Host Preferences and Pathogenomics of Pseudomonas fuscovaginae in Australia Kankanthri Nirodha Sandeepani Weeraratne B.Sc. Agriculture (Hons.) A thesis submitted to Charles Sturt University, Australia for the degree of Doctor of Philosophy December 2017 School of Agricultural and Wine Sciences Faculty of Science Charles Sturt University Table of Contents List of Figures .............................................................................................................. VII List of Tables .................................................................................................................. X Certificate of Authorship ............................................................................................ XII Acknowledgements .................................................................................................... XIII Abstract ............................................................................................................................ 1 Chapter 1. Introduction and Literature Review .......................................................... 6 1.1. Important bacterial diseases of rice ................................................................ 7 1.2. Sheath rot diseases of rice ................................................................................ 9 1.2.1. Symptoms and Diagnosis ............................................................................ 9 1.2.2. Diversity of causal organisms ................................................................... 10 1.2.3. Economic impact and global distribution of the disease ........................... 11 1.2.4. Control ...................................................................................................... 13 1.3. Burkholderia glumae ....................................................................................... 16 1.3.1. Characteristics ........................................................................................... 16 1.3.2. Symptoms and diagnosis ........................................................................... 17 1.3.3. Pathogenicity and virulence ...................................................................... 17 1.3.4. Host range ................................................................................................. 18 1.3.5. Control ...................................................................................................... 19 1.4. Acidovorax avenae ssp. avenae ....................................................................... 20 1.4.1. Characteristics ........................................................................................... 20 1.4.2. Symptoms and diagnosis ........................................................................... 20 1.4.3. Pathogenicity and virulence ...................................................................... 21 1.4.4. Host range ................................................................................................. 22 1.4.5. Control ...................................................................................................... 23 1.5. Pantoea ananatis ............................................................................................. 23 1.5.1. Characteristics ........................................................................................... 24 1.5.2. Symptoms and diagnosis ........................................................................... 24 1.5.3. Pathogenicity and virulence ...................................................................... 25 1.5.4. Host range ................................................................................................. 26 1.5.5. Control ...................................................................................................... 27 II 1.6. Pseudomonas fuscovaginae ............................................................................. 27 1.6.1. Classification and nomenclature ............................................................... 28 1.6.2. Morphological and physiological characteristics ...................................... 28 1.6.3. Disease symptoms and diagnostics ........................................................... 29 1.6.4. Epidemiology ............................................................................................ 30 1.6.5. Geographical distribution .......................................................................... 31 1.6.6. Genetic diversity ....................................................................................... 31 1.6.7. Pathogenicity and virulence ...................................................................... 32 1.6.8. Host range ................................................................................................. 36 1.6.9. Control ...................................................................................................... 37 1.6.10. P. fuscovaginae in Australia ..................................................................... 39 Chapter 2. Potential hosts of P. fuscovaginae strains isolated from rice in Australia and their host-pathogen interactions ........................................................................... 44 2.1. Introduction .................................................................................................... 44 2.1.1 Host range of P. fuscovaginae .................................................................. 44 2.1.2 The range of potential hosts for P. fuscovaginae in Australia .................. 45 2.1.3 Occurrence of P. fuscovaginae in rice cropping regions in Australia....... 47 2.1.4 Sources of host plant resistance to P. fuscovaginae .................................. 49 2.1.5 Techniques for screening of host plant resistance..................................... 52 2.2 Materials and Methods .................................................................................. 54 2.2.1 Strains of P. fuscovaginae ......................................................................... 54 2.2.2 Selection of cultivars ................................................................................. 57 2.2.3 Plant growth conditions ............................................................................ 62 2.2.4 Preparation of inoculum and inoculation techniques ................................ 62 2.2.5 Data collection .......................................................................................... 63 2.2.6 Data analysis ............................................................................................. 63 2.2.7 Survey of sheath brown rot disease ........................................................... 64 2.2.8 Preparation of plant samples collected during the survey ......................... 65 2.2.9 Use of Loop mediated isothermal amplification (LAMP) technique........ 66 2.2.10 Isolation and screening of putative P. fuscovaginae from diseased plant samples ...................................................................................................... 67 2.3 Results .............................................................................................................. 67 2.3.1 Screening of existing collection of putative P. fuscovaginae isolates ...... 67 2.3.2 Response of rice cultivars to inoculation with P. fuscovaginae................ 73 2.3.3 Response of wheat cultivars to inoculation with P. fuscovaginae ............ 77 III 2.3.4 Response of durum-wheat cultivars to inoculation with P. fuscovaginae 84 2.3.5 Response of triticale cultivars to inoculation with P. fuscovaginae ......... 85 2.3.6 Response of barley cultivars to inoculation with P. fuscovaginae............ 87 2.3.7 Outcomes of the disease survey ................................................................ 88 2.3.8 Results of LAMP assay for detecting P. fuscovaginae under field conditions .................................................................................................. 90 2.3.9 Results of screening of bacteria isolated from diseased plant samples from the survey .................................................................................................. 90 2.3.10 Response of rice and wheat to inoculation with P. fuscovaginae strains isolated from wheat ................................................................................... 91 2.4 Discussion ........................................................................................................ 92 2.5 Conclusions ................................................................................................... 101 Chapter 3. Comparative genomics of P. fuscovaginae from a perspective of host- specificity .................................................................................................................. 103 3.1. Introduction .................................................................................................. 103 3.2. Materials and methods ................................................................................. 107 3.2.1. P. fuscovaginae genomes ........................................................................ 107 3.2.2. Whole genome comparisons ................................................................... 109 3.3. Results ............................................................................................................ 110 3.3.1. Rice NRPS I ............................................................................................ 114 3.3.2. Rice NRPS II ..........................................................................................