臺灣博碩士論文加值系統

　　本研究採集台灣花蓮、高雄、屏東三個區域之淡水進行菌株的分離與純化，並從中篩選出具有新種潛力的菌株進行分類及鑑定。三個採集地之樣本中共分離出80株菌，其中包含革蘭氏陽性菌29株以及革蘭氏陰性菌51株。透過16S rRNA基因序列分析進行初步鑑定後，判斷菌株ANT-18、KYPC3、TAPG2、TAPW14具有成為新種細菌的潛力，因此將此四株菌作為本論文之主要研究對象，進行進一步的分類與鑑定。

　　菌株ANT-18分離自高雄茂林谷龍頭山瀑布水下游 (22°54'39"N 120°41'09"E)，為革蘭氏陰性之好氧桿菌，具有滑動性，具莢膜，不具鞭毛。其菌落在R2A培養基上呈西瓜紅色，規則圓形凸起，有光澤並會產生黏液。生長條件為15-37 °C (最適為25 °C)，pH範圍為7-8 (最適為pH 7)，以及0-1 % NaCl (最適為0 %)。經由16S rRNA基因序列進行親緣關係分析，顯示其隸屬於Hymenobacter屬，並與Hymenobacter ocellatus具有最高相似度 (97.93 %)。其主要脂肪酸包含iso-C15:0、anteiso-C15:0、C18:0、Summed Feature 4 (iso-C17:1 I/anteiso-C17:1 B)。主要醌型為MK-7。主要的多胺為homospermidine (HSPD)。極性脂肪組成包含phosphatidylethanolamine (PE)、兩個unidentified aminophospholipids (APL1-APL2)、一個unidentified aminolipid (AL)、兩個unidentified glycolipid (GL1-GL2) 以及七個unidentified lipids (L1-L7)。DNA G+C含量為63.65 mol%。經DNA-DNA雜交反應顯示菌株ANT-18與Hymenobacter ocellatus之雜合程度低於39 %，根據一系列形態、生理生化特性及遺傳特徵鑑定，證實其為Hymenobacter屬之新種細菌，並將其命名為Hymenobacter gummosus。模式菌株為ANT-18T (= LMG 29477T = KCTC 52166T = BCRC 80966T)。

　　菌株KYPC3與TAPG2分別分離自花蓮縣鳳林鎮林榮里的小溪流 (23°48'02"N 121°29'08"E) 以及屏東縣萬安溪 (22°37'21"N 120°38'48"E)，兩者皆為革蘭氏陰性之好氧桿菌，具莢膜，具鞭毛。其菌落在R2A培養基上皆呈現奶油色至灰白色，圓形，中心點呈黃綠色至墨綠色。生長條件分別為10-30 °C (最適為20-25 °C) 以及20-37 °C (最適為25-30 °C)， pH範圍分別為6-8 (最適為pH 7) 以及7-8 (最適為pH 7)，而生長鹽度範圍則分別為0-0.5 % NaCl (最適為0 %)以及0-1.0 % NaCl (最適為0. 5 %)。經16S rRNA基因序列進行親緣關係分析，顯示兩株菌皆隸屬於Rheinheimera屬，KYPC3與Rheinheimera tangshanensis具有最高相似度 (97.84 %)，TAPG2則是與Rheinheimera aquatica具有最高相似度 (98.57 %)。其主要脂肪酸皆為C12:0 3-OH、C16:0、Summed Feature 3 (C16:1ω7c/C16:1ω6c)。主要醌型皆為ubiquinone-8 (Q-8)。極性脂肪組成部分，菌株KYPC3為phosphatidylethanolamine (PE)、phosphatidylglycerol (PG)、unidentified aminophospholipid (APL)、unidentified phospholipid (PL)、unidentified lipid (L)；菌株TAPG2為phosphatidylethanolamine (PE)、phosphatidylglycerol (PG)、uncharacterized aminophospholipids (APL)、unidentified aminolipid (AL)、unidentified phospholipid (PL) 以及uncharacterized lipid (L)。DNA G+C含量分別為51.15 mol% 和53.57 mol%。經過DNA-DNA 雜交反應顯示菌株KYPC3和TAPG2與Rheinheimera屬中鄰近模式菌株之間的雜合程度皆低於40 %，根據一系列形態、生理生化特性及遺傳特徵鑑定，證實菌株KYPC3和TAPG2為Rheinheimera屬之新種細菌，並將KYPC3命名為Rheinheimera riviphila，TAPG2命名為Rheinheimera coerulea。模式菌株分別為KYPC3T (= LMG 29729T = KCTC 52440T = BCRC 81008T )以及TAPG2T (= LMG 30056T = KCTC 52815T = BCRC 81054T)。

