Bioremediation

Protocols

METHODS

IN

BIOTECHNOLOGY

John M. Walker,

SERIESEDITOR

2 BioremediationProtocols,editedby David Sheehan,1997 1, Immobilizationof Enzymesand Cells,editedby GordonF Bderstafi

1997

Bioremediation Protocols Edited by

David Sheehan University College, Cork, Ireland

Humana Press

Totowa, New Jersey

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IO 9 8 7 6 5 4 3 2 I

Library of Congress Cataloging m Publlcatlon Data Mam entry under title Methods m biotechnology’” Bloremedlatlon protocols/edited by David Sheehan cm.-(Methods m biotechnology, 2) P Includes mdex ISBN o-89603-437-2 (alk paper) I Bioremedlatlon-Technique I Sheehan, David TD192 5 B55744 1997 628 5-dc2 I

II Series 97- 16362 CIP

Preface The many thousands of human-made and other chemical compounds present in the environment offer a serious challenge to our btosphere. It is appropriate, therefore, that our response to these products of human knowledge and ingenuity should draw on a body of mtenstve scientific endeavor that is no lessimpressive. Bioremediation offers the possibility of harnessing the diversity of the biosphere to degrade, remove, alter, or otherwise detoxify these various chemicals. It brings together scientists from a wide variety of disciplines and backgrounds, such as microbiology, molecular biology, analytical chemistry, and chemical and environmental engineering, among others. These different fields, each with its own individual approach, have actively contributed to the development of bioremediation research tn recent years. The prmcipal objective of Bioremediation Protocols is to make the fruits of some of this research available in a different format to that of the textbook or journal article. It provides a selection of clearly written laboratory protocols presented as stepwise, easy-to-follow mstructions. In common with prewous volumes in this and the companion Methods in Molecular Biology series, an extensive “Notes” section is provided with each chapter. This contains useful mformation (of a type often not normally included m a research paper) supplementmg the protocol. Reviews and case studies are also included to provide a deeper context to the methods chapters. It is obviously impossible to cover the full range of bioremediation research m a single volume. However, an attempt has been made to address some major issuesm bioremediatton research, such as cell unmobibzatton, design and use of bioreactors, genetic manipulation, preparation, and analysis of envn-onmental samples.It is hoped that many of the protocols provided (which, of necessity,are very specific) may lend themselves to adaptation by other investigators, perhaps to address some of their particular research needs. The international selection of authors are to be commended for agreeing to share detailed descriptions of their research methodologies and expertise with a wider audience in such an accessible format. It is hoped that this will stimulate other workers m this important and growmg field. David Sheehan V

Contents Preface ., .., . .. . . . . .. . . . .. . . .. . . . . . .. . . . . . .. . . . .. . .. . . . . . . .. Contnbutrng Authors . . .. . . . .., . .. . . . . *... *.. . . . . . . .. . .. . . . . PART I. OVERVIEW ., .,... .

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1 Uses of Bacteria in Bioremediation, Emer Colleran .. . . . . .. ,. . . .. . . . . . . . .. . . . . .. . . .. 2 Granular Sludge Consortia for Bioremediation, Nina Christiansen, lndra M. Mathrani, and Birgitte K. Ahring PART II PROTOCOLS. . .. . . . .. . . . ,. . . . .. . . . .. . . . .. . . .

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3 Screemng of Bacterial Products for Their Crude Oil Biodegradation Effectiveness, Albert D. Venosa, John R. Haines, and B. Loye Eberhart.. . . . . . ...47 4 Measurement of Btosurfactant-Enhanced Solubilization and Biodegradation of Hydrocarbons, Raina M. Miller and Yimin Zhang .. . . . . . . .. . . .. . .. . . . . . . . .. . . 59 5 lmmobilrzation of Bacteria in Macro- and Microparticles, David B. Knaebel, Keith E. Stormo, and Ronald L. Crawford . 67 6 Immobilization and Evaluation of Bacterial Ceils In Bioreactors, Samir S. Sofer. . . . ,. . . .. . ..,....... .. . . .. . . . .. . . . ., . ., . . .. . . .. . 79 7 Immobilization of Yeast and Algal Cells for Bioremediation of Heavy Metals, John R. Duncan, Dean Brady, and Brendan Wilhelmi . . .. . . . .. , . . . .97 8 Enumeratron of Hydrocarbon-Degrading Bacteria, Laura E. Rice and Barbara B. Hemmingsen . . . . . . .. . . . .. . . .. .. . . . . 99 9 Molecular Methods for the Detection of Methanotrophs, fan R. McDonald, Andrew J. Holmes, Elizabeth M. Kenna, and J. Co/in Murrell . . . .. . .. . . .. . . . . . . . .. . . .. . . . .. . . .. . . . Iii 10 Measurement of Mutagenic Activity in Contaminated Soils, Shanna L. Collie and Kevin C. Donnelly . . , ,,.,o, ,... ~~.. ,~ . . . .. 127 11 Conjugation-Mediated Gene Transfer in Bacterial Strains to Be Used for Bioremedlation, Max Mergeay and Dirk Springael .. . . . . . . . . .. . , .. . . .., . . .. 153

