Principles of Plant-Microbe Interactions: Microbes for Sustainable Agriculture

Principles of Plant-Microbe Interactions

Ben Lugtenberg

Editor

Principles of Plant-Microbe

Interactions

Microbes for Sustainable Agriculture

2123

Editor

Ben Lugtenberg

Molecular Microbiology and Biotechnology

Leiden University, Sylvius Laboratory

Leiden

The Netherlands

ISBN 978-3-319-08574-6 ISBN 978-3-319-08575-3 (eBook)

DOI 10.1007/978-3-319-08575-3

Springer Cham Heidelberg New York Dordrecht London

Library of Congress Control Number: 2014956088

© Springer International Publishing Switzerland 2015

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I dedicate this book to my wife Faina and my

children Annelieke, Martijn and Marjolein

Preface

The field of Plant Microbe Interactions is very broad. It covers all topics in which mi￾crobes influence or even determine plant activities. Plant enemies can be pathogenic

viruses, microbes or insects which cause pests. Fortunately, these enemies in turn

have natural enemies in the form of beneficial microbes, which can protect plants

against pathogens and pests. As is rather common in this field, we included nema￾todes and insects in the book. Although they are not microbes, they have in common

with microbes that some can cause harm to, and others help protect, the plant. An￾other group of microbes is beneficial for plant growth. Some microbes promote plant

growth, for example by producing “plant” hormones or by making nutrients avail￾able to the plant. Other beneficial microbes can alleviate plant stress or can inactivate

environmental pollutants, thereby cleaning the environment and allowing plants to

grow without toxic residues. The present market share of biologicals is estimated

at 1.6 billion USDs and is growing fast. In the past years the trend is that major

chemical companies buy smaller biotech companies.

For this book I have invited the world’s top scientists to summarize the basic

principles of all these topics in brief chapters which give a helicopter view on the

subjects. The book also contains important techniques, success stories and future

prospects. The topics include basic as well as applied aspects. Hereby we make an

attempt to close the gap that still exists between fundamental and applied research.

In my opinion the two fields need each other and cooperation will create a win-win

situation for both parties. Since space is limited, the authors have often referred to

reviews. For more detailed information, the reader can consult primary articles listed

as references in these reviews.

This book is meant for everybody who is interested in plant-microbe interactions

and in the roles microbes can play in making agriculture and horticulture more

sustainable. These include academic scientists, industrial professionals working in

agriculture, horticulture, biotech and food industry, students, teachers, as well as

government officials and decision makers who quickly want to make themselves

familiar with particular aspects of this broad field. Using this information as a basis,

also a non-specialist reader should be able to understand more complicated articles

and to discuss selected topics with colleagues. To read the book, basic knowledge of

plant science, microbiology, biochemistry, and molecular biology is helpful.

Ben Lugtenberg, editor

vii

Acknowledgement

I am very much indebted to all authors for their contributions. I am particularly

thankful to the following people who have contributed by useful advice and discus￾sions: Gabriele Berg, Rainer Borriss, Frans de Bruijn, Faina Kamilova, Christoph

Keel, Corné Pieterse, and Clara Pliego. I am greatly obliged to Izabela Witkowska

and Melanie van Overbeek of Springer Dordrecht for their help and patience during

the preparation of the manuscript.

The following sponsors made the editing of the book more pleasant. Their con￾tributions will go to a foundation which supports the promotion of knowledge about

plant-microbe interactions and their applications.

