the Ecology, Biology, and Biotechnology of microorganisms from thermal environments. Many of the foundations of thermophile research were laid in Yellowstone National Park, primarily by the research of Professor Thomas Brock's laboratory in the late 1960s and early 1970s. The upper temperature for life was debated, the first thermophilic archeum discovered (although it was only later shown to be an archeum by ribosomal cataloging), and the extremes of light, temperature, pH on the physiology of microorganisms were explored. Interest in thermophiles increased steadily in the 1970s, and with the discovery of deep-sea hydrothermal vents in 1977, thermophilic research began its exponential explosion. The development of Taq polymerase in the polymerase chain reaction (peR) focused interest on the biotechnological potential of thermophilic microorganisms and on the thermal features in Yellowstone National Park. Additionally, the use of Taq polymerase in molecular phylogenetic approaches to assess microbial diversity has identified a plethora of novel types of microbes representing a diverse array of potential metabolic types.

This book aims to provide a source of the recent advances in the biology, biotechnology, and management of thermophilic microorganisms. The contributed chapters include research results, technical information, and reviews that highlight the state of our current knowledge of thermophiles and their habitats. Most of the contributors have drawn specific examples largely from the Yellowstone National Park thermal springs. The volume presents a historical background and gives an overview of research on thermophilic microorganisms (Brock; Prieur et al.). Section II covers what is known about the microbial diversity associated with hydrothermal environments and addresses the unusual physiologies of some of these organisms. Estimates of the diversity of natural microbial communities have been hindered by our inability to enrich and culture the organisms present (Ferris et al.). Yet

xi

xii Preface

such enrichment procedures established the foundations of what we know of their diversity and physiology (Ramaley et al.; Johnson et al.). Recent advances in molecular phylogenetic techniques have eliminated the need to culture organisms to assess diversity. Studies based on these techniques have yielded a plethora of diverse, and, sometimes, novel lineages, such as the Korarchaeota (Graber et al.; Ferris et al.; Stoner et al.). Section III contains papers pertaining to the ecology and evolution of thermal spring microbial communities. These papers address aspects of the ecology of thermophiles and discuss how these organisms influence their environment through their physiological activity (Madigan et al.; Rothschild et al.). Thermal habitats can provide insights into unusual physiologies adapted for conditions similar to the early earth's environment. For example, many laminated stromatolite-like structures are found in the Archaean oceans, which are analogous to the structures formed by microbial mats in thermal springs. Findings from studies in these extant environments may aid interpretations of the nature, distribution, and paleoecology of ancient microorganisms (Lowe et al.; Ward et al.).

The final section in the book addresses some of the applications and potential uses of thermophiles in industry, including the use of carotenoids as antioxidants in food and feed preparations, bioprocessing such as TNT degradation, and coal solubilization and desulfurization (Combie). Given the recent surge of interest in the biotechnological potential of thermophilic microorganisms, there is a need to clarify resource management policies so that microbial resources can be managed effectively to the benefit of all. The volume concludes with a discussion of ways in which the microbial organisms can be managed in areas such as national parks. Some of the specific issues regarding the management of Yellowstone's microbial resources are: inventory and monitoring of the resources, generation and maintenance of research support, habitat protection, legal and ecological ramifications of bioprospecting, and education (Varley et al.). These issues are of global concern and must eventually be confronted by all nations. Many of the initial discussions that started at the meeting in Yellowstone in 1995 were directed toward addressing these issues. The final outcome of those discussions is reflected in the proposed agreement between the biotechnological company, Diversa, and Yellowstone National Park.

The editors thank the authors for their patience in making this project happen. It could not have happened without the help and guidance of Michael Hennelley at Kluwer AcademicIPlenum Publishers. Many thanks.

