可促進植物生長之光合菌Rhodopseudomonas palustris PS3的基因體分析與培養條件優化

Abstract

Rhodopseudomonas palustris PS3 is one of purple non-sulfur phototrophic bacteria that was isolated from Taiwanese paddy soils. It has been demonstrated that PS3 can promote plant growth and increase the agronomic nitrogen use efficiency of the host plant. The first part of this dissertation focuses on the elucidation of the relationship between the phototrophic bacteria and plant growth-promotion from the view of whole genomes of microorganisms. I conducted comparative analyses of genomic structures, physiological responses of microbes, and gene expression profiles with those of an ineffective R. palustris YSC3 strain. Based on the differential data, many putative genes that were associated with known plant growth promotional traits were identified. In this study, Illumina short-reads and PacBio long-reads technologies were integrated and assembled to obtain the whole genome sequences. PS3 and YSC3 individually contains a one circular chromosome with 5.27 and 5.37 Mb bp in size, with 4,799 and 4,907 protein-coding genes, respectively. The PS3 and YSC3 strains are closely related to each other with high identity (95.11%), and have similar genomic structures and compositions. Both strains contain the genes associated with plant growth-promotion, such as nitrogen fixation, phosphate solubilization, indole acetic acid synthesis, 1-aminocyclopropane-1-carboxylate deaminase, etc. Although there was no difference in the growth rate of PS3 and YSC3 strains, both the production of biofilm and the gene expressions of chemotaxis of PS3 were higher than those of YSC3 by the addition of root exudate in culture broth. Since PS3 is an elite strain with commercialization potential, the second part of this dissertation focuses on the optimal fermentation conditions for PS3 through mathematical and statistical models to find out a high-yield and low-cost production strategy. In this study, I evaluated various substrates, including the carbon and nitrogen sources commonly used in industry as well as the agricultural processing by-products. The culture condition was optimized by response surface methodology. The optimum culture condition was found to be at corn steep liquor, 39.41 mL/L; molasses, 32.35 g/L; temperature, 38°C; pH, 7.0; and DO 30%. Under this condition, the maximum yield of PS3 strain was up to 2.18 ± 0.01 g/L, which was approximately 8-fold higher than that with original medium, and the medium cost was approximate 70% reduced. Moreover, the beneficial effect of the new PS3 broth on plant growth was verified by pot experiments. The genomic information established in this study can be used as a research platform to investigate the interaction between phototrophic bacteria and plants as well as the molecular mechanisms of plant growth promotion. In addition, the newly developed medium uses agricultural processing by-products as the main nutrient substrates for phototrophic bacterium growth, which not only effectively reduces production costs, but also promotes the value-added and recycling of agricultural resources.