MANUAL OF Environmental Microbiology THIRD EDITION EDITOR IN CHIEF Christon J. Hurst Department of Biology, Xavier University, Cincinnati, Ohio and Facultad de Ingenierfa, Universidad del Valle, Ciudad Universitaria Melendez, Santiago de Cali, Colombia EDITORS Ronald L. Crawford Aaron L. Mills Environmental Biotechnology Institute Department of Environmental Sciences University of Idaho University of Virginia Moscow, Idaho Charlottesville, Virginia Jay L. Garland Linda D. Stetzenbach Dynamac Corporation Department of Environmental and Kennedy Space Center, Florida Occupational Health School of Public Health University of Nevada, Las Vegas David A. Lipson Las Vegas, Nevada Department of Biology San Diego State University San Diego, California ASM -PRESS Washington, D.C. Address editorial correspondence to ASM Press, 1752 N St. NW, Washington, DC 20036-2904, USA Send orders to ASM Press, P.O. Box 605, Herndon, VA 20172, USA Phone: (800) 546-2416 or (703) 661-1593 Fax: (703) 661-1501 E-mail: [email protected] Online: estore.asm.org Copyright 0 1997, 2002, 2007 ASM Press American Society for Microbiology 1752 N St. NW Washington, DC 20036-2904 Library of Congress Cataloging-in-Publication Data Manual of environmental microbiology / editor in chief, Christon J. Hurst ; editors, Ronald L. Crawford .. [et al.].-3rd ed. p. ; cm. Includes bibliographical references and index. ISBN-13: 978- 1-55581-379-6 (hardcover) ISBN- 10: 1-55581-3 79-8 (hardcover) 1. Microbial ecology-Laboratory manuals. 2. Sanitary microbiology-Laboratory manuals. I. Hurst, Christon J. 11. Crawford, Ronald L., 1947- [DNLM: 1. Environmental Microbiology. QW 55 M294 20071 QR100.M36 2007 579l.174~22 2006034637 10 9 8 7 6 5 4 3 2 1 All Rights Reserved Printed in the United States of America Preface Environmental microbiology is a fascinating field of science readers. Two hundred seven scientists have contributed to this which captured my imagination when I first got out my third edition of the Manual, including more than 100 new trowel 32 years ago to collect soil from beneath a suburban authors, and I welcome each of them. I offer special apprecia- tree. While following the trail which ensued, I have sam- tion for the fact that nearly all of the former editors have pled the drainage from coal mines, dug infiltration basins in remained among our group as authors. the desert, dredged sediments from bays and rivers, and The most difficult part of compiling such a volume is chopped holes through surface ice. I even have learned that deciding which topics will receive center stage and which sometimes the sample bottle gets filled in unusual ways, must be given a reduced representation. It also is important such as when the surf washed over my head or when I to recognize that the research of any given field flows and slipped sideways into a river. The latter event was observed sometimes changes its path over time. The authors and edi- by three of my students, who were courteous enough not to tors of this manual are dedicated to helping you, our read- laugh too loudly. The Manual of Environmental Microbiology ers, keep a balanced perspective. We always will be certain is an effort to combine the results and my excitement from that the basic foundations of environmental microbial my own discoveries with those of many colleagues. I feel methodology are thoroughly covered and also try to keep honored to be a part of this collaborative effort. It is an idea you up to date with the front of that flow. To keep that which began handwritten on the back of an envelope in objective and meet our responsibility to our readers, we January 1991, and I still cherish that envelope. have updated all of those chapters that were carried over The process of organizing, writing, and finally publishing from the second edition, and many of them have been com- this manual has been a joint volunteer effort by many hun- pletely rewritten. You also will find that this edition con- dreds of people, each of whom has contributed generously of tains numerous chapters on new topics. their own experiences and expertise. Together, as a group of In addition to thanking the authors and editors, without 136 scientists, we saw our efforts come to initial fruition with whose selfless volunteer efforts the American Society for publication of the first edition of the Manual in the fall of 1996. Microbiology could not bring forth this manual, I offer par- By bringing to you this third edition, we now present a com- ticular thanks to several specific individuals. Jeff Holtmeier, plete update of our field. Jay Garland, David Lipson, and the director of ASM Press, has lent us his utmost support. Aaron Mills have been added as new volume editors for this Ken April of ASM Press served as our production editor. Ken, edition, replacing Michael McInerney and Guy Knudsen, who most of all, has coordinated the entire process and kept us on now have become emeritus editors. Four of the section editors course. Although his job is not easy, Ken somehow manages from the second edition, Robert Christian, Steven Newell, to seem calm and cheerful while