Advances in MICROBIAL ECOLOGY Volume 11

ADVANCES IN MICROBIAL ECOLOGY

Sponsored by the International Committee on Microbial Ecology (ICOME), a committee of the International Union of

Microbiological Societies (IUMS) and the International Union of Biological Sciences (IUBS)

EDITORIAL BOARD

R. M. Atlas University oj Louisville

Louisville, Kentucky

J. G. Jones Freshwater Biological Association

Ambleside, Cumbria, United Kingdom

B. B. J0rgensen University oj Aarhus

Aarhus, Denmark

A continuation Order Plan is available for this series. A continuation order will bring delivery of each new volume immediately upon publication. Volumes are billed only upon actual shipment. For further information please contact the publisher.

Advances in MICROBIAL ECOLOGY Volume 11

Edited by

K. C. Marshall University of New South Wales Kensington, New South Wales, Australia

PLENUM PRESS· NEW YORK AND LONDON

The Library of Congress cataloged the first volume of this title as follows:

Advances in microbial ecology. v. 1-New York, Plenum Press cI977-v. ill. 24 cm. Key title: Advances in microbial ecology, ISSN 0147-4863 1. Microbial ecology-Collected works.

QR100.A36 576'.15

ISBN 978-1-4684-7614-9 ISBN 978-1-4684-7612-5 (eBook)

DOl: 10.1007/ 978-1-4684-7612-5

© 1990 Plenum Press, New York Softcover reprint of the hardcover 1st editio n 1990 A Division of Plenum Publishing Corporation 233 Spring Street, New York, N.Y. 10013

All rights reserved

77-649698

No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher

Contributors

John Bauld, Division of Continental Geology, Bureau of Mineral Resources, Canberra, ACT 2601, Australia

T. E. Cloete, Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, South Africa

B. J. Finlay, Institute of Freshwater Ecology, Ambleside, Cumbria LA22 OLP, United Kingdom

Tim Ford, Laboratory of Microbial Ecology, Division of Applied Sciences, Harvard University, Cambridge, Massachusetts 02138

A. Gerber, Division of Water Technology, CSIR, Pretoria, South Africa Graham W. Gooday, Department of Genetics and Microbiology, Marischal College,

University of Aberdeen, Aberdeen AB9 lAS, Scotland Don P. Kelly, Department of Biological Sciences, University of Warwick, Coventry

CV 4 7 AL, England Arthur L. Koch, Department of Biology, Indiana University, Bloomington, Indiana

47405 L. H. Lotter, City Health Department, Johannesburg, South Africa Ralph Mitchell, Laboratory of Microbial Ecology, Division of Applied Sciences,

Harvard University, Cambridge, Massachusetts 02138 M. O'Hara, Department of Microbiology and Genetics, Massey University, Palmerston

North, New Zealand Hans W. PaerJ, Institute of Marine Sciences, University of North Carolina, Chapel

Hill, Morehead City, North Carolina 28557 J. I. Prosser, Department of Genetics and Microbiology, Marischal College, University

of Aberdeen, Aberdeen AB9 lAS, Scotland Graham W. Skyring, CSIRO Division of Water Resources, Canberra, ACT 2601,

Australia Neil A. Smith, Department of Biological Sciences, University of Warwick, Coventry

CV 4 7 AL, England Gerald W. Tannock, Department of Microbiology, University of Otago, Dunedin, New

Zealand

v

vi Contributors

E. Terzaghi, Department of Microbiology and Genetics, Massey University, Palmerston North, New Zealand

D. F. Toerien, Division of Water Technology, CSIR, I,!retoria, South Africa David D. Wynn-Williams, British Antarctic Survey, Natural Environment Research

Council, Cambridge CB3 OET, United Kingdom

Preface

The International Committee on Microbial Ecology (ICOME) sponsors both the Interna­tional Symposium on Microbial Ecology, held in various parts of the world at three-year intervals, and the publication of Advances in Microbial Ecology. Advances was estab­lished to provide a vehicle for in-depth, critical, and even provocative reviews in microbial ecology and is now recognized as a major source of information for both practicing and prospective microbial ecologists. The Editorial Board of Advances nor­mally solicits contributions from established workers in particular areas of microbial ecology, but individuals are encouraged to submit outlines of unsolicited contributions to any member of the Editorial Board for consideration for pUblication in Advances.

