Molecular Microbial Ecology of the Rhizosphere, Two Volume Set Book

VOLUME ONE

Chapter 1. Introduction Frans J. de Bruijn

Section 1 Focus Chapters

Chapter 2. Using genomics to unveil bacterial determinants of rhizosphere life style Maria Ramos-Gonzalez

Chapter 3. Benefits of breeding crops for yield response to soil organisms Philip White

Chapter 4. Microbial interactions in the Rhizosphere Jose-Miguel Barea

Chapter 5. Culture-independent molecular approaches to microbial ecology in soil and the rhizosphere Penny Hirsch

Chapter 6. Exploiting new systems-based strategies to elucidate plant-bacterial interactions in the rhizosphere Fergal O’Gara

Chapter 7. Combining molecular microbial ecology with ecophysiology and plant genetics for a better understanding of plant-microbial communities interactions in the rhizosphere Philippe Lemanceau and Christoph Mougel

Chapter 8. Microbially Mediated Plant Functional Traits Maren L. Friesen

Section 2 Plant-mediated Structuring of Bacterial Communities in the Rhizosphere

Chapter 9. Unraveling the shed of unexplored rhizosphere microbial diversity Chandra Nautiyal

Chapter 10. Analysis of bacterial communities in the rhizosphere- what do advanced molecular tools tell us about the ecology of interactions?
Jan Dirk van Elsas

Chapter 11. Challenges in assessing links between root exudates and the structure and function of soil microbial communities Leo Condron

Chapter 12. Root secretions: interrelating genes and molecules to microbial associations. Is it all that simple?
Harsh Bais

Chapter 13. The use of stable isotope labelling and compound-specific analysis of microbial phospholipid fatty acids to quantify the influences of rhizodeposition on microbial community structure and function Eric Paterson

Chapter 14. Metarhizobium robertsii, a rhizosphere-competent insect pathogen that expresses a specific subset of genes in plant root exudate Monica Pava-Ripoll

Chapter 15. Shaping of microbial community structure and function in the rhizosphere by four diverse plant species Wafa Achouak

Chapter 16. Exploration of hitherto-uncultured bacteria from the rhizosphere Leo van Overbeek

Chapter 17. The use of molecular methods to assess chemotactic-competent bacterial populations in the rhizosphere Alison Buchan

Chapter 18. Assessment of rice root-associated bacteria Pablo Hardoim

Chapter 19. Phylogenetic analysis of Azospirillum species isolated from the rhizosphere of field grown wheat based on genetic and phenotypic features Panagiotis Katinakis

Chapter 20. Influence of intercropping and intercropping plus rhizobial inoculation on microbial activity and community composition in rhizosphere of alfalfa (Medicago sativa L.) and siberian wild rye (Elymus sibericus L.)
Hong Li Yuan

Chapter 21. Root exudates, crucial for molecular understanding of interactions in the rhizosphere Nicholas Uren

Chapter 22. Do root exudates exert more influence on rhizosphere bacterial community structure than other rhizodeposits?
Penny Hirsch

Section 3 Plant Genetics and Rhizobacterial Communities

Chapter 23. Arabidopsis thaliana as model in the study of root-inhabiting bacteria Paul Schulze-Lefert

Chapter 24. Genetic and developmental control of rhizosphere bacterial communities Shirley Micallef and Adan Colon-Carmona

Chapter 25. Arabidopsis thaliana: a useful but limited mosel to investigate stress impacts on rhizosphere community composition and function Gordon Wolfe

Chapter 26. Medicago truncatula root proteomics Frank Colditz

Section 4 Hormones and other Signals and Rhizomicrobes

Chapter 27. Control of the cooperation.between plant growth-promoting rhizobacteria and crops by rhizosphere signals Yvan Moenne-Loccoz and Claire Prigent Combaret

Chapter 28. Small molecules involved in transkingdom communication between plants and rhizobacteria Jose Lopez-Bucio

Chapter 29. Bacterial biosynthesis of indole-acetic acid: Signal messenger service Sheela Srivastava

Chapter 30. Fixing and non-fixing Rhizobia affect Arabidopsis root architecture by interfering with the auxin signalling pathway Bruno Touraine

Chapter 31. Terpene production by bacteria and its involvement in plant growth promotion, stress alleviation and yield increase Ruben Bottini

