臺灣博碩士論文加值系統

本研究的主要目的是進行台灣環境水樣之菌株的分離與純化，並從中篩選具有成為新菌種潛力之細菌，進而進行分類與鑑定。實驗樣本來自12處水源，從中共分離純化到131菌株。經過 16S rRNA 基因序列分析的初步結果，得知有14株菌株具有成為新屬與新種菌株的潛能。本論文選用 KYPW7、TLA-22、CHR27、ICH-30、LLJ-11、WWJ-16六株菌株，進行進一步的特性分析。
菌株KYPW7T經16S rRNA基因序列分析，結果顯示與Flavobacteriaceae 科中的其他菌屬成員的相似度小於 96.0%。利用16S rRNA基因序列分析、多位點序列分析 (MLSA) 及最新細菌核心基因組序列分析 (UBCG) 並繪製親緣演化樹圖，證實菌株KYPW7為Flavobacteriaceae 科中的新菌屬。菌株KYPW7T與Flavobacteriaceae 科中的其他鄰近菌屬的菌株相比較，其平均核苷酸相似度 (ANI) 低於72.1%，而數位DNA-DNA雜交相似度 (dDDH) 低於27.9%。這些結果可推測菌株KYPW7T為Flavobacteriaceae 科中的新屬菌株。經由形態、生理生化及遺傳特徵等分析結果，確認菌株KYPW7T為Flavobacteriaceae 科中的新屬新種細菌，並將其命名為Amniculibacterium aquaticum gen. nov., sp. nov.。模式菌種為Amniculibacterium aquaticum，而模式菌株為KYPW7T (=BCRC 81123T =LMG 30598T =KCTC 62512T )。
菌株TLA-22T 與CHR27T經16S rRNA基因序列分析，結果顯示菌株TLA-22T與Sphingobium aromaticiconvertens RW16T具有最高相似度 (97.4%)，而菌株CHR27T與Sphingobium qiguonii X23T具有最高相似度 (97.0%)。利用16S rRNA基因序列分析及最新細菌核心基因組序列分析 (UBCG) 並繪製親緣演化樹圖，證實二菌株TLA-22T 與CHR27T為Sphingobium屬的新種細菌。二菌株與Sphingobium屬中的其他菌株相比較，其平均核苷酸相似度範圍分別在74.8-75.7%與73.2-74.8%，而數位DNA-DNA雜交相似度範圍分別在20.1-22.0%與19.4-22.1%，推測此二菌株為Sphingobium屬的新種細菌。經由表現型、化學分類學特徵和系統親緣關係推論，確認菌株TLA-22T與CHR27T為Sphingobium屬的新種細菌，並將其分別命名為Sphingobium algorifonticola sp. nov. 與 Sphingobium fluviale sp. nov.。Sphingobium algorifonticola的模式菌株為TLA-22T (=BCRC 81097T =LMG 30309T =KCTC 62189T)。Sphingobium fluviale的模式菌株為CHR27T (=BCRC 81121T =LMG 30596T =KCTC 62510T)。
菌株ICH-30T、LLJ-11T、WWJ-16T經16S rRNA基因序列分析，結果顯示菌株ICH-30T與Flavobacterium lacus NP180T具有最高相似度 (97.0%)，而菌株LLJ-11T與Flavobacterium amniphilum KYPY10T有最高相似度 (98.0%)，而菌株WWJ-16T與Flavobacterium fontis MIC3010T有最高相似度 (97.9%)。利用16S rRNA基因序列分析及最新細菌核心基因組序列分析 (UBCG) 並繪製親緣演化樹圖，證實三菌株ICH-30T、LLJ-11T、WWJ-16T為Flavobacterium屬的新種細菌。三菌株與Flavobacterium屬中的其他菌株相比較，菌株ICH-30T的平均核苷酸相似度範圍為70.0-83.1%，而數位DNA-DNA雜交相似度範圍為16.5-23.7%；菌株LLJ-11T的平均核苷酸相似度範圍為70.0-76.3%，而數位DNA-DNA雜交相似度範圍為21.1-23.9%；菌株WWJ-16T的平均核苷酸相似度範圍為68.8-77.4%，而數位DNA-DNA雜交相似度範圍為20.6-24.3%，這些數據可推測此三菌株為Flavobacterium屬的新種細菌。經由表現型、化學分類學特徵和系統親緣關係推論，確認菌株ICH-30T、LLJ-11T、WWJ-16T為Sphingobium屬的新種細菌，並將其分別命名為Flavobacterium piscinae sp. nov.、 Flavobacterium amnicola sp. nov. 與 Flavobacterium stagni sp. nov.。Flavobacterium piscinae的模式菌株為ICH-30T (=BCRC 81122T =LMG 30579T =KCTC 62513T)。Flavobacterium amnicola的模式菌株為LLJ-11T (=BCRC 81124T =LMG 30599T =KCTC 62514T)。Flavobacterium stagni的模式菌株為WWJ-16T (=BCRC 81125T =LMG 30600T =KCTC 62515T)。

Purpose of this study is to isolate and purify bacterial strains from the environmental water samples in Taiwan and to screen bacteria with potential to be as novel genus and novel species. And then, these bacteria were subjected to further identification and classification. Experimental samples come from twelve water sources, and 131 bacterial strains were isolated and purified. After phylogenetic analysis of 16S rRNA gene sequence, 14 bacterial strains were obtained with potential to be as novel genus and novel species. In this study, six strains, KYPW7, TLA-22, CHR27, ICH-30, LLJ-11 and WWJ-16, were selected and subjected to further characterization.
