Microbial Activity in the Rhizosphere

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1 K. G. Mukerji C. Manoharachary J. Singh (Eds.) Microbial Activity in the Rhizosphere With 35 Figures 4y Springer

2 1 Rhizosphere Biology - an Overview 1 Chakravarthula Manoharachary, Krishna G. Mukerji 1.1 Introduction SoilMicrobes Rhizosphere Soil Rhizoplane RootExudates Rhizosphere and Compounds Released by Roots Decomposition of Organic/Inorganic Compounds in Rhizosphere Root Sensing Signals Conclusions 11 References 12 2 Methods and Techniques for Isolation, Enumeration and Characterization of Rhizosphere Microorganisms 17 Nandanavanam Ranganayaki, Kolluru V.B.R. Tilak, Chakravarthula Manoharachary, Krishna G. Mukerji 2.1 Introduction Isolation Sampling Fungi Bacteria Actinomycetes Algae Enumeration Counting Microscopy Microbial Biomass Immunological Detection Methods Molecular Techniques 30

3 VIII Contents 2.4 Mathematical Modeling Mechanistic Models Descriptive Models Enumeration in Real Time Systems Conclusions 33 References 34 3 Root Exudates as Determinant of Rhizospheric Microbial Biodiversity 39 Geeta Singh, Krishna G. Mukerji 3.1 Introduction Composition of Root Exudates Factors Affecting Root Exudates Roles of Root Exudates Root Exudates vs AMF Host Influence Diversity of Microbial Populations in the Rhizosphere of Different Plant Species Bacterial Population Exudation in Genetically Engineered Plants Conclusions 48 References 49 4 Rhizosphere Microbial Community Dynamics 55 Roopam Kapoor, Krishna G. Mukerji 4.1 Introduction Root-Microbe Communication Root Exudates Microbial Interactions Signalling Factors Microbial Dynamics in Terrestrial Ecosystem Soil Microbial Community in Relation to Plant Diversity Microbial Community and Plant Genotype Transgenics Expressing T 4 Lysozyme Atmospheric Carbon Dioxide Microbial Community and Rhizodeposition Agronomical Regimes and Microbial Diversity Crop Sequence Conclusions 66 References 66

4 IX 5 The Role of Rhizotrons and Minirhizotrons in Evaluating the Dynamics of Rhizoplane-Rhizosphere Micro flora 71 Bobbie L. McMichael, John C. Zak 5.1 Introduction Use of Rhizotrons and Minirhizotrons in Root Research Minirhizotrons Data Collection from Rhizotrons and Minirhizotrons Advantages and Disadvantages of Rhizotrons and Minirhizotrons Use of Rhizotrons and Minirhizotrons in Rhizoplane and Rhizosphere Research Mycorrrhizae Soil Borne Pathogens Root Surface or Rhizoplane Phenomena Conclusions 84 References 84 6 Significance of Bacteria in the Rhizosphere 89 David B. Nehl, Oliver G.G. Knox 6.1 Introduction Functional Diversity of Rhizobacteria Soil Structure Phosphate Solubilisation Nitrogen Cycling Symbioses Between Plants and Diazotrophic Rhizobacteria Free-Living Diazotrophic Rhizobacteria The Soil Food Web Interactions Among Rhizosphere Microorganisms Functional Flux in the Rhizosphere Rhizobacteria are Moderators at the Plant-Soil Interface Selective Enrichment and Diversity of Bacteria in the Rhizosphere Competitiveness of Rhizobacteria Selective Plant Factors Evolution of the Rhizosphere Gene Flow in the Rhizosphere Selection Processes in the Rhizosphere Rhizobacteria as Determinants of Plant Diversity Conclusions 109 References 110