Chapters in Volume 11 of Advances in Microbial Ecology include those on micro­bial transformations of chitin by G. W. Gooday, organic sulfur compounds by D. P. Kelly and N. A. Smith, and phosphorus, including its removal in waste water treatment plants, by D. F. Toerien, A. Gerber, L. H. Lotter, and T. E. Cloete. The importance of diffusion processes in microbial ecology is discussed by A. L. Koch, and 1. I. Prosser reviews the application of mathematical modeling to nitrification processes. Considera­tions of particular ecosystems include the Antarctic by D. D. Wynn-Williams and Australian coastal microbial mats by G. W. Skyring and 1. Bauld. Other chapters include the regulation of N2 fixation by H. W. Paerl, the role of microbial plasticity in ecology by E. Terzaghi and M. O'Hara, and the ecology of corrosion by T. Ford and R. Mitchell, of free-living protozoa by B. 1. Finlay, and of lactobacilli in the gastrointestinal tract by G. W. Tannock.

K. C. Marshall, Editor R. M. Atlas 1. G. Jones B. B. J¢rgensen

vii

Contents

Chapter 1

Physiological Ecology of Free-Living Protozoa

B. 1. Finlay

1. Introduction 2. Basic Requirements of Protozoa .................................. 2 3. Water, Food, and Polymorphism .................................. 7

3.1. Dictyostelium-A Slime Mold ............................... 7 3.2. Sorogena-A Polymorphic Ciliate ............................ 11 3.3. Other Responses to Starvation ................................ 12

4. Microaerophily ................................................ 13 4.1. Interstitial Zone of Marine Sands ............................. 14 4.2. Loxodes-A Microaerophilic Ciliate. . . . . . . . . . . . . . . . . . . . . . . . . . . IS 4.3. Zoochlorellae-Bearing Ciliates ................................ 18

5. Other Photosynthetic Symbionts .................................. 21 5.1. Planktonic Foraminifera ..................................... 22 5.2. Sequestered Chloroplasts .................................... 24

6. Anaerobiosis and Methanogenic Symbionts ......................... 25 7. Postscript ..................................................... 28

References .................................................... 29

Chapter 2

Diffusion: The Crucial Process in Many Aspects of the Biology of Bacteria

Arthur L. Koch

1. Introduction ................................................... 37 2. Microorganisms Are Small ....................................... 38

ix

x Contents

3. An Outline of Diffusion ......................................... 39 3.1. Fick's Diffusion Law ....................................... 39 3.2. Steady State. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40 3.3. Diffusion through and around Obstacles ........................ 43 3.4. Reaction along the Diffusion Path. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46 3.5. Dynamics of Diffusion ...................................... 46 3.6. Diffusion in a Stratified Ecosystem: Elementary Treatment. . . . . . . . . 47 3.7. Diffusion Limitation of Growth. . ... . . .. . . .. ....... .. ... . ... . . 47 3.8. Literature on the Mathematics of Diffusion ..................... 49

4. Kinetics of Uptake from the Environment into the Metabolic Pool. . . . . . . 50 4.1. Transport in the Environment ................................ 51 4.2. Transport through a Capsule ................................. 52 4.3. Permeation through the S-layer or through the Outer Membrane .... 52 4.4. Diffusion through the Peptidoglycan ........................... 54 4.5. Role of Periplasmic Enzymes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54 4.6. Uptake via Binding Proteins ................................. 55 4.7. Passage through the Cytoplasmic Membrane .................... 55 4.8. The Role of Peripheral Enzymes .............................. 55 4.9. Colimiting Transport. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

5. Diffusion through a Gel ......................................... 57 5.1. The Ogsten Theory ......................................... 58 5.2. Elaboration of the Renkin Theory ............................. 59

6. Two-Dimensional Cross-Diffusion ................................. 60 7. Efficiency of Uptake Systems .................................... 62 8. Conclusions ................................................... 67

References .................................................... 68

Chapter 3

Ecological Aspects of Antarctic Microbiology

David D. Wynn-Williams

1. Introduction ................................................... 71 2. Why Are Antarctic Habitats Distinctive? . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74

2.1. Continental Drift and the Isolation of Antarctica ................. 74 2.2. The Ice Habitats of Antarctica. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75 2.3. The Cold Deserts of Continental Antarctica ..................... 78 2.4. Seasonal Changes in the Maritime Antarctic .................... 81