Strain KYPW7T shared low level of 16S rRNA gene sequence similarity (less than 96.0%) to members of other genera in the family Flavobacteriaceae. Phylogenetic analyses based on 16S rRNA gene sequence, multilocus sequence (MLS) and up-to-date bacterial core gene (UBCG) sequence showed that strain KYPW7T represents a novel genus of the family Flavobacteriaceae. Strain KYPW7T showed less than 72.1% average nucleotide identity (ANI) and less than 27.9% digital DNA-DNA hybridization (dDDH) identity compared to the type strains of related genera within the family Flavobacteriaceae. These results indicated that strain KYPW7T should be assigned to a novel genus of the family Flavobacteriaceae. On the basis of morphological, physiological, biochemical and genetic data, strain KYPW7T represents a novel species of a new genus in the family Flavobacteriaceae, for which the name Amniculibacterium aquaticum gen. nov., sp. nov. is proposed. The type species is Amniculibacterium aquaticum, and the type strain is KYPW7T (=BCRC 81123T =LMG 30598T =KCTC 62512T).
Strain TLA-22T was most closely related to Sphingobium aromaticiconvertens RW16T with 97.4% 16S rRNA gene sequence similarity, and strain CHR27T was most closely related to Sphingobium qiguonii X23T with 97.0%. Phylogenetic analyses based on 16S rRNA gene sequence and UBCG sequence indicated that both strains, TLA-22T and CHR27T, represent novel species of bacteria in the genus Sphingobium. Strain TLA-22T showed 74.8-75.7% ANI and 20.1-22.0% dDDH values with the strains of other Sphingobium species, and strain CHR27T showed 19.4-22.1% dDDH values and 73.2-74.8% ANI. These data confirmed that both strains should be assigned to novel species in the genus Sphingobium. On the basis of phenotypic, chemotaxonomic properties and phylogenetic inference, it is clear that both strains, TLA-22T and CHR27T, represent two novel species of the genus Sphingobium, for which the names Sphingobium algorifonticola sp. nov. and Sphingobium fluviale sp. nov. are proposed. The type strain of Sphingobium algorifonticola is TLA-22T (=BCRC 81097T =LMG 30309T =KCTC 62189T). The type strain of Sphingobium fluviale is CHR27T (=BCRC 81121T =LMG 30596T =KCTC 62510T).
