Verfügbarkeit: Plant surface microbiology

Plant surface microbiology:

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Format:	Buch
Sprache:	English
Veröffentlicht:	Berlin [u.a.] Springer 2008
Ausgabe:	[Taschenbuch-Ausg.]
Schlagworte:	Plant surfaces > Microbiology Mikrobiologie Pflanzen Aufsatzsammlung
Online-Zugang:	Inhaltsverzeichnis
Beschreibung:	XXXI, 628 S. Ill., graph. Dars.
ISBN:	9783540740506

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Datensatz im Suchindex

_version_	1804137927004913664
adam_text	Contents The State of the Art ................... AjiT Varma, Lynette K. Abbott, Dietrich Werner and Rüdiger Hampp Section A 2 Root Colonisation Following Seed Inoculation ....... 13 Thomas EC. Chin-A-Woeng and Ben J.J. Lugtenberg 1 Introduction ........................... 13 2 Bacterial Root Colonisation .................. 13 3 Analysis of Tomato Root Tip Colonisation After Seed Inoculation Using a Gnotobiotic Assay ...... 14 3.1 Description of the Gnotobiotic System ............ 14 3.2 Seed Disinfection ........................ 15 3.3 Growth and Preparation of Bacteria .............. 16 3.4 Seed Inoculation ........................ 17 3.5 Analysis of the Tomato Root Tip ................ 17 3.6 Confocal Laser Scanning Microscopy ............. 18 4 Genetic Tools for Studying Root Colonisation ........ 18 4.1 Marking and Selecting Bacteria ................ 18 4.2 Rhizosphere-Stable Plasmids ................. 21 4.3 Genetic and Metabolic Burdens ................ 21 5 Behaviour of Root-Colonising Pseudomonas Bacteria in a Gnotobiotic System ....... 22 5.1 Colonisation Strategies of Bacteria .............. 22 5.2 Competitive Colonisation Studies ............... 23 5.3 Monocots versus Dicots ..................... 25 6 Influence of Abiotic and Biotic Factors ............ 25 VIII Contents 6.1 Abiotic Factors ......................... 25 6.2 Biotic Factors .......................... 27 7 Conclusions ........................... 28 References and Selected Reading ..................... 28 3 Methanogenic Microbial Communities Associated with Aquatic Plants ....................... 35 Ralf Conrad 1 Introduction ........................... 35 2 Role of Plants in Emission of CH4 to the Atmosphere .... 35 3 Role of Photosynthates and Plant Debris for CH4 Production 38 4 Methanogenic Microbial Communities on Plant Debris ... 40 5 Methanogenic Microbial Communities on Roots ....... 42 6 Interaction of Methanogens and Methanotrophs ....... 44 References and Selected Reading ..................... 45 4 Role of Functional Groups of Microorganisms on the Rhizosphere Microcosm Dynamics .......... 51 Galdino Andrade 1 Introduction ........................... 51 2 General Aspects of Functional Groups of Soil Microorganisms ..................... 52 3 Carbon Cycle Functional Groups ............... 53 4 Functional Groups of Microorganisms of the Nitrogen Cycle 55 5 Functional Groups of Microorganisms of the Sulphur Cycle 57 6 Functional Groups of Microorganisms of the Phosphorus Cycle .................... 59 7 Dynamics of the Rhizosphere Functional Groups of Microorganisms ....................... 60 8 Relationship Among r and к Strategist Functional Groups . 61 9 Arbuscular Mycorrhizal Fungi Dynamics in the Rhizosphere ....................... 61 10 Dynamics Among the Functional Micro-Organism Groups of the Carbon, Nitrogen, Phosphorus and Sulphur Cycles . . 65 References and Selected Reading ..................... 68 Contents IX 5 Diversity and Functions of Soil Microflora in Development of Plants .................... 71 Ramesh CHandER Kuhad, David Manohar Kothamasi, K.K. Tripathi and Ajay Singh 1 Introduction ........................... 71 2 Functional Diversity of Soil Microflora ............ 72 3 Role of Soil Microflora in Plant Development ........ 76 3.1 Mycorrhiza ............................ 76 3.2 Actinorhiza ........................... 80 3.3 Plant Growth-Promoting Rhizobacteria ........... 82 3.4 Phosphate-Solubilizing Microorganisms ........... 84 3.5 Lignocellulolytic Microorganisms ............... 85 4 Plant Growth Promoting Substances Produced by Soil Microbes ......................... 88 5 Conclusions ........................... 90 References and Selected Reading ..................... 91 6 Signalling in the Rhizobia-Legumes Symbiosis ....... 99 Dietrich Werner 1 Introduction ........................... 99 2 The Signals from the Host Plants ............... 101 2.1 Phenylpropanoids: Simple Phenolics, Flavonoids and Isoflavonoids ........................ 102 2.2 Metabolization of Flavonoids and Isoflavonoids ....... 104 2.3 Vitamins as Growth Factors and Signal Molecules ...... 106 3 Signals from the Microsymbionts ............... 107 3.1 Nod Factors ........................... 107 3.2 Cyclic Glucans .......................... 109 3.3 Lipopolysaccharides ...................... 110 3.4 Exopolysaccharides ....................... 110 4 Signal Perception and Molecular Biology of Nodule Initiation ....................... Ill References and Selected Reading ..................... 114 X Contents Section В 7 The Functional Groups of Micro-organisms Used as Bio-indicator on Soil Disturbance Caused by Biotech Products such as Bacillus thuringiensis and Bt Transgenic Plants .................... 121 Galdino Andrade 1 Introduction ........................... 121 2 General Aspects of Bacillus thuringiensis ........... 122 3 Survival in the Soil ....................... 123 4 History of Bacillus thuringiensis-Tramgmic Plants ..... 124 5 Persistence of the Protein Crystal in the Soil ......... 125 6 Effect of Bacillus thuringiensis and Its Bio-insecticide Protein on Functional Soil Microorganism Assemblage . . . 126 References and Selected Reading ..................... 130 8 The Use of ACC Deaminase-Containing Plant Growth-Promoting Bacteria to Protect Plants Against the Deleterious Effects of Ethylene ......... 133 Bernard R. Glick and Donna M. Penrose 1 Introduction ........................... 133 2 Ethylene ............................. 134 3 ACCDeaminase ......................... 135 3.1 Treatment of Plants with ACC Deaminase Containing Bacteria ....................... 137 4 Conclusions ........................... 140 References and Selected Reading ..................... 141 9 Interactions Between Epiphyllic Microorganisms and Leaf Cuticles ........................ 145 Lukas Schreiber, Ursula Krimm and Daniel Knoll 1 Introduction ........................... 145 2 Physical and Chemical Parameters of the Phyllosphere ... 147 3 Leaf Surface Colonisation and Species Composition ..... 149 4 Alteration of Leaf Surface Wetting ............... 150 5 Interaction of Bacteria with Isolated Plant Cuticles ..... 152 6 Conclusions ........................... 153 References and Selected Reading ..................... 154 Contents XI 10 Developmental Interactions Between Clavidpitaleans and Their Host Plants ..................... 157 James E White Jr., Faith Belanger, Raymond Sullivan, Elizabeth Lewis, Melinda Μου, William Meyer and Charles W. Bacon 1 Introduction ........................... 157 2 Endophyte/Epibiont Niche ................... 