DIAMOND SPONSORS

ix

x Acknowledgement

GOLD SPONSORS

Contents

1 Introduction to Plant-Microbe Interactions ...................... 1

Ben Lugtenberg

Part I Introductory Chapters

2 The Importance of Microbiology in Sustainable Agriculture ........ 5

Thomas Schäfer and Tom Adams

3 Life of Microbes in the Rhizosphere ............................. 7

Ben Lugtenberg

4 Life of Microbes on Aerial Plant Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

Johan H. J. Leveau

5 Life of Microbes Inside the Plant. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25

Jesús Mercado-Blanco

6 Microbial Cell Surfaces and Secretion Systems . . . . . . . . . . . . . . . . . . . 33

Jan Tommassen and Han A. B. Wösten

7 Microbial Biofilms and Quorum Sensing . . . . . . . . . . . . . . . . . . . . . . . . . 45

Aurelien Carlier, Gabriella Pessi and Leo Eberl

8 Bacterial Volatiles as Airborne Signals for Plants and Bacteria . . . . . 53

Choong-Min Ryu

Part II Phytopathogens and Pest Insects

9 Phytopathogenic Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65

Jan van der Wolf and Solke H. De Boer

10 Plant Pathogenic Fungi and Oomycetes . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Pierre J. G. M. de Wit

xi

xii Contents

11 Phytopathogenic Nematodes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

Johannes Helder, Mariëtte Vervoort, Hanny van Megen, Katarzyna

Rybarczyk-Mydłowska, Casper Quist, Geert Smant and Jaap Bakker

12 Herbivorous Insects—A Threat for Crop Production . . . . . . . . . . . . . . 103

Eddy van der Meijden

13 Phytopathogenic Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115

Carmen Büttner, Susanne von Bargen and Martina Bandte

14 Induced Disease Resistance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123

Corné M. J. Pieterse and Saskia C. M. Van Wees

15 Apologies to the Planet—Can We Restore the Damage? . . . . . . . . . . . . 135

Dulce Eleonora de Oliveira and Marc Van Montagu

16 Will the Public Ever Accept Genetically Engineered Plants? . . . . . . . 145

Inge Broer

Part III Control of Plant Diseases and Pests using Beneficial Microbes

17 Microbial Control of Phytopathogenic Nematodes . . . . . . . . . . . . . . . . 155

Xiaowei Huang, Keqin Zhang, Zefen Yu and Guohong Li

18 Microbial Control of Root-Pathogenic Fungi and Oomycetes . . . . . . . 165

Linda Thomashow and Peter A. H. M. Bakker

19 Control of Insect Pests by Entomopathogenic Nematodes . . . . . . . . . . 175

Vladimír Pu◦

ža

20 Bacillus thuringiensis-Based Products for Insect Pest Control . . . . . . 185

Ruud A. de Maagd

21 Post Harvest Control . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193

Emilio Montesinos, Jesús Francés, Esther Badosa

and Anna Bonaterra

Part IV Plant Growth Promotion by Microbes

22 The Nitrogen Cycle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205

Martine A. R. Kox and Mike S. M. Jetten

23 Biological Nitrogen Fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215

Frans J. de Bruijn

24 Phosphate Mobilisation by Soil Microorganisms . . . . . . . . . . . . . . . . . . 225

José-Miguel Barea and Alan E. Richardson

Contents xiii

25 Arbuscular Mycorrhizas: The Lives of Beneficial Fungi and Their

Plant Host . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 235

Paola Bonfante and Alessandro Desirò

26 Plant Hormones Produced by Microbes. . . . . . . . . . . . . . . . . . . . . . . . . . 247

Stijn Spaepen

27 Stress Control and ACC Deaminase . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257

Bernard R. Glick

28 Plant-Microbe Interactions and Water Management in Arid

and Saline Soils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265

Daniele Daffonchio, Heribert Hirt and Gabriele Berg

29 Rhizoremediation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

Sofie Thijs and Jaco Vangronsveld

Part V Important Technologies

30 Microbial Communities in the Rhizosphere Analyzed

by Cultivation-Independent DNA-Based Methods. . . . . . . . . . . . . . . . . 289

Susanne Schreiter, Namis Eltlbany and Kornelia Smalla

31 Visualization of Plant-Microbe Interactions . . . . . . . . . . . . . . . . . . . . . . 299

Massimiliano Cardinale and Gabriele Berg

Part VI Products for Plant Growth-promotion and Disease Suppression

32 Commercialisation of Microbes: Present Situation

and Future Prospects . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309

Willem J. Ravensberg

33 Commercialization of Microbes: Manufacturing, Inoculation,

Best Practice for Objective Field Testing, and Registration . . . . . . . . . 319