3. Microbiology of Antarctic Cold Deserts ............................ 83 3.1. Endolithic Communities ..................................... 83 3.2. Soil Microbial Xero- and Cryotolerance ........................ 90

Contents xi

4. Microbiology of Ice-Covered Water Bodies ......................... 98 4.1. Permanently Ice-Covered Lakes .............................. 98 4.2. Transient Rivers and Streams . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 4.3. Temporarily Ice-Covered Freshwater Lakes ..................... 108 4.4. Sea Ice Microbial Communities (SIMCO) ...................... 113

5. Microbiology of Patterned Ground ................................ 117 5.1. Frost Tolerance in a Wet Habitat .............................. 117 5.2. Microbial Stabilization of Fellfield Soils. . . . . . . . . . . . . . . . . . . . . . . . 119 5.3. A Meeting of Ice and Steam ................................. 123

6. Terrestrial Nutrient Cycling-Peat and Penguins ..................... 125 6.1. Moss-Peat Ecosystems. . .. . .. . .. .. .. .. . . .. . .... ... ... ... . .. . 125 6.2. Ornithogenic Soils ......................................... 126

7. Environmental Impact ........................................... 127 7.1. Dry Valleys Drilling Project (DVDP) .......................... 127 7.2. Microbial Aspects of Conservation in Coastal and Maritime

Antarctica ................................................ 130 8. Future Research Directions ....................................... 131

References .................................................... 132

Chapter 4

The Microecology of Lactobacilli Inhabiting the Gastrointestinal Tract

Gerald W. Tannock

1. Introduction ................................................... 147 2. The Microecology of Lactobacilli: Present Status. . . . . . . . . . . . . . . . . . . . . 149

2.1. Cell Walls of Lactobacilli and Adhesion Mechanisms ............. 151 2.2. Metabolism and Colonization ................................ 153 2.3. Interactions with Other Microbes ............................. 155 2.4. Testing the Colonization Abilities of Lactobacillus Strains ......... 156 2.5. Interactions with the Animal Host. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158

3. The Microecology of Lactobacilli: The Future ....................... 160 3.1. Plasmids ................................................. 161 3.2. Conjugation ............................................... 162 3.3. Transduction .............................................. 162 3.4. Transformation ............................................ 163 3.5. Transposons ............................................... 164

4. Conclusion .................................................... 165 References .................................................... 165

xii Contents

Chapter 5

Enhanced Biological Phosphorus Removal in Activated Sludge Systems

D. F. Toerien, A. Gerber, L. H. Lotter, and T. E. Cloete

1. Introduction ................................................... 173 1.1. Polyphosphates ............................................ 174 1.2. Activated Sludge Treatment .................................. 174

2. Background and Current Practices ................................. 175 2.1. Evolution of Biological P-Removal Processes ................... 175 2.2. Design and Operational Aspects Pertinent to Biological P Removal. 184

3. Nutrient Dynamics in Activated Sludge Systems ..................... 189 3. 1. Factors Influencing P Release ................................ 190 3.2. Factors Influencing P Uptake. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195

4. Microbiology of P-Removal Activated Sludge Systems ................ 196 4.1. Introduction ............................................... 196 4.2. Bacteria Present in Activated Sludge Systems ................... 196 4.3. Numbers of Bacteria in Activated Sludge. . . . . . . . . . . . . . . . . . . . . . . 197 4.4. Selective Pressures in Activated Sludge Systems ................. 199

5. Biochemical Model of Enhanced P Removal ........................ 201 5.1. PolyP Metabolism . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 202 5.2. Carbon Metabolism ........................................ 206 5.3. Transport of Metabolites .................................... 210 5.4. Metabolic Control .......................................... 213 5.5. Current Biochemical Models of Enhanced P Removal ............ 213 5.6. Extended Model ........................................... 215

6. Ecological Implications .......................................... 218 References .................................................... 219

Chapter 6

The Ecology of Microbial Corrosion

Tim Ford and Ralph Mitchell

1. Introduction ................................................... 231 2. The Role of the Surface Microbiota ............................... 232

2.1. Aerobic Processes.......................................... 232 2.2. Anaerobic Processes ........................................ 235 2.3. Exopolymer-Metal Interactions ............................... 236

3. Acid Production .. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239 3.1. Sulfur Oxidation ........................................... 239 3.2. The Role of Fungi ......................................... 240

Contents xiii

4. Influence of Iron and Manganese Deposition ........................ 242 4.1. Thbercle Fonnation ......................................... 242 4.2. Colonization of Welds ...................................... 243