Strain ICH-30T was most closely related to Flavobacterium lacus NP180T with 97.0% 16S rRNA gene sequence similarity, strain LLJ-11T most closely related to Flavobacterium amniphilum KYPY10T with 98.0%, and strain WWJ-16T most closely related to Flavobacterium fontis MIC3010T with 97.9%. Phylogenetic analyses based on 16S rRNA gene sequence and UBCG sequence indicated that three strains, ICH-30T, LLJ-11T and WWJ-16T, represent novel species of bacteria in the genus Flavobacterium. Strain ICH-30T showed 70.0-83.1% ANI and 16.5-23.7% dDDH values with the strains of other Flavobacterium species, strain LLJ-1T showed 21.1-23.9% dDDH values and 70.0-76.3% ANI and strain WWJ-16T showed 20.6-24.3% dDDH values and 68.8-77.4% ANI. These data confirmed that all strains should be assigned to novel species in the genus Flavobacterium. On the basis of phenotypic, chemotaxonomic properties and phylogenetic inference, it is clear that three strains, ICH-30T, LLJ-11T and WWJ-16T, represent three novel species of the genus Flavobacterium, for which the names Flavobacterium piscinae sp. nov., Flavobacterium amnicola sp. nov. and Flavobacterium stagni sp. nov. are proposed. The type strain of Flavobacterium piscinae is ICH-30T (=BCRC 81122T =LMG 30579T =KCTC 62513T). The type strain of Flavobacterium amnicola is LLJ-11T (=BCRC 81124T =LMG 30599T =KCTC 62514T). The type strain of Flavobacterium stagni is WWJ-16T (=BCRC 81125T =LMG 30600T =KCTC 62515T).

摘 要 i
Abstract iii
誌謝 v
目錄 vi
表目錄 ix
圖目錄 xiii
第壹章 緒論 17
一、 前言 17
二、 研究目的 17
第貳章 文獻回顧 18
一、 細菌分類學 18
(一) 簡介 18
(二) 新菌種 (屬) 之定義 19
(三) 新菌種 (屬) 之發表 21
二、 Flavobacteriaceae科簡介 21
三、 Sphingobium屬簡介 21
四、 Flavobacterium屬簡介 22
第參章 材料與方法 23
一、 細菌分類之實驗架構與流程 23
二、 菌株之分離純化與保存 23
(一) 樣品來源 23
(二) 菌株的分離與純化 24
(三) 菌株分類分群 25
三、 菌株初步特徵分析 25
(一) 革蘭氏染色 (Gram staining) 25
(二) 氫氧化鉀試驗 (KOH Test) 26
(三) 氧化酶試驗 (Oxidase Test) 26
(四) 觸酶試驗 (Catalase Test) 27
四、 菌種保存 27
(一) 短期保存 27
(二) 長期保存 27
五、 細菌細胞蛋白質SDS-PAGE電泳圖譜分析與分群 28
(一) 樣品製備處理 28
(二) SDS-PAGE電泳分析 29
(三) 膠片保存與分析 30
六、 遺傳特徵分析 30
(一) 16S rRNA 基因序列分析與親緣演化樹圖建構 30
(二) 細菌全基因序列分析與親緣演化樹圖建構 33
(三) DNA G＋C mol%分析 36
(四) DNA-DNA雜合相似度分析 37
七、 形態分析 38
(一) 菌落形態觀察 38
(二) 菌體形態觀察 38
(三) 運動性觀察 40
八、 生理生化特性分析 40
(一) 最適生長條件測試 40
(二) 氧氣需求試驗 43
(三) 色素分析 43
(四) 剛果紅試驗 44
(五) 抗生素耐受性測試 44
(六) 硝酸還原能力測試 44
(七) 水解能力測試 44
(八) API套組系統之鑑定 46
(九) 單一碳源利用分析 49
(十) 極性脂肪分析 50
(十一) 脂肪酸分析 52
(十二) 多胺分析 54
(十三) 醌型分析 56
第肆章 結果與討論 58
一、 樣品來源、菌株分離純化及初步鑑定 58
二、 新種 (屬) 菌株之鑑定與特性描述 63
(一) 菌株KYPW7之分類鑑定 64
(二) 菌株TLA-22及CHR27之分類鑑定 84
(三) 菌株ICH-30、LLJ-11及WWJ-16之分類鑑定 116
結論 168
參考文獻 173

Allen, T. D., Lawson, P. A., Collins, M. D., Falsen, E. & Tanner, R. S. (2006). Cloacibacterium normanense gen. nov., sp. nov., a novel bacterium in the family Flavobacteriaceae isolated from municipal wastewater. International Journal of Systematic and Evolutionary Microbiology, 56(6), 1311-1316.
An, Q. D., Zhang, G. L., Wu, H. T., Zhang, Z. C., Zheng, G. S., Luan, L., Luan, Y., Murata & Li, X. (2009). Alginate‐deriving oligosaccharide production by alginase from newly isolated Flavobacterium sp. LXA and its potential application in protection against pathogens. Journal of applied microbiology, 106(1), 161-170.
