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Transcriptional Profiling of Bacillus Amyloliquefaciens FZB42 in Response to Seed and Root Exudates Collected Under Different Nutrient Regimes

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Transcriptional Profiling of Bacillus Amyloliquefaciens FZB42 in Response to Seed and Root Exudates Collected Under Different Nutrient Regimes Institute of Plant Nutrition University of Hohenheim Prof. Dr. N. von Wirén Transcriptional profiling of Bacillus amyloliquefaciens FZB42 in response to seed and root exudates collected under different nutrient regimes Dissertation submitted in fulfillment of the requirements for the degree “Doktor der Agrarwissenschaften” (Dr. Sc. Agr. / Ph. D. in Agricultural Sciences) to the Faculty of Agricultural Sciences of the University of Hohenheim presented by Lília Costa Carvalhais from Belo Horizonte, Minas Gerais, Brazil 2010 This thesis was accepted as a doctoral dissertation in fulfillment of the requirements for the degree “Doktor der Agrarwissenschaften” by the Faculty of Agricultural Sciences at the University of Hohenheim. Date of oral examination: 12th July 2010 Examination Committee Supervisor and reviewer Prof. Dr. Nicolaus von Wirén Co-reviewer Prof. Dr. Ellen Kandeler Additional examiner, vice dean and head of the committee Prof. Dr. Andreas Fangmeier I TABLE OF CONTENTS 1. Summary / Zusammenfassung..................................................................................... 1 1.1. Summary...................................................................................................................... 1 1.2. Zusammenfassung ....................................................................................................... 3 2. General Introduction.................................................................................................... 5 2.1. Plant-bacteria interactions............................................................................................ 5 2.2. Root-derived compounds and mechanisms for their release ....................................... 7 2.3. Essential elements in plant nutrition and their functions............................................. 8 2.4. Effect of nutrient deficiencies on the release of root exudates.................................... 9 2.5. Plant-associated bacteria - their effect on plants and use in agriculture.................... 11 2.6. The advantage of microarray analysis for the investigation of plant-bacteria associations ................................................................................................................ 13 2.7. Aims of the thesis ...................................................................................................... 15 3. Material and methods................................................................................................. 17 3.1. Sterilization of maize seeds ....................................................................................... 17 3.2. Plant growth conditions ............................................................................................. 17 3.3. Seed exudates collection............................................................................................ 18 3.4. Root exudate collection ............................................................................................. 18 3.5. Chemical analyses of root exudates........................................................................... 19 3.6. Statistical analysis of seed and root exudates constituents........................................ 20 3.7. Transcriptional profiling experiments ....................................................................... 21 3.7.1. Incubation of cells with seed and root exudates .................................................. 21 3.7.2. RNA purification and labeling of cDNA, hybridization and image acquisition. 22 3.7.3. Microarray Data analysis..................................................................................... 22 3.7.4. Multivariate analysis of microarray experiments ................................................ 23 3.7.5. Real-time PCR..................................................................................................... 24 4. Results........................................................................................................................ 25 4.1. Characterization of metabolites in seed and root exudates........................................ 25 4.2. Seed exudates affected greater levels of bacterial transcripts than root exudates ..... 27 II 4.2.1. Transcriptional profiling of B. amyloliquefaciens FZB42 in response to seed exudates ............................................................................................................... 28 4.2.1.1. Differentially expressed genes in the logarithmic phase (OD 1.0)............. 28 4.2.1.2. Differentially expressed genes in the transitional phase (OD 3.0) ............. 29 4.2.2. Transcriptional profiling of B. amyloliquefaciens FZB42 in response to root exudates ............................................................................................................... 31 4.2.2.1. Differentially expressed genes in the logarithmic phase (OD 1.0)............. 31 4.2.2.2. Differentially expressed genes at the transitional phase (OD 3.0) ............. 31 4.2.3. Shared bacterial transcripts in response to seed and root exudates collected from maize plants grown under optimal nutritional conditions........................... 33 4.2.4. Between Group Analysis comparing bacterial transcriptional responses to seed and root exudates ......................................................................................... 34 4.3. Specific responses to nutritional deficiencies in root exudates ................................. 37 4.3.1. General responses in root exudation to nutrient deficiencies .............................. 38 4.3.2. A possible relationship between root exudation and the diffusion coefficient of nutrients in soils............................................................................................... 40 4.4. Different nutritional deficiencies distinctively affect the transcriptome of Bacillus amyloliquefaciens FZB42.......................................................................................... 41 4.4.1. Transcriptional profile of B. amyloliquefaciens FZB42 in response to nitrogen-deficient maize root exudates................................................................ 42 4.4.1.1. Differentially expressed genes in the logarithmic phase (OD 1.0)............. 42 4.4.1.2. Differentially expressed genes in the transitional phase (OD3.0) .............. 43 4.4.2. Transcriptional profile of B. amyloliquefaciens FZB42 in response to phosphorus-deficient maize root exudates........................................................... 44 4.4.2.1. Differentially expressed genes in the logarithmic phase (OD 1.0)............. 44 4.4.2.2. Differentially expressed genes in the transitional phase (OD 3.0) ............. 45 4.4.3. Transcriptional profile of B. amyloliquefaciens FZB42 in response to iron- deficient maize root exudates .............................................................................. 47 4.4.3.1. Differentially expressed genes in the logarithmic phase (OD 1.0)............. 47 4.4.3.2. Differentially expressed genes in the transitional phase (OD 3.0) ............. 47 4.4.4. Transcriptional profile of B. amyloliquefaciens FZB42 in response to potassium-deficient maize root exudates............................................................. 48 4.4.4.1. Differentially expressed genes in the logarithmic phase (OD 1.0)............. 48 4.4.4.2. Differentially expressed genes in the transitional phase (OD 3.0) ............. 48 III 4.4.5. Shared bacterial transcripts in response to root exudates collected from maize plants grown under different nutritional deficiencies.......................................... 50 4.4.5.1. Logarithmic phase (OD 1.0) – up-regulated genes..................................... 50 4.4.5.2. Transitional phase – up-regulated genes..................................................... 50 4.4.5.3. Transitional phase – down-regulated genes................................................ 51 4.4.6. Real time for validation of the microarray analysis............................................. 54 4.4.7. Between group analysis to identify the most discriminating genes between deficiency treatments ........................................................................................... 54 4.4.8. Interpretation of changes in gene expression using the chemical composition of root exudates.................................................................................................... 58 5. General Discussion.................................................................................................... 60 5.1. Transcriptional responses of B. amyloliquefaciens to seed and root exudates reflect bacterial adaptations to altered substrate and ion availabilities...................... 60 5.2. Nutrient deficiencies affect the composition of primary metabolites in maize root exudates ..................................................................................................................... 65 5.3. Root exudates from nutrient-deficient plants affect differently the transcriptome of Bacillus amyloliquefaciens FZB42........................................................................ 69 5.4. Correlation between metabolite composition of root exudates and bacterial gene expression .................................................................................................................. 77 6. REFERENCES .......................................................................................................... 80 7. APPENDIX...............................................................................................................
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