Modern Soil Microbiology

501 Pages·2019·21.975 MB·English

by  Jan Dirk van Elsas (ed.), Jack T. Trevors (ed.), Alexandre Soares Rosado (ed.), and Paolo Nannipieri (ed.)

Modern Soil Microbiology
Third Edition

Modern Soil Microbiology
Third Edition
Edited by
Jan Dirk van Elsas, Jack T. Trevors,
Alexandre Soares  Rosado, and Paolo Nannipieri
Cover images courtesy of:
Professor Emeritus Jan Dirk van Elsas, University of Groningen, Netherlands (upper picture); Professor Emeritus
Dr. George Barron, University of Guelph, Canada (left and right lower picture inserts); and Professor Raquel Peixoto,
Federal University of Rio de Janeiro, Brazil (middle lower picture insert).
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Library of Congress Cataloging-in-Publication Data
Names: Elsas, J. D. van (Jan D.), 1951- editor.
Title: Modern soil microbiology / editors: Jan Dirk van Elsas, Jack T.
Trevors, Alexandre Soares Rosado, Paolo Nannipieri.
Description: Third edition. | Boca Raton : Taylor & Francis, 2019.
Identifiers: LCCN 2018050977 | ISBN 9781498763530 (hardback : alk. paper) |
ISBN 9780429607929 (pdf) | ISBN 9780429602405 (epub) | ISBN 9780429596889
(mobi/kindle)
Subjects: LCSH: Soil microbiology. | Molecular microbiology.
Classification: LCC QR111 .M58 2019 | DDC 579/.1757—dc23
LC record available at https://lccn.loc.gov/2018050977
Visit the Taylor & Francis Web site at
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Contents
Preface...............................................................................................................................................ix
Editors ...............................................................................................................................................xi
Contributors ...................................................................................................................................xiii
Section i Fundamental chapters
Chapter 1 The Soil Environment ..................................................................................................3
Jan Dirk van Elsas
Chapter 2 The Seven Grand Questions on Soil Microbiology (Selman A. Waksman,
Reexamined by Arthur D. McLaren) .........................................................................21
Jan Dirk van Elsas and Paolo Nannipieri
Chapter 3 The Soil Microbiome—An Overview ........................................................................37
Francisco Dini-Andreote and Jan Dirk van Elsas
Chapter 4 The Bacteria and Archaea in Soil ..............................................................................49
Jan Dirk van Elsas, Anton Hartmann, Michael Schloter, Jack T. Trevors, and
Janet K. Jansson
Chapter 5 The Fungi in Soil ........................................................................................................65
Roger D. Finlay and R. Greg Thorn
Chapter 6 The Viruses in Soil—Potential Roles, Activities, and Impacts .................................91
Akbar Adjie Pratama and Jan Dirk van Elsas
Chapter 7 Horizontal Gene Transfer and Microevolution in Soil .............................................105
Kaare Magne Nielsen and Jan Dirk van Elsas
Chapter 8 The Protists in Soil—A Token of Untold Eukaryotic Diversity...............................125
Michael Bonkowski, Kenneth Dumack, and Anna Maria Fiore-Donno
Chapter 9 Microbial Interactions in Soil...................................................................................141
Jan Dirk van Elsas, Akbar Adjie Pratama, Welington Luis de Araujo, and
Jack T. Trevors
v
vi Contents
Chapter 10 Plant-Associated Bacteria and the Rhizosphere ......................................................163
Abdul Samad, Günter Brader, Nikolaus Pfaffenbichler, and Angela Sessitsch
Chapter 11 Microorganisms Cycling Soil Nutrients ...................................................................179
Penny R. Hirsch
Section ii Methods chapters
Chapter 12 Methods to Determine Bacterial Abundance, Localization, and
General Metabolic Activity in Soil ..........................................................................195
Lise Bonnichsen, Nanna Bygvraa Svenningsen, Mette Haubjerg Nicolaisen,
and Ole Nybroe
Chapter 13 Soil Microbiome Data Analysis ...............................................................................215
Francisco Dini-Andreote
Chapter 14 Soil Metagenomics: Deciphering the Soil Microbial Gene Pool .............................227
Sara Sjöling, Jan Dirk van Elsas, Francisco Dini Andreote, and
Jorge L. Mazza Rodrigues
Chapter 15 Analysis of Transcriptomes to Assess Expression and Activity Patterns
of the Soil Microbiome .............................................................................................245
Stefanie Schulz, Anne Schöler, Michael Schloter, and Shilpi Sharma
Chapter 16 Metaproteomics of Soil Microbial Communities .....................................................257
Paolo Nannipieri, L. Giagnoni, and G. Renella
Chapter 17 Stable Isotope Probing—Detection of Active Microbes in Soil ..............................269
Marie E. Kroeger and Klaus Nüsslein
Chapter 18 Isolation of Uncultured Bacteria ..............................................................................295
Ulisses Nunes da Rocha
Chapter 19 Statistical Analyses of Microbiological and Environmental Data ...........................307
Alexander V. Semenov
Section iii Applied chapters
Chapter 20 Soil Microbial Communities and Global Change ....................................................331
Mark P. Waldrop and Courtney Creamer
Contents vii
Chapter 21 Soil Suppressiveness to Plant Diseases ....................................................................343
Christian Steinberg, Véronique Edel-Hermann, Claude Alabouvette, and
Philippe Lemanceau
Chapter 22 Plant Growth-Promoting Bacteria in Agricultural and Stressed Soils ....................361
Elisa Gamalero and Bernard R. Glick
Chapter 23 Biodegradation and Bioremediation of Organic Pollutants in Soil ..........................381
Kam Tin Leung, Zi-Hua Jiang, Nouf Almzene, Kanavillil Nandakumar,
Kurissery Sreekumari, and Jack T. Trevors
Chapter 24 The Impact of Metal Contamination on Soil Microbial Community Dynamics .....403
David C. Gillan and Rob Van Houdt
Chapter 25 Management Strategies for Soil Used for Cultivation, Including Modulation of
the Soil Microbiome .................................................................................................421
Alexandre Soares Rosado, Paolo Nannipieri, and Jan Dirk van Elsas
Glossary ........................................................................................................................................431
Index ..............................................................................................................................................459