Faina Kamilova, Yaacov Okon, Sandra de Weert and Katja Hora

34 Towards a New Generation of Commercial Microbial Disease

Control and Plant Growth Promotion Products. . . . . . . . . . . . . . . . . . . 329

Rainer Borriss

35 Important Organizations and Companies . . . . . . . . . . . . . . . . . . . . . . . . 339

Ben Lugtenberg

Part VII Paradigms in Plant-Microbe Interactions

36 Trichoderma: A Multi-Purpose Tool for Integrated Pest

Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345

Matteo Lorito and Sheridan L. Woo

xiv Contents

37 Agrobacterium, The Genetic Engineer . . . . . . . . . . . . . . . . . . . . . . . . . . . 355

Paul J. J. Hooykaas

38 Take-All Decline and Beneficial Pseudomonads . . . . . . . . . . . . . . . . . . . 363

David M. Weller

39 The Oomycete Phytophthora infestans, the Irish Potato

Famine Pathogen. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 371

Charikleia Schoina and Francine Govers

40 Bacillus, A Plant-Beneficial Bacterium . . . . . . . . . . . . . . . . . . . . . . . . . . . 379

Rainer Borriss

41 Soybean Production in the Americas . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393

Woo-Suk Chang, Hae-In Lee and Mariangela Hungria

Part VIII Future Prospects and Dreams

42 Exploring the Feasibility of Transferring Nitrogen Fixation

to Cereal Crops . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403

Muthusubramanian Venkateshwaran

43 The Minimal Rhizosphere Microbiome . . . . . . . . . . . . . . . . . . . . . . . . . . 411

Jos M. Raaijmakers

44 The Edible Plant Microbiome: Importance and Health Issues . . . . . . 419

Gabriele Berg, Armin Erlacher and Martin Grube

45 From Nodulation to Antibiotics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427

Eva Kondorosi

Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435

Contributors

Tom Adams Monsanto Company, St. Louis, MO, USA

Carmen Büttner Division Phytomedicine, Faculty of Life Sciences, Humboldt￾Universität zu Berlin, Berlin, Germany

Esther Badosa Laboratory of Plant Pathology, Institute of Food and Agricultural

Technology, University of Girona, Girona, Spain

Jaap Bakker Laboratory of Nematology, Wageningen University, Wageningen,

The Netherlands

Peter A. H. M. Bakker Plant-Microbe Interactions, Institute of Environmental

Biology, Utrecht University, Utrecht, The Netherlands

Martina Bandte Division Phytomedicine, Faculty of Life Sciences, Humboldt￾Universität zu Berlin, Berlin, Germany

José-Miguel Barea Soil Microbiology and Symbiotic Systems Department,

Estación Experimental del Zaidín, CSIC, Granada, Spain

Gabriele Berg Institute of Environmental Biotechnology, Graz University of

Technology, Graz, Austria

Anna Bonaterra Laboratory of Plant Pathology, Institute of Food and Agricultural

Technology, University of Girona, Girona, Spain

Paola Bonfante Department of Life Sciences and Systems Biology, University of

Torino, Torino, Italy

Rainer Borriss ABiTEP GmbH, Berlin, Germany

Inge Broer Agricultural and Environmental Faculty, University of Rostock,

Rostock, Germany

Massimiliano Cardinale Institute of Applied Microbiology, Justus-Liebig￾University Giessen, Giessen, Germany