157 3 Coevolution of Clavicipitalean Fungi with Grass Hosts . . . 158 4 The Jump from Insects to Plants ................ 158 4.1 Trans-Kingdom Jump ...................... 158 4.2 Intermediate Stages in the Transition to Plants ........ 158 4.3 Parasitism of Grass Meristematic Tissues ........... 160 5 Developmental Differentiation of Endophytic and Epiphyllous Mycelium ................... 160 5.1 Plant Cell Wall Alteration .................... 160 5.2 Endophytic Mycelial Growth .................. 160 5.3 Control of Endophytic Mycelial Development ........ 163 5.4 Epiphyllous Mycelial Development .............. 163 5.5 Expression of Fungal Secreted Hydrolytic Enzymes in Infected Plants ................... 164 6 Modifications of Plant Tissues for Nutrient Acquisition . . . 165 6.1 Development of the Stroma in Epichloë ............ 165 6.2 Stroma Development in Myriogenospora ........... 166 6.3 Mechanisms for Modifying Plant Tissues ........... 168 6.4 Evaporative-Flow Mechanism for Nutrient Acquisition . . . 169 6.5 The Cytokinin Induction Hypothesis ............. 169 7 Evolution of Asexual Derivatives of Epichloë ......... 171 7.1 Reproduction and Loss of Sexual Reproduction ....... 171 7.2 The Hypotheses ......................... 172 7.3 The Process of Stroma Development and its Loss ...... 173 7.4 The Shift from Pathogen to Mutualist ............. 174 8 Conclusions ........................... 174 References and Selected Reading ..................... 174 11 Interactions of Microbes with Genetically Modified Plants . 179 Michael Kaldorp, Chi Zhang, Uwe Nehls, Rüdiger Hampp and François Buscot 1 Introduction ........................... 179 2 Changes in Microbial Communities Induced by Genetically Modified Plants ................. 181 XII Contents 3 Impact of Genetically Modified Plants on Symbiotic Interactions ................... 184 4 Horizontal Gene Transfer .................... 186 5 Conclusions ........................... 191 References and Selected Reading ..................... 192 Section С 12 Interaction Between Soil Bacteria and Ectomycorrhiza-Forming Fungi ............. 197 Rüdiger Hampp and AndREAS Maier 1 Introduction ........................... 197 2 Bacteria ............................. 198 3 Bacterial Community Structure ................ 198 4 Association of Bacteria with Fungal/Ectomycorrhizal Structures ............................ 199 5 Bacteria Associated with Sporocarps and Ectomycorrhiza . 200 6 Benefits from Bacteria/Ectomycorrhiza Interactions .... 201 7 Possible Mechanisms of Interaction .............. 202 8 Biochemical Evidence for Interaction ............. 203 9 Impacts of Environmental Pollution .............. 206 10 Conclusions ........................... 206 References and Selected Reading ..................... 207 13 The Surface of Ectomycorrhizal Roots and the Interaction with Ectomycorrhizal Fungi ........... 211 Ingrid Kottke 1 Introduction ........................... 211 2 Long and Short Roots of Ectomycorrhiza-Forming Plants . 212 3 A Cuticle-Like Layer on the Surface of Short Roots ..... 214 4 Involvement of the Cuticle-Like Layer in Mycorrhiza Formation .................... 218 5 Involvement of the Cuticle-Like Layer in Hyphal Attachment 218 6 Digestion of the Suberin Layer and the Cell Wall of the Root Cap ......................... 220 7 Hartig Net Formation ...................... 221 8 Pectins in the Cortical Cell Walls of Nonmycorrhizal Long and Mycorrhizal Short Roots .............. 222 9 Conclusions ........................... 223 References and Selected Reading ..................... 224 Contents XIII 14 Cellular Ustilaginomycete — Plant Interactions ....... 227 Robert Bauer and Franz Oberwinkler 1 Introduction ........................... 227 2 The Term Smut Fungus ..................... 227 3 Life Cycle ............................. 228 4 Hosts ............................... 228 5 Cellular Interactions ...................... 229 5.1 Local Interaction Zones ..................... 230 5.2 Enlarged Interaction Zones .................. 234 6 Conclusions ........................... 235 References and Selected Reading ..................... 236 15 Interaction of Piriformospora indica with Diverse Microorganisms and Plants ........... 237 Giang Huong Pham, Anjana Singh, Rajani Malla, Rina Kumari, , Ram Prasad, Minu Sachdev, Karl-Heinz Rexer, Gerhard Kost, Patricia Luis, Michael Kaldorf, François Buscot, Sylvie Herrmann, Tanja Peskan, Ralf Oelmüller, Anil Kumar Saxena, Stephane Declerck, Maria Mittag, Edith Stabentheiner, Solveig Hehl and Ajit Varma 1 Introduction ........................... 237 2 Interaction with Microorganisms ............... 238 2.1 Rhizobacteria .......................... 238 2.2 Chlamydomonas reinhardtii .................. 239 2.3 Sebacina vermifera ....................... 239 2.4 Other Soil Fungi ......................... 240 2.5 Gaeumannomyces graminis .................. 240 3 Interaction with Bryophyte ................... 242 4 Interaction with Higher Plants ................. 242 4.1 Monocots ............................ 245 4.2 Legumes ............................. 245 4.3 Orchids .............................. 246 4.4 Medicinal Plants ......................... 247 4.5 Economically Important Plants ................ 249 4.6 Timber Plants .......................... 252 4.7 Unexpected Interactions with Wild Type and Genetically Modified Populus Plants ........... 253 4.8 Nonmycorrhizal Plants ..................... 255 XIV Contents 4.9 Arabidopsis thaliana ...................... 256 4.10 Root Organ Culture....................... 259 5 Cell Wall Degrading Enzymes ................. 260 6 Conclusions ........................... 263 References and Selected Reading ..................... 264 16 Cellular Basidiomycete-Fungus Interactions ........ 267 Robert Bauer and Franz Oberwinkler 1 Introduction ........................... 267 2 Occurrence of Mycoparasites Within the Basidiomycota . . 267 3 Hosts ............................... 268 4 Cellular Interactions ...................... 268 4.1 Colacosome-Interactions .................... 268 4.2 Fusion-Interaction ....................... 275 5 Basidiomycetous Mycoparasitism, a Result of Convergent Evolution? ............................ 277 6 Conclusions ........................... 278 References and Selected Reading ..................... 278 Section D 17 Fungal Endophytes ....................... 281 Sita R. Ghimire and Kevin D. Hyde 1 Introduction ........................... 281 2 Definition of a Fungal Endophyte ............... 281 3 Role of Endophytes ....................... 282 4 Modes of Endophytic Infection and Colonization ...... 283 5 Isolation of Endophytes .................... 284 6 Molecular Characterization of Endophytes .......... 285 7 Are Endophytes Responsible for Host Exclusivity/ Recurrence in Saprobic Fungi? ................. 286 8 Conclusions ........................... 287 References and Selected Reading ..................... 288 Contents XV 18 Mycorrhizal Development and Cytoskeleton ......... 293 Marjatta Raudaskoski, Mika Tarkka and Sara Niini 1 Introduction ........................... 293 2 Cytoskeletal Components ................... 