Upload
others
View
2
Download
0
Embed Size (px)
Citation preview
Molecular Microbial Ecologyof the Rhizosphere
Molecular Microbial Ecologyof the Rhizosphere
Edited by
Frans J. de Bruijn
Cover Photo: Bioluminescence image of a barley root system colonized by Pseudomonas fluorescens strain DF57-40E7 visualized by a Hamamatsuphotonic camera system. Strain DF57-40E7 emits bioluminescence due to an inserted Tn5::luxAB gene cassette. Image courtesy of Lene Kragelund, Fransde Bruijn and Ole Nybroe.
Copyright © 2013 by John Wiley & Sons, Inc. All rights reserved.
Published by John Wiley & Sons, Inc., Hoboken, New Jersey.Published simultaneously in Canada.
No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical,photocopying, recording, scanning, or otherwise, except as permitted under Section 107 or 108 of the 1976 United States Copyright Act, without eitherthe prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, Inc.,222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4470, or on the web at www.copyright.com. Requests to the Publisher forpermission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) 748-6011, fax(201) 748-6008, or online at http://www.wiley.com/go/permission.
Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representationsor warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantabilityor fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategiescontained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shallbe liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.
For general information on our other products and services or for technical support, please contact our Customer Care Department within the UnitedStates at (800) 762-2974, outside the United States at (317) 572-3993 or fax (317) 572-4002.
Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic formats. For moreinformation about Wiley products, visit our web site at www.wiley.com.
Library of Congress Cataloging-in-Publication Data:
Molecular microbial ecology of the rhizosphere / edited by Frans J. de Bruijn.p. ; cm.
Includes bibliographical references and index.ISBN 978-1-118-29617-2 (set : cloth : alk. paper) – ISBN 978-1-118-29629-5 (v. 1 : cloth : alk.
paper) – ISBN 978-1-118-29616-5 (v. 2 : cloth : alk. paper)I. Bruijn, F. J. de (Frans J. de)[DNLM: 1. Soil Microbiology. 2. Genetics, Microbial. 3. Microbial Interactions. 4. Rhizosphere.
QW 60]
579′.1757–dc232012032879
Printed in Singapore
10 9 8 7 6 5 4 3 2 1
This work is dedicated to my two daughters Waverly and Vanessa de Bruijn for theirsupport even from a distance and to Marie Lefevre-Fonollosa for her continual
interest in the Book
Contents
Preface xiii
Acknowledgements xv
Contributors xvii
1. Introduction 1
Frans J. de Bruijn
Section 1 Focus Chapters
2. Using Genomics to Unveil Bacterial Determinants of Rhizosphere Life Style 7
Marıa-Isabel Ramos-Gonzalez, Miguel A. Matilla, Jose-Miguel Quesada, Juan L. Ramos,and Manuel Espinosa-Urgel
3. Benefits of Breeding Crops for Yield Response to Soil Organisms 17
Alison E. Bennett, Timothy J. Daniell, and Philip J. White
4. Microbial Interactions in the Rhizosphere 29
Jose-Miguel Barea, Marıa-Jose Pozo, Rosario Azcon, and Concepcion Azcon-Aguilar
5. Culture-Independent Molecular Approaches to Microbial Ecology in Soiland the Rhizosphere 45
Penny R. Hirsch, Tim H. Mauchline, and Ian M. Clark
6. Exploiting New Systems-Based Strategies to Elucidate Plant–Bacterial Interactionsin the Rhizosphere 57
Matthieu Barret, Hao Tan, Frank Egan, John P. Morrissey, Jerry Reen, and Fergal O’Gara
vii
viii Contents
7. Combining Molecular Microbial Ecology with Ecophysiology and Plant Geneticsfor a Better Understanding of Plant–Microbial Communities’ Interactionsin the Rhizosphere 69
Anouk Zancarini, Clementine Lepinay, Judith Burstin, Gerard Duc, Philippe Lemanceau,Delphine Moreau, Nathalie Munier-Jolain, Barbara Pivato, Thierry Rigaud,Christophe Salon, and Christophe Mougel
8. Microbially Mediated Plant Functional Traits 87
Maren L. Friesen
Section 2 Plant-mediated Structuring of Bacterial Communities in the Rhizosphere
9. Unraveling the Shed of Unexplored Rhizosphere Microbial Diversity 105
Puneet S. Chauhan, Vasvi Chaudhry, Sandhya Mishra, Aradhana Mishra,and Chandra S. Nautiyal
10. Advanced Molecular Tools for Analysis of Bacterial Communities and TheirInteractions in the Rhizosphere 115
Jan Dirk van Elsas and Ines Mandic-Mulec
11. Challenges in Assessing Links Between Root Exudates and the Structureand Function of Soil Microbial Communities 125
Shengjing Shi, Alan E. Richardson, Maureen O’Callaghan, Mary Firestone,and Leo Condron
12. Root Secretions: Interrelating Genes and Molecules to Microbial Associations.Is It All That Simple? 137
Meredith L. Biedrzycki and Harsh P. Bais
13. The Use of Stable Isotope Labeling and Compound-Specific Analysis of MicrobialPhospholipid Fatty Acids to Quantify the Influences of Rhizodeposition on MicrobialCommunity Structure and Function 141
