Table Of ContentHeribert Insam Andrea Rangger Microbial Communities
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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
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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