Aziz, R. K., Bartels, D., Best, A. A., DeJongh, M., Disz, T., Edwards, R. A., Formsma, K., Gerdes, S., Glass, E. M., Kubal, M., Meyer, F., Olsen, G. J., Olsen, R., Osterman, A. L., Overbeek, R. A., McNeil, L. K., Paarmann, D., Paczian, T., Parrello, B., Pusch, G. D., Reich, C., Stevens, R., Vassieva, O., Vonstein, V., Wilke, A. & Zagnitko, O. (2008). The RAST Server: rapid annotations using subsystems technology. BMC Genomics, 9(1), 75.
Baek, S. H., Lim, J. H. & Lee, S. T. (2010). Sphingobium vulgare sp. nov., isolated from freshwater sediment. International Journal of Systematic and Evolutionary Microbiology, 60(10), 2473-2477.
Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A. & Pevzner, P. A. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455-477.
Bergey, D. H., Harrison, F. C., Breed, R. S., Hammer, B. W. & Huntoon, F. M. (1923). Genus II. Flavobacterium gen. nov. Bergey’s Manual of Determinative Bacteriology, 97, 117.
Bernardet, J. F., Segers, P., Vancanneyt, M., Berthe, F., Kersters, K. & Vandamme, P. (1996). Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov.(basonym, Cytophaga aquatilis Strohl and Tait 1978). International Journal of Systematic and Evolutionary Microbiology, 46(1), 128-148.
Bodour, A. A., Guerrero-Barajas, C., Jiorle, B. V., Malcomson, M. E., Paull, A. K., Somogyi, A., Trinh, L. N., Bates, R. B. & Maier, R. M. (2004). Structure and characterization of flavolipids, a novel class of biosurfactants produced by Flavobacterium sp. strain MTN11. Appl. Environ. Microbiol., 70(1), 114-120.
Cao, S. J., Deng, C. P., Li, B. Z., Dong, X. Q. & Yuan, H. L. (2010). Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment. International Journal of Systematic and Evolutionary Microbiology, 60(9), 2023-2026.
Chen, W. M., Su, C. L. & Sheu, S. Y. (2017). Flavobacterium lacunae sp. nov., isolated from a freshwater pond. International Journal of Systematic and Evolutionary Microbiology, 67(4), 875-882.
Chun, B. H., Lee, Y., Jin, H. M. & Jeon, C. O. (2017). Cloacibacterium caeni sp. nov., isolated from activated sludge. International Journal of Systematic and Evolutionary Microbiology, 67(6), 1688-1692.
Chun, J., Kang, J. Y. & Jahng, K. Y. (2013). Flavobacterium fontis sp. nov., isolated from freshwater. International Journal of Systematic and Evolutionary Microbiology, 63(5), 1653-1657.
Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D. R., da Costa, M. S., Rooney, A. P., Yi, H., Xu, X. W., De Meyer, S. & Trujillo, M. E. (2018). Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 68(1), 461-466.
Colombo, M., Cavalca, L., Bernasconi, S., & Andreoni, V. (2011). Bioremediation of polyaromatic hydrocarbon contaminated soils by native microflora and bioaugmentation with Sphingobium chlorophenolicum strain C3R: a feasibility study in solid-and slurry-phase microcosms. International biodeterioration & biodegradation, 65(1), 191-197.
del Carmen Montero-Calasanz, M., Göker, M., Rohde, M., Spröer, C., Schumann, P., Busse, H. J., Schmid, M, Klenk, H. P., Tindall, B. J. & Camacho, M. (2014). Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense. Systematic and Applied Microbiology, 37(5), 342-350.
Ewels, P., Magnusson, M., Lundin, S. & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048.
Giri, S., & Pati, B. R. (2004). A comparative study on phyllosphere nitrogen fixation by newly isolated Corynebacterium sp. & Flavobacterium sp. and their potentialities as biofertilizer. Acta microbiologica et immunologica Hungarica, 51(1-2), 47-56.
Hall, T., Biosciences, I. & Carlsbad, C. (2011). BioEdit: an important software for molecular biology. GERF Bull Biosci, 2(1), 60-61.
Hantsis-Zacharov, E. & Halpern, M. (2007). Chryseobacterium haifense sp. nov., a psychrotolerant bacterium isolated from raw milk. International Journal of Systematic and Evolutionary Microbiology, 57(10), 2344-2348.
