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系統識別號 U0026-2508202018552000
論文名稱(中文) 解析土壤微生物相探究草生栽培對台南麻豆文旦果園之影響
論文名稱(英文) Deciphering soil microbiome to investigate the effects of sod culture on pomelo orchards in Madou, Tainan
校院名稱 成功大學
系所名稱(中) 熱帶植物與微生物科學研究所
系所名稱(英) Institute of Tropical Plant Sciences and Microbiology
學年度 108
學期 2
出版年 109
研究生(中文) 林竹君
研究生(英文) Chun-Chun Lin
學號 Z36071015
學位類別 碩士
語文別 中文
論文頁數 73頁
口試委員 指導教授-黃兆立
口試委員-黃浩仁
口試委員-蔣鎮宇
口試委員-江友中
口試委員-劉世慧
中文關鍵字 文旦  草生栽培  清耕栽培  多源基因體學  土壤微生物 
英文關鍵字 Buntan pomelo  sod culture  clean tillage  metagenomics  soil microorganism 
學科別分類
中文摘要 傳統集約式農業管理所帶來的高效率與高產量解決了部分糧食短缺的問題,使人口飛速成長,但其對環境所造成的問題近年來掀起了一番討論,在這股風氣之下,友善農業興起,十幾年前農改場所推行的草生栽培便是友善環境的管理方法之一。藉由適當的雜草管理,可以改善土壤的物理化學性質、提升有機質含量、防止土壤養分快速流失,惟其對土壤微生物群落的影響鮮少被探討。因此本篇研究採用多源基因體學 (metagenomics) 結合細菌 16S rRNA 分子條碼,透過比較台南麻豆施行草生栽培 (S) 與清耕栽培 (CT) 的文旦園,探討植被覆蓋對果園土壤細菌相之影響。本研究選定八個草生果園與六個清耕果園,於二月與八月各採集一次樣本,同時利用離子層析儀測量土壤離子濃度,並以照片記錄樣點草相推估草相差異與土壤性質及微生物相之相關性。分析結果顯示多數土壤離子在八月的濃度顯著低於二月,而在微生物相方面,兩種果園中土壤微生物前三大優勢物種均為變形菌門、酸桿菌門與放線菌門,其中放線菌門之 Streptomyces 與 Nocardioides 屬豐度在草生果園顯著高於清耕果園,而變形菌門的Pseudomonas屬顯著偏向出現在清耕果園。有趣的是,清耕果園的土壤細菌相與土壤化學性質變動有顯著相關性,此效應可能也造成清耕栽培時微生物多樣性在土壤離子濃度較低的八月顯著下降;草生果園則更能維持土壤微生物群聚之穩定,如NMDS分析顯示各草生果園的土壤細菌相在八月更為相似。這種趨同現象暗示草生果園的植生覆蓋能創造較穩定的微環境,使草生果園微生物相不易受施肥行為的影響,讓土壤細菌組成在氮肥缺乏的時期更趨向依賴植物供給的類型。此外,共現網絡 (co-occurrence network) 顯現草生果園具有較高的模組化趨勢 (modularity),此現象可能來自草生果園植被組成差異而形成不同的群聚模組單元,而清耕果園之微生物則依附文旦果樹而形成連結眾多的單一龐大群集。總結以上,文旦果園的草生栽培能使土壤細菌相不易受農業操作造成的劇烈變動影響,藉植物多樣性匯集較多元化的群聚組成,形成果樹與環境友善共生的正向網絡。
英文摘要 Sod culture is an environmental approach frequently applied in orchards to lessen the chemical damages caused by conventional intensive agriculture. The management increases soil organic matters and moisture, but the effects on soil microbiome are still largely unknown. Hence, I utilized targeted metagenomics to investigate the soil microbiome in eight sod culture (S) orchards and six clean tillage (CT) orchards in Madou at two time points, before flowering and before harvest. In both types of orchards, Proteobacteria, Acidobacteria, and Actinobacteria were the predominant bacteria across time points. At genus level, Streptomyces and Nocardioides were enriched in S orchards, while Pseudomonas revealed significantly high abundance in CT orchards. Interestingly, soil microbial communities showed strong correlation with soil chemical properties only in CT orchards. Such effect may also reduce microbial diversity when the supply of nitrogen is limited before harvest. On the contrary, S orchards stabilized soil microbial communities by maintaining species diversity and showed a convergence pattern during the nutrient-depletion period. As a result, microbial communities in S orchards were less affected by agricultural manipulation compared to CT orchards. Besides, co-occurrence network reveals higher modularity index in S orchards, while the microbiome in CT orchards formed a giant module probably due to high dependence to the pomelo tree under low plant diversity. In conclusion, although the microbial community was not drastically changed by sod culture, a positive network between trees and environment was nevertheless strengthened via land cover with native vegetation.
論文目次 摘要..............................i
Extend abstract..............................ii
INTRODUCTON..............................iii
MATERIAL AND METHODS..............................iii
RESULTS AND DISCUSSION..............................iii
CONCLUSION..............................iv
致謝..............................v
目錄..............................vi
表目錄..............................viii
圖目錄..............................ix
引言..............................1
一、慣行農法的興起與缺憾..............................1
二、草生栽培在農業上的應用..............................2
三、文旦在台灣的種植..............................6
四、DNA 分子條碼 (DNA barcode) 與多源基因體學 (metagenomics)..............................7
五、研究動機..............................8
材料與方法..............................9
一、樣本採集..............................9
(一)採樣點選擇:..............................9
(二)土壤採樣時間與樣點分布..............................9
(三)草相觀察..............................10
二、實驗方法..............................10
(一)土壤DNA萃取..............................10
(二)聚合酶連鎖反應 (polymerase chain reaction, PCR) 進行DNA樣本前測..............................10
(三)DNA定序..............................11
(四)土壤化學性質測量..............................11
三、資料分析..............................12
(一)定序資料處理..............................12
(二)重取樣分析 (Rarefaction analysis)..............................12
(三)微生物多樣性分析..............................13
(四)環境因子與β-多樣性相關性分析..............................13
(五)火山圖顯示同時間點草生與清耕果園微生物群落差異性分析..............................13
(六)親緣關係樹的建立..............................13
(七)共現網路分析 (co-occurrence network analysis)..............................14
結果..............................15
一、各樣本讀序數 (reads) 資料與Greengenes基因庫比對資料..............................15
二、果園環境因子與草相觀察..............................16
三、草生與清耕栽培果園微生物相與多樣性分析..............................17
(一)土壤微生物相組成..............................17
(二)土壤微生物多樣性分析..............................18
1. α-微生物多樣性分析..............................18
2. β-微生物多樣性分析..............................19
3. 草生與清耕栽培OTU數變動..............................19
四、環境變量與土壤微生物相相關性..............................20
(一)環境因子與物種多樣性相關性..............................20
(二)環境因子與土壤微生物β-多樣性的相關性..............................20
五、各OTUs在草生與清耕果園中的豐度差異與親緣樹的建立..............................21
六、共出現網路分析 (co-occurrence network analysis)..............................22
討論..............................23
一、草生與清耕果園土壤微生物多樣性與環境因子相關性..............................23
二、草生與清耕果園微生物相隨時間流逝而有不同變動趨勢..............................24
結論..............................26
參考文獻..............................28
附錄..............................33

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