成功大學博碩士論文系統

簡易檢索 / 詳目顯示

回結果列表

研究生：	張新杰 Chang, Shin-Chieh
論文名稱：	微生物來源分析法追蹤地表水糞便污染：指標微生物環境耐受性初探 Microbial Source Tracking on Fecal Contamination of Surface Water: Persistency of Indicator Microorganisms
指導教授：	吳哲宏 Wu, Jer-Horng
學位類別：	碩士 Master
系所名稱：	工學院 - 環境工程學系 Department of Environmental Engineering
論文出版年：	2012
畢業學年度：	100
語文別：	中文
論文頁數：	121
中文關鍵詞：	水質安全、微生物來源追蹤、糞便污染來源追蹤、擬桿菌群、大腸桿菌群、指標微生物耐受性
外文關鍵詞：	Water safety, Microbial source tracking, Fecal contamination source tracking, Bacteroidales, Coliform group, Indicator microorganism persistency
相關次數：	點閱：147 下載：7
分享至:	分享至facebook 分享至twitter

查詢本校圖書館目錄查詢臺灣博碩士論文知識加值系統勘誤回報

水質安全一直是飲用水的重要課題，而以微生物來源追蹤 (microbial source tracking, MST) 技術偵測糞便污染源，近來成為水質安全研究的重心。美國EPA於2005年編寫的MST指南中提出了MST急需要達成的目標，就是建立水體的最大日負荷量 (Total maximum daily load, TMDL)，因此在宿主專一性指標菌群的研究漸趨完整後，即開始探討指標菌群在水體中的耐受性。本研究結合了濾膜法、q-PCR，以及過去已經用於糞便污染來源追蹤並可快速定量多種菌群豐富度的階層寡核苷酸引子延伸技術 (Hierarchical oligonucleotide primer extension, HOPE)，進行糞便污染來源動物的判定，並初步探討實際環境水體中指標菌群的耐受性。
本研究先以純菌培養試驗觀察不同指標菌群的衰亡速率，發現當溫度由攝氏10度提升至30度時，Escherichia coli K-12與Bacteroides fragilis BCRC10620兩株菌的衰亡速率分別自4.6 Day -1與5.7 Day -1上升至大於2.1 Day -1以及大於0.4 Day -1，並且也發現溫度造成的耐受性變異 (P value = 0.08比較10 ℃與20 ℃)，與兩株菌群間的耐受性差異 (P value = 0.23在10 ℃以及20 ℃下) 皆未達顯著差異，但若從20度升至30度時，耐受性會大幅下降，代表溫度以外還有其他因子影響菌群的衰亡。接著選擇金門太湖的山外溪流域做為研究的對象，從HOPE的分析結果發現可能有多個污染源進入山外溪，且其污染來源主要為人類糞便污染。根據衰亡速率觀察顯示各種指標菌群的耐受性並不相同，衰亡速率分布從E. coli uidA gene的1.6 (100m)-1至C367-detected Bacteroidales 16S rRNA gene的 >4.82 (100m)-1，其差異可到種間的差異。
本研究亦探討了Total coliform/lacZ gene與E. coli/uidA gene的比值是否適合做為水體受到污染的時間的長短的參考指標。而從台灣六座水庫的比較中，發現E. coli/uidA gene的比值較能做為水體受到污染的時間的長短的參考指標；從其結果也可以看出在未降雨的情況下，台灣七座水庫中可以使用培養法計數的E. coli數量約在5%以下，代表有大多數的指標菌群無法藉由培養法計數。最後將這兩個比值與山外溪污染來源判定結果相互對照，印證E. coli/uidA gene的比值確實比較適合用做參考的指標 (75 %準確率, n=4)。
本研究成功地建立了q-PCR與HOPE高通量的微生物來源追蹤技術，可快速定性指標菌群以追蹤糞便污染來源的種類，並藉由其定量結果揭露在不同種的微生物間具有不同的耐受性，這些結果未來可應用於不同水環境的糞便污染追蹤，以達到確保水質安全的目標。

Water safety is an important issue in drinking water supply. Application of microbial source tracking (MST) techniques on the detection of fecal contamination source has emerged an inseparable part of water safety, while in 2005, USEPA suggested the use of MST to construct total maximum daily load (TMDL) of water body for better management of water resource. Though, more of host specific biomarkers extensively developed, the persistency of indicator microorganisms is still poorly understood so far. In this research, the membrane filter method combined with the quantitative PCR (q-PCR) method, and the hierarchical oligonucleotide primer extension (HOPE) method that was recently developed and had the advantage to analyze the abundance of multiple groups of indicators quantitatively in short time were applied to identify the fecal contaminations and to preliminarily investigate the persistency of indicators in water body.
Firstly, the pure cultures were used to investigate the decay rate of different indicators. It was found that when the temperature increased from 10 ℃ to 30 ℃, the decay rate of Escherichia coli K-12 and Bacteroides fragilis BCRC10620 were increased from 4.6 Day -1 and 5.7 Day -1 to more than 2.1 Day -1 and more than 0.4 Day -1, respectively. Furthermore, both of two bacterial strains showed little significant persistency responding to the change of incubation temperature between 10 ℃ and 20 ℃ (P = 0.08), but there was a significant persistency decrease for the incubation temperature between 20 ℃to 30 ℃. However, no significant difference of the persistency could be concluded for the two strains (P = 0.23), although Escherichia coli and Bacteroides fragilis are physiologically different. The experimental results indicated that the temperature may not be the only factor, which could affect the decay rate of indicator microorganisms.
Next, the Tai-Hu’s drainage area in Kin-Men, inclusive of the Shan-Wai river was used as a model site in this study. The results showed that the Shan-Wai river had multiple fecal contamination sources. The main contaminant in this site was identified human feces based on the HOPE analyses. According to the different biomarker detected, the decay rate varied from 1.6 (100m)-1 for E. coli uidA gene to > 4.82 (100m)-1 for the C367-detected Bacteroidales 16S rRNA gene. This result indicated that the microbial persistency in environmental water body may vary at the species level.
The ratios of cultivated total coliform to PCR-detected lacZ gene (all of total coliform) and cultivated E. coli to the PCR-detected uidA gene (all of the E. coli) were also investigated to know the effects of traveling time of microbial indicators in water body. After calculating the ratios obtained from 7 reservoirs, the ratio of E. coli to uidA gene was considered a more appropriate index. Furthermore, in the investigation site, the cultural percentage of E. coli was usually lower than 5% without raining, indicating that most of the viale but not culturable E. coli cells could not be detected by the cultivation method. This ratio was applied to the Shan-Wai river system and 75% of contamination source (n = 4) could be identified correctly.
In conclusion, in this study, the q-PCR and HOPE detection systems were successfully developed to investigate the type of fecal contaminations and also microbial persistency with different species. These techniques are able to be carried out in a high-throughput and standardized manners for microbial source tracking, where analysis of a great number of samples is usually needed,. The platform developed in this research can be applied to track the source of fecal contaminations from different water macrocosms and hopefully, it can contribute to ensure the safety of drinking water in the future.