Holmes, B., Owen, R. J., Steigerwalt, A. G. & Brenner, D. J. (1984). Flavobacterium gleum, a new species found in human clinical specimens. International Journal of Systematic and Evolutionary Microbiology, 34(1), 21-25.
Holmes, B., Steigerwalt, A. G., Weaver, R. E. & Brenner, D. J. (1986). Weeksella zoohelcum sp. nov.(formerly group IIj), from human clinical specimens. Systematic and Applied Microbiology, 8(3), 191-196.
HuiJie, L., CaiYun, Y., Yun, T., GuangHui, L., & TianLing, Z. (2011). Using population dynamics analysis by DGGE to design the bacterial consortium isolated from mangrove sediments for biodegradation of PAHs. International Biodeterioration & Biodegradation, 65(2), 269-275.
Hyun, D. W., Shin, N. R., Kim, M. S., Kim, J. Y., Kim, P. S., Oh, S. J., Whon, T.W. & Bae, J. W. (2014). Cloacibacterium haliotis sp. nov., isolated from the gut of an abalone, Haliotis discus hannai. International Journal of Systematic and Evolutionary Microbiology, 64(1), 72-77.
Jooste, P. J. (1985). The taxonomy and significance of Flavobacterium-Cytophaga strains from dairy sources.
Jooste, P. J. & Hugo, C. J. (1999). The taxonomy, ecology and cultivation of bacterial genera belonging to the family Flavobacteriaceae. International Journal of Food Microbiology, 53(2-3), 81-94.
Kämpfer, P., Vaneechoutte, M., Lodders, N., De Baere, T., Avesani, V., Janssens, M., Busse, H. & Wauters, G. (2009). Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense, proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium. International Journal of Systematic and Evolutionary Microbiology, 59(10), 2421-2428.
Kanaly, R. A. & Harayama, S. (2000). Biodegradation of high-molecular-weight polycyclic aromatic hydrocarbons by bacteria. Journal of Bacteriology, 182(8), 2059-2067.
Kanaly, R. A. & Harayama, S. (2010). Advances in the field of high‐molecular‐weight polycyclic aromatic hydrocarbon biodegradation by bacteria. Microbial Biotechnology, 3(2), 136-164.
Khondee, N., Tathong, S., Pinyakong, O., Powtongsook, S., Chatchupong, T., Ruangchainikom, C., & Luepromchai, E. (2012). Airlift bioreactor containing chitosan-immobilized Sphingobium sp. P2 for treatment of lubricants in wastewater. Journal of hazardous materials, 213, 466-473.
Lee, I., Kim, Y. O., Park, S. C. & Chun, J. (2016). OrthoANI: an improved algorithm and software for calculating average nucleotide identity. International Journal of Systematic and Evolutionary Microbiology, 66(2), 1100-1103.
Li, A., Liu, H., Sun, B., Zhou, Y. & Xin, Y. (2014). Flavobacterium lacus sp. nov., isolated from a high-altitude lake, and emended description of Flavobacterium filum. International Journal of Systematic and Evolutionary Microbiology, 64(3), 933-939.
Li, A. H., Liu, H. C. & Zhou, Y. G. (2017). Flavobacterium orientale sp. nov., isolated from lake water. International Journal of Systematic and Evolutionary Microbiology, 67(1), 108-112.
Na, S. I., Kim, Y. O., Yoon, S. H., Ha, S. M., Baek, I. & Chun, J. (2018). UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. Journal of Microbiology, 56(4), 281-285.
Nguyen, N. L., Kim, Y. J., Hoang, V. A. & Yang, D. C. (2013). Chryseobacterium ginsengisoli sp. nov., isolated from the rhizosphere of ginseng and emended description of Chryseobacterium gleum. International Journal of Systematic and Evolutionary Microbiology, 63(8), 2975-2980.
Park, M., Joung, Y., Nam, G. G., Kim, S. & Cho, J. C. (2017). Flavobacterium inkyongense sp. nov., isolated from an artificial freshwater pond. International Journal of Systematic and Evolutionary Microbiology, 67(1), 82-86.
