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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 劉啓德(Chi-Te Liu) | |
dc.contributor.author | Kai-Jiun Lo | en |
dc.contributor.author | 羅凱軍 | zh_TW |
dc.date.accessioned | 2021-05-20T00:50:01Z | - |
dc.date.available | 2020-08-24 | |
dc.date.available | 2021-05-20T00:50:01Z | - |
dc.date.copyright | 2020-08-24 | |
dc.date.issued | 2020 | |
dc.date.submitted | 2020-08-18 | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/8201 | - |
dc.description.abstract | 沼澤紅假單胞菌 (Rhodopseudomonas palustris) PS3菌株是一株由台灣水稻田土壤所篩選出的紫色非含硫光合菌。在先前研究中已證明該菌株具有促進各種作物生長的能力,並且可以提升植物氮肥使用效率。本論文的第一部份是從微生物全基因體的角度來探討光合菌與促進植物生長的關係。藉由與另一株不具促進植物生長功能之YSC3光合菌 (Rhodopseudomonas palustris)做比較分析,依基因構造、微生物生理反應以及基因表現的結果找出PS3菌株可能參與促進植物生長的相關基因。本研究結合了短片段與長片段定序技術,並完成序列組裝與註解後,分別得到PS3與YSC3菌株的基因體全長為527萬與537萬鹼基對,含有4,799以及4,907編碼序列。PS3與YSC3菌株有極高的序列相似度 (約95.11%),而且大部分的基因群的組成與排列方式類似,都有固氮、溶磷、吲哚乙酸合成、氨基環丙烷羧酸脫胺酶等代表性的植物生長促進相關基因群。雖然PS3與YSC3菌株的生長速率沒有差異,在微生物生理試驗結果發現,添加植物的根分泌液至兩株菌的培養液中會促使PS3菌株的生物膜生成量以及化學趨向性的相關基因表現量都較YSC3菌株高。這意味著PS3菌株對於植物的反應可能是其促進植物生長的重要關鍵。 PS3光合菌是具有產業化潛力的菌株,本論文的第二部分藉由數學統計模式探討最適化發酵條件,找出高產量與低成本的生產方式。在本研究中評估了各種較低成本的基質,包括了工業發酵常用的碳氮源以及農產加工副產物等作為培養基配方的可行性,並藉由回應曲面法優化培養條件。實驗結果顯示,當以39.41 mL/L的玉米浸漬液加上32.35 g/L的蔗糖糖蜜作為氮源和碳源,利用5公升桌上型發酵槽於38°C,pH 7以及溶氧濃度30%的條件下進行24小時培養,得到 PS3菌株的最大生物量約為2.18 ± 0.01 g/L。該新配方所生產的PS3發酵液產量約為使用傳統光合菌培養條件的8倍,成本卻只需原先的30%,而且在植物盆栽試驗上證實可以促進作物生長。 在本研究中所建立的基因體資訊,可作為探討光合菌與植物間的交互作用以及促進生長機制的研究平台。此外,新開發的培養基配方是以農產加工副產物作為光合菌的主要營養基質,不僅可有效降低生產成本,也促進了農業資源的加值與循環再利用。 | zh_TW |
dc.description.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. | en |
dc.description.provenance | Made available in DSpace on 2021-05-20T00:50:01Z (GMT). No. of bitstreams: 1 U0001-1408202015035600.pdf: 25879232 bytes, checksum: 749a1827e640a0cafb6af2f704c33c4c (MD5) Previous issue date: 2020 | en |
dc.description.tableofcontents | 口試委員會審定書 i 謝辭 ii 中文摘要 iii ABSTRACT v CONTENTS vii LIST OF FIGURES xi LIST OF TABLE xiii CHAPTER I 1 INTRODUCTION 1 Plant growth promoting rhizobacteria 1 PGPR with nitrogen fixing ability 2 PGPR with phosphate solubilizing ability 3 PGPR with phytohormone producing ability 4 Phototrophic bacteria 5 Purple non-sulfur phototrophic bacteria 6 Application of purple non-sulfur photosynthetic bacteria 7 Rhodopseudomonas palustris 9 R. palustris PS3 10 Specific aims 11 CHAPTER II 22 Whole-Genome Sequencing and Comparative Analysis of Two Plant-Associated Strains of Rhodopseudomonas palustris (PS3 and YSC3) 22 Summary 23 Introduction 23 Materials and methods 27 Preparation of phototrophic bacterial inoculant 27 Genomic DNA preparation 27 Whole-genome sequencing 28 De novo genome assembly 29 Genome annotation 29 Phylogenetic analysis 30 Biofilm formation assay 31 Phosphate-solubilizing activity assay 32 Indole acetic acid production of R. palustris 32 Comparative genomic analyses 33 Collection of Chinese cabbage root exudate solution 