目錄

摘要 ........................................................................................................ I
ABSTRACT ....................................................................................... III
致謝 ..................................................................................................... VI
目錄 .................................................................................................... VII
圖目錄 ............................................................................................... XIV
表目錄 ............................................................................................. XVII
第一章前言 ......................................................................................... 1
1-1 背景 ................................................................................................ 1
1-2 研究目標 ........................................................................................ 3
1-3 研究架構 ........................................................................................ 3
1-4 研究流程 ........................................................................................ 4
第二章文獻回顧 ................................................................................. 5
2-1 水生病原菌 .................................................................................... 5
2-2 動物腸道菌群結構 ........................................................................ 6
2-2-1 人類腸道菌群結構 ......................................................... 6
2-2-2 牛腸道菌群結構 ............................................................. 6
2-2-3 豬腸道菌群結構 ............................................................. 7
2-3 指標菌群 ........................................................................................ 7
2-3-1 傳統水質指標菌群 ......................................................... 7
2-3-2 大腸菌群的角色 ............................................................. 9
2-4 宿主專一性指標腸道菌群 .......................................................... 10
2-4-1 擬桿菌群 ....................................................................... 10
2-4-2 大腸桿菌 ....................................................................... 11
2-4-3 其他菌群或微生物 ....................................................... 11
2-4-4 指標菌群之環境意義 ................................................... 12
2-5 指標微生物偵測方式 .................................................................. 13
2-5-1 傳統偵測方式 ............................................................... 13
2-5-1-1 濾膜法 ....................................................................... 13
2-5-1-2 MPN 法 ...................................................................... 14
2-5-2 分子生物偵測方式 ....................................................... 15
2-5-2-1 聚合.鏈鎖反應 (Polymerase Chain Reaction,
PCR) .......................................................................... 17
2-5-2-2 即時定量聚合.鏈鎖反應 (Quantitative real-time
Polymerase Chain Reaction, q-PCR) ........................ 19
2-5-2-3 變性梯度明膠電泳 (Denaturation Gradient Gel
Electrophoresis, DGGE) ........................................... 20
2-5-2-4 端點限制片段長度多形性 (Terminal Restriction
Fragment Length Polymorphism, T-RFLP) .............. 21
2-5-2-5 階層寡核.酸引子延伸技術 (Hierarchical
Oligonucleotide Primer Extension, HOPE) .............. 21
2-6 台灣水體指標微生物分布 .......................................................... 22
2-6-1 台灣水質趨勢 ............................................................... 22
2-6-2 台灣各流域水生病原菌之潛勢 ................................... 25
2-6-3 台灣各分區之大腸桿菌群平均濃度 ........................... 27
2-7 糞便污染來源追蹤 ...................................................................... 30
2-7-1 傳統糞便污染來源指標 ............................................... 31
2-7-2 宿主專一性生物標記 (Host Specific Biomarker) ....... 32
2-8 水體指標菌群耐受性 .................................................................. 32
2-8-1 大腸菌群與環境之關聯性 ........................................... 33
2-8-2 宿主專一性指標菌群耐受性 ....................................... 34
2-9 問題分析 ...................................................................................... 36
第三章材料與方法 ........................................................................... 37
3-1 樣本來源 ...................................................................................... 37
3-1-1 純菌細胞 ....................................................................... 37
3-1-2 實際環境樣本 ............................................................... 37
3-1-2-1 金門太湖 ................................................................... 37
3-1-2-2 金門金沙水庫 ........................................................... 38
3-1-2-3 基隆新山水庫 ........................................................... 39
3-1-2-4 桃園石門水庫 ........................................................... 40
3-1-2-5 台南南化水庫 ........................................................... 41
3-1-2-6 嘉義仁義潭水庫 ....................................................... 42
3-1-2-7 新竹寶山水庫 ........................................................... 43
3-1-3 糞便樣本來源 ................................................................ 44
3-2 樣本前處理 .................................................................................. 44
3-2-1 純菌於水庫水之培養樣本 ........................................... 44
3-2-2 糞便樣本 ....................................................................... 44
3-2-3 實際環境樣本 ............................................................... 44
3-2-3-1 採樣及運送方式 ....................................................... 44
3-2-3-2 傳統指標菌群培養前處理 ....................................... 45
3-2-3-3 DNA 萃取前處理 ...................................................... 45
3-3 傳統指標菌群培養 ...................................................................... 46
3-3-1 水中總大腸桿菌群檢測 ............................................... 46
3-3-2 水中糞生大腸桿菌群檢測 ........................................... 46
3-3-3 水中大腸桿菌檢測 ....................................................... 47
3-4 DNA 萃取................................................................................... 47
3-4-1 純菌DNA 萃取............................................................. 47
3-4-2 糞便樣本DNA 萃取 .................................................... 48
3-4-3 水樣DNA 萃取............................................................. 48
3-5 引子設計 ...................................................................................... 48
3-5-1 聚合.鏈鎖反應引子設計 ........................................... 48
3-5-2 定量聚合.鏈鎖反應引子設計 ................................... 49
3-5-2-1 總大腸桿菌群 ........................................................... 49
3-5-2-2 Escherichia coli .......................................................... 50
3-5-2-3 Bacteroidales .............................................................. 51
3-5-3 HOPE 引子設計 ............................................................. 51
3-6 聚合.鏈鎖反應 (Polymerase Chain Reaction, PCR) ............ 55
3-7 純菌16S rRNA gene 選殖 .......................................................... 55
3-8 DNA 序列分析 .......................................................................... 55
3-9 即時定量聚合.鏈鎖反應 (Quantitative real-time
Polymerase Chain Reaction, q-PCR) ........................................ 56
3-9-1 q-PCR 檢量線製作 ........................................................ 57
3-10 階層寡核.酸引子延伸技術 (Hierarchical Oligonucleotide
Primer Extension, HOPE) ......................................................... 57
3-11 毛細管電泳 ................................................................................ 58
3-12 結果計算 .................................................................................... 58
3-12-1 q-PCR 結果計算 .......................................................... 58
3-12-2 HOPE 結果計算 ........................................................... 58
3-12-3 菌群衰亡率計算 ......................................................... 59
第四章結果與討論 ........................................................................... 60
4-1 專一性指標菌群的選定 .............................................................. 60
4-2 探針設計 ...................................................................................... 60
4-2-1 q-PCR 探針設計結果 .................................................... 61
4-2-1-1 lacZ 引子評估及測試 ............................................... 61
4-2-1-2 uidA 引子的評估 ....................................................... 62
4-2-2 HOPE 探針設計結果 ..................................................... 64
4-3 純菌標準品最佳化 ...................................................................... 66
4-3-1 q-PCR 標準菌最佳化 .................................................... 66
4-3-1-1 lacZ 基因即時定量PCR 校正曲線 .......................... 66
4-3-1-2 uidA gene 以及Bacteroidaels 16S rRNA gene 即時
定量PCR 校正曲線 ................................................. 67
4-3-2 HOPE 標準菌最佳化 ..................................................... 70
4-4 純菌培養分析結果 ...................................................................... 74
4-5 實際水庫樣本分析 ...................................................................... 77
4-5-1 水庫指標菌群分析結果 ............................................... 77
4-5-2 水庫污染來源動物判定結果 ....................................... 80
4-5-3 金門太湖水庫指標菌群定性定量分析結果 ............... 83
4-5-3-1 傳統指標菌群培養及q-PCR 偵測結果 .................. 83
4-5-3-2 糞便污染來源鑑定結果 ........................................... 87
4-5-3-3 宿主專一性指標菌群定量結果 ................................ 89
4-5-4 各指標菌群在山外溪水體的耐受性 ........................... 92
4-5-5 水庫水體可培養率之探討 ........................................... 94
4-5-6 可培養率與污染源之關聯性 ....................................... 96
第五章結論與建議 ........................................................................... 98
5-1 結論 .............................................................................................. 98
5-2 建議 .............................................................................................. 99
參考文獻 ................................................................................ 101
附錄 ........................................................................................ 113
自述 .................................................................................................... 121