293 2.1 Expression of Tubulin-Encoding Genes............ 294 2.2 Expression of Actin-Encoding Genes ............. 297 3 Organization of Cytoskeleton in Endomycorrhiza...... 298 3.1 Root Cells ............................ 298 3.2 Fungal Hyphae ......................... 300 4 Organization of Cytoskeleton in Ectomycorrhiza ...... 300 4.1 Root Cells ............................ 300 4.2 Fungal Hyphae ......................... 304 5 Regulation of Actin Cytoskeleton Organization in Fungal Hyphae and Plant Cells ............... 305 6 Actin Binding-Proteins ..................... 307 7 Microtubule-Associated Proteins ............... 308 7.1 Plant Cells ............................ 308 7.2 Fungal Hyphae ......................... 310 8 Cell Cycle and Cytoskeleton in Mycorrhiza .......... 313 9 Cytoskeletal Research Methods ................ 315 9.1 Indirect Immunofluorescence Microscopy .......... 316 9.2 Microinjection Method ..................... 317 9.3 Green Fluorescence Protein Technique ............ 317 References and Selected Reading ..................... 318 19 Functional Diversity of Arbuscular Mycorrhizal Fungi on Root Surfaces ........................ 331 M. Zakaria Solaiman and Lynette K. Abbott 1 Introduction ........................... 331 2 Mycorrhiza Formation and Ecological Specificity ...... 332 2.1 Establishment of the Symbiosis ................ 333 2.2 Spore Germination and Hyphal Growth ........... 333 2.3 Role of Plant Root Exudates .................. 333 3 Functioning of Arbuscular Mycorrhizas in Nutrient Exchange ...................... 334 3.1 Metabolic Activity During Mycorrhiza Formation ...... 335 3.2 Gene Expression During Mycorrhiza Formation ....... 336 3.3 Nutrient Exchange Mechanisms in Arbuscular Mycorrhizas 336 4 Functional Diversity of Arbuscular Mycorrhizal Fungi in Root and Hyphal Interactions ................ 338 XVI Contents 4.1 Diversity of Arbuscular Mycorrhizal Fungi Inside Roots . . 339 4.2 Relationship Between Hyphae in the Root and in the Soil . . 340 5 Role of Arbuscular Mycorrhizal Fungi Associated with Roots in Soil Aggregation ................. 340 6 Environmental Influence on Functional Diversity of Arbuscular Mycorrhizal Fungi ............... 341 7 Role of Plant Mutants in Studying the Interactions Between Arbuscular Mycorrhizal Fungi and Roots ..... 341 8 Conclusion and Future Research Needs ............ 343 References and Selected Reading ..................... 343 20 Mycorrhizal Fungi and Plant Growth Promoting Rhizobacteria ................... 351 José-Miguel Barba, Rosario Azcón and Concepción Azcón-Aguilar 1 Introduction ........................... 351 2 Main Types of Rhizosphere Microorganisms ......... 352 3 Mycorrhizal Fungi ........................ 353 4 Plant Growth Promoting Rhizobacteria ............ 354 5 Reasons for Studying Arbuscular Mycorrhizal Fungi and Plant Growth Promoting Rhizobacteria Interactions and Main Scenarios ....................... 356 6 Effect of Plant Growth Promoting Rhizobacteria on Mycorrhiza Formation ................... 357 7 Effect of Mycorrhizas on the Establishment of Plant Growth Promoting Rhizobacteria in the Rhizosphere .... 357 8 Interactions Involved in Nutrient Cycling and Plant Growth Promotion ....................... 359 9 Interactions for the Biological Control of Root Pathogens . . 361 References and Selected Reading ..................... 362 21 Carbohydrates and Nitrogen: Nutrients and Signals in Ectomycorrhizas ................ 373 Uwe Nehls 1 Introduction ........................... 373 2 Trehalose Utilization by Ectomycorrhizal Fungi ....... 374 3 Carbohydrate Uptake ...................... 374 4 Carbohydrate Metabolism ................... 376 5 Carbohydrate Storage ...................... 376 Contents XVII 6 Carbohydrates as Signal, Regulating Fungal Gene Expression in Ectomycorrhizas ............. 377 7 Nitrogen ............................. 380 8 Utilization of Inorganic Nitrogen ............... 381 9 Utilization of Organic Nitrogen ................ 382 10 Proteolytic Activities of Ectomycorrhizal Fungi ....... 383 11 Uptake of Amino Acids ..................... 383 12 Regulation of Fungal Nitrogen Export in Mycorrhizas by the Nitrogen-Status of Hyphae ............... 385 13 Carbohydrate and Nitrogen-Dependent Regulation of Fungal Gene Expression ................... 385 14 Conclusions ........................... 385 References and Selected Reading ..................... 386 22 Nitrogen Transport and Metabolism in Mycorrhizal Fungi and Mycorrhizas ............ 393 Arnaud Javelle, Michel Chalot, Annick Brun and Bernard Botton 1 Introduction ........................... 393 1.1 Ecological Significance of Ectomycorrhizas ......... 393 1.2 Nitrogen Uptake and Translocation by Ectomycorrhizas . . 394 2 Nitrate and Nitrite Transport .................. 395 2.1 Uptake Kinetics ......................... 395 2.2 Characterization of Nitrate and Nitrite Transporters .... 395 3 Ammonium Transport ..................... 398 3.1 Physico-Chemical Properties of Ammonium: Active Uptake Versus Diffusion ................ 398 3.2 Physiology of Ammonium Transport in Ectomycorrhizas . . 399 3.3 Isolation of Ammonium Transporter Genes ......... 400 3.4 Regulation of the Ammonium Transporters ......... 400 3.5 Other Putative Functions of Ammonium Transporters . . . 402 4 Amino Acid Transport ..................... 403 4.1 Utilization of Amino Acids by Ectomycorrhizal Partners . . 403 4.2 Molecular Regulation of Amino Acid Transport ....... 404 5 Reduction of Nitrate to Nitrite and Ammonium ....... 405 5.1 Reduction of Nitrate to Nitrite ................. 405 5.2 Reduction of Nitrite to Ammonium .............. 406 5.3 Molecular Characterization of Nitrate Reductase and Nitrite Reducíase ...................... 406 6 Assimilation of Ammonium .................. 409 6.1 Role and Properties of Glutamate Dehydrogenase ...... 410 XVIII Contents 6.2 Role and Properties of Glutaminę Synthetase ........ 413 6.3 Role and Properties of Glutamate Synthase .......... 415 7 Amino Acid Metabolism .................... 417 7.1 Utilization of Proteins by Ectomycorrhizal Fungi and Ectomycorrhizas ...................... 417 7.2 Amino Acids Used as Nitrogen and Carbon Sources ..... 418 8 Conclusion and Future Prospects ............... 419 References and Selected Reading ..................... 421 Section E 23 Visualisation of Rhizosphere Interactions of Pseudomonas and ВасШкѕ Biocontrol Strains ...... 431 Thomas F.C. Chin-A- Wo eng, Anastasia L. Lagopodi, Ine H.M. Mulders, Guido V. Bloemberg and Ben J.J. Lugtenberg 1 Introduction ........................... 431 2 Tomato Foot and Root Rot and the Need for Biological Control ...................... 431 3 Selection of Antagonistic Strains ............... 432 3.1 Selection of Antagonistic Pseudomonas and Bacillus sç. . . . 432 3.2 In Vitro Antifungal Activity Test ................ 434 4 In Vivo Biocontrol Assays .................... 434 4.1 Fusarium oxysporum — Tomato Biocontrol Assay in a Potting Soil System ..................... 434 4.2 Gnotobiotic Fusarium oxysporum-Pythium ultimum and Rhizoctonia solani-Tomato Bioassays .......... 