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Molecular Markers, Indicator Taxa, and Community Indices: the Issue of Bioindication Accuracy

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Molecular Markers, Indicator Taxa, and Community Indices: the Issue of Bioindication Accuracy NEMATODES AS ENVIRONMENTAL INDICATORS This page intentionally left blank NEMATODES AS ENVIRONMENTAL INDICATORS Edited by Michael J. Wilson Institute of Biological and Environmental Sciences, The University of Aberdeen, Aberdeen, Scotland, UK Thomais Kakouli-Duarte EnviroCORE Department of Science and Health, Institute of Technology, Carlow, Ireland CABI is a trading name of CAB International CABI Head Office CABI North American Office Nosworthy Way 875 Massachusetts Avenue Wallingford 7th Floor Oxfordshire OX10 8DE Cambridge, MA 02139 UK USA Tel: +44 (0)1491 832111 Tel: +1 617 395 4056 Fax: +44 (0)1491 833508 Fax: +1 617 354 6875 E-mail: [email protected] E-mail: [email protected] Website: www.cabi.org © CAB International 2009. All rights reserved. No part of this publication may be reproduced in any form or by any means, electronically, mechanically, by photocopying, recording or otherwise, without the prior permission of the copyright owners. A catalogue record for this book is available from the British Library, London, UK. Library of Congress Cataloging-in-Publication Data Nematodes as environmental indicators / edited by Michael J. Wilson, Thomais Kakouli-Duarte. p. cm. Includes bibliographical references and index. ISBN 978-1-84593-385-2 (alk. paper) 1. Nematodes–Ecology. 2. Indicators (Biology) I. Wilson, Michael J. (Michael John), 1964- II. Kakouli-Duarte, Thomais. III. Title. QL391.N4N382 2009 592'.5717--dc22 2008049111 ISBN-13: 978 1 84593 385 2 Typeset by SPi, Pondicherry, India. Printed and bound in the UK by the MPG Books Group. The paper used for the text pages in this book is FSC certified. The FSC (Forest Stewardship Council) is an international network to promote responsible man- agement of the world’s forests. Contents Contributors vii Preface xi Part I Nematodes and Bioindication – General Considerations 1 The Role of Nematodes in Ecosystems 1 G.W. Yeates, H. Ferris, T. Moens and W.H. Van der Putten 2 Nematode Diversity in Terrestrial, Freshwater Aquatic 45 and Marine Systems M. Hodda, L. Peters and W. Traunspurger 3 Molecular Markers, Indicator Taxa, and Community 94 Indices: the Issue of Bioindication Accuracy K. Ekschmitt and G. Korthals Part II Analysis of Nematode Assemblages in Environmental Samples 4 General Community Indices that can be used for 107 Analysis of Nematode Assemblages D.A. Neher and B.J. Darby 5 Indices Developed Specifi cally for Analysis of 124 Nematode Assemblages H. Ferris and T. Bongers v vi Contents 6 Case Studies Using Nematode Assemblage Analysis in 146 Aquatic Habitats R. Danovaro, C. Gambi, S. Höss, S. Mirto, W. Traunspurger and A. Zullini 7 Case Studies Using Nematode Assemblage Analysis in 172 Terrestrial Habitats P. Nagy 8 Molecular Tools for Analysing Nematode Assemblages 188 R. Neilson, S. Donn, B. Griffi ths, T. Daniell, K.D. Rybarczyk, S. van den Elsen, P. Mooyman and J. Helder Part III Nematode Ecotoxicity Tests and Gene Expression Analysis 9 Ecotoxicity Testing with Nematodes 208 S. Höss and P.L. Williams 10 Transgenic Caenorhabditis elegans as Biosensors 225 C. Lagido 11 Caenorhabditis elegans and Chemical Environmental Stressors: 253 from DNA Microarrays and Data Analysis to Genomic Data of True Ecotoxicological Relevance R. Menzel, C.E.W. Steinberg and S.R. Stürzenbaum Part IV Commercial Use of Nematodes as Bioindicators 12 Commercial Aspects of the Use of Nematodes as Bioindicators 275 M.W. Trett, B.C. Urbano, S.J. Forster and S.P. Trett Index 315 Contributors Tom Bongers, Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands (Email: [email protected]) Brian J. Darby, Department of Plant and Soil Science, University of Vermont, 105 Carrigan Drive, Burlington, Vermont, 05405, USA (Email: brian. [email protected]) Tim Daniell, Environment Plant Interactions Programme, SCRI, Invergowrie, Dundee, DD2 5DA, UK (Email: [email protected]) Roberto Danovaro, Dipartimento di Scienze del Mare, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy (Email: r.danovaro@ univpm.it) Suzanne Donn, Environment Plant Interactions Programme, SCRI, Inver- gowrie, Dundee, DD2 5DA, UK (Email: [email protected]) Klemens Ekschmitt, Justus Liebig University, IFZ – Department of Animal Ecology, H.