圖目錄

圖 2- 1 宿主專一性指標微生物及其宿主 (本研究整理) .................... 12
圖2- 2 糞便污染來源追蹤技術分類圖 (EPA, 2005)，虛線框為本研
究新加入之技術 .............................................................................. 16
圖2- 3 聚合酶鏈鎖反應 (Freyer, 1990) ................................................ 18
圖2- 4 CT值的決定 (固定的閾值是偵測到螢光開始要指數成長的值)
(本研究整理) .................................................................................... 20
圖2- 5 台灣河川分級水體標準全台測站大腸桿菌群總達成率 (本
研究整理) ......................................................................................... 23
圖2- 6 全台各區域河川分級水體大腸桿菌群平均達成率 (本研究
整理) ................................................................................................. 24
圖2- 7 全台各分級水體大腸桿菌群總達成率 (本研究整理) ............ 25
圖2- 8 2008-2009 台灣各流域上中下游大腸桿菌群濃度圖 (本研究
整理) ................................................................................................. 26
圖2- 9 全台各分區2002 至2009 年大腸桿菌群濃度變化圖 (虛線代
表丙級水體大腸桿菌群的最高限值) (本研究整理) ..................... 28
圖2- 10 2002 至2009 年分區全河段平均總大腸桿菌群濃度 (虛線代
表丙級水體大腸桿菌群的最高限值) (本研究整理) ..................... 29
圖3- 1 金沙水庫採樣點，黃色標點為採樣點 ..................................... 38
圖3- 2 新山水庫採樣點，黃色標點為採樣點 ..................................... 39
圖3- 3 石門水庫採樣點，黃色標點為採樣點 ..................................... 40
圖3- 4 南化水庫採樣點，黃色標點為採樣點 ...................................... 41
圖3- 5 仁義潭水庫採樣點，黃色標點為採樣點 .................................. 42
圖3- 6 寶山水庫採樣點，黃色標點為採樣點 ...................................... 43
圖4- 1 lacZ 引子測試 ............................................................................. 61
圖4- 2 LZL-389~LZR-653 溫度梯度測試 ............................................. 62
圖4- 3 Bacteroides 與Prevotella 之親源樹，圖中標記者為本研究之
參考標準菌株，右方為偵測該些菌群所使用的探針 .................. 65
圖4- 4 lacZ gene 的q-PCR 螢光成長曲線 ............................................ 66
圖4- 5 lacZ gene 的q-PCR 檢量線 ........................................................ 67
圖4- 6 uidA gene 以及Bacteroidales 16S rRNA gene 的q-PCR 螢光成
長曲線............................................................................................... 67
圖4- 7 uidA gene 以及Bacteroidales 16S rRNA gene 的q-PCR 檢量線
........................................................................................................... 68
圖4- 8 (A) HPCMix-2 混合引子與C11 clone 187、P3 clone 18 和B.
fragilis 混合標準品測試 (B) HMix-3 混合引子與混合標準品B.
fragilis、B. uniformis、B. vulgatus 測試 (C) PCMix-3 混合引子
與C11 clone 18、P3 clone 73、P3 clone 18 混合標準品測試 (RFU
為relative fluorescence unit) ............................................................ 73
圖4- 9 純菌培養衰亡圖 (A) E. coli K-12 培養衰亡趨勢圖 (B) B.
fragilis BCRC10620 培養衰亡趨勢圖，虛線代表偵測極限 ........ 75
圖4- 10 山外溪水樣採樣點，黃點為採樣點，黑色箭頭為排水口位
置 ....................................................................................................... 85
圖4- 11 太湖樣本毛細管電泳訊號圖 (A) 太湖B，(B) 太湖C，(C) 太
湖E，(D) 太湖F (RFU 為relative fluorescence unit) .................. 88
圖4- 12 各水庫採樣點 (A) Total coliform (B) E. coli 的可培養率，實
線代表平均可培養率，虛線代表95 %信賴區間 (以百分比表示)
........................................................................................................... 95
圖4- 13 培養菌群與基因測定的比例變化圖 ....................................... 97



