Heribert Insam Andrea Rangger Microbial Communities Springer Berlin Heidelberg New York Barcelona Budapest Hong Kong London Milan Paris Santa Clara Singapore Tokyo H.Insam A. Rangger (Eds.) Microbial Communities Functional Versus Structural Approaches With 83 Figures and 54 Tables Springer Univ. Doz. Dr. HERIBERT INSAM Mag. ANDREA RANGGER Universitat Innsbruck Institut fUr Mikrobiologie TechnikerstraBe 25 A-6020 Innsbruck Gedruckt mit Unterstiitzung des Bundesministeriums fUr Wissenschaft und Verkehr in Wien. ISBN-13:978-3-642-64S11-2 Library of Congress Cataloging-in-Publication Data Microbial communities: funtional versus structural approaches I Heribert Insam , Andrea Rangger, eds. p. em. Includes bibliographical references and index. ISBN-13:978-3-642-645U-2 e-ISBN-13:978-3-642-60694-6 DOl: 10.1001/978-3-642-60694-6 1. Soil ,microbiology--Reserarch--Methodology. 2. Microbial ecology--Research--Methodology. I. Insam, Heribert, 1957- II. Rangger, Andrea. 1966- QRll1.M379 1997 579'. 1757--dc21 97-22416 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is con cerned, specifically the rights of translation, reprinting reuse of illustrations, recitation, broadcasting, repro duction on microfilm or in any other way, and storage in data banks. Duplication of this publication or parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965, in its current version, and permissions for use must always be obtained from Springer-Verlag. Violations are lia ble for prosecution under the German Copyright Law. @Springer-Verlag Berlin Heidelberg 1997 Softcover reprint of the hardcover 1st edition 1997 The use of general descriptive names, registered names, trademarks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. Cover design: Design & Production, Heidelberg Cover photograph: Judith Ascher Typesetting: Camera ready by authors SPIN 10544412 3113137. 5432 1 0 -Printed on acid-free paper Preface Research on decomposer communities of terrestrial ecosystems for a long time has focussed on microbial biomass and gross turnover parameters. Recently, more and more attempts are made to look beyond the biomass, and more specifically determine functions and populations on a smaller scale-in time and space. A multitude of techniques is being improved and developed. Garland and Mills (1991) triggered a series of publications on substrate utilization tests in the field of microbial ecology. Despite several promising results for different applications in different laboratories, many problems concerning the assay and the interpretation of results became evident. After individual discussions on the approach with colleagues from various laboratories we started to plan a workshop on the matter. The response on our first circular was extraordinary, and instead of a small workshop it became a meeting with almost 150 participants. The meeting was named 'Substrate use for characterization of microbial communities in terrestrial ecosystems' (SUBMECO) and was held in Innsbruck, Austria, from Oct. 16-18, 1996. The very focussed scope attracted enthusiastic advocates of the approach, and also serious critics. Some of the topics concerned improvements of current inoculation and incubation techniques, ranging from sample pre-treatment, inoculum density and incubation temperature to statistical data handling. New methods for calculating microbial diversity were proposed, as well as bootstrap methods that allow statistics with many variables on a relatively low number of replicates. One of the main aims of the meeting was to link the functional approach with structural ones, like the determination of biochemical markers or DNA and RNA based methods. It was discussed under which circumstances substrate use tests are advisable, and for which studies other approaches offer much more information. The selection of substrates offered on commercially available multisubstrate plates is not targeted at environmental samples. Unequivocally, the need for a set of substrates meeting the requirements of environmental analyses was recognized. In a follow-up workshop it was proposed to screen the data available in the different labs to come up with such a set of substrates. As a result of previous experience and the workshop, an EcoPlate was designed with only 31 substrates, but in three replications per plate. Prototypes of these plates are VI currently in the test phase in several labs. For further communication on the topic, an internet discussion forum was initiated (http:www.biolog.com). The editors express their thanks to the members of the scientific committee of the meeting, Erland Baath (Sweden), Ann Kennedy, Aaron Mills, Jay Garland, John Zak (USA), Lars Bakken, Shivcharn Dhillion (Norway), Colin Bell (Canada), Roland Psenner (Austria), Christoph Tebbe (Germany), Anne Winding (Denmark) and Bryan Griffiths (UK) for their initial ideas that helped to focus the meeting, their involvement in heading sessions and perform the reviewing process. The editors also thank the sponsors of the meeting for their support, among them the University of Innsbruck, the Austrian Federal Ministry of Science, the European Union (MICS and grant for Eastern European participants) and Tyrolean Airways. The help and support by colleagues and students of the Institute of Microbiology is also gratefully acknowledged. The contents of this book range from agricultural topics to global change issues, they relate to pollutant effects and bioremediation studies, and they cover microbial community dynamics during decomposition and food fermentation processes. You will further find method comparisons (substrate use tests versus PLF A and genetic approaches) and, last but not least, critical evaluations. Papers focussing on methods improvement can be found in a Special Issue of the Journal ofM icrobiological Methods. The Editors Heribert Insam Andrea Rangger Contents Relationship between Functional Diversity and Genetic Diversity in Complex Microbial Communities ................................................................... 