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Contents

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VIII

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Analysis of Pentachlorophenol In Soils for Use In Bioremediation Studies, Ruth McGrath and Ian Singleton . . . .. . . . . .. . . . .. . . . .. . . . . .. . .. . .. .. . . . .. . . . 169 Generation of Species Specific DNA Probes for the Lignin Peroxidase Genes of White Rot Fungr, Patrick J. Collins and Alan D. W. Dobson .. . . . .. . .. . .. . . . .. . . . . .. .. . . 177 Biodegradation of Nttroaromatics by Microbes, Juan L. Ramos, Asuncibn Delgado, Estrella Duque, Maria-Dolores Fandila, Matilde Gil, Ali Hai’dour, Gloria Lucchesi, Carmen MichBn, and Rafael Salto.

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The Determination of Trace Elements in Biological and Environmental Samples Using Atomic Absorptron Spectroscopy, 201 John O’Halloran, Andrew R. Walsh, and Patrick J. Fitzpatrick. Quantifying Organic and Inorganic Tin Compounds in Environmental Samples, . . .. . . . ,.... . . . .. . . . . . . . . . ,. . . . 273 Joseph J. Cooney . .. . .. . . . .

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Protocol for Determining Bioavailability and Biodegradation Kinetics of Organic Soil Pollutants in Soil Systems to Enhance Bioremediatron of Polluted So11 Sites, Henry H. Tabak, Rakesh Govind, Chunsheng Fu, and Chao Gao . .. . . ,. . . . . . .. . . . .. .. . . . . .. . . . .. .. . .. . . .. . .. ,. . . . . . 223

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Methods for Evaluation of PCB Dechlorination in Sediments, John F. Quensen, III and James M. Tiedje .. . . . .. .. . . . .. . . . . .. . .. . .. . . .. 24 I

PART III CASESTUDIES ...

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Evaluation of PCB Dechlorination in Sediments, John F. Quensen, 111and James M. Tiedje . . . .,. . ,.. . . . . . . .. . .. . . . 257 Microbial Degradation of Alkenylbenzenes, . . . 275 Kevin E. O’Connor and Alan D. W. Dobson . . . . . .. . . Heavy Metal Broremediation of SolI, Ludo Diels . .. . .. . ,. . . . . .. . . .. . .. . . . .. .. . .. . . .. . .. . . . . .. .. . . . . .. . . . .. . . . . . . .. . . . . . .. , . . 283 Application of Bioavarlability and Brokinetics Protocol to Phenol and Polycyclic Aromatic Hydrocarbon Contaminants in Soil and Development of Broavailabrlity and Biokinetic Models for Soil Systems, Henry H. Tabak, Rakesh Govind, Chunsheng Fu, and Chao Gao. . .,.. . .. .,.. .. . . . . .. . ,.. . . .. .., . . . .. .. .. . .. . . . . 297

Appendix. Index

Glossary of Abbreviations and Acronyms . . .. . . . .. . .. . .. . . . . . . . 325 . . . . . . . . . . . . .. . . .. .. . . ,. . . . . . . . . . . . . . .. . . 329

