Aquatic Microbial Ecology: Biochemical and Molecular Approaches

199 Pages·1990·8.92 MB·English

by  Ryszard J. Chróst

Brock/Springer Series in Contemporary Bioscience
Aquatic Microbial
Ecology
Brock/Springer Series in Contemporary Bioscience
Series Editor: Thomas D. Brock
University of Wisconsin-Madison
Tom Fenchel
ECOLOGY OF PROTOZOA:
The Biology of Free-living Phagotrophic Protists
Johanna Diibereiner and Fabio o. Pedrosa
NITROGEN-FIXING BACTERIA IN NONLEGUMINOUS
CROP PLANTS
Tsutomu Hattori
THE VIABLE COUNT: Quantitative and Environmental Aspects
Roman Saliwanchik
PROTECTING BIOTECHNOLOGY INVENTIONS:
A Guide for Scientists
Hans G. Schlegel and Botho Bowien (Editors)
AUTOTROPHIC BACTERIA
Barbara Javor
HYPERSALINE ENVIRONMENTS: Microbiology and Biogeochemistry
Ulrich Sommer (Editor)
PLANKTON ECOLOGY: Succession in Plankton Communities
Stephen R. Rayburn
THE FOUNDATIONS OF LABORATORY SAFETY:
A Guide for the Biomedical Laboratory
Gordon A. McFeters (Editor)
DRINKING WATER MICROBIOLOGY:
Progress and Recent Developments
Mary Helen Briscoe
A RESEARCHER'S GUIDE TO SCIENTIFIC AND
MEDICAL ILLUSTRATIONS
Max M. Tilzer and Colette Serruya (Editors)
LARGE LAKES: Ecological Structure and Function
Jurgen Overbeck and Ryszard J. Chr6st (Editors)
AQUATIC MICROBIAL ECOLOGY:
Biochemical and Molecular Approaches
Jiirgen Overbeck
Ryszard J. Chrost
Editors
Aquatic Microbial
Ecology
Biochemical and Molecular Approaches
With 40 Figures and 12 Tables
Springer-Verlag
New York Berlin Heidelberg
London Paris Tokyo Hong Kong
Jiirgen Overbeck Ryszard J. Chrost
Max-Planck Institute of limnology Institute of Microbiology
Department of Microbial Ecology University of Warsaw
D-2320 PIon PI-OO-064 Warsaw
Federal Republic of Germany Poland
library of Congress Cataloging-in-Publication Data
Aquatic microbial ecology : biomechanical and molecular approaches /
edited by Jiirgen Overbeck and Ryszard J. Chrost ; contributors,
Ryszard J. Chrost ... ret al.l.
p. em. - (Brock/Springer series in contemporary bioscience)
Includes bibliographical references.
1. Aquatic microbiology. 2. Microbial ecology. I. Overbeck,
Jiirgen. II. Chrost, Ryszard J. III. Series.
QRI05.A694 1990
576'.15'0916-dc20 89-26242
Printed on acid-free paper.
© 1990 Springer-Verlag New York Inc.
Softcover reprint of the hardcover 1s t edition 1990
All rights reserved. This work may not be translated or copied in whole or in part without
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The use of general descriptive names, trade names, trademarks, etc., in this publication,
even if the former are not especially identified, is not to be taken as a sign that such names,
as understood by the Trade Marks and Merchandise Marks Act, may accordingly be used
freely by anyone.
Production and editorial supervision: Science Tech Publishers.
987654321
ISBN-13:978-1-4612-7991-4 e-ISBN-13:978-1-4612-3382-4
001: 10.1007/978-1-4612-3382-4
Preface
This book was written because of a conviction that although aquatic microbial
ecology has developed rapidly it has become compartmentalized into many
research areas and specialist disciplines. Microbial ecologists are confronted
with the complexity of natural microbial communities and are attempting to
unravel and describe the interactions and activities occurring in such com
munities in situ. Microbial ecology has become very difficult for both the
student and the specialist to approach in a comprehensive manner. The facts
are often so discrete and disconnected that they do not form a story, and
many of the important truths of the discipline are still unknown.
This book discusses the state-of-the-art research in selected fields of
aquatic microbial ecology. It provides examples of areas of aquatic research
where new methods and approaches available in biochemistry, molecular
biology, and microbial genetics are being applied. This work has been made
possible through the rapid development of advanced methods in the labo
ratory and the subsequent modification and adaptation of these methods to
field studies.
This text is addressed to postgraduate students and scientists who will
apply these methods to aquatic microbial ecology. There are many fascinating
questions to be answered through future aquatic microbial research. Success
in this field will depend on causal analysis of complex ecological systems on
different levels, measurement of structures and functions of microbial pop
ulations in the field, and analysis of functional relationships in laboratory
experiments. Field and laboratory work are equally important and must pro
ceed in parallel. These different approaches imply an interdisciplinary col
laboration of specialists. We hope that this book will initiate both new projects