Pflanz, M. & Zude, M. (2008). Spectrophotometric analyses of chlorophyll and single carotenoids during fruit development of tomato (Solanum lycopersicum L.) by means of iterative multiple linear regression analysis. Applied Optics, 47(32), 5961-5970.
Raina, V., Suar, M., Singh, A., Prakash, O., Dadhwal, M., Gupta, S. K., Dogra, C., Lawlor, K., Lal, S., van der Meer, J. R., Holliger, C., & Lal, R. (2008). Enhanced biodegradation of hexachlorocyclohexane (HCH) in contaminated soils via inoculation with Sphingobium indicum B90A. Biodegradation, 19(1), 27-40.
Rainey, F. A. (2011). How to describe new species of prokaryotes. In Methods in Microbiology (Vol. 38, pp. 7-14). Academic Press.
Rappé, M. S. & Giovannoni, S. J. (2003). The uncultured microbial majority. Annual Reviews in Microbiology, 57(1), 369-394.
Reichenbach, H. (1992). The order cytophagales. In The prokaryotes (pp. 3631-3675). Springer, New York, NY.
Rubbenstroth, D., Ryll, M., Hotzel, H., Christensen, H., Knobloch, J. K. M., Rautenschlein, S. & Bisgaard, M. (2013). Description of Riemerella columbipharyngis sp. nov., isolated from the pharynx of healthy domestic pigeons (Columba livia f. domestica), and emended descriptions of the genus Riemerella, Riemerella anatipestifer and Riemerella columbina. International Journal of Systematic and Evolutionary Microbiology, 63(1), 280-287.
Sang, M. K., & Kim, K. D. (2012). The volatile‐producing Flavobacterium johnsoniae strain GSE09 shows biocontrol activity against Phytophthora capsici in pepper. Journal of applied microbiology, 113(2), 383-398.
Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics, 30(14), 2068-2069.
Segers, P., Mannheim, W., Vancanneyt, M., De Brandt, K., Hinz, K. H., Kersters, K. & Vandamme, P. (1993). Riemerella anatipestifer gen. nov., comb. nov., the causative agent of septicemia anserum exsudativa, and its phylogenetic affiliation within the Flavobacterium-Cytophaga rRNA homology group. International Journal of Systematic and Evolutionary Microbiology, 43(4), 768-776.
Sheu, S. Y., Chen, Y. L. & Chen, W. M. (2016). Flavobacterium verecundum sp. nov., isolated from a freshwater river. International Journal of Systematic and Evolutionary Microbiology, 66(9), 3337-3344.
Sheu, S. Y., Lin, Y. S. & Chen, W. M. (2013). Flavobacterium squillarum sp. nov., isolated from a freshwater shrimp culture pond, and emended descriptions of Flavobacterium haoranii, Flavobacterium cauense, Flavobacterium terrae and Flavobacterium aquatile. International Journal of Systematic and Evolutionary Microbiology, 63(6), 2239-2247.
Sheu, S. Y., Shiau, Y. W. & Chen, W. M. (2013). Sphingobium sufflavum sp. nov., isolated from a freshwater lake. International Journal of Systematic and Evolutionary Microbiology, 63(9), 3444-3450.
Sheu, S. Y., Su, C. L., Kwon, S. W. & Chen, W. M. (2017). Flavobacterium amniphilum sp. nov., isolated from a stream. International Journal of Systematic and Evolutionary Microbiology, 67(12), 5179-5186.
Shoemaker, C. A., Klesius, P. H., Drennan, J. D., & Evans, J. J. (2011). Efficacy of a modified live Flavobacterium columnare vaccine in fish. Fish & shellfish immunology, 30(1), 304-308.
Siddiqi, M. Z., Choi, G. M., Kim, M. S. & Im, W. T. (2017). Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water. International Journal of Systematic and Evolutionary Microbiology, 67(8), 2665-2671.
Singh, H., Du, J., Won, K., Yang, J. E., Akter, S., Kim, K. Y. & Yi, T. H. (2015). Flavobacterium vireti sp. nov., isolated from soil. Antonie van Leeuwenhoek, 107(6), 1421-1428.
Stolz, A. (2009). Molecular characteristics of xenobiotic-degrading sphingomonads. Applied Microbiology and Biotechnology, 81(5), 793-811.
Takeuchi, M., Hamana, K. & Hiraishi, A. (2001). Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. International Journal of Systematic and Evolutionary Microbiology, 51(4), 1405-1417.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10), 2731-2739.