435 5 Microscope Analysis of Infection and Biocontrol ...... 435 5.1 Marking Fungi with Autofluorescent Proteins ........ 437 5.2 Marking Rhizosphere Bacteria with Autofluorescent Proteins ............................. 438 5.3 Confocal Laser Scanning Microscopy of Rhizosphere Interactions .................. 442 6 Conclusions ........................... 443 References and Selected Reading ..................... 443 Contents XIX 24 Microbial Community Analysis in the Rhizosphere by in Situ and ex Situ Application of Molecular Probing, Biomarker and Cultivation Techniques ............ 449 Anton Hartmann, Rüdiger Pukall, Michael Rothballes, Stephan Gantner, SiGRUN Metz, Michael Schloter and Bernhard Mogge 1 Introduction ........................... 449 2 In Situ Studies of Microbial Communities Using Specific Fluorescence Labeling and Confocal Laser Scanning Microscopy .................. 451 2.1 Fluorescence in Situ Hybridization .............. 451 2.2 Immunofluorescence Labeling Combined with Fluorescence in Situ Hybridization .............. 453 2.3 Application of Fluorescence Tagging and Reporter Constructs ............................ 456 3 Ex Situ Studies of Microbial Communities After Separation of Rhizosphere Compartments ....... 457 3.1 Recovery of Bacteria from Bulk Soil, Ecto- and Endorhizosphere ........................ 457 3.2 Community Analysis by Cultivation and Dot Blot Studies . . 458 3.3 Community Analysis by Fluorescence in Situ Hybridization on Polycarbonate Filters ........ 460 3.4 Community Analysis by (RT) PCR- Amplification of Phylogenetic Marker Genes, D/TGGE-Fingerprinting and Clone Bank Studies ..................... 461 3.5 Community Analysis by Fatty Acid Pattern and Community Level Physiological Profile Studies ..... 463 4 Conclusions ........................... 463 References and Selected Reading ..................... 464 25 Methods for Analysing the Interactions Between Epiphyllic Microorganisms and Leaf Cuticles .............. 471 Daniel Knoll and Lukas Schreiber 1 Introduction ........................... 471 2 Physical Characterisation of Cuticle Surfaces by Contact Angle Measurements ................ 471 3 Chemical Characterisation of Cuticle Surfaces ........ 473 4 A New in Vitro System for the Study of Interactions Between Microbes and Cuticles ....... 475 XX Contents 4.1 Isolated Cuticles as Model Surfaces for Phyllosphere Studies 475 4.2 Enzymatic Isolation of Plant Cuticles ............. 476 4.3 The Experimental Set-Up of the System ............ 476 4.4 Inoculation of Cuticular Membranes with Epiphytic Microorganisms ................ 477 4.5 Measurement of Changes in Cuticular Transport Properties 479 4.6 Measuring Penetration of Microorganisms Through Cuticular Membranes ................ 481 4.7 Determination of the Viable Cell Number on the Cuticle Surface ...................... 483 4.8 Microscopic Visualisation of Microorganisms on the Cuticle 483 5 Conclusions ........................... 486 References and Selected Reading ..................... 486 26 Quantifying the Impact of ACC Deaminase-Containing Bacteria on Plants ........................ 489 Donna M. Penrose and Bernard R. Glick 1 Introduction ........................... 489 2 Selection of Bacterial Strains that Contain ACC Deaminase . 489 3 Culture Conditions for the Induction of Bacterial ACC Deaminase Activity ............. 491 4 Gnotobiotic Root Elongation Assay .............. 492 5 Measurement of ACC Deaminase Activity .......... 493 5.1 Assay of ACC Deaminase Activity in Bacterial Extracts . . . 494 6 Measurement of ACC in Plant Roots, Seed Tissues and Seed Exudates ....................... 495 6.1 Collection of Canola Seed Tissue and Exúdate During Germination ...................... 495 6.2 Preparation of Plant Extracts ................. 496 6.3 Protein Concentration Assay .................. 497 6.4 Measurement of ACC by HPLC ................. 498 References and Selected Reading ..................... 501 Contents XXI 27 Applications of Quantitative Microscopy in Studies of Plant Surface Microbiology ................. 503 Frank B. Dazzo 1 Introduction ........................... 503 2 Quantitation of Symbiotic Interactions Between Rhizobium and Legumes by Visual Counting Techniques . . 504 2.1 The Modified Fåhraeus Slide Culture Technique for Studies of the Root — Nodule Symbiosis .......... 504 2.2 Attachment of Rhizobia to Legume Root Hairs ........ 506 2.3 Rhizobium-lnduced Root Hair Deformations ........ 508 2.4 Primary Entry of Rhizobia into Legume Roots ........ 509 2.5 In Situ Molecular Interactions Between Legumes Roots and Surface-Colonizing Rhizobia ............ 511 2.6 Cross-Reactive Surface Antigens and Trifoliin A Host Lectin 511 2.7 Rhizobium Acidic Heteropolysaccharides ........... 513 2.8 Rhizobium Lipopolysaccharides ................ 516 2.9 Chitolipooligosaccharide Nod Factors ............ 518 2.10 Epidermal Pit Erosions ..................... 522 2.11 Elidtation of Root Hair Wall Peroxidase by Rhizobia .... 524 2.12 In Situ Gene Expression .................... 525 3 Quantitation of Symbiotic Interactions Between Rhizobium and Legumes by Image Analysis ......... 526 3.1 Definitive Elucidation of the Nature of Rhizobium Extracellular Microfibrils .................... 526 3.2 Rhizobial Modulation of Root Hair Cytoplasmic Streaming 527 3.3 Motility of Rhizobia in the External Root Environment . . . 527 3.4 Root Hair Alterations Affecting Their Dynamic Growth Extension and Primary Host Infection ........ 528 4 A Working Model for Very Early Stages of Root Hair Infection by Rhizobia ................... 529 5 Improvements in Specimen Preparation and Imaging Optics for Plant Rhizoplane Microbiology ..... 529 6 CMEIAS: A New Generation of Image Analysis Software for in Situ Studies of Microbial Ecology ...... 531 6.1 CMEIAS v. 1.27: Major Advancements in Bacterial Morphotype Classification ................... 531 6.2 CMEIAS v. 3.0: Comprehensive Image Analysis of Microbial Communities ................... 532 6.3 CMEIAS v. 3.0: Plotless and Plot-Based Spatial Distribution Analysis of Root Colonization .......... 533 6.4 CMEIAS v. 3.0: In Situ Analysis of Microbial Communities on Plant Phylloplanes .............. 535 XXII Contents 6.5 CMEIAS v. 3.0: In Situ Geostatistical Analysis of Root Colonization by Pioneer Rhizobacteria ....... 540 6.6 CMEIAS v. 3.0: Quantitative Autecological Biogeography of the Rhizobium-Blce Association .............. 541 6.7 CMEIAS v. 3.0: Spatial Scale Analysis of in Situ Quorum Sensing by Root-Colonizing Bacteria ........ 543 7 Conclusions ........................... 544 References and Selected Reading ..................... 544 28 Analysis of Microbial Population Genetics .......... 551 Emanuele G. Biondi, Alessio Mengoni and Marco Bazzicalupo 1 Introduction ........................... 551 2 Materials for RAPD,AFLP and ITS .............. 552 3 RAPD ............................... 553 4 AFLP ............................... 556 5 ITS-RFLP Analysis ....................... 559 6 Statistical analysis........................ 561 7 Concluding Remarks ...................... 563 References and Selected Reading ..................... 