　　菌株TAPW14分離自屏東縣萬安溪 (22°37'21"N 120°38'48"E)，為革蘭氏陰性之好氧桿菌，不具莢膜，不具鞭毛。其菌落在R2A培養基上呈現灰白色的半透明不規則粘液狀。生長條件為15-30 °C (最適為25-30 °C)， pH範圍為6-8 (最適為pH 7)，以及0-2 % NaCl (最適為0.5 %)。由16S rRNA基因序列進行親緣關係分析，顯示其隸屬於Flavobacterium屬，並與Flavobacterium akiainvivens具有最高相似度 (96.54 %)。其主要脂肪酸包含iso-C15:0、C16:0、Summed Feature 3 (C16:1ω7c/C16:1ω6c)。主要醌型為menaquinone-6 (MK-6)。極性脂肪組成包含phosphatidylethanolamine (PE)、uncharacterized aminophospholipids (APL1-APL3)、uncharacterized lipids (L1-L2)。DNA G+C含量為45.97 mol%。經過一系列形態、生理生化特性及遺傳特徵鑑定，證實菌株TAPW14為Flavobacterium屬之新種細菌，並命名為Flavobacterium album。模式菌株為TAPW14T (= LMG 30057T = KCTC 52808T = BCRC 81055T)。

In this study, four novel species bacteria isolated from freshwater in three cities of Taiwan (Hualien, Kaohsiung and Pingtung) were identified and classified.

Strain ANT-18T, isolated from a water sample taken from Longtoushan, Maolin Valley, Kaohsiung City in Taiwan (22°54'39"N 120°41'09"E), was characterized taxonomically using a polyphasic approach. Cells of strain ANT-18T were Gram-stain-negative, aerobic, motile by gliding rods that were covered by large capsules and formed red colonies. Growth occurred at 15-37 °C (optimum 25 °C), at pH 7-8 (optimum pH 7) and with 0-1 % NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ANT-18T belonged to the genus Hymenobacter and was most closely related to Hymenobacter ocellatus Myx 2105T with a sequence similarity of 97.93 %. The predominant fatty acids contained iso-C15:0, anteiso-C15:0, C18:0 and Summed Feature 4 (iso-C17:1 I/anteiso-C17:1 B). The major isoprenoid quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminophospholipids, an unidentified glycolipid and seven unidentified lipids. The major polyamine was homospermidine. The DNA G+C content of the genomic DNA was 63.65 mol%. The DNA-DNA relatedness of strain ANT-18T with respect to Hymenobacter ocellatus Myx 2105T was less than 39 %. On the basis of the phylogenetic inference and phenotypic data, strain ANT-18T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter gummosus sp. nov. is proposed. The type strain is ANT-18T (=LMG 29477T = KCTC 52166T = BCRC 80966T).

Bacterial strains KYPC3T and TAPG2T, isolated from water samples taken from Fenglin Township, Hualien County and Wan-An creek, Pingtung County in Taiwan, were characterized taxonomically using a polyphasic approach. Cells of strains KYPC3T and TAPG2T were Gram-stain-negative, aerobic, off-white with yellow-green to dark-green centres, rod-shaped, and motile by means of a single polar flagellum. Growth of strain KYPC3T occurred at 10-30 °C (optimum, 20-25 °C), at pH 6-8 (optimum, pH 7) and with 0-0.5 % NaCl (optimum, 0 %). Growth of strain TAPG2T occurred at 20-37 °C (optimum, 25-30 °C), at pH 7-8 (optimum, pH 7) and with 0-1 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strains KYPC3T and TAPG2T were belonged to genus Rheinheimera. Strain KYPC3T was most closely related to Rheinheimera tangshanensis JA3-B52T with sequence similarity of 97.84 %, and strain TAPG2T was most closely related to Rheinheimera aquatica GR5T with sequence similarity of 98.57 %. The major fatty acids of strains KYPC3T and TAPG2T were C12:0 3-OH, C16:0, Summed Feature 3 (C16:1ω7c/C16:1ω6c). The major respiratory quinone of both strains was Q-8. The DNA G+C content of the genomic DNA of both strains was 51.15 mol% and 53.57 mol%, respectively. The polar lipid profile of KYPC3T consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminophospholipid and an unidentified lipid; TAPG2T consisted of phosphatidylethanolamine、phosphatidylglycerol、an uncharacterized aminophospholipids、an unidentified aminolipid、an unidentified phospholipid and an uncharacterized lipid. The DNA-DNA relatedness of strains KYPC3T and TAPG2T with respect to recognized members of the genus Rheinheimera were less than 37 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strains KYPC3T and TAPG2T represent two novel species in the genus Rheinheimera, for which the name Rheinheimera riviphila sp. nov. and Rheinheimera coerulea sp. nov. are proposed, respectively. The type strains are KYPC3T (=LMG 29729T = KCTC 52440T = BCRC 81008T) and TAPG2T (= LMG 30056T = KCTC 52815T = BCRC 81054T).