Chapter 32 Rapid identification of plant growth promoting rhizobacteria using an agar plate co-cultivation system with Arabidopsis Jose Lopez-Bucio

Chapter 33. Strigolactone biosynthesis and biology Harro Bouwmeester

Chapter 34. Chemistry of strigolactones: why and how do plants produce so many strigolactones?
Koichi Yoneyama

Chapter 35. Strigolactones: crucial cues in the rhizosphere Juan Lopez-Raez

Section 5 Endophytes

Chapter 36. Bacterial endophytes: Who and where and what they are doing there Natalia Malfanova and Gabriele Berg

Chapter 37. Properties of bacterial endophytes leading to maximized host fitness Jan Dirk van Elsas

Chapter 38. DNA-Based stable isotope probing for identifying active bacterial endophytes in potato Frank Rasche

Chapter 39. Visualization of niches of colonization of Firmicuyes with Bacillus spp in the rhizosphere, rhizoplane and endorhiza of grapevine plants at flowering stage of development by FISH microscopy Stephane Compant; Angela Sessitsch

Chapter 40. The poplar endophyte Pseudomonas putida W619 as a key to a succesfull phytoremediation of volatile organic contaminants Nele Weyens

Chapter 41. NifH gene expression and nitrogen fixation by diazotrophic endophytes in sugarcane and sweet potato Tadakatsu Yoneyama

Chapter 42. Surveying diverse Zea seed for populations of bacterial endophytes Manish Raizada Robert Johnston Monje

Section 6 Symbiotic Plant-Microbe Interactions

Chapter 43. Molecular mechanisms governing arbuscular mycorrhiza development and function Martin Parniske

Chapter 44. Diversity and evolution of nitrogen-fixing legume symbionts Catharine Masson

Chapter 45. Lipochitooligosaccharide perception and the basis of partner recognition in root endosymbioses Julie Cullimore and Clare Gough

Chapter 46. Rhizobial genetic repertoire to inhabit legume- and non-legume rhizospheres Esperanza Martinez Romero

Chapter 47. Who is controlling whom within the ectomycorrhizal symbiosis: Insights from genomic and functional analyses Francis Martin and Claire Fourrey

Chapter 48. Role of carotenoid metabolism in the arbuscular mycorrhizal symbiosis Michael Walter

Chapter 49. Bacterial colonization of the arbuscular mycorrhizal.fungal hyposphere Tanja Scheublin

Chapter 50. Role of Quorum Sensing in the Sinorhizobium meliloti-Alfalfa Symbiosis Juan Gonzalez

Chapter 51. Roles for flavonoids in symbiotic root-rhizosphere interactions Ulrike Mathesius

Chapter 52. Exopolysaccharides and Nodule Invasion in the Sinorhizobium meliloti-Alfalfa Symbiosis Juan Gonzalez

VOLUME TWO

Section 7 PGPR, Biocontrol and Disease-Suppressive Bacteria

Chapter 53. Plant growth promotion by microbes Ben Lugtenberg and Gabriele Berg

Chapter 54. Microbial control of plant root diseases Ben Lugtenberg and Gabriele Berg

Chapter 55. Biocontrol and Osmoprotection for Plants under Saline Conditions Gabriela Berg

Chapter 56. Genetics and evolution of 2,4 di acetylphloroglucinol synthesis in Pseudomonas fluorescence John Morrissey

Chapter 57. Suppression of crown gall disease by rhizosphere bacteria and Agrobacterium-specific bacteriophages Leonid Chernin

Chapter 58. Molecular-based strategies to exploit the inorganic phosphate solubilization ability of Pseudomonas in sustainable agriculture Fergal O’Gara

Chapter 59. The biocontrol bacterium Pseudomonas fluoresens Pf29Arp strain affects the pathogenesis-related gene expression of the take-all fungus Gaeumannomyces graminis var. tritici on wheat roots Stephanie Daval

Chapter 60. Marker-Assisted Selection of Novel Bacteria Contributing to Soilborne Plant Disease Suppression Brian McSpadden Gardener

Chapter 61. Combined effects of wheat roots and pathogenic fungus Gaeumannomyces graminis vartritici on Gene Expression of the biocontrol bacterium Pseudomonas fluorescens Pf29Arp Alain Sarniguet