Eric Paterson
14. Metarhizium robertsii, a Rhizosphere-Competent Insect Pathogen 149
Monica Pava-Ripoll
15. Shaping of Microbial Community Structure and Function in the Rhizosphereby Four Diverse Plant Species 161
Wafa Achouak and Feteh ElZahar Haichar
16. Exploration of Hitherto-Uncultured Bacteria from the Rhizosphere 169
Leonard S. van Overbeek
17. The Use of Molecular Methods to Assess Chemotactic-Competent BacterialPopulations in the Rhizosphere 179
Alison Buchan and Gladys M Alexandre
Contents ix
18. Assessment of Rice Root-Associated Bacteria 191
Pablo Rodrigo Hardoim and Jan Dirk van Elsas
19. Phylogenetic Analysis of Azospirillum Species Isolated from the Rhizosphereof Field-Grown Wheat Based on Genetic and Phenotypic Features 203
Vezyri Eleni, Venieraki Anastasia, Dimou Maria, Chatzipavlidis Iordanis,Tampakaki Anastasia, and Panagiotis Katinakis
20. Influence of Intercropping and Intercropping plus Rhizobial Inoculationon Microbial Activity and Community Composition in Rhizosphere of Alfalfa(Medicago sativa L.) and Siberian Wildrye (Elymus sibiricus L.) 211
YanMei Sun, NanNan Zhang, En Tao Wang, HongLi Yuan, JinShui Yang, and WenXin Chen
21. Root Exudates and Soil: Crucial for Molecular Understanding of Interactionsin the Rhizosphere 221
Nicholas C. Uren
22. Do Root Exudates Exert More Influence on Rhizosphere Bacterial CommunityStructure Than Other Rhizodeposits? 229
Penny R. Hirsch, Anthony J. Miller, and Paul G. Dennis
Section 3 Plant Genetics and Rhizobacterial Communities
23. Arabidopsis thaliana as Model for Studies on the Bacterial Root Microbiota 245
Klaus Schlaeppi, Emiel Ver Loren van Themaat, Davide Bulgarelli, and Paul Schulze-Lefert
24. Genetic and Developmental Control of Rhizosphere Bacterial Communities 257
Shirley Micallef and Adan Colon-Carmona
25. Arabidopsis thaliana: A Useful but Limited Model to Investigate Stress Impactson Rhizosphere Community Composition and Function 265
Kristopher Blee, John Hein, and Gordon V. Wolfe
26. Medicago truncatula Root Proteomics 271
Frank Colditz
Section 4 Hormones and other Signals and Rhizomicrobes
27. Control of the Cooperation Between Plant Growth-Promoting Rhizobacteriaand Crops by Rhizosphere Signals 281
Benoıt Drogue, Emeline Combes-Meynet, Yvan Moenne-Loccoz, Florence Wisniewski-Dye,and Claire Prigent-Combaret
28. Small Molecules Involved in Transkingdom Communication between Plantsand Rhizobacteria 295
Randy Ortiz Castro and Jose Lpopez Bucio
x Contents
29. Bacterial Biosynthesis of Indole-3-Acetic Acid: Signal Messenger Service 309
Mandira Kochar, A Vaishnavi, Anamika Upadhyay, and Sheela Srivastava
30. Fixing and Non-Fixing Rhizobia Affect Arabidopsis Root Architecture by Interferingwith the Auxin Signaling Pathway 327
Guilhem Desbrosses, Nelly Queruel, Arthur Poitout, and Bruno Touraine
31. Terpene Production by Bacteria and its Involvement in Plant Growth Promotion,Stress Alleviation, and Yield Increase 335
Patricia Piccoli and Ruben Bottini
32. Rapid Identification of Plant-Growth-Promoting Rhizobacteria Using an Agar PlateCocultivation System with Arabidopsis 345
Randy Ortiz Castro, Jesus Campos Garcıa, and Jose Lopez Bucio
33. Strigolactone Biosynthesis and Biology 355
Yanxia Zhang, Imran Haider, Carolien Ruyter-Spira, and Harro J. Bouwmeester
34. Chemistry of Strigolactones: Why and How do Plants Produce so ManyStrigolactones? 373
Koichi Yoneyama, Takaya Kisugi, Xiaonan Xie, and Kaori Yoneyama
35. Strigolactones: Crucial Cues in the Rhizosphere 381
Juan A. Lopez-Raez
Section 5 Endophytes
36. Bacterial Endophytes: Who and Where, and What Are They Doing There? 393
Natalia Malfanova, Ben J.J. Lugtenberg, and Gabriele Berg
37. Properties of Bacterial Endophytes Leading to Maximized Host Fitness 405
Pablo R. Hardoim and Jan Dirk van Elsas
38. DNA-Based Stable Isotope Probing for Identifying Active Bacterial Endophytesin Potato 413
Frank Rasche, Michael Schloter, Tillmann Luders, and Angela Sessitsch
39. Visualization of Niches of Colonization of Firmicutes with Bacillus spp. in the Rhizo-sphere, Rhizoplane, and Endorhiza of Grapevine Plants at Flowering Stage of Develop-ment by FISH Microscopy 423
Stephane Compant, Helmut Gangl, and Angela Sessitsch
40. The Poplar Endophyte Pseudomonas putida W619 as a Key to a SuccessfulPhytoremediation of Volatile Organic Contaminants 429
Nele Weyens, Daniel van der Lelie, Safiyh Taghavi, and Jaco Vangronsveld
Contents xi
41. NifH Gene Expression and Nitrogen Fixation by Diazotrophic Endophytesin Sugarcane and Sweet Potatoes 437
Junko Terakado-Tonooka, Shotaro Ando, Yoshinari Ohwaki,and Tadakatsu Yoneyama
42. Surveying Diverse Zea Seed for Populations of Bacterial Endophytes 445
David Johnston-Monje and Manish N. Raizada
Section 6 Symbiotic Plant–Microbe Interactions