Tatusov, R. L., Galperin, M. Y., Natale, D. A., & Koonin, E. V. (2000). The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic acids research, 28(1), 33-36.
Vancanneyt, M., Vandamme, P., Segers, P., Torck, U., Coopman, R., Kersters, K. & Hinz, K. H. (1999). Riemerella columbina sp. nov., a bacterium associated with respiratory disease in pigeons. International Journal of Systematic and Evolutionary Microbiology, 49(1), 289-295.
Vandamme, P., Bernardet, J. F., Segers, P., Kersters, K. & Holmes, B. (1994). New Perspectives in the Classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. International Journal of Systematic and Evolutionary Microbiology, 44(4), 827-831.
Wayne, L. G., Brenner, D. J., Colwell, R. R., Grimont, P. A. D., Kandler, O., Krichevsky, M. I., Moore, L. H., Moore, W. E. C., Murray, R. G. E., Stackebrandt, E., Starr, M. P. & Truper, H. G. (1987). Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic and Evolutionary Microbiology, 37(4), 463-464.
Weon, H. Y., Song, M. H., Son, J. A., Kim, B. Y., Kwon, S. W., Go, S. J. & Stackebrandt, E. (2007). Flavobacterium terrae sp. nov. and Flavobacterium cucumis sp. nov., isolated from greenhouse soil. International Journal of Systematic and Evolutionary Microbiology, 57(7), 1594-1598.
Wittich, R. M., Busse, H. J., Kämpfer, P., Tiirola, M., Wieser, M., Macedo, A. J. & Abraham, W. R. (2007). Sphingobium aromaticiconvertens sp. nov., a xenobiotic-compound-degrading bacterium from polluted river sediment. International Journal of Systematic and Evolutionary Microbiology, 57(2), 306-310.
Wu, Y. F., Wu, Q. L. & Liu, S. J. (2013). Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum. International Journal of Systematic and Evolutionary Microbiology, 63(3), 913-919.
Yabuuchi, E., Yano, I., Oyaizu, H., Hashimoto, Y., Ezaki, T. & Yamamoto, H. (1990). Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb, nov., and Two Genospecies of the Genus Sphingomonas. Microbiology and immunology, 34(2), 99-119.
Yan, Q. X., Wang, Y. X., Li, S. P., Li, W. J. & Hong, Q. (2010). Sphingobium qiguonii sp. nov., a carbaryl-degrading bacterium isolated from a wastewater treatment system. International Journal of Systematic and Evolutionary Microbiology, 60(12), 2724-2728.
Zamora, L., Domínguez, L., Fernández-Garayzábal, J. F. & Vela, A. I. (2016). Bergeyella porcorum sp. nov., isolated from pigs. Systematic and Applied Microbiology, 39(3), 160-163.
Zhang, J., Lang, Z. F., Zheng, J. W., Hang, B. J., Duan, X. Q., He, J. & Li, S. P. (2012). Sphingobium jiangsuense sp. nov., a 3-phenoxybenzoic acid-degrading bacterium isolated from a wastewater treatment system. International Journal of Systematic and Evolutionary Microbiology, 62(4), 800-805.
Zhang, J., Lin, X., Liu, W., Wang, Y., Zeng, J., & Chen, H. (2012). Effect of organic wastes on the plant-microbe remediation for removal of aged PAHs in soils. Journal of Environmental Sciences, 24(8), 1476-1482.
Zhou, N. A., & Gough, H. L. (2016). Enhanced biological trace organic contaminant removal: A lab-scale demonstration with bisphenol A-degrading bacteria Sphingobium sp. BiD32. Environmental science & technology, 50(15), 8057-8066.
周德慶 (2011)。微生物學教程（第三版）。高等教育出版社，中國北京。
許銘元 (2016)。好氧異營的硝化與脫氮細菌之特性研究。國立高雄海洋科技大學海洋生物技術系暨研究所碩士論文，台灣高雄。
李懿書 (2015)。台灣本土魚塭及冷泉的新屬新種細菌之分類。國立高雄海洋科技大學水產食品科學系暨研究所碩士論文，台灣高雄。
蕭淯文 (2012)。淡水與土壤環境中的新種細菌之鑑定與分類。國立高雄海洋科技大學海洋生物技術系暨研究所碩士論文，台灣高雄。