Microbial ecology l barton, d northup (wiley, 2011)

MICROBIAL ECOLOGY MICROBIAL ECOLOGY Larry L Barton and Diana E Northup A JOHN WILEY & SONS, INC., PUBLICATION Copyright  2011 by Wiley-Blackwell All rights reserved Published by John Wiley & Sons, Inc., Hoboken, New Jersey Published simultaneously in Canada Wiley-Blackwell is an imprint of John Wiley & Sons, formed by the merger of Wiley’s global Scientific, Technical and Medical business with Blackwell Publishing No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax (201) 748-6008, or online at http://www.wiley.com/go/permission Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose No warranty may be created or extended by sales representatives or written sales materials The advice and strategies contained herein may not be suitable for your situation You should consult with a professional where appropriate Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages For general information on our other products and services or for technical support, please contact our Customer Care Department within the United States at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002 Wiley also publishes its books in a variety of electronic formats Some content that appears in print may not be available in electronic formats For more information about Wiley products, visit our web site at www.wiley.com Library of Congress Cataloging-in-Publication Data: Barton, Larry, 1940Microbial ecology / Larry L Barton and Diana E Northup p cm Includes index ISBN 978-0-470-04817-7 (hardback) Microbial ecology I Northrup, Diana E II Title QR100.B37 2011 579 17–dc22 2010043470 Printed in the United States of America oBook ISBN: 978-1-118-01584-1 ePDF ISBN: 978-1-118-01582-7 ePUB ISBN: 978-1-118-01583-4 10 Dedicated to Sandra, Kenneth, and the many students who inspired us to write this book CONTENTS PREFACE xvii GLOSSARY xix MICROBIAL ECOLOGY: BEGINNINGS AND THE ROAD FORWARD 1.1 1.2 Central Themes Introduction 1.2.1 Roots of Microbial Ecology 1.2.2 Current Perspectives 1.3 Timeline 1.4 Microfossils 1.5 Early Life 1.5.1 The Precellular World 1.5.2 The First Cell 1.5.3 Development of Cellular Biology 1.5.4 Evolution of Metabolic Pathways 1.6 Characteristics of Microbial Life 1.6.1 Structure and Evolution of Cell Shape 1.6.2 Metabolism and Use of Energy 1.6.3 Growth, Reproduction, and Development 1.6.4 Adaptations and Response to Stimuli 1.7 Classification and Taxonomy: The Species Concept 1.8 The Three Domains: Tree of Life 1.9 Relationship of Microbial Ecology to General Ecology 1.10 Changing Face of Microbial Ecology 1.10.1 Change in Focus 1.10.2 Diversity: From Culturing to Molecular Phylogeny 1.11 Summary 1.12 Delving Deeper: Critical Thinking Questions Bibliographic Material 1 9 10 11 12 13 13 16 17 18 18 19 22 23 23 24 25 26 26 vii viii CONTENTS DIVERSITY OF MICROORGANISMS 29 2.1 2.2 2.3 Central Themes The Ubiquity of Microorganisms The Amazing Diversity of Morphologies 2.3.1 Comparison of the Three Domains 2.3.2 What’s in a Name: Prokaryotes 2.3.3 Winogradsky’s Experiments with Chemolithotrophs 2.4 Diversity of Bacterial Groups 2.4.1 Expansion of the Number of Bacterial Phyla 2.4.2 Bacterial Portrait Gallery: Processes and Players 2.5 Discovery of Archaea as a Separate Domain 2.6 Archaeal Diversity 2.6.1 Archaeal Portrait Gallery 2.7 Archaea–Bacteria Differences 2.8 Eukarya: A Changing Picture of Phylogenetic Diversity 2.9 Protist Diversity 2.9.1 Protist Gallery 2.10 Fungal Diversity 2.11 Algal