Strain TAPW14T, isolated from a water sample taken from Wan-An creek, Pingtung County in Taiwan, was characterized taxonomically using a polyphasic approach. Cells of strain TAPW14T were Gram-negative rods, aerobic, no flagella. Flexirubin-type pigments were not produced. Growth occurred at 15-30 °C (optimum 25-30 °C), at pH 6-8 (optimum pH 7) and with 0-2% NaCl (optimum 0.5%). Based on phylogenetic analyses of 16S rRNA gene sequences, the closest neighbour of strain TAPW14T was Flavobacterium akiainvivens IK-1T with 96.54% identity. The predorminant fatty acids of TAPW14T were iso-C15:0, C16:0 and Summed Feature 3 (C16:1ω7c/C16:1ω6c). The polar lipid profile consisted of phosphatidylethanolamine, three unidentified aminophospholipids and two unidentified lipids. The major respiratory quinone was MK-6. The G+C content of the genomic DNA was 45.97 mol%. Based on distance from its nearest phylogenetic neighbours and phenotypic differences, the species Flavobacterium album sp. nov. is proposed to accommodate strain TAPW14T (= LMG 30057T = KCTC 52808T = BCRC 81055T ) as the type strain.

摘要 I
Abstract IV
致謝 VIII
目錄 X
圖目錄 XIV
表目錄 XVI
第一章 緒論 1
一、前言 1
二、研究目的 2
第二章 文獻回顧 3
一、細菌分類學 3
(一) 簡介 3
(一) 歷史發展 3
(二) 分類方式 5
(三) 新菌種／屬之定義標準 6
(四) 正式命名 6
(五) 新種／屬細菌之發表 7
二、菌屬介紹 7
(一) Hymenobacter屬 7
(二) Rheinheimera屬 8
(三) Flavobacterium屬 8
第三章 材料與方法 10
一、實驗架構與流程 10
二、菌株之分離純化與保存 11
(一) 樣品來源 11
(二) 菌株之分離與純化 11
(三) 菌株保存 12
三、細菌形態學分析 13
(一) 菌落形態特徵 13
(二) 菌體形態特徵 15
(三) 運動性觀察 20
四、細菌細胞蛋白質電泳圖譜分析與分群 20
(一) 樣品製備與處理 21
(二) SDS-PAGE分析 22
(三) 電泳膠片之保存與分析 23
五、遺傳特徵分析 24
(一) 16S rRNA基因序列分析與比對 24
(二) 建立演化樹 27
(三) DNA-DNA雜交 (DNA-DNA hybridization) 27
(四) DNA G+C組成分析 30
六、生理特性分析 31
(一) 最適生長條件 31
(二) 氧氣需求測試 - 厭氧缸測試法 32
(三) 抗生素感受性測試 33
七、生化特性分析 34
(一) 氧化酶試驗 34
(二) 觸酶試驗 35
(三) 水解能力測試 35
(四) Biomerieux微生物鑑定套組 38
(五) BIOLOG GN II碳源利用鑑定 44
(六) 色素分析 46
(七) 極性脂肪組成分析 46
(八) 脂肪酸組成分析 49
(九) 多胺分析 51
(十) 醌分析 54
第四章 結果與討論 57
一、菌株分離純化與初步鑑定 57
二、菌株ANT-18之分類鑑定 59
(一) 形態特徵分析 59
(二) 生理特徵分析 60
(三) 生化特徵分析 62
(四) 遺傳特徵分析 70
(五) 與同屬鄰近菌株之差異比較 71
三、菌株KYPC3與TAPG2之分類鑑定 73
(一) 形態特徵分析 73
(二) 生理特徵分析 75
(三) 生化特徵分析 77
(四) 遺傳特徵分析 84
(五) 與同屬鄰近菌株之差異比較 87
四、菌株TAPW14之分類鑑定 89
(一) 形態特徵分析 89
(二) 生理特徵分析 91
(三) 生化特徵分析 93
(四) 遺傳特徵分析 99
(六) 與同屬鄰近菌株之差異比較 101
第五章 結論 103
第六章 參考文獻 108

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