Chapter 62. Biocontrol of Tree Root Diseases Francisco Cazorla and Clara Piego

Chapter 63. Plant growth modulation by bacterial volatiles: a focus on Burkholderia species Laure Weisskopf

Chapter 64. Plant growth promoting microorganisms: The road from an academically promising result to a commercial product Faina Kamilova and H. Mikkelsen

Chapter 65. The effect of agricultural practices on resident soil microbial communities: Focus on biocontrol and biofertilization Susana Castro-Sowinski

Section 8 Biofilm Formation and Attachment to Roots

Chapter 66. Biofilm Formation in the Rhizosphere: Multispecies Interactions and Implications for Plant Growth Ann Hirsch

Chapter 67. Probiotics for plants: Rhizospheric microbiome and plant fitness Harsh Bais

Chapter 68. Motility, biofilm formation and rhizosphere colonization by Pseudomonas fluorescens F113
Rafael Rivilla and Marta Martin

Chapter 69. CMEIAS: An improved computing technology for quantitative image analysis of root colonization by rhizobacteria In Situ at single-cell resolution Frank Dazzo and Youssef Yanni

Section 9 Quorum Sensing and Signalling

Chapter 70. Understanding root-microbiome interactions Jorge Vivanco

Chapter 71. An interkingdom signaling mechanism in rhizosphere Pseudomonas Vittorio Venturi

Chapter 72. N-Acylhomoserine-lactone quorum-sensing signalling in phenazine and cyclic lipopeptide-producing Pseudomonas sp. CMR12 from the red cocoyam rhizosphere Monica. Hofte

Chapter 73. The response of plants towards N-acyl homoserine lactones of quorum sensing active bacteria in the rhizosphere Anton Hartmann

Chapter 74. In situ calling distances and high population independent N-acylhomoserine lactone- mediated communication on plant root surfaces Frank Dazzo Stephan Gantner

Chapter 75. Quorum-sensing quenching by volatile organic compounds emitted by rhizosphere bacteria Leonid Chernin

Chapter 76. The biological significance of the degradation of N-acylhomoserine lactones-Quorum sensing and quorum quenching in Burkholderia and Agrobacterium Kok-Gan Chan and Yves Dessaux

Chapter 77. Altering Plant-Microbe Interactions Through Artificially Manipulating Bacterial Quorum Sensing Rupert Fray

Chapter 78. Rhizosphere microbial communication in soil nutrient acquisition Kristen DeAngelis

Chapter 79 Agony to harmony- What decides? Calcium signalling in beneficial and pathogenic plant-microbe interactions: What we can learn from the Arabidopsis/Piriformospora indica symbiosis Ralf Oelmuller

Section 10 Genomic Sequencing and Screening of Genes/Promoters Activated in the Natural Environment

Chapter 80 Genome transcriptome analysis and functional characterization of a nitrogen fixation island in root-associated Pseudomonas stutzeri Min Lin and Claudine Elmerich

Chapter 81. Genome analysis, ecology and plant growth promotion of the endophyte Burkholderia phytofirmans strain PsJN Angela Sessitsch

Chapter 82. Identification and mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in complex environments Robert Jackson

Chapter 83. Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42
Rainer Borriss

Chapter 84. Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638
Daniel van der Lelie

Section 11 Marker and Reporter Genes For Plant-Host Interaction Studies

Chapter 85. Approaches for the design of genetically engineered bacteria for ecological studies and biotechnological applications Humberto Ramos

Chapter 86. Construction of signature-tagged mutant libraries and application to plant-symbiotic bacteria Anke Becker

Chapter 87 Us e of DOPE-FISH tool to better visualize colonization of plants by beneficial bacteria? An example with Saccharothrix algeriensis NRRL B-24137 colonizing grapevine plants Stephane Compant

Chapter 88. Combining rhizobox, reporter gene systems and molecular analysis to assess the effects of humic substances on plant-microbes interactions in soil rhizosphere Marco Trevisan

Chapter 89. Multi-parameter flow cytometry for characterization of physiological states in Pseudomonas fluorescens DR54 biocontrol inoculants under dry formulation and long-term storage in clay carrier Jan Sorensen

