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 the written permission of the publisher (Springer-Verlag New York, Inc., 175 Fifth Avenue, New York, NY 10010, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed is forbidden. 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