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Visit the Taylor & Francis Web site at http://www.com and the CRC Press Web site at http://www.com Preface Soil teems with diverse microorganisms, most still unknown yet highly appreciated because of their suspected capacities to produce compounds that are important for biotechnology and medicine. Additionally, soil has an indispensable ecological function, primarily in the anabolic and catabolic cycles of carbon, nitrogen and sulfur, without which the diversity of life forms that have evolved on the planet would likely not have been possible. Given its enormous relevance for bioprospecting and ecosystem functioning, soil microbiology has been termed the “last true scientific frontier” on Earth. Over the last decade, the study of soil microbiology has undergone significant changes, both in the understanding of the diversity and functioning of soil microbial communities and in the methods that are being used to dissect and reconstruct the soil in microbiological terms.
In particular, the ever- increasing development and use of DNA- or RNA-based molecular detection methods have revolutionized our knowledge of the living soil, as well as the strategies available to analyze it. Several examples of outstanding recent breakthroughs come to mind. For example, we now know that acidobacteria are major constituents of many terrestrial habitats on the planet, although we do not yet fully understand what this means in terms of their function. Additionally, the role of archaea—previously believed to encompass primarily organisms that thrive under extreme conditions—in soil systems, in particular in nitrogen transformations, is becoming increasingly better understood.
We also currently accept and appreciate the astounding microbial diversity in the terrestrial habitat more than we ever did before, and this growing insight has been spurred by the application of powerful molecular methods. The apparent wealth of different niches in soil has also given rise to a range of diversification processes. Although much still remains to be learned, we now appreciate the importance of the key horizontal gene transfer processes in these genome adaptations that result in the accelerated evolution of microorganisms. Finally, we are at the beginning of what may be a second revolution in soil microbiology and that is the increasing success in culturing microorganisms that previously were thought of as unculturable.
This book, Modern Soil Microbiology, Second Edition, is a fully revised version of the highly successful book Modern Soil Microbiology that appeared in 1997 (Dekker Inc. It covers most relevant current topics of soil microbiology to provide a broad (cutting-edge) picture of this fascinating discipline that encompasses aspects of ecology, physiology, genetics, molecular biology, and biotechnology, and that also makes use of biochemical and biophysical approaches. The book is divided into three DK3097—PRELIMS —17/11/2006—10:54—SRIDHAR—XML MODELCRC3b1 – pp. 1–19 sections that progress from the fundamental to the applied levels.
The first section covers the soil, as well as rhizosphere, as habitats in which microorganisms live, and describes the different microbial groups (in particular bacteria, archaea, fungi, and protozoa), their diversities and adaptive responses, as well as their respective processes in interactive and functional terms. The current understanding of the involvement of terrestrial microorganisms in the cycling of nitrogen and carbon is a major topic. The second section describes the use of the varied advanced methods that have provided a great thrust to the discipline of soil microbiology, and will continue to do so. The third section focuses on a range of applied aspects of soil microbiology, including the nature of disease-suppressive soils, the use of biological control agents, biopesticides and bioremediation agents, and the need for correct statistics in the analyses of the data obtained from soil systems.
The bold italicized terms in this book are defined in the glossary. Modern Soil Microbiology, Second Edition is designed as a basic textbook for use in soil microbiology courses and other courses that aim to explore the current developments in this field. It will also be very useful as a basic work that provides scientists and professionals with a quick introduction into the specific topics, as well as the most relevant literature. The editors sincerely thank all of the authors and the publisher for their excellent cooperation and contributions to this text.
As with all scientific and scholarly pursuits, the expansion of knowledge is based on the discoveries of past and present generations of dedicated scholars, to whom we feel indebted. We hope that present and future generations will use the knowledge in this text for the betterment of humanity. We welcome any comments from all who use this text. DK3097—PRELIMS —17/11/2006—10:54—SRIDHAR—XML MODELCRC3b1 – pp.
1–19 Editors Jan Dirk van Elsas is a professor of microbial ecology, Groningen University, Groningen, The Netherlands. Professor van Elsas has worked in Wageningen (most recently at Plant Research International, 1985–2003), where he was a pioneer in the development of molecular tools to address questions in soil microbiology. In addition to his other achievements, he described the importance of horizontal gene transfer, by both conjugation and transformation, in the rhizosphere and discovered particular mobile genetic elements (plasmids) that confer tremendous genetic plasticity to the popu- lations that harbor these. He also showed how bacterial genetic systems could be induced by particular conditions in soil and rhizosphere.
The group led by Professor van Elsas is currently focusing on the fundamental principles at the genome level that enable bacteria in soil to adapt to their fluctuating niches. The horizontal transfer of genes that confer adaptive traits in the system is a key phenomenon studied. Jansson is a professor of environmental microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden. Professor Jansson was one of the first molecular microbial ecologists, beginning with her doctoral studies in the laboratory of Professor James Tiedje, Michigan State University, in the mid 1980s.
She has since developed a range of molecular tools for assessment of specific microorganisms and microbial communities in environ- mental samples. Her focus has been on bioremediation and biocontrol applications of soil organisms. She is currently coordinating the Uppsala Microbiomics Center, a strong research environment in Uppsala centered on the development of novel molecular tools for characterization of complex microbial communities (www. Trevors is a professor of microbiology and environmental biology, Department of Environmental Biology, University of Guelph, Ontario, Canada.