5. Corrosion by Hydrogen-Consuming Bacteria ........................ 245 5.1. Sulfate-Reducing Bacteria ................................... 245 5.2. Activity of Methanogens .................................... 246 5.3. Iron-Reducing Bacteria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246

6. Corrosion by Hydrogen-Producing Bacteria ......................... 246 7. Thennophilic Corrosion Processes ................................. 248 8. The Role of Consortia .......................................... 251 9. Future Studies ................................................. 252

References .................................................... 252

Chapter 7

Mathematical Modeling of Nitrification Processes

1. I. Prosser

1. Introduction ................................................... 263 2. Nitrification ................................................... 264 3. Mathematical Modeling ......................................... 265 4. Pure-Culture Studies ............................................ 266

4.1. Basic Growth Kinetics ...................................... 266 4.2. Short-Tenn Measurements ................................... 266 4.3. Measurement of Growth and Activity in Batch Culture. . . . . . . . . . .. 267 4.4. Effect of Substrate Concentration ............................. 269 4.5. Growth in Continuous Culture. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270 4.6. Effect of Temperature on Nitrification. . . . . . . . . . . . . . . . . . . . . . . . .. 272 4.7. Effect of pH and Inhibitors .................................. 273 4.8. Surface Growth ............................................ 275 4.9. Summary ................................................. 277

5. Nitrification in Soil ............................................. 277 5.1. Measurement of Rates of Nitrification ......................... 277 5.2. Effects of Environmental Factors.. ... . .. . .. . . .. . . . . . .. . . . . . . .. 281 5.3. Other Nitrogen Transfonnations .............................. 282 5.4. Soil Columns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 285

6. Nitrification in Aquatic Ecosystems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 287 6.1. Measurement of Rates of Nitrification ......................... 287 6.2. System Models ............................................ 287

7. Nitrification in Sewage and Waste Water Treatment Processes .......... 289 7.1. Basic Kinetics ............................................. 290 7.2. Measurement of Growth Constants ............................ 290

xiv Contents

7.3. Effect of Biomass Concentration ........ , ... ... .... ... . .. . . ... 293 7.4. Effects of Temperature, pH, and Inhibition ..................... 294 7.5. Surface Growth ............................................ 296 7.6. Summary ................................................. 298

8. Concluding Remarks... .. . ... ... . . .. . .... . .. .. . . . ... . . .. . .. . . . .. 299 References .................................................... 300

Chapter 8

Physiological Ecology and Regulation of N2 Fixation in Natural Waters

Hans W. Paerl

1. Historical and Current Perspectives ................................ 305 2. Aquatic N2-Fixing Microorganisms: Their Diversity and Habitats ....... 307 3. The Physiological Ecology of Aquatic N2 Fixation ................... 319 4. Environmental Constraints and Limitations on Aquatic N2 Fixation ...... 323 5. Roles of Organic Matter and Microzone Formation ................... 327 6. Evolutionary and Ecological Considerations ......................... 333 7. Ecosystem-Level Regulation of N2 Fixation: Are There Fundamental

Differences between Freshwater and Marine Habitats? . . . . . . . . . . . . . . . .. 334 8. Conclusions ................................................... 336

References .................................................... 337

Chapter 9

Organic Sulfur Compounds in the Environment: Biogeochemistry, Microbiology, and Ecological Aspects

Don P. Kelly and Neil A. Smith

1. Introduction ................................................... 345 1.1. Background ............................................... 345 1.2. The Atmospheric Component of the Sulfur Cycle ................ 346

2. Organic Sulfur Compounds in the Natural Environment ............... 348 2.1. Methylated Sulfides, Carbon Sulfide, and Carbonyl Sulfide ........ 349 2.2. Carbon Disulfide and Carbonyl Sulfide ......................... 358 2.3. Sulfoxides and Sulfonates ................................... 360 2.4. Higher Alkyl and Aromatic Sulfides and Poly sulfur Compounds .... 361 2.5. Naturally Occurring Aromatic and Heterocyclic Sulfur Compounds. . 362 2.6. Mammalian Odors: Pheromones, Attractants, and Repellants ....... 363

3. Microbiological Degradation of Organic Sulfur Compounds ............ 368 3.1. Methylated Sulfides ........................................ 368 3.2. Other Sulfides ............................................. 369