564 29 Functional Genomic Approaches for Studies of Mycorrhizal Symbiosis ................... 567 Gopi K. Podila and Luisa Lanfranco 1 Introduction ........................... 567 2 Material and Methods ...................... 568 2.1 Equipment ............................ 568 2.2 Biological Material ....................... 569 2.3 RNA Extraction ......................... 569 3 RNA Quantification ....................... 570 3.1 Construction of a cDNA Library ................ 570 4 Conversion Protocol ...................... 577 4.1 Evaluation of the Quality of the cDNA Library ........ 577 5 Troubleshooting ......................... 578 6 Sequencing Strategies ...................... 578 6.1 Data Analysis .......................... 579 6.2 Sequence Homology Comparisons .............. 579 Contents XXIII 6.3 Examples of Expressed Sequence Tag Data Analysis ..... 579 7 Macroarrays ........................... 582 7.1 PCR Amplification of cDNA Inserts .............. 582 7.2 Purification and Quantification of PCR Products ...... 583 7.3 Printing of Macroarrays .................... 583 7.4 Generation of Exponential cDNA Probes from RNA for Macroarrays and Hybridization Analysis ...... 584 7.5 Exponential Amplification of the sscDNAs .......... 585 8 Generation of Radiolabeled Probes .............. 585 9 Hybridization of Macroarrays to Radiolabeled Probes . . . 586 10 Data Analysis .......................... 586 10.1 Data Analysis Autoradiography Images on X-ray Films . . . 587 11 Example of Laccarla bicolor Macroarrays ........... 588 12 Conclusions ........................... 590 References and Selected Reading ..................... 591 30 Axenic Culture of Symbiotic Fungus Piriformospora indica 593 Giang Huong Pham, Rina Kumari, Anjana Singh, Rajani Malla, Ram Prasad, Minu Sachdev, Michael Kaldorf, Francois Buscot, Ralf Oelmuller, Rüdiger Hampp, Anil Kumar Saxena, Karl-Heinz Rexer, Gerhard Kost and Ajit Varma 1 Introduction ........................... 593 2 Morphology ........................... 593 3 Taxonomy of the Fungus .................... 595 4 Chlamydospore Formation and Germination ........ 597 5 Cultivation ............................ 597 6 Carbon and Energy Sources .................. 600 7 Biomass on Individual Amino Acids .............. 604 8 Growth on Complex Media ................... 604 9 Phosphatic Nutrients ...................... 605 10 Composition of Media ..................... 606 11 Conclusions ........................... 612 References and Selected Reading ..................... 612 Subject Index ................................ 615
adam_txt	Contents The State of the Art . AjiT Varma, Lynette K. Abbott, Dietrich Werner and Rüdiger Hampp Section A 2 Root Colonisation Following Seed Inoculation . 13 Thomas EC. Chin-A-Woeng and Ben J.J. Lugtenberg 1 Introduction . 13 2 Bacterial Root Colonisation . 13 3 Analysis of Tomato Root Tip Colonisation After Seed Inoculation Using a Gnotobiotic Assay . 14 3.1 Description of the Gnotobiotic System . 14 3.2 Seed Disinfection . 15 3.3 Growth and Preparation of Bacteria . 16 3.4 Seed Inoculation . 17 3.5 Analysis of the Tomato Root Tip . 17 3.6 Confocal Laser Scanning Microscopy . 18 4 Genetic Tools for Studying Root Colonisation . 18 4.1 Marking and Selecting Bacteria . 18 4.2 Rhizosphere-Stable Plasmids . 21 4.3 Genetic and Metabolic Burdens . 21 5 Behaviour of Root-Colonising Pseudomonas Bacteria in a Gnotobiotic System . 22 5.1 Colonisation Strategies of Bacteria . 22 5.2 Competitive Colonisation Studies . 23 5.3 Monocots versus Dicots . 25 6 Influence of Abiotic and Biotic Factors . 25 VIII Contents 6.1 Abiotic Factors . 25 6.2 Biotic Factors . 27 7 Conclusions . 28 References and Selected Reading . 28 3 Methanogenic Microbial Communities Associated with Aquatic Plants . 35 Ralf Conrad 1 Introduction . 35 2 Role of Plants in Emission of CH4 to the Atmosphere . 35 3 Role of Photosynthates and Plant Debris for CH4 Production 38 4 Methanogenic Microbial Communities on Plant Debris . 40 5 Methanogenic Microbial Communities on Roots . 42 6 Interaction of Methanogens and Methanotrophs . 44 References and Selected Reading . 45 4 Role of Functional Groups of Microorganisms on the Rhizosphere Microcosm Dynamics . 51 Galdino Andrade 1 Introduction . 51 2 General Aspects of Functional Groups of Soil Microorganisms . 52 3 Carbon Cycle Functional Groups . 53 4 Functional Groups of Microorganisms of the Nitrogen Cycle 55 5 Functional Groups of Microorganisms of the Sulphur Cycle 57 6 Functional Groups of Microorganisms of the Phosphorus Cycle . 59 7 Dynamics of the Rhizosphere Functional Groups of Microorganisms . 60 8 Relationship Among r and к Strategist Functional Groups . 61 9 Arbuscular Mycorrhizal Fungi Dynamics in the Rhizosphere . 61 10 Dynamics Among the Functional Micro-Organism Groups of the Carbon, Nitrogen, Phosphorus and Sulphur Cycles . . 65 References and Selected Reading . 68 Contents IX 5 Diversity and Functions of Soil Microflora in Development of Plants . 71 Ramesh CHandER Kuhad, David Manohar Kothamasi, K.K. Tripathi and Ajay Singh 1 Introduction . 71 2 Functional Diversity of Soil Microflora . 72 3 Role of Soil Microflora in Plant Development . 76 3.1 Mycorrhiza . 76 3.2 Actinorhiza . 80 3.3 Plant Growth-Promoting Rhizobacteria . 82 3.4 Phosphate-Solubilizing Microorganisms . 84 3.5 Lignocellulolytic Microorganisms . 85 4 Plant Growth Promoting Substances Produced by Soil Microbes . 88 5 Conclusions . 90 References and Selected Reading . 91 6 Signalling in the Rhizobia-Legumes Symbiosis . 99 Dietrich Werner 1 Introduction . 99 2 The Signals from the Host Plants . 101 2.1 Phenylpropanoids: Simple Phenolics, Flavonoids and Isoflavonoids . 102 2.2 Metabolization of Flavonoids and Isoflavonoids . 104 2.3 Vitamins as Growth Factors and Signal Molecules . 106 3 Signals from the Microsymbionts . 107 3.1 Nod Factors . 107 3.2 Cyclic Glucans . 109 3.3 Lipopolysaccharides . 110 3.4 Exopolysaccharides . 110 4 Signal Perception and Molecular Biology of Nodule Initiation . Ill References and Selected Reading . 114 X Contents Section В 7 The Functional Groups of Micro-organisms Used as Bio-indicator on Soil Disturbance Caused by Biotech Products such as Bacillus thuringiensis and Bt Transgenic Plants . 121 Galdino Andrade 1 Introduction . 121 2 General Aspects of Bacillus thuringiensis . 122 3 Survival in the Soil . 123 4 History of Bacillus thuringiensis-Tramgmic Plants . 124 5 Persistence of the Protein Crystal in the Soil . 125 6 Effect of Bacillus thuringiensis and Its Bio-insecticide Protein on Functional Soil Microorganism Assemblage . . . 126 References and Selected Reading . 130 8 The Use of ACC Deaminase-Containing Plant Growth-Promoting Bacteria to Protect Plants Against the Deleterious Effects of Ethylene . 133 Bernard R. Glick and Donna M. Penrose 1 Introduction . 133 2 Ethylene . 134 3 ACCDeaminase . 135 3.1 Treatment of Plants with ACC Deaminase Containing Bacteria . 137 4 Conclusions . 140 References and Selected Reading . 141 9 Interactions Between Epiphyllic Microorganisms and Leaf Cuticles . 145 Lukas Schreiber, Ursula Krimm and Daniel Knoll 1 Introduction . 