Professor Trevors is a fellow of the American Academy of Microbiology, The Linnean Society, World Academy of Arts and Sciences, World Innovation Foundation and The Institute of Biology of the UK. He is also an academic and research microbiologist (ARMCCM) of the Canadian College of Micro- biology. Professor Trevors is an editor of The Journal of Microbiological Methods and Antonie van Leeuwenhoek. He is also the editor-in-chief of Water, Air and Soil Pollution; Water, Air and Soil Pollution:FOCUS and co-editor-in- chief of The Environmentalist and The Environmental Pollution book series.
His research includes the origin of genetic instructions, gene transfer in DK3097—PRELIMS —17/11/2006—10:54—SRIDHAR—XML MODELCRC3b1 – pp. 1–19 bacteria, soil bioremediation, gene expression in soil, pathogens in the environment, cytoplasmic membrane polarization in bacteria, and applications of molecular and biophysical methods in soil bacteriology. He has published over 300 articles in these areas. DK3097—PRELIMS —17/11/2006—10:54—SRIDHAR—XML MODELCRC3b1 – pp.
1–19 Contributors Claude Alabouvette Ralf Conrad UMR Microbiologie et Géochimie Max Planck Institute for Terrestrial des Sols Microbiology INRA/Université de Bourgogne Marburg, Germany Dijon, France Rodrigo Costa Manish Kumar Aneja Federal Biological Research Centre Institute of Soil Ecology for Agriculture and Forestry (BBA) GSF-National Research Centre Braunschweig, Germany for Environment and Health München, Germany Don A. Bailey Department of Biotechnology Molecular Microbial Ecology Advanced Research Centre for NERC, CEH-Oxford Applied Microbiology Oxford, United Kingdom University of Western Cape Bellville, South Africa Michael Bonkowski Institut für Zoologie Véronique Edel-Hermann Rhizosphere Ecology Group UMR Microbiologie et Géochimie Technische Universität des Sols Darmstadt INRA/Université de Bourgogne Darmstadt, Germany Dijon, France Kristian K. Finlay Genetics and Microbiology Department of Forest Mycology and Group Pathology, SLU Department of Ecology Uppsala, Sweden Royal Veterinary and Agricultural University Frederiksberg, Denmark Berndt Gerhardson The MASE Laboratories Marianne Clarholm Uppsala, Sweden Department of Forest Mycology and Pathology Bernard R. Glick Swedish University of Agricultural Department of Biology Sciences University of Waterloo Uppsala, Sweden Waterloo, Ontario, Canada DK3097—PRELIMS —17/11/2006—10:54—SRIDHAR—XML MODELCRC3b1 – pp.
1–19 Bryan Griffiths Ken Killham Environment Plant Interaction School of Biological Sciences Programme University of Aberdeen Scottish Crop Research Institute Scotland, United Kingdom Dundee, United Kingdom Robert I. Griffiths Hung Lee Molecular Microbial Ecology Lakehead University NERC, CEH-Oxford Thunder Bay, Ontario, Canada Oxford, United Kingdom Philippe Lemanceau Lars Hestbjerg Hansen UMR Microbiologie et Géochimie Department of Microbiology des Sols Institute of Biology INRA/Université de Bourgogne University of Copenhagen Dijon, France Copenhagen, Denmark Anton Hartmann Kam Tin Leung Department of Microbe–Plant Lakehead University Interactions Thunder Bay, Ontario, Canada GSF-National Research Centre for Environment and Health Neuherberg, München, Germany Brian B. McSpadden Gardener OARDC Department of Plant Pathology Holger Heuer Ohio State University Federal Biological Research Centre Wooster, Ohio for Agriculture and Forestry (BBA) Braunschweig, Germany Kanavillil Nandakumar Janet K. Jansson Lakehead University Department of Microbiology Thunder Bay, Ontario, Canada University of Agricultural Sciences Genetics Centre Uppsala, Sweden Mette H.
Nicolaisen Genetics and Microbiology Pål Johnsen Group Faculty of Medicine Department of Ecology Department of Pharmacy Royal Veterinary and University of Tromsø Agricultural University Tromsø, Norway Frederiksberg, Denmark DK3097—PRELIMS —17/11/2006—10:54—SRIDHAR—XML MODELCRC3b1 – pp. Nielsen Saleema Saleh-Lakha Faculty of Medicine Department of Biology Department of Pharmacy University of Waterloo University of Tromsø Waterloo, Ontario, Canada Tromsø, Norway Michael Schloter Ole Nybroe Institute of Soil Ecology Genetics and Microbiology Group GSF-National Research Centre for Department of Ecology Environment and Health Royal Veterinary and Agricultural München, Germany University Frederiksberg, Denmark Michael Schmid Miruna Oros-Sichler Department of Microbe–Plant Federal Biological Research Centre Interactions, for Agriculture and Forestry GSF-National Research Centre for (BBA) Environment and Health Braunschweig, Germany München, Germany Lise Øvreås Angela Sessitsch Department of Biology Department of Bioresources University of Bergen ARC Seibersdorf Research GmbH Bergen, Norway Seibersdorf, Austria Pernille Hasse Busk Poulsen Department of Microbiology Shilpi Sharma Institute of Biology Institute of Soil Ecology University of Copenhagen GSF-National Research Centre for Copenhagen, Denmark Environment and Health München, Germany Jim I.