Contents xv

3.3. Carbon Disulfide and Carbonyl Sulfide ........................ 370 3.4. Sulfonates ................................................ 372 3.5. Thiophenes and Aromatic Sulfur Compounds. . . . . . . . . . . . . . . . . . . . 372 3.6. Miscellaneous Sulfur Compounds ............................. 374

4. Some Effects of Organic Sulfur Compounds on Global Ecology ........ 374 References .................................................... 375

Chapter 10

The Ecology of Chitin Degradation

Graham W. Gooday

1. Chitin and Its Occurrence ........................................ 387 1.1. Chitin Structure ............................................ 387 1.2. Occurrence of Chitin ....................................... 388 1.3. Fossil Chitin .............................................. 389 1.4. Annual Production of Chitin ................................. 390 1.5. Amount of Chitin in the Biosphere ............................ 390

2. Pathways of Chitin Degradation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 391 3. Chitin Digestion by Microbes .................................... 393 4. Chitin Degradation in the Sea .................................... 393

4.1. Degradation in the Water Column ............................. 393 4.2. Degradation in Sediments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 394 4.3. Degradation in the Deep Sea ................................. 395 4.4. Rates of Degradation ....................................... 397

5. Chitin Degradation in Estuaries ................................... 398 5.1. Estuarine Chitinoclastic Microbes ............................. 398 5.2. Rates of Degradation ....................................... 400

6. Chitin Degradation in Freshwaters ................................. 402 6.1. Freshwater Chitinoclastic Microbes ............................ 403 6.2. Rates of Degradation ....................................... 403

7. Chitin Degradation in Soil ....................................... 405 7.1. Microbial Degradation ...................................... 405 7.2. Soil Chitinase Activity ...................................... 408 7.3. Effects of Addition of Chitin to Soil ........................... 409 7.4. Addition of Chitin to Soil for Biological Control of Disease ....... 410

8. Adhesion of Microbes to Chitin. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 411 9. Chitin Digestion in Animals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 416

10. Involvement of Chitin Degradation in Pathogenesis and Symbiosis ...... 418 11. Summary ..................................................... 419

References .................................................... 419

xvi Contents

Chapter 11

Microbial Plasticity: The Relevance to Microbial Ecology

E. Terzaghi and M. O'Hara

1. Introduction ................................................... 431 2. Interorganismal Exchange. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 433 3. Progranuned Rearrangement ...................................... 434

3.1. Topology of Rearrangement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 434 3.2. Inversions ................................................ 434 3.3. Transposition and Deletion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437

4. Unprogrammed Rearrangement ................................... 438 4.1. Agents of Change .......................................... 438 4.2. Evolution of Function ....................................... 442 4.3. Cryptic Functions .......................................... 444

5. Evidence for Genomic Change .................................... 446 5.1. Chromosomal ............................................. 446 5.2. Plasmid .................................................. 447

6. Phenotypic Changes of Unknown Genetic Basis ..................... 449 7. Significance of Microbial Plasticity to Microbial ~cblogy . . . . . . . . . . . . . . 451

References .................................................... 453

Chapter 12

Microbial Mats in Australian Coastal Environments

Graham W. Skyring and John Bauld

1. Introduction ................................................... 461 2. Occurrence and Characteristics of Australian Microbial Mats ........... 463

2.1. Location and Habitat ....................................... 463 2.2. Conununity Structure and Microbial Components ................ 468

3. Phototrophic Activity and Environmental Constraints ................. 471 3.1. Light .................................................... 471 3.2. Photoautotrophic Activity and Primary Productivity .............. 473 3.3. Photoheterotrophic Activity .................................. 476 3.4. Environmental Controls on Phototrophic Processes ............... 477 3.5. Interactions with Other Biota. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .. 478 3.6. Nitrogen Fixation .......................................... 480

4. Degradative Processes and Environmental Constraints. . . . . . . . . . . . . . . . . 481 4.1. Aerobic Processes .......................................... 481 4.2. Fermentation and Sulfate Reduction ........................... 482 4.3. Methanogenesis ............................................ 486

Contents xvii

5. Conclusions ................................................... 486 5.1. Ecology .................................................. 487 5.2. Minerals, Petroleum, and Modeling ........................... 487 5.3. Serendipity, Controversy, and Speculation ...................... 488 5.4. Some Unsolved Problems and Unanswered Questions. . . . . . . . . . . . . 489 References .................................................... 491

Index ............................................................ 499