145 2 Physical and Chemical Parameters of the Phyllosphere . 147 3 Leaf Surface Colonisation and Species Composition . 149 4 Alteration of Leaf Surface Wetting . 150 5 Interaction of Bacteria with Isolated Plant Cuticles . 152 6 Conclusions . 153 References and Selected Reading . 154 Contents XI 10 Developmental Interactions Between Clavidpitaleans and Their Host Plants . 157 James E White Jr., Faith Belanger, Raymond Sullivan, Elizabeth Lewis, Melinda Μου, William Meyer and Charles W. Bacon 1 Introduction . 157 2 Endophyte/Epibiont Niche . 157 3 Coevolution of Clavicipitalean Fungi with Grass Hosts . . . 158 4 The Jump from Insects to Plants . 158 4.1 Trans-Kingdom Jump . 158 4.2 Intermediate Stages in the Transition to Plants . 158 4.3 Parasitism of Grass Meristematic Tissues . 160 5 Developmental Differentiation of Endophytic and Epiphyllous Mycelium . 160 5.1 Plant Cell Wall Alteration . 160 5.2 Endophytic Mycelial Growth . 160 5.3 Control of Endophytic Mycelial Development . 163 5.4 Epiphyllous Mycelial Development . 163 5.5 Expression of Fungal Secreted Hydrolytic Enzymes in Infected Plants . 164 6 Modifications of Plant Tissues for Nutrient Acquisition . . . 165 6.1 Development of the Stroma in Epichloë . 165 6.2 Stroma Development in Myriogenospora . 166 6.3 Mechanisms for Modifying Plant Tissues . 168 6.4 Evaporative-Flow Mechanism for Nutrient Acquisition . . . 169 6.5 The Cytokinin Induction Hypothesis . 169 7 Evolution of Asexual Derivatives of Epichloë . 171 7.1 Reproduction and Loss of Sexual Reproduction . 171 7.2 The Hypotheses . 172 7.3 The Process of Stroma Development and its Loss . 173 7.4 The Shift from Pathogen to Mutualist . 174 8 Conclusions . 174 References and Selected Reading . 174 11 Interactions of Microbes with Genetically Modified Plants . 179 Michael Kaldorp, Chi Zhang, Uwe Nehls, Rüdiger Hampp and François Buscot 1 Introduction . 179 2 Changes in Microbial Communities Induced by Genetically Modified Plants . 181 XII Contents 3 Impact of Genetically Modified Plants on Symbiotic Interactions . 184 4 Horizontal Gene Transfer . 186 5 Conclusions . 191 References and Selected Reading . 192 Section С 12 Interaction Between Soil Bacteria and Ectomycorrhiza-Forming Fungi . 197 Rüdiger Hampp and AndREAS Maier 1 Introduction . 197 2 Bacteria . 198 3 Bacterial Community Structure . 198 4 Association of Bacteria with Fungal/Ectomycorrhizal Structures . 199 5 Bacteria Associated with Sporocarps and Ectomycorrhiza . 200 6 Benefits from Bacteria/Ectomycorrhiza Interactions . 201 7 Possible Mechanisms of Interaction . 202 8 Biochemical Evidence for Interaction . 203 9 Impacts of Environmental Pollution . 206 10 Conclusions . 206 References and Selected Reading . 207 13 The Surface of Ectomycorrhizal Roots and the Interaction with Ectomycorrhizal Fungi . 211 Ingrid Kottke 1 Introduction . 211 2 Long and Short Roots of Ectomycorrhiza-Forming Plants . 212 3 A Cuticle-Like Layer on the Surface of Short Roots . 214 4 Involvement of the Cuticle-Like Layer in Mycorrhiza Formation . 218 5 Involvement of the Cuticle-Like Layer in Hyphal Attachment 218 6 Digestion of the Suberin Layer and the Cell Wall of the Root Cap . 220 7 Hartig Net Formation . 221 8 Pectins in the Cortical Cell Walls of Nonmycorrhizal Long and Mycorrhizal Short Roots . 222 9 Conclusions . 223 References and Selected Reading . 224 Contents XIII 14 Cellular Ustilaginomycete — Plant Interactions . 227 Robert Bauer and Franz Oberwinkler 1 Introduction . 227 2 The Term Smut Fungus . 227 3 Life Cycle . 228 4 Hosts . 228 5 Cellular Interactions . 229 5.1 Local Interaction Zones . 230 5.2 Enlarged Interaction Zones . 234 6 Conclusions . 235 References and Selected Reading . 236 15 Interaction of Piriformospora indica with Diverse Microorganisms and Plants . 237 Giang Huong Pham, Anjana Singh, Rajani Malla, Rina Kumari, , Ram Prasad, Minu Sachdev, Karl-Heinz Rexer, Gerhard Kost, Patricia Luis, Michael Kaldorf, François Buscot, Sylvie Herrmann, Tanja Peskan, Ralf Oelmüller, Anil Kumar Saxena, Stephane Declerck, Maria Mittag, Edith Stabentheiner, Solveig Hehl and Ajit Varma 1 Introduction . 237 2 Interaction with Microorganisms . 238 2.1 Rhizobacteria . 238 2.2 Chlamydomonas reinhardtii . 239 2.3 Sebacina vermifera . 239 2.4 Other Soil Fungi . 240 2.5 Gaeumannomyces graminis . 240 3 Interaction with Bryophyte . 242 4 Interaction with Higher Plants . 242 4.1 Monocots . 245 4.2 Legumes . 245 4.3 Orchids . 246 4.4 Medicinal Plants . 247 4.5 Economically Important Plants . 249 4.6 Timber Plants . 252 4.7 Unexpected Interactions with Wild Type and Genetically Modified Populus Plants . 253 4.8 Nonmycorrhizal Plants . 255 XIV Contents 4.9 Arabidopsis thaliana . 256 4.10 Root Organ Culture. 259 5 Cell Wall Degrading Enzymes . 260 6 Conclusions . 263 References and Selected Reading . 264 16 Cellular Basidiomycete-Fungus Interactions . 267 Robert Bauer and Franz Oberwinkler 1 Introduction . 267 2 Occurrence of Mycoparasites Within the Basidiomycota . . 267 3 Hosts . 268 4 Cellular Interactions . 268 4.1 Colacosome-Interactions . 268 4.2 Fusion-Interaction . 275 5 Basidiomycetous Mycoparasitism, a Result of Convergent Evolution? . 277 6 Conclusions . 278 References and Selected Reading . 278 Section D 17 Fungal Endophytes . 281 Sita R. Ghimire and Kevin D. Hyde 1 Introduction . 281 2 Definition of a Fungal Endophyte . 281 3 Role of Endophytes . 282 4 Modes of Endophytic Infection and Colonization . 283 5 Isolation of Endophytes . 284 6 Molecular Characterization of Endophytes . 285 7 Are Endophytes Responsible for Host Exclusivity/ Recurrence in Saprobic Fungi? . 286 8 Conclusions . 287 References and Selected Reading . 288 Contents XV 18 Mycorrhizal Development and Cytoskeleton . 293 Marjatta Raudaskoski, Mika Tarkka and Sara Niini 1 Introduction . 293 2 Cytoskeletal Components . 293 2.1 Expression of Tubulin-Encoding Genes. 294 2.2 Expression of Actin-Encoding Genes . 297 3 Organization of Cytoskeleton in Endomycorrhiza. 298 3.1 Root Cells . 298 3.2 Fungal Hyphae . 300 4 Organization of Cytoskeleton in Ectomycorrhiza . 300 4.1 Root Cells . 300 4.2 Fungal Hyphae . 304 5 Regulation of Actin Cytoskeleton Organization in Fungal Hyphae and Plant Cells . 305 6 Actin Binding-Proteins . 307 7 Microtubule-Associated Proteins . 308 7.1 Plant Cells . 308 7.2 Fungal Hyphae . 310 8 Cell Cycle and Cytoskeleton in Mycorrhiza . 313 9 Cytoskeletal Research Methods . 315 9.1 Indirect Immunofluorescence Microscopy . 316 9.2 Microinjection Method . 317 9.3 Green Fluorescence Protein Technique . 317 References and Selected Reading . 318 19 Functional Diversity of Arbuscular Mycorrhizal Fungi on Root Surfaces . 331 M. Zakaria Solaiman and Lynette K. Abbott 1 Introduction . 331 2 Mycorrhiza Formation and Ecological Specificity . 332 2.1 Establishment of the Symbiosis . 333 2.2 Spore Germination and Hyphal Growth . 333 2.3 Role of Plant Root Exudates . 333 3 Functioning of Arbuscular Mycorrhizas in Nutrient Exchange . 334 3.1 Metabolic Activity During Mycorrhiza Formation . 335 3.2 Gene Expression During Mycorrhiza Formation . 