5 Interactions Among Beneficial Microorganisms 121 Anil Kumar Saxena, Rasika Shende, Minakshi Grover 7.1 Introduction Interaction Between Rhizobium and PGPR Rhizobium and Nodulation Promoting Rhizobacteria Rhizobium and Biocontrol Agents Interaction Between AM Fungi and Rhizobium Influence on Nodulation and Nitrogen Fixation Specific Compatibility and Yield Interaction Under Stress Interaction of AM Fungi with PGPR Mycorrhiza Development and Population Density of PGPR Interaction of AMF and PGPR in Plant Growth Promotion Conclusions 131 References 132 Bacterial Community Composition and Activity in Rhizosphere of Roots Colonized by Arbuscular Mycorrhizal Fungi 139 Petra Marschner, Sari Timonen 8.1 Introduction Rhizosphere Colonization by Bacteria Soil Bacteria Pseudomonads N 2 Fixing Bacteria and P Solubilizers Biological Control Organisms Bacterial Community Composition Bacterial Activity Effects of Bacteria on AM Fungi Bacteria in AM Fungi Conclusions 149 References 149 Mycorrhizosphere Concept 155 Sari Timonen, Petra Marschner 9.1 Introduction Mycorrhizosphere Structure Evolution and Occurrence of Mycorrhizospheres Mycorrhizospheres as Habitats Microorganisms Involved in Forming Mycorrhizospheres Mycorrhizal Fungi 161

6 XI Other Fungi Bacteria Archaea Protozoa Ecological Significance of Mycorrhizospheres Conclusions 167 References Molecular Techniques for Understanding the Microbial Community Structure in Mycorrhizosphere 173 Pankaj Krishna, Mondem S. Reddy, Tulasi Satyanarayana 10.1 Introduction Culture-Dependent Methods for Identification of Bacteria Culture-Independent (Molecular) Methods Determination of the DNA Base Ratio (Mole Percent G+C) DNA:DNA Hybridization DNA:rRNA Hybridization Ribosomal RNA (rrna) and Spacer Region Amplification by Polymerase Chain Reaction (PCR) Primers Random Amplified Polymorphic DNA (RAPD) Amplification Fragment Length Polymorphism (AFLP) Restriction Fragment Length Polymorphism (RFLP) Gradient Gel Electrophoresis Terminal Restriction Fragment Length Polymorphism (T-RFLP) Screening of Libraries of Amplified 16S rdna Sequence In Situ Hybridization Limitation of rdna Technology Conclusions 191 References Arbuscular Mycorrhizal Fungi and the Form and Functioning of the Root System 199 David Atkinson 11.1 Introduction AMF Infection and Whole Plant Functioning AMF and Root Form and Function Root System Size 204

7 XII Contents Root and Root System Morphology Root Longevity Infection and Root Function Effects on Infection Hyphae Functioning AMF and Resource Acquisition Effects on Nutrient Uptake from the Soil AMF and Water Relations Conclusions 216 References Fungal Recognition Responses to Host Derived Signals by Arbuscular Mycorrhizal Fungi 223 Cristiana Sbrana 12.1 Introduction AM Fungal Life Cycle Chemotropic Responses Pre-Contact Host Recognition Does Non-Host Signalling Occur? Signalling at Host Contact Conclusions 238 References Interactions Between Ectomycorrhizal Fungi and Rhizospheric Microbes 245 Mondem S. Reddy, Tulasi Satyanarayana 13.1 Introduction Interaction with MHBs Inhibitory Effects Interactions with PGPRs Interations to Improve Soil Quality Conclusions 258 References Role of Beneficial Microsymbionts on the Plant Performance and Plant Fitness 265 Borbala Bird, Krisztina Koves-Pichy, Merope Tsimilli-Michael, Reto J. Strasser 14.1 Introduction Managing the Beneficial Effect of Microsymbionts Isolation and Selection of Beneficial Microsymbionts Microcosm Experiments for the Inoculation Studies. 268

8 XIII Micropropagated Plants and Microsymbiont Inoculations Assessment of Plant Performance and Plant Fitness Plant Performance Parameters Plant Fitness Parameters Interpretation of Data Plant Performance and Fitness by Microsymbiont Co-Inoculations Establishment of Inoculated Microsymbionts in the Rhizosphere Performance of Microsymbiont Inoculated Plants Plant Physiological Parameters Conclusions 291 References Bacteria Helping Mycorrhiza Development 297 Robin Duponnois 15.1 Introduction Setting in Evidence Mycorrhiza Helper Bacteria (MHB) Biological Properties of MHBs Mechanisms Involved in the MHB Effect Application of MHBs Conclusions 307 References Rhizosphere Regulation of Preinfection Behavior of Oomycete Plant Pathogens 311 Eric B. Nelson 16.1 Introduction Exudate Elicitors of Pathogen Responses to Plants Oomycete Pathogens Aphanomyces Species Pythium Species Phytophthora Species Conclusions 332 References 334 Subject Index 345

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