43. Molecular Mechanisms Governing Arbuscular Mycorrhiza Developmentand Function 459
Kristina Haage and Martin Parniske
44. Diversity and Evolution of Nitrogen-Fixing Legume Symbionts 467
Delphine Capela, Suhua Guan, and Catherine Masson-Boivin
45. Lipochitooligosaccharide Perception and the Basis of Partner Recognitionin Root Endosymbioses 483
Julie Cullimore and Clare Gough
46. Rhizobial Genetic Repertoire to Inhabit Legume and NonlegumeRhizospheres 495
Martha G. Lopez-Guerrero, Miguel A. Ramırez,and Esperanza Martınez-Romero
47. Who is Controlling Whom within the Ectomycorrhizal Symbiosis: Insightsfrom Genomic and Functional Analyses 501
Claire Veneault-Fourrey, Jonathan M. Plett, and Francis Martin
48. Role of Carotenoid Metabolism in the Arbuscular Mycorrhizal Symbiosis 513
Michael H. Walter
49. Bacterial Colonization of the Arbuscular Mycorrhizal Fungal Hyphosphere 525
Tanja R. Scheublin
50. Role of Quorum Sensing in the Sinorhizobium meliloti–Alfalfa Symbiosis 535
Luciana V. Rinaudi-Marron and Juan E. Gonzalez
51. Roles of Flavonoids in Symbiotic Root–Rhizosphere Interactions 541
Samira Hassan and Ulrike Mathesius
52. Exopolysaccharides and Nodule Invasion in the Sinorhizobium meliloti–AlfalfaSymbiosis 551
Luciana V. Rinaudi-Marron and Juan E. Gonzalez
Contents
Preface xv
Acknowledgements xvii
Contributors xix
Section 7 PGPR, Biocontrol, and Disease-Suppressive Bacteria
53. Plant Growth Promotion by Microbes 561
Ben J.J. Lugtenberg, Natalia Malfanova, Faina Kamilova, and Gabriele Berg
54. Microbial Control of Plant Root Diseases 575
Ben J.J. Lugtenberg, Natalia Malfanova, Faina Kamilova, and Gabriele Berg
55. Biocontrol and Osmoprotection for Plants under Salinated Conditions 587
Gabriele Berg, Mohammadali Alavi, Christoph S. Schmidt, Christin Zachow, DilfuzaEgamberdieva, Faina Kamilova, and Ben J.J. Lugtenberg
56. Genetics and Evolution of 2,4-Diacetylphloroglucinol Synthesis inPseudomonas fluorescens 593
Danielle M. Troppens, Jennifer A. Moynihan, Mathieu Barret, Fergal O’Gara,and John Morrissey
57. Suppression of Crown Gall Disease by Rhizosphere Bacteriaand Agrobacterium-Specific Bacteriophages 607
Leonid Chernin, Natela Toklikishvili, Natalia Dandurishvili, Marina Tediashvili,and Alexander Vainstein
58. Molecular-Based Strategies to Exploit the Inorganic Phosphate-SolubilizationAbility of Pseudomonas in Sustainable Agriculture 615
Patrick Browne, Matthieu Barret, John P. Morrissey, and Fergal O’Gara
vii
viii Contents
59. The Biocontrol Bacterium Pseudomonas Fluorescens Pf29Arp Strain Affects thePathogenesis-Related Gene Expression of the Take-All Fungus GaeumannomycesGraminis Var. Tritici on Wheat Roots 629
Stephanie Daval, Lionel Lebreton, and Alain Sarniguet
60. Marker-Assisted Selection of Novel Bacteria Contributing to Soil-Borne PlantDisease Suppression 637
Jun-Kyung Park, Seung-Hwan Lee, Songhee Han, Jin-Cheol Kim, Young Cheol Kim,and Brian McSpadden Gardener
61. Combined Effects of Wheat Roots and Pathogenic Fungus Gaeumannomyces graminisvar. tritici on Gene Expression of the Biocontrol Bacterium Pseudomonas fluorescensPf29Arp 643
Matthieu Barret, Pascale Frey-Klett, Anne-Yvonne Guillerm-Erckelboudt, Morgane Boutin,Gregory Guernec, Muriel Marchi, Stephanie Daval, and Alain Sarniguet
62. Biocontrol of Tree Root Diseases 655
Clara Pliego and Francisco M. Cazorla
63. Plant Growth Modulation by Bacterial Volatiles—A Focus on Burkholderia Species 665
L Weisskopf and A Bailly
64. Plant Growth Promoting Microorganisms: The Road from an AcademicallyPromising Result to a Commercial Product 677
Faina Kamilova and Roland de Bruyne
65. The Effect of Agricultural Practices on Resident Soil Microbial Communities:Focus on Biocontrol and Biofertilization 687
Natalia Bajsa, Marıa A. Morel, Victoria Brana, and Susana Castro-Sowinski
Section 8 Biofilm Formation and Attachment to Roots
66. Biofilm Formation in the Rhizosphere: Multispecies Interactions and Implicationsfor Plant Growth 703
Annette A. Angus and Ann M. Hirsch
67. Probiotics for Plants: Rhizospheric Microbiome and Plant Fitness 713
Carla Spence and Harsh Bais
68. Motility, Biofilm Formation, and Rhizosphere Colonization byPseudomonas fluorescens F113 723
Rafael Rivilla, Francisco Martınez-Granero, and Marta Martın
69. CMEIAS: An Improved Computing Technology for Quantitative Image Analysisof Root Colonization by Rhizobacteria In Situ At Single-Cell Resolution 733
Frank B. Dazzo and Youssef G. Yanni
Contents ix
Section 9 Quorum Sensing and Signaling
70. Understanding Root–Microbiome Interactions 745
Gaston Zolla, Matthew G Bakker, Dayakar V Badri, Jacqueline M Chaparro,Amy M Sheflin, Daniel K Manter, and Jorge Vivanco
71. An Inter-Kingdom Signaling Mechanism in Rhizosphere Pseudomonas 755
Juan F. Gonzalez, Sujatha Subramoni, and Vittorio Venturi
