臺灣博碩士論文加值系統

植物內共生微生物與作物生長發育密切相關，也會影響作物產量及品質，許多有益內共生微生物已被證實具有促進作物生長、增進作物逆境耐受性的能力。有鑑於慣行農業操作法在維繫農田土壤健康及生態多樣性的限制，以維持生產、生活及生態平衡為出發點的永續農法應運而生，然而不同農業操作是否會透過改變作物根圈及根內共生微生物的多樣性及組成，進而影響作物健康，目前瞭解有限；另一方面，有益微生物共生的時間點及族群結構關係著其對作物的效益，但內共生微生物群落組成是否會隨著作物發育時期的推進而產生變化，相關研究並不多。為瞭解耕作模式及生育時期對內共生菌組成的影響，本研究藉由16S核糖體RNA基因定序技術，在2018至2019年間3個期作，以苗栗縣苑裡鎮慣行及有機等2種管理水稻田為樣區，調查水稻根部內共生細菌群落組成，並於2019年兩個期作調查秧苗期和分蘗期根部內共生細菌群落之變化。結果顯示不同管理方式對水稻根內共生細菌α-多樣性並無顯著影響，但對菌相的組成在三個期作都具有顯著差異，而生育期的不同對水稻根部內共生細菌組成及β-多樣性的影響更為顯著，推測水稻隨發育階段演進，會透過改變根部代謝而營造出相對應的菌相組成。另外經由指標物種分析，鑑定出對生育期及管理方式敏感的OTUs，未來可再擴大檢視這些OTUs在水稻田的角色。本次試驗水稻雖來自相近區位，仍可見田間樣品受到區域環境因子的影響，建議未來可擴大樣區並進行長期的研究，以確認管理方式對於作物根內共生微生物組成及功能的影響。

Plant endophytic microorganisms have great impacts on crop growth, development and yield. Many beneficial endophytic microbes have been identified which can enhance the crop growth and stress tolerance. Because the conventional agricultural practices are not good for soil health and agricultural biodiversity, sustainable agricultural practices which aim to balance the crop production, people’s living and ecosystem attract more and more attention. However, little is known about the impacts of agricultural practices on crop health via modifying the diversity and composition of endophytic and rhizosphere microbial communities. On the other hand, the timing that the beneficial microbe association forms and their composition influence the benefits that crops receive. However, it is still unclear that whether endophyte composition and structure change temporally during plant growth and development. In order to address these questions, we examined rice root microbiome by using the 16S ribosomal RNA gene sequencing from 2018 to 2019. The samples from organic and conventional-cultivated rice fields in Yuanli Town, Miaoli County were harvested for investigating the composition of the rice root bacterial endophyte under different practices at two different growth stages. The results showed that different managements only affected the composition of bacterial endophyte but not α-diversity. However, the bacterial composition and β-diversity were significantly different between two growth stages. It is possible that the modification of metabolite accumulation during the growing season leads to the change of endophytic community structure. In addition, by performing indicator species analysis, several growth stage- and field management-sensitive OTUs were identified. Further studies are required to examine their role in rice fields. Although our experimental sites were very close, the variation between samples were still observed, suggesting the presence of local environmental effects. Thus, we suggest that more experimental sites and long-term research are needed in the future to dissect the impacts of cropping practices on root endophyte composition and function in crops.

致謝 I
摘要 II
Abstract III
目錄 V
圖目錄 VIII
表目錄 IX
附錄目錄 X
第1章 前言 1
1.1 永續農業 1
1.1 耕作模式與土壤性質 1
1.2 植物內共生微生物 2
1.2.1 植物內共生微生物對植物生長的效益 2
1.2.2 植物內共生微生物與耕作模式 3
1.2.3 植物生育期對根圈菌相之影響 4
1.3 植物根圈土壤及內共生微生物研究方法 4
1.3.1 傳統微生物分離培養法 5
1.3.2 土壤酶活性測定 5
1.3.3 次世代定序技術 5
1.3.4 利用次世代定序分析微生物群落多樣性 6
1.4 研究目的 7
第2章 材料及方法 9
2.1 樣品採集 9
2.2 田間施作方法 9
2.3 樣本採樣與處理 9
2.4 內共生細菌DNA萃取 10
2.5 16s rRNA基因次世代定序 11
2.5.1 16S rRNA基因聚合酶連鎖反應（polymerase chain reaction, PCR） 11
2.5.2 樣本基因體建庫及定序 11
2.5.3 定序資料處理 11
2.6 生物資訊分析 12
2.6.1 OTU聚類和物種注釋 12
2.6.2 樣品複雜度分析（α-多樣性；α-diversity） 12
2.6.3 樣本分組比較分析（β-多樣性；β-diversity） 13
2.6.4 環境因子分析 13
2.6.5 基因功能預測 13
2.6.6 敏感物種（OTUs）分析 13
2.6.7 熱圖（heatmap）製作 13
2.7 數據統計分析 14
第3章 結果 15
3.1 試驗取樣點環境概況 15
3.2 水稻根部內共生細菌群落組成與生育地土壤性質關係 16
3.3 水稻根部內共生細菌門組成在不同期作及管理方式下的差異 16
3.4 水稻根部內共生細菌群落組成在不同期作α-多樣性的差異 17
3.5 水稻根部內共生細菌群落組成在不同期作β-多樣性的差異 19
3.6 分析對管理方式及生育時期敏感的水稻內共生細菌指標OTUs 25
3.7 不同期作水稻根部內共生細菌群落的功能預測分析 26
第4章 討論 28
4.1 田間管理方式對水稻內共生細菌群落結構及功能的影響 28
4.2 生育期對水稻內共生細菌群落結構及功能的影響 30
4.3 生育期及田間管理方式的交互作用共同影響水稻內共生細菌相 33
4.4 田間管理方式對土壤特性及微生物相的影響 34
4.5 品種及氣候環境條件對根內共生菌相的影響 35
第5章 參考文獻 37
附錄 82

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