34 Gene expression analysis of R. palustris in response to root exudates 35 Statistical analysis 35 Results 36 General characteristics of the genomes 36 Carbon source utilization 38 Nitrogen fixation and nitrogen utilization 40 Root colonization 41 Deduced plant growth promotion-related genes 42 Effect of root exudates of Chinese cabbage on biofilm formation and relative gene expression levels 44 Transcriptomic profiling of R. palustris PS3 response to root exudate 44 Discussion 46 CHAPTER III 76 Development of A Low-Cost Culture Medium For Rapid Production of Plant Growth-Promoting Rhodopseudomonas palustris PS3 Strain 76 Summary 77 Introduction 77 Materials and Methods 81 Microorganism and bacterial preparation 81 Measurement of cell growth 81 Screening of nitrogen and carbon sources for medium optimization 82 Evaluate the effects of fermentation factors on the growth of R. palustris by fractional factorial design (FFD) 82 Maximum region improvement of factors by steepest ascent method 84 Construction of the response surface model by central composite design (CCD) 84 Batch-culture experiments in a benchtop bioreactor 85 Quantification of total organic carbon 86 Quantification of total nitrogen 86 In planta experiments to verify the plant-growth promotion effect of the newly developed fermentation broth 87 Statistical analysis 89 Results 89 Selection of appropriate components for optimization of R. palustris strain PS3 medium 89 Screening suitable fermentation conditions by FFD 90 Optimization of culture conditions by RSM 92 Effects of various factors on R. palustris PS3 biomass production 93 Verification of optimization 94 Validation of the plant growth-promoting effect of the newly developed fermentation broth 94 Discussion 95 Chapter IV 118 Concluding remarks and discussion 118 References 125 APPENDIX 155 | |
dc.language.iso | en | |
dc.title | 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 | zh_TW |
dc.title | Genome analysis and fermentation optimization of plant growth promoting strain Rhodopseudomonas palustris PS3 | en |
dc.type | Thesis | |
dc.date.schoolyear | 108-2 | |
dc.description.degree | 博士 | |
dc.contributor.oralexamcommittee | 劉嚞睿(Je-Ruei Liu),陳仁治(Jen-Chih Chen),林詩舜(Shih-Shun Lin),李昆達(Kung-Ta Lee),郭志鴻(Chih-Horng Kuo) | |
dc.subject.keyword | 沼澤紅假單胞菌,全基因體比較分析,回應曲面法,農產加工副產物,玉米浸漬液,糖蜜,促進作物生長, | zh_TW |
dc.subject.keyword | Rhodopseudomonas palustris,whole genomic comparative analysis,response surface methodology,agricultural processing by-products,corn steep liquor,molasses,plant growth promotion, | en |
dc.relation.page | 190 | |
dc.identifier.doi | 10.6342/NTU202003422 | |
dc.rights.note | 同意授權(全球公開) | |
dc.date.accepted | 2020-08-19 | |
dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
dc.contributor.author-dept | 生物科技研究所 | zh_TW |
顯示於系所單位: | 生物科技研究所 |
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