72. N-Acyl-homoserine-Lactone Quorum-Sensing Signaling in Phenazine and CyclicLipopeptide-Producing Pseudomonas sp. CMR12a from the RedCocoyam Rhizosphere 763
Katrien De Maeyer, Jolien D’aes, Gia K.H. Hua, Nam Phuong Kieu,and Monica Hofte
73. The Response of Plants toward N-Acyl Homoserine Lactonesof Quorum-Sensing-Active Bacteria in the Rhizosphere 775
Anton Hartmann, Sebastian T. Schenk, Tina Riedel, Peter Schroder,and Adam Schikora
74. In Situ Calling Distances and High Population IndependentN-Acylhomoserine Lactone-Mediated Communication on Plant Root Surfaces 785
Frank B. Dazzo and Stephan Gantner
75. Quorum-Sensing Quenching by Volatile Organic CompoundsEmitted by Rhizosphere Bacteria 791
Leonid Chernin, Natela Toklikishvili, Marianna Ovadis,and Inessa Khmel
76. The Biological Significance of the Degradation of N-Acyl HomoserineLactones—Quorum Sensing and Quorum Quenching in Burkholderiaand Agrobacterium 801
Kok G. Chan, Denis Faure, and Yves Dessaux
77. Altering Plant–Microbe Interactions Through Artificially ManipulatingBacterial Quorum Sensing 813
Katalin Kovacs and Rupert Fray
78. Rhizosphere Microbial Communication in Soil Nutrient Acquisition 823
Kristen M. DeAngelis
79. Agony to Harmony—What Decides? Calcium Signaling in Beneficialand Pathogenic Plant–Fungus Interactions—What We Can Learn from theArabidopsis/Piriformospora indica Symbiosis 833
Joy Michal Johnson and Ralf Oelmuller
x Contents
Section 10 Genomic Sequencing and Screening of Genes/Promoters Activatedin the Natural Environment
80. Genome Transcriptome Analysis and Functional Characterizationof a Nitrogen-Fixation Island in Root-Associated Pseudomonas stutzeri 853
Yongliang Yan, Wei Lu, Ming Chen, Jin Wang, Wei Zhang, Yunhua Zhang, Shuzhen Ping,Claudine Elmerich, and Min Lin
81. Genome Analysis, Ecology, and Plant Growth Promotion of the EndophyteBurkholderia phytofirmans Strain PsJN 865
Birgit Mitter, Alexandra Petric, Patrick SG Chain, Friederike Trognitz, Jerzy Nowak,Stephane Compant and Angela Sessitsch
82. Identification and Mutational Activation of Niche-Specific Genes Provide Insightinto Regulatory Networks and Bacterial Function in Complex Environments 875
Robert W. Jackson, Xue-Xian Zhang, and Mark W. Silby
83. Comparative Analysis of the Complete Genome Sequence of the PlantGrowth-Promoting Bacterium Bacillus amyloliquefaciens FZB42 883
Rainer Borriss
84. Genome Sequence of the Plant Growth-Promoting Endophytic BacteriumEnterobacter sp. 638 899
Safiyh Taghavi and Daniel van der Lelie
Section 11 Marker and Reporter Genes For Plant-Host Interaction Studies
85. Approaches for the Design of Genetically Engineered Bacteria for Ecological Studiesand Biotechnological Applications 911
Humberto J.O. Ramos, Marshall Geoffrey Yates, Fabio O. Pedrosa, and Emanuel M. Souza
86. Construction of Signature-Tagged Mutant Libraries and Its Applicationto Plant-Symbiotic Bacteria 921
Anke Becker and Nataliya Pobigaylo
87. Use of DOPE-FISH Tool to Better Visualize Colonization of Plants by BeneficialBacteria? An Example with Saccharothrix algeriensis NRRL B-24137 ColonizingGrapevine Plants 929
Stephane Compant and Florence Mathieu
88. Combining Rhizobox, Reporter Gene Systems, and Molecular Analysesto Assess the Effects of Humic Substances on Plant–Microbes Interactionsin Soil Rhizosphere 933
Edoardo Puglisi and Marco Trevisan
Contents xi
89. Multiparameter Flow Cytometry for Characterization of Physiological Statesin Pseudomonas Fluorescens DR54 Biocontrol Inoculants UnderDry Formulation and Long-Term Storage in Clay Carrier 943
Jan Sørensen and Ole Sjøholm
90. Endophytic Lifestyle of Biocontrol Strains of Pseudomonas spp. in Olive Roots 951
Jesus Mercado-Blanco and Pilar Prieto
Section 12 Phytoremediation and heavy-metal tolerance in the Rhizosphere
91. Improving Phytoremediation through Plant-Associated Bacteria 963
Kieran J. Germaine, Martina McGuinness, and David N. Dowling
92. Ecology of Alkane-Degrading Bacteria and Their Interaction with the Plant 975
Muhammad Afzal, Sohail Yousaf, Thomas G. Reichenauer, and Angela Sessitsch
93. Abiotic Stress Remediation by the Arbuscular Mycorrhizal Symbiosisand Rhizosphere Bacteria/Yeast Interactions 991
Rosario Azcon, Almudena Medina, Ricardo Aroca, and Juan M. Ruiz-Lozano
94. Potential Plant-Growth-Promoting and Nitrogen-Fixing Bacteria Associatedwith Pioneer Plants Growing on Mine Tailings 1003
Yendi E. Navarro-Noya, Esperanza Martınez-Romero, and Cesar Hernandez-Rodrıguez
95. Stimulation of Rhizosphere Microbial Communities During Chemophytostabilizationof a Pb–Zn Mine Soil 1013
Marıa A. Galende, Lur Epelde, M T. Gomez-Sagasti, Oihana Barrutia, Antonio Hernandez,Jose M. Becerril, George A. Kowalchuk, and Carlos Garbisu
96. Arbuscular Mycorrhiza in Glucosinolate-Containing Plants: The Story of the MetalHyperaccumulator Noccaea (Thlaspi) praecox (Brassicaceae) 1023