表目錄

表 2- 1 台灣各種飲用水水體大腸菌群指標 ........................................... 8
表2- 2 不同培養基的培養條件 ............................................................. 13
表2- 3 糞便污染來源辨識方法 (Sargeant, 1999) ................................ 31
表3- 1 各水樣體積建議過濾體積 ......................................................... 45
表3- 2 本研究使用的PCR 引子 ........................................................... 49
表3- 3 本研究候選的SYBR Green q-PCR 引子及探針 ..................... 52
表3- 4 本研究候選的TaqMan q-PCR 引子及探針 ............................. 53
表3- 5 HOPE 試驗中使用的引子 ........................................................ 54
表4- 1 本研究使用之q-PCR 引子及探針 ........................................... 69
表4- 2 設計的探針與標準菌單一測試結果 ......................................... 72
表4- 3 Multiplex 引子之個別內容物 .................................................... 72
表4- 4 E. coli 與B. fragilis 於不同時間及溫度的衰亡速率 ................ 77
表4- 5 各水庫水樣以傳統培養法及q-PCR 法分析大腸菌群的結果 79
表4- 6 太湖以外之水庫各採樣點人類糞便污染來源判定 ................. 81
表4- 7 太湖以外之水庫各採樣點動物糞便污染來源判定 ................. 82
表4- 8 各排水口之污染情況 (金門縣環境保護局, 2006) .................. 85
表4- 9 金門太湖傳統培養及q-PCR 結果 ............................................ 86
表4- 10 以豐富度推算的各點專一性指標菌群數量 ........................... 91
表4- 11 山外溪各指標菌群的衰亡速率 ............................................... 93
                                    