-Buff-Ring 26-32, D-35392 Giessen, Germany (Email: Klemens. [email protected]) Howard Ferris, Department of Nematology, University of California Davis, Davis, CA 95616, USA (Email: [email protected]) Simon J. Forster, Physalia Limited, Consultant & Forensic Ecologists, Sedgefen House, Meadow Walk, Harpenden, Hertfordshire AL5 5TF, UK (Email: [email protected]) Cristina Gambi, Dipartimento di Scienze del Mare, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy (Email: c.gambi@ univpm.it) Bryan Griffiths, Teagasc, Environmental Research Centre, Johnstown Castle, Wexford, Ireland (Email: [email protected]) Johannes Helder, Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands (Email: [email protected]) vii viii Contributors Mike Hodda, Nematode Biosystematics & Ecology, Australian National Insect Collection, CSIRO Entomology, GPO Box 1700, Canberra ACT 2601, Australia (Email: [email protected]) Sebastian Höss, Ecossa, Giselastr. 6, 82319 Starnberg, Germany (Email: hoess @ecossa.de) Thomais Kakouli-Duarte, Envirocore Department of Science and Health, Institute of Technology, Carlow, Kilkenny Road, Carlow, Ireland (Email: [email protected]) Gerard Korthals, Wageningen UR, Applied Plant Research, P.O. Box 430, NL-8200 AK Lelystad, The Netherlands (Email: [email protected]) Cristina Lagido, School of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK (Email [email protected]) Ralph Menzel, Department of Biology, Freshwater and Stress Ecology, Humboldt University at Berlin, Unter den Linden 6, 10099 Berlin, Germany (Email: [email protected]) Simone Mirto, Istituto per l’Ambiente Marino Costiero (IAMC), CNR, Spianata San Raineri, 86, 98122, Messina, Italy (Email: simone.mirto@ iamc.cnr.it) Tom Moens, Marine Biology Section, Department of Biology, Ghent Univer- sity, Krijgslaan 281/S8, B-9000 Ghent, Belgium (Email: Tom.Moens@ UGent.be) Paul Mooyman, Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands (Email: [email protected]) Péter Nagy, Department of Zoology and Animal Ecology, Szent István University, Gödöllo˝, Hungary (Email: [email protected]) Deborah A. Neher, Department of Plant and Soil Science, University of Vermont, 105 Carrigan Drive, Burlington, VT 05405, USA (Email: deborah. [email protected]) Roy Neilson, Environment Plant Interactions Programme, SCRI, Invergowrie, Dundee, DD2 5DA, UK (Email: [email protected]) Lars Peters, Department of Animal Ecology, University of Bielefeld, Morgenbreede 45, 33615 Bielefeld, Germany (Email: lars.peters@ uni-bielefeld.de) Katarzyna D. Rybarczyk, Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands (Email: [email protected]) Christian E.W. Steinberg, Department of Biology, Freshwater and Stress Ecology, Humboldt University at Berlin, Unter den Linden 6, 10099 Berlin, Germany (Email: [email protected]) Stephen R. Stürzenbaum, School of Biomedical and Health Sciences, King’s College London, 150 Stamford Street, London SE1 9NH, UK (Email: [email protected]) Walter Traunspurger, Department of Animal Ecology, University of Bielefeld, Morgenbreede 45, 33615 Bielefeld, Germany (Email: traunspurger@ uni-bielefeld.de) Contributors ix Marcus W. Trett, Physalia Limited, Consultant & Forensic Ecologists, Sedgefen House, Meadow Walk, Harpenden, Hertfordshire AL5 5TF, UK (Email: [email protected]) Simon P. Trett, Physalia Limited, Consultant & Forensic Ecologists, Sedgefen House, Meadow Walk, Harpenden, Hertfordshire AL5 5TF, UK (Email: [email protected]) Beatriz Calvo Urbano, Nebalia S.L. Consultoría Medioambiental, Calle de Amor de Dios, 4, bajo A, 28014 Madrid, Spain (Email: [email protected]) Sven van den Elsen, Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands (Email: [email protected]) Wim H. Van der Putten, NIOO-KNAW, Centre for Terrestrial Ecology, PO Box 40, 6666 ZG Heteren, The Netherlands and Laboratory of Nematology, Department of Plant Sciences, Wageningen University, Binnenhaven 5, 6709 PD Wageningen, The Netherlands (Email: [email protected]) Phillip L. Williams, College of Public Health, University of Georgia, Paul D. Coverdell Center, Athens, GA 30602-7396, USA (Email: [email protected]) Michael J. Wilson, Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen AB24 3UU, UK (Email: m.j.wilson@ abdn.ac.uk) Gregor W. Yeates, P.O. Box 1758, Palmeston North 4440, New Zealand (Email: [email protected]) Aldo Zullini, Dipartimento di Biotecnologie & Bioscienze, Università di Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy (Email: aldo. [email protected]) This page intentionally left blank Preface Both of us are relatively new to the field of nematodes as biological indica- tors. We have backgrounds in crop protection and particularly the use of parasitic nematodes as biological control agents. In the late 1990s, we both obtained tenure track positions in institutions
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