Paula Pongrac, Katarina Vogel-Mikus, Charlotte Poschenrieder, Juan Barcelo,Roser Tolra, and Marjana Regvar
97. Novel Metal-Resistance Genes from the Rhizosphere of Extreme Environments:A Functional Metagenomics Approach 1033
Salvador Mirete and Jose E. Gonzalez-Pastor
Section 13 Climate Change Effects on Soil/Rhizosphere Microbial Communities
98. Soil Warming Effects on Beneficial Plant–Microbe Interactions 1047
Stephane Compant, Marcel van der Heijden, and Angela Sessitsch
xii Contents
99. Soil Respiration, Climate Change, and the Role of Microbial Communities 1055
O. Roger Anderson
100. Rhizosphere Responses to Elevated CO2 1063
Barbara Drigo and George A. Kowalchuk
101. Applying Stable Isotope Probing of Phospholipid Fatty Acids and Ribosomal RNAin Rice Fields to Study the Composition of the Active MethanotrophicBacterial Community In Situ 1075
Ralf Conrad and Yahai Lu
Section 14 Metagenomics and the Soil/Rhizosphere
102. Impact of Mangrove Roots on Bacterial Composition 1083
Newton C.M. Gomes and Daniel F.R. Cleary
103. Prediction of an Ectomycorrhizal Metabolome from Transcriptomic Data 1089
Peter E. Larsen, Leland J. Cseke, and Frank R. Collart
104. Metagenomic Analysis of the Rhizosphere Soil Microbial Community 1099
Yusuke Unno and Takuro Shinano
105. Bacterial Diversity in Rhizosphere Soil from Antarctic Vascular Plantsof Admiralty Bay in Maritime Antarctica 1105
Lia C. R. S. Teixeira, Raquel S. Peixoto, and Alexandre S. Rosado
106. Arbuscular Mycorrhizal Fungi throughout the Year: Using MassivelyParallel Pyrosequencing to Quantify Spatiotemporal Seasonal Dynamics 1113
Alex J. Dumbrell
107. Transcriptomics and Metatranscriptomic Analysis of the Response of RhizosphereBacteria to Environmental Change 1123
Thomas Turner and Philip Poole
108. Unraveling the Rhizosphere Using the cpn60 Genomic Marker and Pyrosequencing 1129
George Lazarovits, Amy L. Turnbull, Brenda Haug, Matthew G. Links, Janet E. Hill,and Sean M. Hemmingsen
109. Rhizosphere Metatranscriptomics: Challenges and Opportunities 1137
Lilia C. Carvalhais, Paul G. Dennis, Gene W. Tyson, and Peer M. Schenk
Section 15 Engineering the Rhizosphere: The “Biased Rhizosphere” Concept
110. The “Biased Rhizosphere” Concept and Advances in the OmicsEra to Study Bacterial Competitiveness and Persistence in the Phytosphere 1147
Michael A. Savka, Yves Dessaux, Brian B. McSpadden Gardener, Samuel Mondy,Petra R.A. Kohler, Frans J. de Bruijn, and Silvia Rossbach
Contents xiii
111. Bacterial Inositol Catabolism—A Sweet Ride into the Host 1163
Petra R. A. Kohler and Silvia Rossbach
112. Exogenous Glucosinolate Produced by Transgenic Arabidopsis thalianahas an Impact on Microbes in the Rhizosphere and Plant Roots 1173
Melanie Bressan, Wafa Achouak, and Odile Berge
113. Reciprocal Interactions between Plants and Fluorescent Pseudomonadsin Relation to Iron in the Rhizosphere 1181
Philippe Lemanceau, Sylvie Mazurier, Laure Avoscan, Agnes Robin,and Jean-Francois Briat
114. Enhancement of Plant–Microbe Interactions using RhizosphereMetabolomics-Driven Approach and its Application in the Removalof Polychlorinated Biphenyls 1191
Yong J. Lee, Kothandaraman Narasimhan, and Sanjay Swarup
Section 16 Concluding Chapters
115. Rhizophagy—A New Dimension of Plant–Microbe Interactions 1201
Chanyarat Paungfoo-Lonhienne, Susanne Schmidt, Richard I. Webb,and Thierry G. A. Lonhienne
116. The Rhizosphere as a Reservoir for Opportunistic Human Pathogenic Bacteria 1209
Gabriele Berg, Mohammadali Alavi, Michael Schmid, and Anton Hartmann
117. Mechanisms of Plant Colonization by Human Pathogenic Bacteria: An Emphasison the Roots and Rhizosphere 1217
Nicola J. Holden, Leighton Pritchard, Kathryn Wright, and Ian K. Toth
118. Perspectives for Rhizosphere Research 1227
Jos M. Raaijmakers and Ben J.J. Lugtenberg
Index 1233
Preface
Having worked on symbiotic plant-microbe interactionsand molecular microbial ecology for nearly 30 years,I have become very cognizant and appreciative of the“Black Box” of the plant Rhizosphere, the below groundzone of soil immediately adjacent to plant roots (“rhiza”)and influenced by these roots (“sphere”). The Rhizospheresupports high levels of microbial activity, as comparedto the bulk soil, although microbial diversity in theRhizosphere may be reduced. The plant roots secrete amagnitude of compounds into the Rhizosphere, includingsugars (up to 20% of the available photosynthate),amino acids, organic acids, fatty acids, sterols, vitamins,enzymes, flavonones, nucleotides, and other inorganicmolecules. These root exudates differ from plant to plant,ecotype to ecotype, and depend on the growth stageof the plant, but the exudates benefit the growth andaction of the Rhizosphere microbial communities. Infact, one may speculate that plants structure microbialcommunities through the root exudates, selecting forbeneficial microbes and warding off pathogens.