1. Ahmed, W., M. Hargreaves, A. Goonetilleke and M. Katouli. 2008. Population similarity analysis of indicator bacteria for source prediction of faecal pollution in a coastal lake. Marine Pollution Bulletin 56:1469-1475.
2. Ahmed, W., R. Neller and M. Katouli. 2005. Host species-specific metabolic fingerprint database for enterococci and Escherichia coli and its application to identify sources of fecal contamination in surface waters. Applied and Environmental Microbiology 71:4461-4468.
3. Ahmed, W., J. Stewart, T. Gardner, D. Powell, P. Brooks, D. Sullivana and N. Tindale. 2007a. Sourcing faecal pollution: A combination of library-dependent and library-independent methods to identify human faecal pollution in non-sewered catchments. Water Research 41:3771-3779.
4. Ahmed, W., J. Tucker, K. A. Bettelheim, R. Neller and M. Katouli. 2007b. Detection of virulence genes in Escherichia coli of an existing metabolic fingerprint database to predict the sources of pathogenic E. coli in surface waters. Water Research 41:3785-3791.
5. Ahmed, W., J. Tucker, J. Harper, R. Neller and M. Katouli. 2006. Comparison of the efficacy of an existing versus a locally developed metabolic fingerprint database to identify non-point sources of faecal contamination in a coastal lake. Water Research 40:2339-2348.
6. Aktas, Z., M. Day, C. B. Kayacan, S. Diren and E. J. Threlfall. 2007. Molecular characterization of Salmonella Typhimurium and Salmonella Enteritidis by plasmid analysis and pulsed-field gel electrophoresis. International Journal of Antimicrobial Agents 30:541-545.
7. Anderson, M. A., J. E. Whitlock and V. J. Harwood. 2006. Diversity and distribution of Escherichia coli genotypes and antibiotic resistance phenotypes in feces of humans, cattle, and horses. Applied and Environmental Microbiology 72:6914-6922.
8. Anderson, M. L., J. E. Whitlock and V. J. Harwood. 2005. Persistence and differential survival of fecal indicator bacteria in subtropical waters and sediments. Applied and Environmental Microbiology 71:3041-3048.
9. Arias, C., M. R. Sala, A. Dominguez, R. Bartolome, A. Benavente, P. Veciana, A. Pedrol and G. Hoyo. 2006. Waterborne epidemic outbreak of Shigella sonnei gastroenteritis in Santa Maria de Palautordera, Catalonia, Spain. Epidemiology and Infection 134:598-604.
10. Bae, S. and S. Wuertz. 2009. Rapid decay of host-specific fecal Bacteroidales cells in seawater as measured by quantitative PCR with propidium monoazide. Water Research 43:4850-4859.
11. Bae, S. and S. Wuertz. 2012. Survival of Host-Associated Bacteroidales Cells and Their Relationship with Enterococcus spp., Campylobacter jejuni, Salmonella enterica Serovar Typhimurium, and Adenovirus in Freshwater Microcosms as Measured by Propidium Monoazide-Quantitative PCR. Applied and Environmental Microbiology 78:922-932.
12. Balleste, E. and A. R. Blanch. 2010. Persistence of Bacteroides species populations in a river as measured by molecular and culture techniques. Applied and Environmental Microbiology 76:7608-7616.
13. Bej, A. K., M. H. Mahbubani, J. L. Dicesare and R. M. Atlas. 1991a. Polymerase Chain Reaction-Gene Probe Detection of Microorganisms by Using Filter-Concentrated Samples. Applied and Environmental Microbiology 57:3529-3534.
14. Bej, A. K., S. C. McCarty and R. M. Atlas. 1991b. Detection of coliform bacteria and Escherichia coli by multiplex polymerase chain reaction: comparison with defined substrate and plating methods for water quality monitoring. Applied and Environmental Microbiology 57:2429-2432.
15. Bej, A. K., R. J. Steffan, J. Dicesare, L. Haff and R. M. Atlas. 1989. Detection of Coliform Bacteria in Water by Polymerase Chain Reaction and Gene Probes. Applied and Environmental Microbiology 56:8.
16. Bernhard, A. E. and K. G. Field. 2000a. Identification of nonpoint sources of fecal pollution in coastal waters by using host-specific 16S ribosomal DNA genetic markers from fecal anaerobes. Applied and Environmental Microbiology 66:1587-1594.
17. Bernhard, A. E. and K. G. Field. 2000b. A PCR assay to discriminate human and ruminant feces on the basis of host differences in Bacteroides-Prevotella genes encoding 16S rRNA. Applied and Environmental Microbiology 66:4571-4574.
18. Bonjoch, X., E. Ballese and A. R. Blanch. 2004. Multiplex PCR with 16S rRNA gene-targeted primers of Bifidobacterium spp. to identify sources of fecal pollution. Applied and Environmental Microbiology 70:3171-3175.
19. Bouchet, V., H. Huot and R. Goldstein. 2008. Molecular genetic basis of ribotyping. Clinical Microbiology Reviews 21:262-+.
20. Brennan, F. P., F. Abram, F. A. Chinalia, K. G. Richards and V. O'Flaherty. 2010. Characterization of environmentally persistent Escherichia coli isolates leached from an Irish soil. Applied and Environmental Microbiology 76:2175-2180.
21. Buchan, A., M. Alber and R. E. Hodson. 2001. Strain-specific differentiation of environmental Escherichia coli isolates via denaturing gradient gel electrophoresis (DGGE) analysis of the 16S-23S intergenic spacer region. FEMS Microbiology Ecology 35:313-321.
22. Byappanahalli, M. N., R. L. Whitman, D. A. Shively, M. J. Sadowsky and S. Ishii. 2006. Population structure, persistence, and seasonality of autochthonous Escherichia coli in temperate, coastal forest soil from a Great Lakes watershed. Environmental Microbiology 8:504-513.
23. Carson, C. A., B. L. Shear, M. R. Ellersieck and A. Asfaw. 2001. Identification of fecal Escherichia coli from humans and animals by ribotyping. Applied and Environmental Microbiology 67:1503-1507.
24. Chee-Sanford, J. C., R. I. Aminov, I. J. Krapac, N. Garrigues-Jeanjean and R. I. Mackie. 2001. Occurrence and diversity of tetracycline resistance genes in lagoons and groundwater underlying two swine production facilities. Applied and Environmental Microbiology 67:1494-1502.
25. Cimenti, M., N. Biswas, J. K. Bewtra and A. Hubberstey. 2005. Evaluation of microbial indicators for the determination of bacterial groundwater contamination sources. Water Air and Soil Pollution 168:157-169.
26. Cole, D., S. C. Long and M. D. Sobsey. 2003. Evaluation of F+ RNA and DNA coliphages as source-specific indicators of fecal contamination in surface waters. Applied and Environmental Microbiology 69:6507-6514.
27. Cooper, K. E. and F. M. Ramadan. 1955. Studies in the differentiation between human and animal pollution by means of faecal streptococci. Journal of General Microbiology 12:180-190.
28. Craig, D. L., H. J. Fallowfield and N. J. Cromar. 2003. The Effects of Temperature and Sediment Characteristics on Survival of Escherichia Coli in Recreational Coastal Water and Sediment. Environmental Health.