Anna-Louise Reysenbach Mary Voytek

Rocco Mancinelli

Contents

Chapter 1

The Origins of Research on Thermophiles 1

Thomas D. Brock

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 2. Early Bacteriological Research on Thermophiles .. . . . . . . . . . . . . . . . . . . . . . 2 3. Ecological Observations of Geothermal Environments .................. 3 4. Yellowstone National Park. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 5. Thermus Aquaticus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 6. Discovery of Extreme Thermophiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 7. Thermoplasma, Sulfolobus, and the Archaea .......................... 6 8. Yellowstone Research and the Deep-Sea Thermal ...................... 6 9. Microbial Prospecting in Thermal Habitats ........................... 7

10. Conservation of Yellowstone's Thermal Resources ..................... 7 11. Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

Chapter 2

Deep.Sea Thermophilic Prokaryotes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

Daniel Prieur; Mary Voytek, Christian Jeanthon, and Anna-Louise Reysenbach

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 2. Hydrothermal Vent Environments ................................... 12 3. Biological Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12 4. Ecological Studies ............................................... 12

4.1. Locating the Niche . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 4.2. Microbial Abundances ........................................ 13 4.3. Origin and Biogeography. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 4.4. Barotolerance and Barophily ................................... 14 4.5. Temperature: Optima and Limits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14

xiii

xiv Contents

5. Diversity: Thermophilic and Hyperthermophilic Isolates. . . . . . . . . . . . . . . . . 14 6. Assessments of Molecular Diversity ................................. 18 7. Bioprospecting and Biotechnology .................................. 18 8. Hydrothermal Vents and the Origin of Life ........................... 18 9. Summary....................................................... 19

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

Chapter 3

Biodiversity of Acidophilic Moderate Thermophiles Isolated from Two Sites in Yellowstone National Park, and Their Roles in the Dissimilatory Oxido-Reduction of Iron .................................................. 23

D. Barrie Johnson, Deborah A. Body, Toni A. M. Bridge, Debby F. Bruhn, and Francisco F. Roberto

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 2. Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

2.1. Isolation of Acidophilic Microorganisms ......................... 24 2.2. Measurement of Oxido-Reduction of Iron by Yellowstone Isolates .... 25 2.3. Determination of Specific Rates of Iron Oxidation and Reduction ..... 26 2.4. Genomic DNA Isolation ...................................... 26 2.5. PCR Amplification of 16S rRNA Genes. . . . . . . . . . . . . . . . . . . . . . . . . . 26 2.6. Cloning of Amplified Sequences ................................ 27 2.7. Sequencing of Cloned 16S rRNA Genes ......................... 27 2.8. Sequence Analysis and Phylogenetic Tree Assembly. . . . . . . . . . . . . . . . 27

3. Results......................................................... 27 3.1. Moderately Thermophilic Acidophiles Isolated from the Yellowstone

Sites. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 3.2. Oxidation of Ferrous Iron by Yellowstone Isolates ................. 28 3.3. Reduction of Ferric Iron by Yellowstone Isolates .................. 28 3.4. Phylogenetic Analyses ........................................ 31

4. Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 5. Summary....................................................... 35

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Chapter 4

Presence of Thermophilic Naegleria Isolates in the Yellowstone and Grand Teton National Parks ............................................... 41

Robert F. Ramaley, Pamela L. Scanlan, and William D. O'Dell


2.1. Collection and Isolation of Naegleria Isolates ..................... 42 2.2. Determination of Virulence of the Naegleria Isolates ............... 42 2.3. Determination of Growth of Naegleria on Thermus Strains .......... 43

3. Results......................................................... 43 3.1. Isolation of Thermophilic Amoebae from the Yellowstone/Grand Teton

Ecosystem . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

Contents xv

4. Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 5. Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49

Chapter 5

Examining Bacterial Population Diversity Within the Octopus Spring Microbial Mat Community .......................................... 51

Michael J. Ferris, Steven C. Nold, C. M. Santegoeds, and David M. Ward

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51 2. Octopus Spring Mat Cyanobacterial Diversity as Revealed by Microscopy,

Cultivation, Probing, Cloning, and Sequencing ........................ 53 3. Standardization of Methodology, Environmentally Meaningful Sampling

Points, and Increased Sample Throughput are Necessary to Understand Octopus Spring Population Dynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56

4. DGGE Analysis of Octopus Spring Mat Samples ...................... 58 5. DGGE Analyses of Aerobic Chemoorganotrophic Enrichment Cultures