336 3.3 Nutrient Exchange Mechanisms in Arbuscular Mycorrhizas 336 4 Functional Diversity of Arbuscular Mycorrhizal Fungi in Root and Hyphal Interactions . 338 XVI Contents 4.1 Diversity of Arbuscular Mycorrhizal Fungi Inside Roots . . 339 4.2 Relationship Between Hyphae in the Root and in the Soil . . 340 5 Role of Arbuscular Mycorrhizal Fungi Associated with Roots in Soil Aggregation . 340 6 Environmental Influence on Functional Diversity of Arbuscular Mycorrhizal Fungi . 341 7 Role of Plant Mutants in Studying the Interactions Between Arbuscular Mycorrhizal Fungi and Roots . 341 8 Conclusion and Future Research Needs . 343 References and Selected Reading . 343 20 Mycorrhizal Fungi and Plant Growth Promoting Rhizobacteria . 351 José-Miguel Barba, Rosario Azcón and Concepción Azcón-Aguilar 1 Introduction . 351 2 Main Types of Rhizosphere Microorganisms . 352 3 Mycorrhizal Fungi . 353 4 Plant Growth Promoting Rhizobacteria . 354 5 Reasons for Studying Arbuscular Mycorrhizal Fungi and Plant Growth Promoting Rhizobacteria Interactions and Main Scenarios . 356 6 Effect of Plant Growth Promoting Rhizobacteria on Mycorrhiza Formation . 357 7 Effect of Mycorrhizas on the Establishment of Plant Growth Promoting Rhizobacteria in the Rhizosphere . 357 8 Interactions Involved in Nutrient Cycling and Plant Growth Promotion . 359 9 Interactions for the Biological Control of Root Pathogens . . 361 References and Selected Reading . 362 21 Carbohydrates and Nitrogen: Nutrients and Signals in Ectomycorrhizas . 373 Uwe Nehls 1 Introduction . 373 2 Trehalose Utilization by Ectomycorrhizal Fungi . 374 3 Carbohydrate Uptake . 374 4 Carbohydrate Metabolism . 376 5 Carbohydrate Storage . 376 Contents XVII 6 Carbohydrates as Signal, Regulating Fungal Gene Expression in Ectomycorrhizas . 377 7 Nitrogen . 380 8 Utilization of Inorganic Nitrogen . 381 9 Utilization of Organic Nitrogen . 382 10 Proteolytic Activities of Ectomycorrhizal Fungi . 383 11 Uptake of Amino Acids . 383 12 Regulation of Fungal Nitrogen Export in Mycorrhizas by the Nitrogen-Status of Hyphae . 385 13 Carbohydrate and Nitrogen-Dependent Regulation of Fungal Gene Expression . 385 14 Conclusions . 385 References and Selected Reading . 386 22 Nitrogen Transport and Metabolism in Mycorrhizal Fungi and Mycorrhizas . 393 Arnaud Javelle, Michel Chalot, Annick Brun and Bernard Botton 1 Introduction . 393 1.1 Ecological Significance of Ectomycorrhizas . 393 1.2 Nitrogen Uptake and Translocation by Ectomycorrhizas . . 394 2 Nitrate and Nitrite Transport . 395 2.1 Uptake Kinetics . 395 2.2 Characterization of Nitrate and Nitrite Transporters . 395 3 Ammonium Transport . 398 3.1 Physico-Chemical Properties of Ammonium: Active Uptake Versus Diffusion . 398 3.2 Physiology of Ammonium Transport in Ectomycorrhizas . . 399 3.3 Isolation of Ammonium Transporter Genes . 400 3.4 Regulation of the Ammonium Transporters . 400 3.5 Other Putative Functions of Ammonium Transporters . . . 402 4 Amino Acid Transport . 403 4.1 Utilization of Amino Acids by Ectomycorrhizal Partners . . 403 4.2 Molecular Regulation of Amino Acid Transport . 404 5 Reduction of Nitrate to Nitrite and Ammonium . 405 5.1 Reduction of Nitrate to Nitrite . 405 5.2 Reduction of Nitrite to Ammonium . 406 5.3 Molecular Characterization of Nitrate Reductase and Nitrite Reducíase . 406 6 Assimilation of Ammonium . 409 6.1 Role and Properties of Glutamate Dehydrogenase . 410 XVIII Contents 6.2 Role and Properties of Glutaminę Synthetase . 413 6.3 Role and Properties of Glutamate Synthase . 415 7 Amino Acid Metabolism . 417 7.1 Utilization of Proteins by Ectomycorrhizal Fungi and Ectomycorrhizas . 417 7.2 Amino Acids Used as Nitrogen and Carbon Sources . 418 8 Conclusion and Future Prospects . 419 References and Selected Reading . 421 Section E 23 Visualisation of Rhizosphere Interactions of Pseudomonas and ВасШкѕ Biocontrol Strains . 431 Thomas F.C. Chin-A- Wo eng, Anastasia L. Lagopodi, Ine H.M. Mulders, Guido V. Bloemberg and Ben J.J. Lugtenberg 1 Introduction . 431 2 Tomato Foot and Root Rot and the Need for Biological Control . 431 3 Selection of Antagonistic Strains . 432 3.1 Selection of Antagonistic Pseudomonas and Bacillus sç. . . . 432 3.2 In Vitro Antifungal Activity Test . 434 4 In Vivo Biocontrol Assays . 434 4.1 Fusarium oxysporum — Tomato Biocontrol Assay in a Potting Soil System . 434 4.2 Gnotobiotic Fusarium oxysporum-Pythium ultimum and Rhizoctonia solani-Tomato Bioassays . 435 5 Microscope Analysis of Infection and Biocontrol . 435 5.1 Marking Fungi with Autofluorescent Proteins . 437 5.2 Marking Rhizosphere Bacteria with Autofluorescent Proteins . 438 5.3 Confocal Laser Scanning Microscopy of Rhizosphere Interactions . 442 6 Conclusions . 443 References and Selected Reading . 443 Contents XIX 24 Microbial Community Analysis in the Rhizosphere by in Situ and ex Situ Application of Molecular Probing, Biomarker and Cultivation Techniques . 449 Anton Hartmann, Rüdiger Pukall, Michael Rothballes, Stephan Gantner, SiGRUN Metz, Michael Schloter and Bernhard Mogge 1 Introduction . 449 2 In Situ Studies of Microbial Communities Using Specific Fluorescence Labeling and Confocal Laser Scanning Microscopy . 451 2.1 Fluorescence in Situ Hybridization . 451 2.2 Immunofluorescence Labeling Combined with Fluorescence in Situ Hybridization . 453 2.3 Application of Fluorescence Tagging and Reporter Constructs . 456 3 Ex Situ Studies of Microbial Communities After Separation of Rhizosphere Compartments . 457 3.1 Recovery of Bacteria from Bulk Soil, Ecto- and Endorhizosphere . 457 3.2 Community Analysis by Cultivation and Dot Blot Studies . . 458 3.3 Community Analysis by Fluorescence in Situ Hybridization on Polycarbonate Filters . 460 3.4 Community Analysis by (RT) PCR- Amplification of Phylogenetic Marker Genes, D/TGGE-Fingerprinting and Clone Bank Studies . 461 3.5 Community Analysis by Fatty Acid Pattern and Community Level Physiological Profile Studies . 463 4 Conclusions . 463 References and Selected Reading . 464 25 Methods for Analysing the Interactions Between Epiphyllic Microorganisms and Leaf Cuticles . 471 Daniel Knoll and Lukas Schreiber 1 Introduction . 471 2 Physical Characterisation of Cuticle Surfaces by Contact Angle Measurements . 471 3 Chemical Characterisation of Cuticle Surfaces . 473 4 A New in Vitro System for the Study of Interactions Between Microbes and Cuticles . 475 XX Contents 4.1 Isolated Cuticles as Model Surfaces for Phyllosphere Studies 475 4.2 Enzymatic Isolation of Plant Cuticles . 476 4.3 The Experimental Set-Up of the System . 476 4.4 Inoculation of Cuticular Membranes with Epiphytic Microorganisms . 477 4.5 Measurement of Changes in Cuticular Transport Properties 479 4.6 Measuring Penetration of Microorganisms Through Cuticular Membranes . 481 4.7 Determination of the Viable Cell Number on the Cuticle Surface . 483 4.8 Microscopic Visualisation of Microorganisms on the Cuticle 483 5 Conclusions . 486 References and Selected Reading . 486 26 Quantifying the Impact of ACC Deaminase-Containing Bacteria on Plants . 489 Donna M. Penrose and Bernard R. Glick 1 Introduction . 489 2 Selection of Bacterial Strains that Contain ACC Deaminase . 