29. Craig, D. L., H. J. Fallowfield and N. J. Cromar. 2004. Use of microcosms to determine persistence of Escherichia coli in recreational coastal water and sediment and validation with in situ measurements. Journal of Applied Microbiology 96:922-930.
30. Davies, C. M., J. A. Long, M. Donald and N. J. Ashbolt. 1995. Survival of fecal microorganisms in marine and freshwater sediments. Applied and Environmental Microbiology 61:1888-1896.
31. de Motes, C. M., P. Clemente-Casares, A. Hundesa, M. Martin and R. Girones. 2004. Detection of bovine and porcine adenoviruses for tracing the source of fecal contamination. Applied and Environmental Microbiology 70:1448-1454.
32. Dick, L. K., A. E. Bernhard, T. J. Brodeur, J. W. Santo Domingo, J. M. Simpson, S. P. Walters and K. G. Field. 2005. Host distributions of uncultivated fecal Bacteroidales bacteria reveal genetic markers for fecal source identification. Applied and Environmental Microbiology 71:3184-3191.
33. Dick, L. K. and K. G. Field. 2004. Rapid estimation of numbers of fecal Bacteroidetes by use of a quantitative PCR assay for 16S rNA genes. Applied and Environmental Microbiology 70:5695-5697.
34. Dick, L. K., E. A. Stelzer, E. E. Bertke, D. L. Fong and D. M. Stoeckel. 2010. Relative decay of Bacteroidales microbial source tracking markers and cultivated Escherichia coli in freshwater microcosms. Applied and Environmental Microbiology 76:3255-3262.
35. Dombek, P. E., L. K. Johnson, S. T. Zimmerley and M. J. Sadowsky. 2000. Use of repetitive DNA sequences and the PCR to differentiate Escherichia coli isolates from human and animal sources. Applied and Environmental Microbiology 66:2572-2577.
36. Eisenstein, L., D. Bodager and D. Ginzl. 2008. Outbreak of giardiasis and cryptosporidiosis associated with a neighborhood interactive water fountain--Florida, 2006. Journal of Environmental Health 71:18-22; quiz 49-50.
37. EPA. 2005. Microbial source tracking guide document. In U. S. E. P. Agency (ed.), Cincinnati.
38. Evans, T. M., C. E. Waarvick, R. J. Seidler and M. W. LeChevallier. 1981. Failure of the most-probable-number technique to detect coliforms in drinking water and raw water supplies. Applied and Environmental Microbiology 41:130-138.
39. Farag, A. M., J. N. Goldstein, D. F. Woodward and M. Samadpour. 2001. Water quality in three creeks in the backcountry of Grand Teton National Park, USA. Journal of Freshwater Ecology 16:135-143.
40. Farber, J. M. 1996. An introduction to the hows and whys of molecular typing. Journal of Food Protection 59:1091-1101.
41. Farnleitner, A. H., N. Kreuzinger, G. G. Kavka, S. Grillenberger, J. Rath and R. L. Mach. 2000. Simultaneous detection and differentiation of Escherichia coli populations from environmental freshwaters by means of sequence variations in a fragment of the beta-D-glucuronidase gene. Applied and Environmental Microbiology 66:1340-1346.
42. Field, K. G., E. C. Chern, L. K. Dick, J. Fuhrman, J. Griffith, P. A. Holden, M. G. LaMontagne, J. Le, B. Olson and M. T. Simonich. 2003. A comparative study of culture-independent, library-independent genotypic methods of fecal source tracking. Journal of Water and Health 1:181-194.
43. Foley, S. L., A. M. Lynne and R. Nayak. 2009. Molecular typing methodologies for microbial source tracking and epidemiological investigations of Gram-negative bacterial foodborne pathogens. Infection Genetics and Evolution 9:430-440.
44. Foley, S. L., D. G. White, P. F. McDermott, R. D. Walker, B. Rhodes, P. J. Fedorka-Cray, S. Simjee and S. H. Zhao. 2006. Comparison of subtyping methods for differentiating Salmonella enterica serovar Typhimurium isolates obtained from food animal sources. Journal of Clinical Microbiology 44:3569-3577.
45. Foulds, I. V., A. Granacki, C. Xiao, U. J. Krull, A. Castle and P. A. Horgen. 2002. Quantification of microcystin-producing cyanobacteria and E. coli in water by 5'-nuclease PCR. Journal of Applied Microbiology 93:825-834.
46. Frahm, E. and U. Obst. 2003. Application of the fluorogenic probe technique (TaqMan PCR) to the detection of Enterococcus spp. and Escherichia coli in water samples. Journal of Microbiological Methods 52:123-131.
47. Freyer, D. A. M. G. A. 1990. DNA amplification useing polemearse chain reaction, p. 144. In M. V. Bloom (ed.), DNA science: A first course in recombinant DNA technology. Carolina biological supply company, America.
48. Grabow, W. O. K., T. E. Neubrech, C. S. Holtzhausen and J. Jofre. 1995. Bacteroides fragilis and Escherichia coli Bacteriophages - Excretion by Humans and Animals. Water Science and Technology 31:223-230.
49. Guillot, E. and J.-F. Loret. 2010. Waterborne Pathogens: Review for the Drinking Water Industry. IWA Publishing, UK.
50. Hager, M. C. 2001a. Detecting bacteria in coastal waters. Part 1. The Journal for Surface Water Quality Professionals 2 3:16–25.
51. Hager, M. C. 2001b. Detecting bacteria in coastal waters. Part 2. The Journal for Surface Water Quality Professionals 2 4.
52. Harmsen, H. J., G. C. Raangs, T. He, J. E. Degener and G. W. Welling. 2002. Extensive set of 16S rRNA-based probes for detection of bacteria in human feces. Applied and Environmental Microbiology 68:2982-2990.
53. Hartel, P. G., C. Hagedorn, J. L. McDonald, J. A. Fisher, M. A. Saluta, J. W. Dickerson, L. C. Gentit, S. L. Smith, N. S. Mantriprayada, K. J. Ritter and C. N. Belcher. 2007a. Exposing water samples to ultraviolet light improves fluorometry for detecting human fecal contamination. Water Research 41:3629-3642.
54. Hartel, P. G., J. L. McDonald, L. C. Gentit, S. N. J. Hemmings, K. Rodgers, K. A. Smith, C. N. Belcher, R. L. Kuntz, Y. Rrvera-Torres, E. Otero and E. C. Schroder. 2007b. Improving fluorometry as a source tracking method to detect human fecal contamination. Estuaries and Coasts 30:551-561.
55. Hartel, P. G., J. D. Summer, J. L. Hill, J. V. Collins, J. A. Entry and W. I. Segars. 2002. Geographic variability of Escherichia coli ribotypes from animals in Idaho and Georgia. Journal of Environmental Quality 31:1273-1278.
56. Hayashi, H., M. Sakamoto and Y. Benno. 2002. Phylogenetic analysis of the human gut microbiota using 16S rDNA clone libraries and strictly anaerobic culture-based methods. Microbiology and Immunology 46:535-548.
57. Hayashi, H., M. Sakamoto, M. Kitahara and Y. Benno. 2003. Molecular analysis of fecal microbiota in elderly individuals using 16S rDNA library and T-RFLP. Microbiology and Immunology 47:557-570.