1 B.s. Griffiths, K. Ritz, R.E. Wheatley Use of Molecular Probing to Assess Microbial Activities in Natural Ecosystems ....................................................................................... 10 J. e. Gottschal, W G. Meijer, Y Oda Phenetic and Genetic Analyses of Bacterial Populations in Fermented Food and Environmental Samples ................................................... 19 H. W van Verseveld, WF.M Roling, D. van Rossum, A.M Laverman, S. van Dijck, M Braster, F.e. Boogerd Comparison of Biolog and Phospholipid Fatty Acid Patterns to Detect Changes in Microbial Community ..................................................... 37 A. Paloj arvi, S. Sharma, A. Rangger, M von Liltzow, H. Insam Combined Application of Biolog and MIS/SHERLOCK for Identifying Bacterial Isolates from Hydrocarbon-polluted Argentinian Soils ....................... 49 L. Wilnsche, e. Hartig, H. 0. Pucci, W Babel Diversity of Anthropogenically Influenced or Disturbed Soil Microbial Communities .................................................................................................... 57 E. Laczko, A. Rudaz, M Aragno Impact of Fertilizers on the Humus Layer Microbial Community of Scots Pine Stands Growing Along a Gradient of Heavy Metal Pollution ........... 68 H. Fritze, T. Pennanen, P. Vanhala Disturbances and their Influence on Substrate Utilization Patterns in Soil Microbial Communities ......................................................................... 84 M V. Gorlenko, T.N. Majorova, P.A. Kozhevin VIII Evaluation of Remediation by Community-Level Physiological Profiles ....................................................................................... 94 M. Lehman, SP. 0 'Connell, J.L. Garland, FS Colwell Carbon Source Utilization by Microbial Communities in Soils under Organic and Conventional Farming Practice ......................................... 109 A. Fliefibach, P. Mader Characterization of Microbial Communities in Agroecosystems ...................... 121 A. C Kennedy, VL. Gewin Different Carbon Source Utilization Profiles of Four Tropical Soils from Ethiopia ......................................................................................... 132 S Sharma, A. Piccolo, H insam Fallow Age Influences Microbial Functional Abilities, Soil Properties and Plant Functional Groups .................................................... 140 SS Dhillion Substrate Utilization Patterns of Extractable and Non-Extractable Bacterial Fractions in Neutral and Acidic Beech Forest Soils ........................... 149 S Kreitz, T. -H Anderson Biolog Metabolic Fingerprints for Clustering Marine Oligotrophic Bacteria from Polar Regions ....................................................... 161 T.L. Tan The Influence of Microbial Community Structure and Function on Community-Level Physiological Profiles ...................................... 171 J.L. Garland, K.L. Cook, CA. Loader, B.A. Hungate Strain and Function Stability in Gnotobiotic Reactors ...................................... 184 A.L. Mills, J.E. Bouma Biolog Substrate Utilisation Assay for Metabolic Fingerprints of Soil Bacteria: Incubation Effects .................................................................. 195 A. Winding, N.B. Hendriksen A Novel Approach for Assessing the Pattern of Catabolic Potential of Soil Microbial Communities .......................................... 206 B. Degens Chirality is a Factor in Substrate Utilization Assays ........................................ 215 D. W. Hopkins, R. W. O'Dowd IX Analysis of the Bacterial Community according to Colony Development on Solid Medium ........................................................... 229 T. Hattori, H. Mitsui, R. Hattori, S. Shikano, K. Gorlach, Y. Kasahara, A. El-Beltagy The Complexity ofthe Flux of Natural Substrates in Soils: A Freeze-thaw can Increase the Formation ofIschemic or Anaerobic Microsites ..................... 236 A. Zsolnay Carbon Transformations During Substrate Utilization by the Microbial Community in an Organic Soil: A Solid-State NMR. Study .............................. 242 E.A. Webster, J.A. Chudek, D. W Hopkins Ammonification of Amino Acids in Field, Grassland and Forest soils ............. 248 0. Dilly A New Set of Substrates Proposed for Community Characterization in Environmental Samples .............................. , ............................................... 259 H.lnsam Index ............................................................................................................... 261