Preface
“Essentially, all life depends upon the soil. There can be no life without soil and no soil without life;
they have evolved together.” (Charles E. Kellogg, 1938).
Living soils are indispensable for human persistence as they are the environments where key bio-
geochemical processes take place. Such life-support processes, for example, the cycling of carbon,
nitrogen, sulfur, and phosphorus, are primarily carried out by different members of the soil microbi-
omes. Moreover, soil microbiomes are useful given their potential capacities to produce compounds
that are important for biotechnology, industry and medicine.
In light of its relevance for the functioning of Earth’s ecosystem, soil microbiology has been
termed one of the last “frontiers” in science.
Over the last decade, the study of soil microbiology has undergone significant changes, with
respect to both the understanding of the diversity and functioning of soil microbial communities
and the methods that are being used to dissect soil microbiomes into their components. In particu-
lar, the rapid development and use of DNA- or RNA-based molecular methods, giving rise to soil
metagenomics and soil metatranscriptomics, respectively, have revolutionized our knowledge of
the living soils across the globe. Moreover, soil proteomics has also undergone significant break-
throughs. Finally, the current capacities to generate big “molecular” soil data and analyze them using
advanced algorithms and deep learning approaches have also enabled unprecedented advances in
soil microbiology. In 2012, Paul and Nannipieri suggested that these important advancements have
given rise to an emergent “second golden age of soil microbiology.” The previous “golden age”
of soil microbiology was named by Waksman in 1932 and reflected the important discoveries of
diverse soil microorganisms being involved in key steps of the soil decomposition processes and of
the nitrogen and sulfur cycles.
What are the current advances about? Several instances of outstanding breakthroughs come to
mind. We have an improved knowledge of the acidobacteria and their diversity as major constitu-
ents of many terrestrial habitats. In addition, the role of archaea, previously believed to encompass
mainly extremophiles, in soil systems, particularly in nitrogen transformations (ammonia oxida-
tion), is becoming increasingly better understood. We also have an increased understanding of the
significance and drivers of the astounding microbial diversity in soils and the relevance of this
diversity for the mechanism of suppressing plant disease. The wealth of diverse niches in soil has
given rise to a range of diversification processes, and we now appreciate the importance of the key
horizontal gene transfer (HGT) processes in soil bacterial genome adaptations.
This book, Modern Soil Microbiology, Third edition, constitutes a thorough update of the highly
successful second edition. It covers all relevant topics in soil microbiology, with the aim to provide
a broad understanding of this fascinating interdisciplinary area that encompasses aspects of soil sci-
ence, ecology, physiology, genetics, molecular biology, biotechnology, biochemistry, and biophysics.
The book is divided into three sections that go from the fundamental, methods, to the applied side.
After depicting the soil and examining the seven grand questions posed by Selman A. Waksman,
as reexamined by Arthur D. McLaren, Section I addresses the aspects of soil as the habitat (matrix)
for microorganisms, describing the different organismal groups in it, including the bacteria, archaea,
viruses, fungi, and protozoa. The section examines their diversities and adaptive responses, as well
as their functioning in interactive and functional terms.
Section II describes the state of the art methods currently used in soil microbiology, examining
the novel knowledge these have provided and will continue to do so. Thus, traditional soil micro-
biology methods, next to soil metagenomics, soil metatranscriptomics, and soil metaproteomics
methods; stable-isotope probing, and novel methods of culturing are examined. Moreover, the use of
appropriate statistical methods, next to machine learning approaches, in soil analyses is examined.
ix