58. Holloway, P. 2001. Tracing the source of E. coli fecal contamination of water using rep-PCR, Manitoba Livestock Manure Management Initiative Project: MLMMI 00-02-08. University of Winnipeg.
59. Hong, P. Y., J. H. Wu and W. T. Liu. 2009. A high-throughput and quantitative hierarchical oligonucleotide primer extension (HOPE)-based approach to identify sources of faecal contamination in water bodies. Environmental Microbiology 11:1672-1681.
60. Hong, P. Y., J. H. Wu and W. T. Liu. 2008. Relative abundance of Bacteroides spp. in stools and wastewaters as determined by hierarchical oligonucleotide primer extension. Applied and Environmental Microbiology 74:2882-2893.
61. Hutchinson, M. and J. W. Ridgway. 1977. Microbiological Aspects of Drinking Water Supplies. Academic Press, London.
62. Ishii, S., T. Yan, D. A. Shively, M. N. Byappanahalli, R. L. Whitman and M. J. Sadowsky. 2006. Cladophora (Chlorophyta) spp. harbor human bacterial pathogens in nearshore water of Lake Michigan. Applied and Environmental Microbiology 72:4545-4553.
63. Jimenez-Clavero, M. A., E. Escribano-Romero, C. Mansilla, N. Gomez, L. Cordoba, N. Roblas, F. Ponz, V. Ley and J. C. Saiz. 2005. Survey of bovine enterovirus in biological and environmental samples by a highly sensitive real-time reverse transcription-PCR. Applied and Environmental Microbiology 71:3536-3543.
64. Jimenez-Clavero, M. A., C. Fernandez, J. A. Ortiz, J. Pro, G. Carbonell, J. V. Tarazona, N. Roblas and V. Ley. 2003. Teschoviruses as indicators of porcine fecal contamination of surface water. Applied and Environmental Microbiology 69:6311-6315.
65. Jin, G., H. W. Jeng, H. Bradford and A. J. Englande. 2004. Comparison of E. coli, enterococci, and fecal coliform as indicators for brackish water quality assessment. Water Environment Research 76:245-255.
66. Kildare, B. J., C. M. Leutenegger, B. S. McSwain, D. G. Bambic, V. B. Rajal and S. Wuertz. 2007. 16S rRNA-based assays for quantitative detection of universal, human-, cow-, and dog-specific fecal Bacteroidales: A Bayesian approach. Water Research 41:3701-3715.
67. King, R. C. and W. D. Stansfield. 2002. A Dictionary of Genetics, sixth ed. Oxford University Press:530.
68. Kreader, C. A. 1995. Design and Evaluation of Bacteroides DNA Probes for the Specific Detection of Human Fecal Pollution. Applied and Environmental Microbiology 61:1171-1179.
69. Layton, A., L. McKay, D. Williams, V. Garrett, R. Gentry and G. Sayler. 2006. Development of Bacteroides 16S rRNA gene TaqMan-based real-time PCR assays for estimation of total, human, and bovine fecal pollution in water. Applied and Environmental Microbiology 72:4214-4224.
70. Lee, C. M., T. Y. Lin, C. C. Lin, G. A. Kohbodi, A. Bhattl, R. Lee and J. A. Jay. 2006a. Persistence of fecal indicator bacteria in Santa Monica Bay beach sediments. Water Research 40:2593-2602.
71. Lee, D. Y., K. Shannon and L. A. Beaudette. 2006b. Detection of bacterial pathogens in municipal wastewater using an oligonucleotide microarray and real-time quantitative PCR. Journal of Microbiological Methods 65:453-467.
72. Lee, J. E., S. Lee, J. Sung and G. Ko. 2010. Analysis of human and animal fecal microbiota for microbial source tracking. ISME Journal.
73. Leser, T. D., J. Z. Amenuvor, T. K. Jensen, R. H. Lindecrona, M. Boye and K. Moller. 2002. Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Applied and Environmental Microbiology 68:673-690.
74. Ley, V., J. Higgins and R. Fayer. 2002. Bovine enteroviruses as indicators of fecal contamination. Applied and Environmental Microbiology 68:3455-3461.
75. Lynch, P. A., B. J. Gilpin, L. W. Sinton and M. G. Savill. 2002. The detection of Bifidobacterium adolescentis by colony hybridization as an indicator of human faecal pollution. Journal of Applied Microbiology 92:526-533.
76. Maier, R. M., I. L. Pepper and C. P. Gerba. 2009. Environmental Microbiology- Second edition, 2 ed. A Macmillan company, USA.
77. Manz, W., R. Amann, W. Ludwig, M. Vancanneyt and K. H. Schleifer. 1996. Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment. Microbiology 142 ( Pt 5):1097-1106.
78. Marshall, M. M., D. Naumovitz, Y. Ortega and C. R. Sterling. 1997. Waterborne protozoan pathogens. Clinical Microbiology Reviews 10:67-&.
79. McFeters, G. A., S. C. Cameron and M. W. LeChevallier. 1982. Influence of diluents, media, and membrane filters on detection fo injured waterborne coliform bacteria. Applied and Environmental Microbiology 43:97-103.
80. Meays, C. L., K. Broersma, R. Nordin and A. Mazumder. 2004. Source tracking fecal bacteria in water: a critical review of current methods. Journal of Environmental Management 73:71-79.
81. Mieszkin, S., J. P. Furet, G. Corthier and M. Gourmelon. 2009. Estimation of pig fecal contamination in a river catchment by real-time PCR using two pig-specific Bacteroidales 16S rRNA genetic markers. Applied and Environmental Microbiology 75:3045-3054.
82. Mohapatra, B. R., K. Broersma, R. Nordin and A. Mazumder. 2007. Evaluation of Repetitive Extragenic Palindromic-PCR for discrimination of fecal Escherichia coli from humans, and different domestic- and wild-animals. Microbiology and Immunology 51:733-740.
83. Moore, W. E. C. and L. H. Moore. 1995. Intestinal Floras of Populations That Have a High-Risk of Colon-Cancer. Applied and Environmental Microbiology 61:3202-3207.
84. Nemerow, N. E. 1974. Scientific stream pollution analysis. Scripta book company, Washinton.
85. Noble, R. T., S. M. Allen, A. D. Blackwood, W. Chu, S. C. Jiang, G. L. Lovelace, M. D. Sobsey, J. R. Stewart and D. A. Wait. 2003. Use of viral pathogens and indicators to differentiate between human and non-human fecal contamination in a microbial source tracking comparison study. Journal of Water and Health 1:195-207.
86. Nocker, A., T. Richter-Heitmann, R. Montijn, F. Schuren and R. Kort. 2010. Discrimination between live and dead cellsin bacterial communities from environmental water samples analyzed by 454 pyrosequencing. International Microbiology 13:59-65.
87. Okabe, S., N. Okayama, O. Savichtcheva and T. Ito. 2007. Quantification of host-specific Bacteroides-Prevotella 16S rRNA genetic markers for assessment of fecal pollution in freshwater. Applied Microbiology and Biotechnology 74:890-901.
88. Okabe, S. and Y. Shimazu. 2007. Persistence of host-specific Bacteroides-Prevotella 16S rRNA genetic markers in environmental waters: effects of temperature and salinity. Applied Microbiology and Biotechnology 76:935-944.
89. Parveen, S., R. L. Murphree, L. Edmiston, C. W. Kaspar, K. M. Portier and M. L. Tamplin. 1997. Association of multiple-antibiotic-resistance profiles with point and nonpoint sources of Escherichia coli in Apalachicola bay. Applied and Environmental Microbiology 63:2607-2612.