In addition, in the Rhizosphere, multiple signalsgo back and forth between plants and microorganisms,which are responsible for recognition of microorganisms;plant growth and development, (Plant Growth PromotingBacteria; PGPR); plant protection from pathogenic attack(Biocontrol); nodulation and symbiotic nitrogen fixation(primarily in legumes); mycorrhization (increased P andN uptake); and resistance to stresses, such as drought,salinity, extreme temperatures, and nutrient deficiencies.Pathogens and stresses cause an average yield loss of50% for most crops worldwide. Yield losses due to stressmay increase with global warming and the expansion ofagriculture into marginal lands. While pest control is stillmostly managed by pesticide application and nutrientdeficiencies by applying nitrogen and phosphorus, thelatter are not only expensive, but lead to runoff, resultingin environmental problems, such as euthrophication ofrivers and lakes and pollution of the drinking water.Since the world’s population is still growing, the pro-duction of food should be increased, without further
damaging the environment and with a decreased inputof chemical hormones and fertilizers. These realizationshave led to an increased interest in the use of beneficialmicrobes as sustainable and inexpensive alternatives foragrochemicals, especially for the production of cerealssuch as wheat, maize, and rice, accounting for onehalf of the human calorie intake. In addition to foodproblems, anthropogenic activities such as mining, oilcollection and refining, as well as the production ofother hazardous chemicals have led to large areas ofheavy metals and organics-polluted sites, which can onlybe decontaminated at high costs, if at all. Against thisbackdrop, the interest in microbial biofertilizers andthe combination of certain plants together with specificmicrobes for phytoremediation purposes is steadilyincreasing. Strategies are being developed to use benefi-cial microbes and these constitute a substantial portionof this two-volume book on the Molecular MicrobialEcology of the Rhizosphere. However, the design ofthese strategies must be based on solid knowledge aboutthe soil, the Rhizosphere, and the plant and its associatedmicroorganisms. This knowledge gathering is the mainpurpose of this book. The development of moleculartechniques, especially high throughput DNA and RNAsequencing to investigate microbes, the microbiome, plantroots, plant-microbe interactions and the Rhizospherehave allowed an increased knowledge base, which cannow be used to design better strategies for the use ofspecific microorganisms and plants for applied purposes,some of which are described in the book. This bookis aimed at soil microbiologists, molecular microbialecologists, plant biologists, and scientists studying plant-microbe interactions, as well as students in these fields.The combination of basic and applied studies is a specialfeature of the book, as is the mixture of reviews andoriginal research papers. I hope that it will be as enlight-ening for you as it has been for me putting these volumestogether.
Frans J. de Bruijn
xiii
Acknowledgements
I greatfully acknowledge Ben Lugtenberg for his mutlti-ple inputs into the Book and Hans Lambers for providingthe Program of the Rhizosphere 3 Conference in advanceof the Meeting. I would like to thank Claude Bruandand Marcel Soon for their help with the computer work.
The Laboratory for Plant Microbe Interactions (LIPM),the Institut National de Recherche Agronomique (INRA);the Centre National de Recherche Scientifique (CNRS)and the Labex TULIP are acknowledged for their supportof the Project.
xv
Contributors
Editor
Frans J. de Bruijn, INRA-CNRS Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441-2594BP52627, F-31320 Castanet-Tolosan, France
Authors
Wafa Achouak, Laboratoire d’Ecologie Microbienne de la Rhizosphere et Environnements extremes, CEA, DSV,IBEB, 13108 Saint-Paul-lez-Durance, France; CNRS, UMR 7265, 13108 Saint-Paul-lez-Durance, France; Univer-site Aix-Marseille, 13108 Saint-Paul-lez-Durance, France; CNRS, UMR 6191, 13115 Saint-Paul-lez-Durance, France;Universite Aix-Marseille, 13115 Saint-Paul-lez-Durance, France
Gladys M. Alexandre, Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville,TN, USA
Tampakaki Anastasia, Department of Agricultural Biotechnology, Laboratory of General and Agricultural Microbiology,Agricultural University of Athens, Iera Odos 75, Votanikos 11855, Athens, Greece
Venieraki Anastasia, Department of Agricultural Biotechnology, Laboratory of General and Agricultural Microbiology,Agricultural University of Athens, Iera Odos 75, Votanikos 11855, Athens, Greece
Shotaro Ando, Japan International Research Center for Agricultural Sciences, Tropical Agriculture Research Front,Maezato-Kawarabaru 1091-1, Ishigaki, Okinawa 907-0002, Japan
Rosario Azcon, Departamento de Microbiologıa del Suelo y Sistemas Simbioticos, Estacion Experimental del Zaidın,CSIC, Profesor Albareda 1, 18008 Granada, Spain
Concepcion Azcon-Aguilar, Departamento de Microbiologıa del Suelo y Sistemas Simbioticos, Estacion Experimentaldel Zaidın, CSIC, Profesor Albareda 1, 18008 Granada, Spain
Harsh P. Bais, Plant and Soil Sciences Department, 531 South College Avenue, Newark, DE 19716, USA; DelawareBiotechnology Institute, 15 Innovation Way, Newark, DE 19711.