Demonstrates the Incongruence among Populations within Natural Microbial Communities and Those Obtained from Selective Enrichment Cultures . . . . . 59

6. Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61

Chapter 6

Direct 5S rRNA Assay for Microbial Community Characterization 65

Daphne L. Stoner, C. K. Browning, D. K. Bulmer, T. E. Ward, and M. T. MacDonell


2.1. Microorganisms ............................................. 67 2.2. RNA Extraction ............................................. 67 2.3. Denaturing Gradient Gel Electrophoresis ......................... 68

3. Results......................................................... 68 4. Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72 5. Summary....................................................... 78

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Chapter 7

Community Structure Along a Thermal Gradient in a Stream near Obsidian Pool, Yellowstone National Park . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Joseph R. Graber, Julie Kirshtein, Mark Speck, and Anna-Louise Reysenbach


2.1. Sample Collection ........................................... 83

xvi Contents

2.2. DNA Extraction ............................................. 83 2.3. DNA Amplification .......................................... 83 2.4. Cloning and Sequencing ...................................... 83 2.5. Phylogenetic Analysis ........................................ 84

3. Results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84 3.1. Cloning and Sequence Analysis ................................ 84 3.2. Phylogenetic Analysis ........................................ 85

4. Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Chapter 8

Isolation of Hyperthermophilic Archaea Previously Detected by Sequencing rDNA Directly from the Environment ................................. 93

Siegfried Burggraf, Robert Huber, Thomas Mayer, Petra Rossnagel, and Reinhard Rachel


2.1. Sampling and Enrichment of Thennophiles ....................... 94 2.2. Cell Fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 2.3. Whole Cell Hybridization ..................................... 94 2.4. Fluorescence Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 2.5. Cell Separation ..................................... -. . . . . . . . . 95 2.6. Sequencing of 16S rDNA ..................................... 95

3. Results......................................................... 95 3.1. Whole Cell Hybridization ..................................... 95 3.2. Isolation of Different Morphotypes .............................. 96 3.3. Phylogeny and Physiology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

4. Summary ............................. ......... ...... . .......... 97 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99

Chapter 9

Thermophilic Anoxygenic Phototrophs Diversity and Ecology ....................... . . . . . . . . . . . . . . . . . . . . . . . . 103

Michael T. Madigan

1. Introduction........ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103 2. Diversity and Phylogeny of Hot Spring Anoxyphototrophs . . . . .. . . . . . . . . . 103

2.1. Purple Bacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105 2.2. Green Bacteria and Heliobacteria ............................... 106 2.3. Ultrastructure of Some Thennophilic Anoxyphototrophs . . . . . . . . . . . . . 106

3. Physiology of Hot Spring Anoxyphototrophs .......................... 107 3.1. Temperature Relationships ..................................... 107 3.2. Autotrophy ................................................. 109

Conren~ xvil

3.3. Nitrogen Fixation ............................................ 111 3.4. Thennostable Enzymes ....................................... 113

4. Ecological Studies of Thennophilic Anoxyphototrophs ... . . . . . . . . . . . . . . . 113 4.1. Adaptation by Chloroflexus to Reduced Light Intensity. . . . . . . . . . . . . . 113 4.2. Autotrophy in Natural Populations of Chromatium tepidum .......... 117

5. Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120

Chapter 10

Algal Physiology at High Temperature, Low pH, and Variable pC02 Implications for Evolution and Ecology . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125

Lynn J. Rothschild

1. Introduction: Why the Microbial Mats of Yellowstone .................. 125 2. Material and Methods ............................................ 127

2.1. Description of Organisms ..................................... 127 2.2. Primary Productivity ......................................... 127 2.3. DNA Synthesis .............................................. 129 2.4. Partitioning of Photosynthate into DNA .......................... 130

3. Results......................................................... 130 3.1. Primary Productivity ......................................... 130 3.2. DNA Synthesis .............................................. 133 3.3. Partitioning of Photosynthate into DNA .......................... 135