90. Payment, P., M. Waite and A. Dufour. 2003. Introducing parameters for the assessment of drinking water quality. OECD Publications.
91. Picone, T., T. Young and E. Fricker. 1997. Detection of Legionella and Legionella pneumophila in environmental water samples using the polymerase chain reaction, p. 159-182, Environmental applications of nucleic acid amplification techniques. Environmental applications of nucleic acid amplification techniques, Lancaster, PA.
92. Rompre, A., P. Servais, J. Baudart, M. R. de-Roubin and P. Laurent. 2002. Detection and enumeration of coliforms in drinking water: current methods and emerging approaches. Journal of Microbiological Methods 49:31-54.
93. Sachse, K. 2004. Specificity and performance of PCR detection assays for microbial pathogens. Molecular Biotechnology 26:61-80.
94. Samadpour, M. 2002. Microbial source tracking: principles and practice. US EPA Workshop on Microbial Source Tracking:5–9.
95. Samadpour, M. and N. Chechowitz. 1995. Little Soos Creek Microbial Source Tracking. Department of Environmental Health, University of Washington.
96. Sargeant, D. 1999. Fecal Contamination Source Identification Methods in Surface Water. Washington State Department of Ecology:19.
97. Savichtcheva, O. and S. Okabe. 2009. Qualitative and quantitative estimation of host-specific fecal pollution using Bacteroides-Prevotella 16S rRNA genetic markers by T-RFLP and real-time PCR analyses. Water Science and Technology 59:1831-1840.
98. Schaper, M., J. Jofre, M. Uys and W. O. K. Grabow. 2002. Distribution of genotypes of F-specific RNA bacteriophages in human and non-human sources of faecal pollution in South Africa and Spain. Journal of Applied Microbiology 92:657-667.
99. Scheidegger, E. M., S. A. Fracalanzza, L. M. Teixeira and P. Cardarelli-Leite. 2009. RFLP analysis of a PCR-amplified fragment of the 16S rRNA gene as a tool to identify Enterococcus strains. Memórias do Instituto Oswaldo Cruz 104:1003-1008.
100. Schulz, C. J. and G. W. Childers. 2011. Fecal Bacteroidales Diversity and Decay in Response to Variations in Temperature and Salinity. Applied and Environmental Microbiology 77:2563-2572.
101. Scott, T. M., S. Parveen, K. M. Portier, J. B. Rose, M. L. Tamplin, S. R. Farrah, A. Koo and J. Lukasik. 2003. Geographical variation in ribotype profiles of Escherichia coli isolates from humans, swine, poultry, beef, and dairy cattle in Florida. Applied and Environmental Microbiology 69:1089-1092.
102. Scott, T. M., J. B. Rose, T. M. Jenkins, S. R. Farrah and J. Lukasik. 2002. Microbial source tracking: Current methodology and future directions. Applied and Environmental Microbiology 68:5796-5803.
103. Seurinck, S., T. Defoirdt, W. Verstraete and S. D. Siciliano. 2005a. Detection and quantification of the human-specific HF183 Bacteroides 16S rRNA genetic marker with real-time PCR for assessment of human faecal pollution in freshwater. Environmental Microbiology 7:249-259.
104. Seurinck, S., W. Verstraete and S. D. Siciliano. 2005b. Microbial source tracking for identification of fecal pollution. Reviews in Environmental Science and Bio/Technology 4:19-37.
105. Shaban, A. B. and H. I. Malkawi. 2007. Rapid Detection of Human Enteric Pathogens (Viruses and Bacteria) in Water Resources from Jordan Using Polymerase Chain Reaction (PCR). Journal of Applied Sciences Research 3:10.
106. Silkie, S. S., M. P. Tolcher and K. L. Nelson. 2008. Reagent decontamination to eliminate false-positives in Escherichia coli qPCR. Journal of Microbiological Methods 72:275-282.
107. Simmons, G. M., D. F. Waye, S. Herbein, S. Myers and E. Walker. 2000. Estimating nonpoint fecal coliform sources in Northern Virginia’s four mile run watershed, in: Younos, T., Poff, J. (Eds.). Proceedings of the Virginia Water Research Symposium:248–267.
108. Simpson, J. M., J. W. Santo Domingo and D. J. Reasoner. 2002. Microbial source tracking: State of the science. Environmental Science & Technology 36:5279-5288.
109. Stoeckel, D. M., M. V. Mathes, K. E. Hyer, C. Hagedorn, H. Kator, J. Lukasik, T. L. O'Brien, T. W. Fenger, M. Samadpour, K. M. Strickler and B. A. Wiggins. 2004. Comparison of seven protocols to identify fecal contamination sources using Escherichia coli. Environmental Science & Technology 38:6109-6117.
110. Suzuki, M., M. S. Rappe and S. J. Giovannoni. 1998. Kinetic bias in estimates of coastal picoplankton community structure obtained by measurements of small-subunit rRNA gene PCR amplicon length heterogeneity. Applied and Environmental Microbiology 64:4522-4529.
111. Tartera, C., F. Lucena and J. Jofre. 1989. Human-Origin of Bacteroides fragilis Bacteriophages Present in the Environment. Applied and Environmental Microbiology 55:2696-2701.
112. Toze, S. 1999. PCR and the detection of microbial pathogens in water and wastewater. Water Research 33:3545-3556.
113. Tynkkynen, S., R. Satokari, M. Saarela, T. Mattila-Sandholm and M. Saxelin. 1999. Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains. Applied and Environmental Microbiology 65:3908-3914.
114. Unno, T., J. Jang, D. Han, J. H. Kim, M. J. Sadowsky, O. S. Kim, J. Chun and H. G. Hur. 2010. Use of Barcoded Pyrosequencing and Shared OTUs To Determine Sources of Fecal Bacteria in Watersheds. Environmental Science & Technology 44:7777-7782.
115. von Wintzingerode, F., U. B. Gobel and E. Stackebrandt. 1997. Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis. FEMS Microbiology Reviews 21:213-229.
116. Walk, S. T., E. W. Alm, D. M. Gordon, J. L. Ram, G. A. Toranzos, J. M. Tiedje and T. S. Whittam. 2009. Cryptic lineages of the genus Escherichia. Applied and Environmental Microbiology 75:6534-6544.
117. Walters, S. P. and K. G. Field. 2009. Survival and persistence of human and ruminant-specific faecal Bacteroidales in freshwater microcosms. Environmental Microbiology 11:1410-1421.
118. Wang, R. F., W. W. Cao and C. E. Cerniglia. 1997. PCR detection of Ruminococcus spp. in human and animal faecal samples. Molecular and Cellular Probes 11:259-265.
119. WHO. 2008. Guidelines for drinking-water quality, third edition, incoporating first and second addenda. In W. H. Organization (ed.), Switzerland.
120. Wu, J. H. and W. T. Liu. 2007. Quantitative multiplexing analysis of PCR-amplified ribosomal RNA genes by hierarchical oligonucleotide primer extension reaction. Nucleic Acids Research 35:-.
121. 金門縣環境保護局. 2006. 金門太湖、榮湖水庫污染整治規劃與初步設計計畫.
122. 黃馨. 2011. 以宿主專一性聚合酶鏈鎖反應及指標生物法應用於河川糞便污染評估. 台灣大學.

校內：2017-02-17公開
校外：2017-02-17公開

簡易檢索 / 詳目顯示

相關論文