Jose-Miguel Barea, Departamento de Microbiologıa del Suelo y Sistemas Simbioticos, Estacion Experimental del Zaidın,CSIC, Profesor Albareda 1, 18008 Granada, Spain
Matthieu Barret, Department of Microbiology, BIOMERIT Research Centre, University College Cork, Cork, Ireland
Alison E. Bennett, Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
Gabriele Berg, Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
Meredith L. Biedrzycki, Department of Plant and Soil Sciences, 531 South College Avenue, Newark, DE 19716, USA;Delaware Biotechnology Institute, 15 Innovation Way, Newark, DE 19711, USA
Kristopher Blee, Department of Biological Sciences, California State University, Chico, Chico, CA 95929-0515, USA
xvii
xviii Contributors
Ruben Bottini, Laboratorio de Bioquımica Vegetal, Instituto de Biologıa Agrıcola de Mendoza, Facultad de CienciasAgrarias, Universidad Nacional de Cuyo-Consejo Nacional de Investigaciones Cientıficas y Tecnicas, Almirante Brown500, M5528AHB Chacras de Coria, Argentina
Harro J. Bouwmeester, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PBWageningen, The Netherlands; Centre for Biosystems Genomics, Wageningen, The Netherlands
Alison Buchan, Department of Microbiology, University of Tennessee, Knoxville, TN, USA
Davide Bulgarelli, Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne,Germany
Judith Burstin, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17, rue Sully, B.P. 86510,21065 Dijon Cedex, France
Jesus Campos Garcıa, Instituto de Investigaciones Quımico-Biologicas, Universidad Michoacana de San Nicolas deHidalgo, Edificio B3, Ciudad Universitaria, C. P. 58030 Morelia, Michoacan, Mexico
Vasvi Chaudhry, Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana Pratap Marg,Lucknow 226001, India
Puneet S. Chauhan, Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana PratapMarg, Lucknow 226001, India
WenXin Chen, State Key Laboratory for Agrobiotechnology, College of Biological Sciences and Center for BiomassEngineering, China Agricultural University, Beijing 100193, China
Ian M. Clark, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
Frank Colditz, Department of Plant Molecular Biology III, Institute for Plant Genetics, Leibniz University of Hannover,Herrenhauser Straße 2, 30419 Hannover, Germany
Adan Colon-Carmona, Department of Biology, University of Massachusetts Boston, Boston, MA, USA
Emeline Combes-Meynet, Universite de Lyon, F-69622 Lyon, France; Universite Lyon 1, Villeurbanne, France; CNRS,UMR5557, Ecologie Microbienne, Villeurbanne, France
Stephane Compant, Dept Bioprocedes et Systemes Microbiens, ENSAT-INP de Toulouse, Universite de Toulouse, LGCUMR 5503 (CNRS/INPT/UPS), 1 Avenue de l’Agrobiopole, B.P. 32607, F-31326 Castanet-Tolosan Cedex 1, France
Leo Condron, Faculty of Agriculture and Life Sciences, Lincoln University, PO Box 84, Lincoln 7647, Christchurch,New Zealand; Bio-Protection Research Centre, Lincoln University, PO Box 84, Lincoln 7647, Christchurch, NewZealand
Julie Cullimore, INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326 Castanet-Tolosan, France
Timothy J. Daniell, Ecological Sciences Group, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
Paul G. Dennis, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland 4072, Aus-tralia; Advanced Water Management Centre, The University of Queensland, Brisbane, Queensland 4072, Australia
Guilhem Desbrosses, Laboratoire des Symbioses Tropicales et Mediterraneennes (UM2/IRD/Cirad/SupAgro/INRA), Uni-versite Montpellier 2, CC 002, Place Eugene Bataillon, 34095 Montpellier Cedex 05, France
Jan Dirk van Elsas, Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University ofGroningen, Linneausborg, Nijenborgh 7, 9747 AG Groningen, The Netherlands
Benoıt Drogue, Universite de Lyon, F-69622 Lyon, France; Universite Lyon 1, Villeurbanne, France; CNRS, UMR5557,Ecologie Microbienne, Villeurbanne, France
Gerard Duc, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17 rue Sully, B.V.86510,21065 Dijon Cedex, France
Feteh Elzachar Haichar, Laboratoire d’Ecologie Microbienne de la Rhizosphere et Environnements Extremes, CEA,DSV, IBEB, 13108 Saint-Paul-lez-Durance, France; CNRS, UMR 7265, 13108 Saint-Paul-lez-Durance, France; Uni-versite Aix-Marseille, 13108 Saint-Paul-lez-Durance, France
Frank Egan, Department of Microbiology, BIOMERIT Research Centre, University College Cork, Cork, Ireland
Vezyri Eleni, Department of Agricultural Biotechnology, Laboratory of General and Agricultural Microbiology, Agri-cultural University of Athens, Iera Odos 75, Votanikos 11855, Athens, Greece
Contributors xix
Manuel Espinosa-Urgel, Department of Environmental Protection, Estacion Experimental del Zaidın, Consejo Superiorde Investigaciones Cientıficas (CSIC), Profesor Albareda 1, 18008 Granada, Spain
Mary Firestone, Department of Environmental Science, Policy and Management, University of California, Berkeley,CA, USA
Maren L. Friesen, Section of Molecular and Computational Biology, Department of Biology, University of SouthernCalifornia, Los Angeles, CA 90089, USA; Department of Plant Bilogy, Michigan State University, USA
Helmut Gangl, Bundesamt fur Weinbau, Golbeszeile 1, A-7000 Eisenstadt, Austria
Juan E. Gonzalez, Department of Molecular and Cell Biology, RL11, 800 W. Campbell Rd., University of Texas atDallas, Richardson, TX 75080, USA
Clare Gough, CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, F-31326 Castanet-Tolosan, France
Suhua Guan, INRA/CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441-UMR2594,F-31326 Castanet-Tolosan, France
Kristina Haage, Institute of Genetics, Biocenter University of Munich (LMU), Großhaderner Str. 2-4, Martinsried 82152,Germany
Imran Haider, Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen,The Netherlands
Samira Hassan, Division of Plant Science, Research School of Biology, Australian National University, Linnaeus Way,Canberra ACT 0200, Australia