and the means of studying them.
Finally, another aspect of microbial ecological studies at the biochemical
and molecular level should be addressed. The structures and functions of
microbial populations are the result of natural selection. Metabolic regulation,
operating at the molecular level, increases the fitness of the microbial cell in
the habitat and assures its preservation by natural selection. From this point
of view, the study of the ecology of microorganisms can lead to a better
understanding of the biochemical and molecular processes that are the end
product of the evolutionary interactions of microorganisms with complex nat
ural environments.
v
vi Preface
If we can motivate one researcher to devote his or her life to aquatic
microbial ecology, or to any aspect thereof, we believe we will have achieved
our purpose in presenting this book.
Jiirgen Overbeck
Ryszard J. Chrost
Contents
Preface v
Contributors x
1 Introduction: Aims, Problems, and Solutions in Aquatic
Microbial Ecology 1
Ryszard J. Chrost and Jurgen Overbeck
1.1 The aims of microbial ecology 1
1.2 Novel solutions to "old" problems 2
References 6
2 Origin, Composition and Microbial Utilization of
Dissolved Organic Matter 8
Uwe Munster and Ryszard J. Chrost
2.1 Introduction 8
2.2 Origin and fate of dissolved organic matter 11
2.3 Concentration and characteristics of dissolved organic
matter 17
2.4 Dissolved organic matter released by phytoplankton 20
2.5 Glycolic acid: a model compound of algal release 24
2.6 Dissolved free amino acids 26
2.7 Dissolved free carbohydrates 28
2.8 Polyphenols 32
2.9 Conclusions 35
References 37
3 Microbial Ectoenzymes in Aquatic Environments 47
Ryszard J. Chrost
3.1 Introduction 47
3.2 Definition of an ectoenzyme 48
3.3 Association of ectoenzymes with microbial cells 49
3.4 Ectoenzyme secretion 52
3.5 Molecular control of ectoenzyme synthesis 54
vii
viii Contents
3.6 Environmental control of ectoenzyme synthesis and
activity in aquatic ecosystems 55
3.7 Methods for assaying ectoenzymes 62
3.8 Significance of ectoenzymes in aquatic environments 68
References 74
4 Aspects of Aquatic Microbial Carbon Metabolism:
Regulation of Phosphoenolpyruvate Carboxylase 79
Jiirgen Overbeck
4.1 Introduction 79
4.2 Basic strategies of biochemical adaptation to the
environment 80
4.3 Anaplerotic reactions 80
4.4 Complexity of CO dark uptake 82
2
4.5 Phosphoenolpyruvate carboxylase 84
4.6 Assays, preparation and kinetic properties of
phoshoenolpyruvate carboxylase 86
4.7 Regulation of phosphoenolpyruvate carboxylase by
effectors 89
4.8 Phosphoenolpyruvate carboxylase and
phosphoenolpyruvate carboxykinase 91
4.9 Concluding remarks: biochemical approaches at the
ecosystem level 92
References 93
5 Approaches to Bacterial Population Dynamics 96
Karl-Paul Witzel
5.1 Introduction 96
5.2 Numerical taxonomic approaches 97
5.3 Immunological approaches 102
5.4 Molecular approaches 108
5.5 Isoenzymes and genetic diversity 113
5.6 Future prospects 116
References 118
6 RNA Chemotaxonomy of Bacterial Isolates and Natural
Microbial Communities 129
Manfred G. H6fle
6.1 Ecological relevance of bacterial taxonomy 129
6.2 Systematics of bacteria based on nucleic acids analysis 130
6.3 The concept of RNA chemotaxonomy 133
6.4 Methodology for the analysis of pure cultures by RNA
profiles 134
Contents ix
6.5 General results of RNA profiles from pure cultures 137
6.6 Identification of bacterial isolates by RNA
chemotaxonomy 143
6.7 Analysis of mixed bacterial cultures 146
6.8 Analysis of natural bacterial communities 149
6.9 Conclusions and future developments 153
References 154
7 Plasmids and Their Role in Natural Aquatic Bacterial
Communities 160
Christian Schutt
7.1 Introduction 160
7.2 Ecogenetics: a new concept of microbial ecology 162
7.3 Plasmids in natural bacterial communities of some
aquatic habitats 164
7.4 Open questions 171
7.5 Molecular techniques 173
7.6 Future ecogenetics 177
References 180
Index 185
Contributors
Ryszard J. Chrost Institute of Microbiology, University of Warsaw,
PI-00-064 Warsaw, Poland
Manfred G. Hofle Max-Planck Institute of Limnology, Department of
Microbial Ecology, 0-2320 PIon, Federal Republic of Germany
Uwe Minster Max-Planck Institute of Limnology, Department of
Microbial Ecology, 0-2320 PIon, Federal Republic of Germany
Jiirgen Overbeck Max-Planck Institute of Limnology, Department of
Microbial Ecology, 0-2320 PIon, Federal Republic of Germany
Christian Schitt Max-Planck Institute of Limnology, Department of
Microbial Ecology, 0-2320 PIon, Federal Republic of Germany
Karl-Paul Witzel Max-Planck Institute of Limnology, Department of
Microbial Ecology, 0-2320 PIon, Federal Republic of Germany
x