Aurelien Carlier Institute of Plant Biology, University of Zurich, Zurich,

Switzerland

xv

xvi Contributors

Woo-Suk Chang Department of Biology, University of Texas-Arlington, Arlington,

Texas, USA

Daniele Daffonchio DeFENS, Department of Food, Environmental and Nutritional

Sciences, University of Milan, Milan, Italy

BESE Division, King Abdullah University of Science and Technology, Thuwal,

Kingdom of Saudi Arabia

Solke H. De Boer Emeritus Scientist, Charlottetown, PE, Canada

Frans J. de Bruijn INRA/CNRS Laboratory of Plant-Microbe Interactions,

Castanet-Tolosan Cedex, France

Ruud A. de Maagd Plant Research International, Wageningen UR, Wageningen,

The Netherlands

Dulce Eleonora de Oliveira VIB–Institute of Plant Biotechnology Outreach,

Department of Biotechnology and Bioinformatics, Ghent University, Gent￾Zwijnaarde, Belgium

Sandra de Weert Koppert Biological Systems, Berkel en Rodenrijs, The

Netherlands

Pierre J. G. M. de Wit Laboratory of Phytopathology, Wageningen University,

Wageningen, The Netherlands

Alessandro Desirò Department of Life Sciences and Systems Biology, University

of Torino, Torino, Italy

Leo Eberl Institute of Plant Biology, University of Zurich, Zurich, Switzerland

Namis Eltlbany Julius Kühn-Institut, Federal Research Centre for Cultivated Plants

(JKI), Braunschweig, Germany

Armin Erlacher Institute of Environmental Biotechnology, Graz University of

Technology, Graz, Austria

Institute of Plant Sciences, University of Graz, Graz, Austria

Jesús Francés Laboratory of Plant Pathology, Institute of Food and Agricultural

Technology, University of Girona, Girona, Spain

Bernard R. Glick Department of Biology, University of Waterloo, Waterloo, ON,

Canada

Francine Govers Laboratory of Phytopathology, Wageningen University,

Wageningen, The Netherlands

Martin Grube Institute of Plant Sciences, University of Graz, Graz, Austria

Johannes Helder Laboratory of Nematology, Wageningen University,

Wageningen, The Netherlands

Contributors xvii

Heribert Hirt BESE Division, King Abdullah University of Science and

Technology, Thuwal, Kingdom of Saudi Arabia

Paul J. J. Hooykaas Institute of Biology, Sylvius Laboratory, Leiden University,

Leiden, The Netherlands

Katja Hora Koppert Biological Systems, Berkel en Rodenrijs, The Netherlands

Xiaowei Huang Yunnan University, Kunming, People’s Republic of China

Mariangela Hungria Embrapa Soja, Londrina, Paraná, Brazil

Mike S. M. Jetten Department of Microbiology, Institute of Water and Wet￾land Research, Faculty of Science, Radboud University Nijmegen, Nijmegen, The

Netherlands

Faina Kamilova Koppert Biological Systems, Berkel en Rodenrijs, The

Netherlands

Eva Kondorosi Institute of Biochemistry, Biological Research Centre of the

Hungarian Academy of Sciences, Szeged, Hungary

Martine A. R. Kox Department of Microbiology, Institute of Water and

Wetland Research, Faculty of Science, Radboud University Nijmegen, Nijmegen,

The Netherlands

Hae-In Lee Department of Biology, University of Texas-Arlington, Arlington,

Texas, USA

Johan H. J. Leveau Department of Plant Pathology, University of California, Davis,

CA, USA

Guohong Li Yunnan University, Kunming, People’s Republic of China

Matteo Lorito Department of Agriculture, University of Naples Federico II, and

Institute of Plant Protection IPP–CNR, Portici (NA), Italy

Ben Lugtenberg Institute of Biology, Sylvius Laboratory, Leiden University,

Leiden, The Netherlands

Jesús Mercado-Blanco Department of Crop Protection, Institute for Sustainable

Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC),

Córdoba, Spain

Emilio Montesinos Laboratory of Plant Pathology, Institute of Food and

Agricultural Technology, University of Girona, Girona, Spain

Yaacov Okon Department of Plant Pathology and Microbiology, Faculty of

Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot,

Israel

Vladimír Pu◦

ža Institute of Entomology, Biology Centre of the AS CR, Ceské ˇ

Budˇejovice, Czech Republic