Diversity 2.12 Viral Diversity 2.13 Summary 2.14 Delving Deeper: Critical Thinking Questions Bibliographic Material 29 29 30 32 32 32 33 33 35 38 39 39 45 46 46 49 51 54 56 57 58 58 COMPLEXITY AND SIMPLICITY OF CELL SYSTEMS 61 3.1 3.2 3.3 61 62 63 64 66 68 71 74 75 76 78 82 84 84 86 3.4 3.5 3.6 3.7 3.8 Central Themes Introduction Cell Parameters 3.3.1 Life at the Lowest Level 3.3.2 Large Microorganisms Cell Movement and Chemotaxis Structures of Sporulation Nutrient Reserves and Storage Materials Cell–Cell Associations 3.7.1 Cell Attachment 3.7.2 Biofilms 3.7.3 Filamentous Growth Cell Physiology and Metabolism 3.8.1 Sensory Response 3.8.2 Global Regulation 406 Subsurface habitats, 119–121 metabolic reactions, 121 radiolysis of water, 121 Succession, 249, 253–254, 269 Sulfate reducing bacteria, 121, 255, 309, 317, 320 Sulfide, 33, 41, 42, 120, 121, 154, 226, 228, 230, 231, 232, 384 Suflita, Joseph, 343 Sulfobacillus, 308 Sulfolobus, 126 Sulfur, see Cycles Sulfur metabolism, 279, 285, 310–311 Sulfuric acid-driven speleogenesis, 310–312 Surface-to-volume ratio, 67 Swimming, 69, 70 Symbiogenesis, 218 Symbiosis, 218–236 See also Endosymbiosis animal, 223–236 associations, 186–187 bacteria, 37, 197 beetles-fungi, 226, 228–229 benefits, 221, 223 cactus, 204 cockroaches, 225 cyanobacteria, 168, 173 definition, 65, 168, 173, 174 diatoms, 168 dual, 66 establishing, 176 fungi, 174, 178, 219, 226, 228–229, 234 fungi–bacteria, 174 genomics, 221, 225, 236 gut, 224, 225, 227, 228, 233–236 host immune response, 222, 224 host reproduction, 224 human-bacterial/archaeal, 236 legumes, 195–201 lichens, 169–173 nitrogen fixing bacteria, 227 pathogenetic mechanisms, 223 primary, 222, 223, 229, 230 protists, 221, 227, 228 protozoa-bacteria, 173–174 ruminants, 226, 233–235 secondary, 222–223, 229 squid-bacterial, 226, 230 termites, 226–228 three partners, 211 Vibrio fischeri, 226, 230 Symbiosis motility, 227 Symbiosomes, 200 INDEX Synechococcus, 168, 319 Synergistes, 227, 234 Synthesis gas, 343 Syntrophic communities, 375 Syntrophism, 43, 167, 294 Syntrophomonas, 294 Syntrophobacter, 167 Syntrophus aciditrophicus, 168 Syntrophomonas, 294 TAME, 370, 372 Tar, decomposition, 373 TCA cycle, 90 Tea, 342 Tebo, Brad, 291, 292 Terceira, Azores, Portugal, 31 Terminal electron acceptors, 305 Termite Groups 1, 2, and 3, 227, 228 Termites, 225–228, 234 Terrabacteria, 24 Tetrazolium, 137, 146 Textile dyes, decomposition, 378 Thallus, 170 Thauera, 370, 385 Thermoactinomyces, 335 Thermocline, 107 Thermocrinis ruber, 265 Thermonospora, 334 Thermophiles, 5–6, 30, 36, 41, 351 Thermoproteus, Thermatoga, 125 Thiobacillus, 311 Thiodendron, 220 Thiomargarita, 67 Thrombolites, 320 Ti-plasmid, 209, 210 TM7, 235 TOL pathway, 369 Toluene, degradation, 368 Total cell counts, 135 Toxic organic compounds, 361 Toxin, Bacillus thuringiensis, 213 Transcriptomics, 151 Travertine, 321–323 Treponema, 227 Tree of life, 19 Trichodesmium, 262–263 Trichonympha agilis, 37 Tufa, 321–323 Ultramicroscopic bacteria (UMB), 65 Ultraviolet radiation, 124 407 INDEX Universal ancestor, 11 Uranium (VI) reduction, 383 Vampirococcus, 175 van Leeuwenhoek, Anton, 3, 23 Varnish, rock, 117–118, 315–318 Vents, deep-sea, 36 Vents, hot, 41 Vents, deep-sea hydrothermal, 120 Verrucomicrobia, 219, 235 Vesicular-arbuscular mycorrhizae, see endomycorrhizae Vibrio fischeri, 226, 230 Vibrionaceae, 124–125 Virulence, 224 Viruses, 56–57, 224, 255, 260 abundance, 57 bacterial species diversity, 139 bacteriophages, 57, 177, 224, 234 