489 3 Culture Conditions for the Induction of Bacterial ACC Deaminase Activity . 491 4 Gnotobiotic Root Elongation Assay . 492 5 Measurement of ACC Deaminase Activity . 493 5.1 Assay of ACC Deaminase Activity in Bacterial Extracts . . . 494 6 Measurement of ACC in Plant Roots, Seed Tissues and Seed Exudates . 495 6.1 Collection of Canola Seed Tissue and Exúdate During Germination . 495 6.2 Preparation of Plant Extracts . 496 6.3 Protein Concentration Assay . 497 6.4 Measurement of ACC by HPLC . 498 References and Selected Reading . 501 Contents XXI 27 Applications of Quantitative Microscopy in Studies of Plant Surface Microbiology . 503 Frank B. Dazzo 1 Introduction . 503 2 Quantitation of Symbiotic Interactions Between Rhizobium and Legumes by Visual Counting Techniques . . 504 2.1 The Modified Fåhraeus Slide Culture Technique for Studies of the Root — Nodule Symbiosis . 504 2.2 Attachment of Rhizobia to Legume Root Hairs . 506 2.3 Rhizobium-lnduced Root Hair Deformations . 508 2.4 Primary Entry of Rhizobia into Legume Roots . 509 2.5 In Situ Molecular Interactions Between Legumes Roots and Surface-Colonizing Rhizobia . 511 2.6 Cross-Reactive Surface Antigens and Trifoliin A Host Lectin 511 2.7 Rhizobium Acidic Heteropolysaccharides . 513 2.8 Rhizobium Lipopolysaccharides . 516 2.9 Chitolipooligosaccharide Nod Factors . 518 2.10 Epidermal Pit Erosions . 522 2.11 Elidtation of Root Hair Wall Peroxidase by Rhizobia . 524 2.12 In Situ Gene Expression . 525 3 Quantitation of Symbiotic Interactions Between Rhizobium and Legumes by Image Analysis . 526 3.1 Definitive Elucidation of the Nature of Rhizobium Extracellular Microfibrils . 526 3.2 Rhizobial Modulation of Root Hair Cytoplasmic Streaming 527 3.3 Motility of Rhizobia in the External Root Environment . . . 527 3.4 Root Hair Alterations Affecting Their Dynamic Growth Extension and Primary Host Infection . 528 4 A Working Model for Very Early Stages of Root Hair Infection by Rhizobia . 529 5 Improvements in Specimen Preparation and Imaging Optics for Plant Rhizoplane Microbiology . 529 6 CMEIAS: A New Generation of Image Analysis Software for in Situ Studies of Microbial Ecology . 531 6.1 CMEIAS v. 1.27: Major Advancements in Bacterial Morphotype Classification . 531 6.2 CMEIAS v. 3.0: Comprehensive Image Analysis of Microbial Communities . 532 6.3 CMEIAS v. 3.0: Plotless and Plot-Based Spatial Distribution Analysis of Root Colonization . 533 6.4 CMEIAS v. 3.0: In Situ Analysis of Microbial Communities on Plant Phylloplanes . 535 XXII Contents 6.5 CMEIAS v. 3.0: In Situ Geostatistical Analysis of Root Colonization by Pioneer Rhizobacteria . 540 6.6 CMEIAS v. 3.0: Quantitative Autecological Biogeography of the Rhizobium-Blce Association . 541 6.7 CMEIAS v. 3.0: Spatial Scale Analysis of in Situ Quorum Sensing by Root-Colonizing Bacteria . 543 7 Conclusions . 544 References and Selected Reading . 544 28 Analysis of Microbial Population Genetics . 551 Emanuele G. Biondi, Alessio Mengoni and Marco Bazzicalupo 1 Introduction . 551 2 Materials for RAPD,AFLP and ITS . 552 3 RAPD . 553 4 AFLP . 556 5 ITS-RFLP Analysis . 559 6 Statistical analysis. 561 7 Concluding Remarks . 563 References and Selected Reading . 564 29 Functional Genomic Approaches for Studies of Mycorrhizal Symbiosis . 567 Gopi K. Podila and Luisa Lanfranco 1 Introduction . 567 2 Material and Methods . 568 2.1 Equipment . 568 2.2 Biological Material . 569 2.3 RNA Extraction . 569 3 RNA Quantification . 570 3.1 Construction of a cDNA Library . 570 4 Conversion Protocol . 577 4.1 Evaluation of the Quality of the cDNA Library . 577 5 Troubleshooting . 578 6 Sequencing Strategies . 578 6.1 Data Analysis . 579 6.2 Sequence Homology Comparisons . 579 Contents XXIII 6.3 Examples of Expressed Sequence Tag Data Analysis . 579 7 Macroarrays . 582 7.1 PCR Amplification of cDNA Inserts . 582 7.2 Purification and Quantification of PCR Products . 583 7.3 Printing of Macroarrays . 583 7.4 Generation of Exponential cDNA Probes from RNA for Macroarrays and Hybridization Analysis . 584 7.5 Exponential Amplification of the sscDNAs . 585 8 Generation of Radiolabeled Probes . 585 9 Hybridization of Macroarrays to Radiolabeled Probes . . . 586 10 Data Analysis . 586 10.1 Data Analysis Autoradiography Images on X-ray Films . . . 587 11 Example of Laccarla bicolor Macroarrays . 588 12 Conclusions . 590 References and Selected Reading . 591 30 Axenic Culture of Symbiotic Fungus Piriformospora indica 593 Giang Huong Pham, Rina Kumari, Anjana Singh, Rajani Malla, Ram Prasad, Minu Sachdev, Michael Kaldorf, Francois Buscot, Ralf Oelmuller, Rüdiger Hampp, Anil Kumar Saxena, Karl-Heinz Rexer, Gerhard Kost and Ajit Varma 1 Introduction . 593 2 Morphology . 593 3 Taxonomy of the Fungus . 595 4 Chlamydospore Formation and Germination . 597 5 Cultivation . 597 6 Carbon and Energy Sources . 600 7 Biomass on Individual Amino Acids . 604 8 Growth on Complex Media . 604 9 Phosphatic Nutrients . 605 10 Composition of Media . 606 11 Conclusions . 612 References and Selected Reading . 612 Subject Index . 615
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id	DE-604.BV035007671
illustrated	Illustrated
index_date	2024-07-02T21:42:47Z
indexdate	2024-07-09T21:20:04Z
institution	BVB
isbn	9783540740506
language	English
oai_aleph_id	oai:aleph.bib-bvb.de:BVB01-016676967
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physical	XXXI, 628 S. Ill., graph. Dars.
publishDate	2008
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publisher	Springer
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spelling	Plant surface microbiology Ajit Varma ... (eds.) [Taschenbuch-Ausg.] Berlin [u.a.] Springer 2008 XXXI, 628 S. Ill., graph. Dars. txt rdacontent n rdamedia nc rdacarrier Plant surfaces Microbiology Mikrobiologie (DE-588)4316357-9 gnd rswk-swf Pflanzen (DE-588)4045539-7 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Pflanzen (DE-588)4045539-7 s Mikrobiologie (DE-588)4316357-9 s DE-604 Varma, Ajit 1939- Sonstige (DE-588)120066718 oth Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016676967&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Plant surface microbiology Plant surfaces Microbiology Mikrobiologie (DE-588)4316357-9 gnd Pflanzen (DE-588)4045539-7 gnd
subject_GND	(DE-588)4316357-9 (DE-588)4045539-7 (DE-588)4143413-4
title	Plant surface microbiology
title_auth	Plant surface microbiology
title_exact_search	Plant surface microbiology
title_exact_search_txtP	Plant surface microbiology
title_full	Plant surface microbiology Ajit Varma ... (eds.)
title_fullStr	Plant surface microbiology Ajit Varma ... (eds.)
title_full_unstemmed	Plant surface microbiology Ajit Varma ... (eds.)
title_short	Plant surface microbiology
title_sort	plant surface microbiology
topic	Plant surfaces Microbiology Mikrobiologie (DE-588)4316357-9 gnd Pflanzen (DE-588)4045539-7 gnd
topic_facet	Plant surfaces Microbiology Mikrobiologie Pflanzen Aufsatzsammlung
url	http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016676967&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA
work_keys_str_mv	AT varmaajit plantsurfacemicrobiology

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