surviving it all. The editors David Stahl, and Linda Thomashow, likewise have become also thank the following individuals who assisted us by serv- emeritus editors. It is with pride that I welcome in their stead ing as ad hoc reviewers for this edition of the Manual: Anne Meredith Hullar, Jonathan Lloyd, Se6n OConnell, and Ming Bernhard, Haluk Beyenal, Rima Franklin, Jim Fredrickson, Tien, who have joined the editorial board as new section edi- Robert Genter, Tim Griffin, Jo Handelsman, Heribert Insam, tors for this edition. Many of the contributing authors from the Scott Kelley, George Kling, Mike Lehman, John Lindquist, first two editions have been called in other directions, and Henry Mainwaring, Andrew Martin, Andrzej Paszczynski, those departing contributors now are our alumni, each of Gary Sayler, Kathleen T. Scott, Claus Sternberg, Ben Van whom knows that his or her efforts were appreciated by our Mooy, and Darla Wise. CHRISTON J . HURST xxi Contents Editorial Board / xi 7 Cultivation of Algae and Protozoa / 79 Contributors / xiii JOHN G. DAY, UNDINE ACHILLES-DAY, Preface / xxi SUSAN BROWN, AND ALAN WARREN 8 Cultivation and Assay of Animal Viruses / 93 SECTION I PIERRE PAYMENT INTRODUCTION TO ENVIRONMENTAL MICROBIOLOGY / 1 9 Cultivation of Microbial Consortia VOLUME EDITOR JAY L. GARLAND and Communities / 101 GIDEON M. WOLFAARDT, DARREN R. KORBER, 1 Introduction to Environmental AND JOHN R. LAWRENCE Microbiology / 3 CHRISTON J. HURST 10 Lipid Analyses for Viable Microbial Biomass, Community Composition, Metabolic 2 Neighborhoods and Community Status, and In Situ Metabolism / 112 Involvement: No Microbe Is an Island / 6 DAVID B. HEDRICK, AARON D. PEACOCK, CHRISTON J. HURST AND DAVID C. WHITE 3 Prokaryotic Diversity: Form, Ecophysiology, 11 Physiological Profiling of Microbial and Habitat / 20 Communities / 126 FREDERICK S. COLWELL JAY L. GARLAND, COLIN D. CAMPBELL, AND EDWARD R. LEADBETTER AND AARON L. MILLS 12 Molecular Approaches for the SECTION II Measurement of Density, Diversity, GENERAL METHODOLOGY / 35 and Phylogeny / 139 WEN-TSO LIU AND DAVID A. STAHL VOLUME EDITOR JAY L. GARLAND SECTION EDITOR SEAN P. O'CONNELL 13 Phylogenetic and Genomic Analysis / 157 DIRK GEVERS AND TOM COENYE 4 Overview: General Microbiology / 37 JAY L. GARLAND AND SEAN P. O'CONNELL 14 Bioreporters, Biosensors, and Microprobes / 169 5 Analytical Imaging and Microscopy ROBERT S. BURLAGE Techniques / 40 J. R. LAWRENCE, D. R. KORBER, AND T. R. NEU 15 Ecology at Long-Term Research Sites: Integrating Microbes and Ecosystems / 182 6 Cultivation of Bacteria and Fungi / 69 JOHN E. HOBBIE, MICHELE BAHR, RALPH S. TANNER AND ANNA-LOUISE REYSENBACH V vi H CONTENTS 16 Quality Assurance / 190 28 Modeling the Fate of Microorganisms in A. J. CROSS-SMIECINSKI Water, Wastewater, and Soil / 355 CHRISTON J. HURST 17 Issues of Study Design and Statistical Analysis for Environmental Microbiology / 199 29 Estimating the Risk of Infectious Disease KENNETH M. PORTIER AND RONALD CORSTANJE Associated with Pathogens in Drinking Water 1365 CHRISTON J. HURST SECTION Ill WATER MICROBIOLOGY IN PUBLIC 30 Toxic Photosynthetic Microbes / 378 HEALTH / 217 WESLEY CLINTON JACKSON, JR. VOLUME EDITOR CHRISTON J. HURST SECTION EDITOR GARY A. TORANZOS SECTION IV AQUATIC ENVIRONMENTS / 391 18 Overview of Water Microbiology as It VOLUME EDITOR CHRISTON J. HURST Relates to Public Health / 219 SECTION EDITOR MEREDITH A. J. HULLAR CHRISTON J. HURST 19 Waterborne Transmission of Infectious 31 An Overview of Methodologies in Aquatic Agents / 222 Microbial Ecology / 393 CHRISTINE L. MOE MEREDITH A. J. HULLAR 20 Detection of Microorganisms in 32 Cultivating Microorganisms from Dilute Environmental Freshwaters and Drinking Aquatic Environments: Melding Traditional Waters / 249 Methodology with New Cultivation Techniques GARY A. TORANZOS, GORDON A. McFETERS, and Molecular Methods / 399 JUAN JOSE BORREGO, AND MARION SAVILL JAMIE W. BECKER, MARINA L. BRANDON, AND MICHAEL S. RAPPE 21 Detection of Protozoan Parasites in Primary Productivity and Producers / Source and Finished Drinking Water / 265 33 407 HANS W. PAERL FRANK W. SCHAEFER I11 34 Bacterial Secondary Productivity / 421 22 Microbial Indicators of Marine GERARD0 CHIN-LEO AND COLLEEN T. EVANS Recreational Water Quality / 280 STEPHEN B. WEISBERG, RACHEL T. NOBLE, 35 Community Structure: Bacteria AND JOHN F. GRIFFITH and Archaea / 434 JED A. FUHRMAN 23 Detection of Viruses in Environmental Waters, Sewage, and Sewage Sludges I 290 36 Viral Community Structure / 445 CHRISTON J. HURST AND KELLY A. REYNOLDS ALEXANDER I. CULLEY AND CURTIS A. SUTTLE 24 Detection of Bacterial Pathogens in 37 Protistan Community Structure / 454 Wastewater and Sludge / 300 DAVID A. CARON AND ASTRID SCHNETZER RICHARD E. DANIELSON AND ROBERT C. COOPER 38 Decomposition and Fungal Community 25 Detection of Pathogenic Bacteria, Viruses, Structure in Aquatic Environments / 469 and Parasitic Protozoa in Shellfish / 31 1 FELIX BARLOCHER LEE-ANN JAYKUS 39 Bacterial Organic Carbon Cycling 26 Control of Microorganisms in Source in Aquatic Environments / 479 Water and Drinking Water / 325 MATTHEW T.