Chapter 90. Endophytic lifestyle of biocontrol strains of Pseudomonas spp. in olive roots Jesus Mercado-Blanco and Pilar Prieto

Section 12 Phytoremediation and heavy metal tolerance in the Rhizosphere

Chapter 91. Improving phytoremediation through plant associated bacteria David Dowling

Chapter 92. Ecology of alkane-degrading bacteria and their interaction with the plant.
Angela Sessitsch

Chapter 93. Abiotic stress remediation by the arbuscular mycorrhizal symbiosis and rhizosphere bacteria /yeast interactions Rosario Azcon

Chapter 94. Potentially plant growth promoting and nitrogen fixing rhizobacteria associated with pioneer plants growing on mine tailings Cesar Hernandez-Rodriguez

Chapter 95. Stimulation of rhizosphere microbial communities during chemophytostabilization of a Pb-Zn mine soil George Kowalchuk and Lur Epelde

Chapter 96. Arbuscular mycorrhiza in glucosinolate-containing plants: The story of the metal hyperaccumulator Thlaspi praecox (Brassicaceae)
Marjana Regvar

Chapter 97. Novel metal resistance genes from the rhizosphere of extreme environments: A functional metagenomics approach Jose Gonzalez-Pastor and Salvator Mirete

Section 13 Climate Change Effects on Soil/Rhizosphere Microbial Communities

Chapter 98. Soil warming effects on beneficial plant-microbe interactions Angela Sessitsch Stephane Compant

Chapter 99. Soil respiration, climate change and the role of microbial communities.
O. Roger Anderson

Chapter 100. Rhizosphere responses to elevated atmospheric CO2
George Kowalchuk and Barbara Drigo

Chapter 101. Applying stable isotope probing of phospholipid fatty acids and ribosomal RNA in rice fields to study the composition of the active methanotrophic bacterial communities in situ Ralph Conrad

Section 14 Metagenomics and the Soil/Rhizosphere

Chapter 102. Impact of mangrove roots on bacterial composition Newton Gomes

Chapter 103. Prediction of an ectomycorrhizal metabolome from transcriptomic data Peter Larsen

Chapter 104. Metagenomic analysis on the rhizosphere soil microbial community Takuro Shinano

Chapter 105. Bacterial diversity in rhizosphere soil from antarctic vascular plants of Admiralty Bay, in maritime Antarctica Alexandre Rosado

Chapter 106. Arbuscular mycorrhizal fungi throughout the year: Using massively parallel pyrosequencing to quantify spatio-temporal seasonal dynamics Alex Dumbrell

Chapter 107. Transcriptomics and metatranscriptomic analysis of the response of rhizosphere bacteria to environmental change Phil Poole

Chapter 108. Unraveling the rhizosphere using the CPN60 genomic marker and pyrosequencing George Lavarovits

Chapter 109. Rhizosphere metatranscriptomics: Challenges and opportunities Peer Schenk

Section 15 Engineering the Rhizosphere : The « Biased Rhizosphere « Concept

Chapter 110. The “Biased Rhizosphere” concept and advances in the Omics era to study bacterial competitiveness and persistence in the phytosphere.
Yves Dessaux and Silvia Rossbach

Chapter 111. Bacterial inositol and rhizopine catabolism- a sweet ride into the host Silvia Rossbach

Chapter 112. Exogenous glucosinolate produced by transgenic Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots Odile Berge and Mélanie Bressan C
hapter 113. Reciprocal interactions between plants and fluorescent pseudomonads in relation to iron in the rhizosphere Philippe Lemanceau

Chapter 114. Enhancement of plant-microbe interactions using rhizosphere metabolomics driven approach and its application in the removal of polychlorinated biphenyls Sanjay Swarup

Section 16 Concluding Chapters

Chapter 115. Rhizophagy – a new dimension of plant-microbe interactions Chanyarat Puangfoo-Lonhienne

Chapter 116. The Rhizosphere as a Reservoir for Opportunistic Human Pathogenic Bacteria Gabriele Berg and Anton Hartmann

Chapter 117. Mechanisms of plant colonization by human pathogenic bacteria: an emphasis on the roots and rhizosphere Nicola Holden

Chapter 118. Perspectives on the Molecular Microbial Ecology of the Rhizosphere B.J.J. Lugtenberg and Jos Raaijmakers