diversity, 57 ecology, 57 evolution, 139 genome size, 56 lysogenic, 56–57 lytic, 56–57 marine, 57 myoviruses, 57 roles, 57 soil ecology, 57 survival, 224 Waiotapu geothermal region, New Zealand, 313–314 Walsby’s square “bacterium”, 30, 44–45 Wasps, 226 Wetland, 352 Whale falls, 227–228, 254 White rot fungi, 331, 334, 373, 375 Wigglesworthia glossinidia, 222 Wine, 266–268, 342 Winogradsky, Sergei, 3, 23, 32–33 Woese, Carl, 21, 33, 38, 42, 133 Wolbachia, 223, 224–225 Woods Hole Marine Biological Laboratory, MA, 43 Wool, 338 Xanthomonas, 308 Xenobiotics, degradation, 373 Xenorhabdus, 226 Xylanase, 334 Yeasts, 266, 267, 268 Yersinia pestis, 247 Young, Lily, 371–372 Zetaproteobacteria, 35, 36 ZoBell, Claude, 247 Zooxanthellae, 49 Zymomonas, 308, 309 Zygomycota, 52, 54 (A) (B) Figure 1.1A Figure 1.3 (B) (A) Figure 1.4 (C) Figure 2.2 (A) (B) Figure 2.7 ESODWHLQGG Figure 2.9 30 Figure 2.11 (A) Anaerobic Aerobic Figure 2.19 Cyanobacteria and algae Green phototrophs Purple phototrophs Figure 3.28 (B) Figure 3.11 Figure 3.29 ESODWHLQGG 30 Figure 4.1 Organic matter Clay Water Silt Sand Air Figure 4.4 Figure 4.9 (C) (J) (F) (A) (K) (B) ESODWHLQGG (D) (G) (E) (H) 1st Level 2nd Level 3rd Level Photosystems Decomposers Mutualists Root feeders Shredders Grazers Predators (I) (L) 4th Level Higher level predator Decomposers (M) (N) 5th Level Highest level predators Figure 4.10 30 Bacterial cells Virus-like particles appear as fine pin pricks of light Numerous bacterial cell can be seen in this image, some clustered and some single Virus-like Afghan soil 1000x oil mag Afghan soil sample, 400x mag., small bright fluorescing dots scattered throughout this image are bacteria attached to soil particles Arrows point to a few of many Figure 4.14 (A) (C) Gram positive cells (D) (A) (B) Gram negative cells (B) Figure 5.3 Figure 5.4 Red formazan crystals Figure 5.5 ESODWHLQGG 30 (A) (B) Figure 5.6 Figure 5.10 Figure 5.13 ESODWHLQGG 30 Figure 6.5 Figure 6.6 Figure 5.14 Figure 6.7 ESODWHLQGG 30 Peribacteroid membrane N2 NH3 NH3 G lu ta m in e Bacteroid Root Leghemoglobin Figure 7.17 Acetogens Protist A Protist B CO2 Wood CO2 H2 H2 Sugar Glucose-6-P Acetate TG1 (endosymbiont) Amino acids & cofactors Gln Amino acids & cofactors N2 NH3 Bacteria Figure 8.1 Esophagus N2 Termite host NH3 Spirochetes & other bacteria Bacteria Figure 8.4 Omasum Abomasum Intestine Reticulum 100–250 L Rumen Dry matter = 10–18% Bacteria = 1010–1011/g Protozoa = 104–106/g Gas phase = CO2 (65%) CH4 (27%) N2 (7%) Figure 8.9 ESODWHLQGG Figure 9.2 30 Figure 9.12 (A) (B) Figure 9.9 Figure 9.13 (A) (B) (C) (D) Figure 10.1 ESODWHLQGG 30 Figure 10.17 (B) (A) (E) (D) (C) Figure 11.1 (A) (B) Figure 11.5 ESODWHLQGG 30 (B) (C) (A) (E) (D) (F) Figure 12.1 (A) Figure 12.3 (B) Figure 12.4 (C) Figure 11.12 ESODWHLQGG 30 Figure 12.11 A B Figure 12.12 Ensilage Figure 12.17 ESODWHLQGG 30 Figure 12.21 Figure 13.9 Figure 13.22 ESODWHLQGG 30 ... MICROBIAL ECOLOGY MICROBIAL ECOLOGY Larry L Barton and Diana E Northup A JOHN WILEY & SONS, INC., PUBLICATION Copyright  2011 by Wiley-Blackwell All rights reserved Published by John Wiley... the development of a theoretical basis that draws on principles identified in general ecology Microbial Ecology, First Edition Larry L Barton, Diana E Northup  2011 Wiley-Blackwell Published 2011... potentially leading to eutrophication in which oxygen levels become very low and algal blooms occur extracellular polymeric matrix (EPM) Polysaccharide material surrounding bacterial cells along