Contributors BIRGITTE K. AHRING

Institute of Environmental Sctence and Engineering, Technical Untversity ofDenmark, Lyngby, Denmark DEAN BRADY Department of Biochemistry and Microbiology, Rhodes Universtty, Grahamstown, South Africa NINA CHRISTIANSEN Institute of Environmental Science and Engineering, Techntcal Untversity of Denmark, Lyngby, Denmark EMER COLLERAN Department of Microbiology, University College, Galway, Ireland SHANNA L. COLLIE Department of VAPH, Texas A&M Universtty, College Statton, TX PATRICK J. COLLINS Department of Microbiology, Untversity College, Cork, Ireland JOSEPH J. COONEY Environmental Sciences Program, University of Massachusetts, Boston, MA RONALD L. CRAWFORD Department of Biology, Clarkson University, Potsdam, NY ASUNCION DELGADO CSIC, Granada, Spain LUDO DIELS Environmental Technology, VITO, Mol, Belgium ALAN D. W. DOBSON Department of Microbiology, Untversity College, Cork, Ireland KEVIN C. DONNELLY Department of VAPH, Texas A&M University, College Station, TX JOHN R. DUNCAN Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa ESTRELLA DUQUE CSIC, Granada, Spatn B. LOYE EBERHART US Environmental Protection Agency, Cincinnati, OH MARIA-DOLORES FANDILA CSIC, Granada, Spain PATRICK J. FITZPATRICK Department of Biochemistry, University College, Cork, Ireland CHIJNSHENG Fu Department of Chemical Engtneering, Universtty of . Cincinnati, OH l

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Contributors

X CHAO GAO

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Department of Chemical Engtneertng, University of Cincinnati,

MATILDE GIL CSIC, Granada, Spatn RAKESH GOVIND Department of Chemical Engineering, Untversity of l

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Cincinnati, OH ALI HAIDOUR CSIC, Granada, Spain JOHN R. HAINES US Environmental Protection Agency, Cincinnatt, OH BARBARA B. HEMMINGSEN Department of Btologv, San Diego State University, San Diego, CA ANDREW J. HOLMES Department of Btologtcal Sciences, University of Warwick, Coventry, UK ELEABETH M. KENNA Department of Biological Sciences, Untverstty of Warwtck, Coven try, UK DAVID B. KNAEBEL Department of Biology, Clarkson University, Potsdam, NY GLORIA LUCCHESI CSIC, Granada, Spatn INDRA M MATHRAN~ 9Institute of Envtronmental Science and Engtneenng, Techntcal Untversity of Denmark, Lyngby, Denmark IAN R. MCDONALD Department of Biological Sciences, Untversrty of Warwick, Coventry, UK RUTH MCGRATH Department of Mtcrobtology, University College, Dublin, Ireland MAX MERGEAY Environmental Technology, VITO, Mel, Belgium CARMEN MICHAN CSIC, Granada, Spatn RAINA M MILLER Department of Soil, Water, and Envtronmental Science, Untverstty of Artzona, Tucson, AZ J. COLIN MURRELL * Department of Btologtcal Sciences, Untversity of Warwtck, Coventry, UK KEVIN E. O’CONNOR Department of Mcrobtology, University College, Cork, Ireland JOHN O’HALLORAN Department of Zoology, Untverstty College, Cork, Ireland JOHN F QUENSEN, III* Department of Crop and Soil Science, Michigan State Unrverstty, East Lansing, MI JUAN L RAMOS CSIC, Granada, Spain LAURA E. RICE Department of Btology San Diego State University, San Diego, CA RAFAEL SALTO CSIC, Granada, Spain l

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Contributors

9 Department of Soil Science, University of Adelatde, Glen Osmond, Australia SAMIR S. SOFER Department of Chemical Engineering, New Jersey Institute of Technology, Newark, NJ DIRK SPRINGAEL Envtronmental Technology, VITO, Mel, Belgium KEITH E STORMO* Department of Biology, Clarkson University, Potsdam, NY HENRYH. TABAK National RuskManagement Research Laboratory, ORD, US Environmental Protectton Agency, Cincinnatt, OH JAMESM. TIEDJE Department of Crop and Soil Sctence, Mtchtgan State Universtty, East Lansing, MI ALBERT D. VENOSA US Envtronmental Protection Agency, Cinctnnatt, OH ANDREWR. WALSH Department of Zoology, Untverstty College, Cork, Ireland BRENDAN WILHELMI Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa YIMIN ZHANG Department of Soil, Water, and Environmental Science, Universtty of Artzona, Tucson, AZ IAN SINGLETON

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