4. Discussion...................................................... 135 4.1. Is There an Effect of High Temperature, Low pH, and Low pC02 .•.. 135 4.2. Ecological and Evolutionary Implications . . . . . . . . . . . . . . . . . . . . . . . . . 136

5. Summary....................................................... 139 References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139

Chapter 11

The Zonation and Structuring of Siliceous Sinter Around Hot Springs, Yellowstone National Park, and the Role of Thermophilic Bacteria in Its Deposition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 143

Donald R. Lowe, Kai S. Anderson, and Deena Braunstein

1. Introduction..................................................... 143 2. Geologic Setting of Yellowstone Geothennal System ................... 145 3. Morphological Subdivisions of Outflow Systems. . . . . . . . . . . . . . . . . . . . . . . 147

3.1. Vent Pool and Near-Vent Outflow Area .......................... 148 3.2. Proximal Outflow Channel. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 3.3. Channel and Terrace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155 3.4. Sinter-Debris Apron .......................................... 155 3.5. Diatom Marsh and Meadow ................................... 156

4. Temperature and Bacterial Subdivisions of Outflow Systems ............. 156

xviii Contents

4.1. High Temperature Zone. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 4.2. Synechococcus-Chlorotlexus Zone .............................. 157 4.3. Phormidium Zone. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158 4.4. Calothrix Zone .............................................. 159

5. The Role of Bacteria in the Deposition and Structuring of Siliceous Sinter 161 6. Discussion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 7. Summary....................................................... 164

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165

Chapter 12

Use of 16S rRNA, Lipid, and Naturally Preserved Components of Hot Spring Mats and Microorganisms to Help Interpret the Record of Microbial Evolution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 167

David M. Ward, Mary M. Bateson, and Jan W. de Leeuw

1. Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167 2. 16S rRNA Biomarker Studies Link Biodiversity, Ecology, and Evolution. . . 169

2.1. Cyanobacterial Diversity, Ecology, and Evolution ... . . . . . . . . . . . . . . . 170 2.2. Diversity, Ecology, and Evolution of Green Nonsulfur-Like Bacteria .. 173 2.3. Chlorofiexus sp. of Sulfidic Mats is Closely Related to C. aurantiacus 174

3. Lipid Biomarker Studies Help Link Chemical Fossils to Their Microbial Sources ........................................................ 174

4. Naturally Preserved Biomarkers can be Related to Their Microbial Sources 176 5. Summary....................................................... 178

References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178

Chapter 13

Research Accomplishments of a Small Business Using Yellowstone's Extremophiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183

Joan Combie and Kenneth Runnion

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183 2. Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184

2.1. Diversity of Collection and Isolation Techniques. . . . . . . . . . . . . . . . . . . 184 2.2. Heat-Stable Enzymes ......................................... 185 2.3. Carotenoids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 2.4. TNT Degradation ............................................ 186 2.5. Coal Bisolubilization ......................................... 186 2.6. Microbial Coal Desulfurization ................................. 187 2.7. Polyurethane Paint Removal ................................... 188

3. Conclusions..................................................... 188 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189

Contents xix

Chapter 14

The Yellowstone Microbiology Program Status and Prospects ................................................ 191

John D. Varley, Robert F. Lindstrom, and Charles C. Chester

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191 2. Inventory and Monitoring of YNP Microorganisms . . . . . . . . . . . . . . . . . . . . . 193

2.1. Current Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193 2.2. Prospects ................................................... 193

3. Microbiological Research Support. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 3.1. Current Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194 3.2. Prospects ................................................... 194

4. Protection of Geothermal Habitat ................................... 195 4.1. Current Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 4.2. Prospects................................................... 195

5. Benefit-SharinglBioprospecting ..................................... 195 5.1. Current Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195 5.2. Prospects .... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196

6. Education ...................................................... 197 6.1. Current Status. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 6.2. Prospects ................................................... 197

7. Summary....................................................... 198 Appendix I ..................................................... 198 Appendix II . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 200

Index............................................................. 201


Documents

Thermophiles - Springer978-1-4615-1197-7/1.pdf · Thermophiles Biodiversity, Ecology, and Evolution Edited Ьу Anna-Louise Reysenbach Portland State University Portland, Oregon Mary