John Hein, Whitman College, Walla Walla, WA 99362, USA; Department of Biological Sciences, California StateUniversity, Chico, Chico, CA 95929-0515, USA
Penny R. Hirsch, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK
Chatzipavlidis Iordanis, Department of Agricultural Biotechnology, Laboratory of General and Agricultural Microbiol-ogy, Agricultural University of Athens, Iera Odos 75, Votanikos 11855, Athens, Greece
David Johnston-Monje, Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1 Canada
Faina Kamilova, Koppert Biological Systems, Veilingweg 14, PO Box 155, 2650 AD Berkel en Rodenrijs, The Nether-lands
Panagiotis Katinakis, Department of Agricultural Biotechnology, Laboratory of General and Agricultural Microbiology,Agricultural University of Athens, Iera Odos 75, Votanikos 11855, Athens, Greece
Takaya Kisugi, Weed Science Center, Utsunomiya University, 350 Mine-machi, Utsunomiya 321-8505, Japan
Mandira Kochar, Centre for Mycorrhizal Research, The Energy and Resources Institute [TERI], India Habitat Centre,Lodhi Road, New Delhi 110003, India
Daniel van der Lelie, Center for Agriculture and Environmental Biotechnology, Research Triangle Institute (RTI) Inter-national, 3040 Cornwallis Road, PO Box 12194, Research Triangle Park, NC 27709-2194, USA
Philippe Lemanceau, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17 Rue Sully,B.V.86510, 21065 Dijon Cedex, France
Clementine Lepinay, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17 Rue Sully,B.V.86510, 21065 Dijon Cedex, France
Jose Lopez Bucio, Instituto de Investigaciones Quımico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo,Edificio B3, Ciudad Universitaria, C. P. 58030 Morelia, Michoacan, Mexico
Martha G. Lopez-Guerrero, Centro de Ciencias Genomicas, UNAM, Av. Universidad SN, Chamilpa, Cuernavaca,Morelos, Mexico
Juan A. Lopez-Raez, Department of Soil Microbiology and Symbiotic Systems, Estacion Experimental del Zaidın(CSIC), Profesor Albareda 1, 18008 Granada, Spain
Tillmann Luders, Helmholtz Center Munich, Institute of Groundwater Ecology, 85764 Neuherberg, Germany
Ben J.J. Lugtenberg, Institute of Biology, Sylvius Laboratory, Leiden University, Sylviusweg 72, PO Box 9505, 2300RA Leiden, The Netherlands
xx Contributors
Natalia Malfanova, Institute of Biology, Sylvius Laboratory, Leiden University, Sylviusweg 72, PO Box 9505, 2300 RALeiden, The Netherlands; All-Russian Research Institute for Agricultural Microbiology (ARRIAM), Saint-Petersburg-Pushkin, Russia; Koppert Biological Systems, Veilingweg 14, PO Box 155, 2650 AD Berkel en Rodenrijs, TheNetherlands
Ines Mandic-Mulec, Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, Vecnapot 111, 1000 Ljubljana, Slovenia
Dimou Maria, Department of Agricultural Biotechnology, Laboratory of General and Agricultural Microbiology, Agri-cultural University of Athens, Iera Odos 75, Votanikos 11855, Athens, Greece
Francis Martin, Interactions Arbres-Microorganismes, UMR 1136, INRA-Universite de Lorraine, INRA Nancy 54280,Champenoux, France; Faculte des Sciences et Techniques, BP 239 54 506 Vandoeuvre, les Nancy Cedex, France
Esperanza Martınez-Romero, Centro de Ciencias Genomicas, Universidad Nacional Autonoma de Mexico, Av. Uni-versidad SN, Chamilpa, Cuernavaca, Morelos, Mexico
Catherine Masson-Boivin, INRA/CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441-UMR2594, F-31326 Castanet-Tolosan, France
Ulrike Mathesius, Division of Plant Science, Research School of Biology, Australian National University, LinnaeusWay, Canberra, ACT 0200, Australia
Miguel A. Matilla, Department of Environmental Protection, Estacion Experimental del Zaidın, Consejo Superior deInvestigaciones Cientıficas (CSIC), Profesor Albareda 1, 18008 Granada, Spain; Department of Biochemistry, Univer-sity of Cambridge, Tennis Court Road, Cambridge CB2 1QW, UK
Tim H. Mauchline, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
Shirley Micallef, Department of Plant Science and Landscape Architecture, Center for Food Safety and Security Systems,University of Maryland, College Park, MD, USA
Anthony J. Miller, John Innes Centre, Norwich, Norfolk NR4 7UH, UK
Aradhana Mishra, Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana PratapMarg, Lucknow 226001, India
Sandhya Mishra, Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana Pratap Marg,Lucknow 226001, India
Yvan Moenne-Loccoz, Universite de Lyon, F-69622 Lyon, France; Universite Lyon 1, Villeurbanne, France; CNRS,UMR5557, Ecologie Microbienne, Villeurbanne, France
Delphine Moreau, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17 Rue Sully, B.V.86510,21065 Dijon Cedex, France
John P. Morrissey, Department of Microbiology, BIOMERIT Research Centre, University College Cork, Cork, Ireland;Environmental Research Institute, University College Cork, Cork, Ireland
Christophe Mougel, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17 Rue Sully, B.V.86510, 21065 Dijon Cedex, France
Nathalie Munier-Jolain, INRA, UMR 1347 Agroecologie, Universite de Bourgogne, AgroSup Dijon, 17 Rue Sully,B.V. 86510, 21065 Dijon Cedex, France
Chandra S. Nautiyal, Division of Plant Microbe Interactions, CSIR-National Botanical Research Institute, Rana PratapMarg, Lucknow 226001, India
Maureen O’Callaghan, AgResearch, Private Bag 4749, Christchurch 8140, New Zealand
Fergal O’Gara, Department of Microbiology, BIOMERIT Research Centre, University College Cork, Cork, Ireland;Environmental Research Institute, University College Cork, Cork, Ireland
Randy Ortiz Castro, Instituto de Investigaciones Quımico-Biologicas, Universidad Michoacana de San Nicolas deHidalgo, Edificio B3, Ciudad Universitaria, C. P. 58030 Morelia, Michoacan, Mexico
Leonard S. van Overbeek, Plant Research International, Wageningen University and Research Centre, Wageningen, TheNetherlands
Martin Parniske, Institute of Genetics, Biocenter University of Munich (LMU), Großhaderner Str. 2-4, Martinsried82152, Germany