Classification and identification of novel species bacteria isolated from freshwater in Taiwan

• Main Authors: Nian-Tsz Cho, 卓念慈
• Other Authors: Wen-Ming Chen
• Format: Others
• Language: zh-TW
• Published: 2010
• Online Access: http://ndltd.ncl.edu.tw/handle/73544098722190491417

碩士 === 國立高雄海洋科技大學 === 水產食品科學研究所 === 98 === In this study, we isolate and identify 233 strains including 183 Gram-negative bacteria and 50 Gram-positive bacteria, collected from freshwater in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences indicate that these strains belong to the class Alphaproteobacteria, class Betaproteobacteria, class Gammaproteobacteria, class Bacilli, class Flavobacteria, class Cytophagia and class Actinobacteria. The results suggest that strains RIB1-20、NAA-13、RIB1-6、NAA16、RG-4、JS-43 and ABP-4 might be the novel species, and they are subjected to further identification and classification. A yellow-pigmented bacterial strain, designated RIB1-20T, isolated from fresh water was investigated by means of a polyphasic taxonomic approach. The cells were Gram-negative, rodshaped and non-spore-forming. Phylogenetic analyses with the 16S rRNA gene sequence showed that the strain formed a monophyletic branch towards the periphery of the evolutionary radiation occupied by the genus Luteimonas, its two closest neighbours being Luteimonas composti CC-YY255T (96.1% sequence similarity) and Luteimonas mephitis B1953/27.1T (95.8%). Strain RIB1-20T was clearly distinguished from both of those type strains using phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strain RIB1-20T represents a novel species of the genus Luteimonas, for which the name Luteimonas aquatica sp. nov. is proposed. The type strain is RIB1-20T (= BCRC 17731T = LMG 24212T). A Gram-positive, rod-shaped, yellow-pigmented actinomycete, designated strain NAA-13T, was isolated from a freshwater spring located in Kaoshiung, southern Taiwan. This strain was characterized using a polyphasic taxonomic approach. The organism had chemotaxonomic and morphological properties consistent with its classification in the genus Nocardioides. The strain contained LL-diaminopimelic acid as the principal diamino acid of the peptidoglycan, MK-8(H4) as the major menaquinone, and iso-C16:0 and C17:0 as the predominant fatty acids. 16S rRNA gene sequence studies showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Nocardioides; its closest neighbours were Nocardioides insulae DS-51T (94.9% similarity), Nocardioides pyridinolyticus KCTC 0074BPT (96.5% similarity) and Nocardioides aquiterrae GW-9T (96.6% similarity). The DNA G+C content of strain NAA-13T was 71.8 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain NAA-13T represents a novel species of the genus Nocardioides, for which the name Nocardioides fonticola sp. nov. is proposed. The type strain is NAA-13T (= LMG 24213T = BCRC 16874T). A yellow pigmented bacterial strain designated RIB1-6T was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Strain RIB1-6T was aerobic, Gram-staining-negative, rod-shaped, non-motile and non-spore forming. Growth occurred at 10-37 oC, at pH 7.0-8.0 and with 0-1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain RIB1-6T belonged to the genus Terrimonas and its two closest neighbours were Terrimonas ferruginea JCM 21559T and Terrimonas lutea JCM 21735T with sequence similarities of 97.4% and 93.5%, respectively. Strain RIB1-6T contained iso-C15:0, iso-C17:0 3-OH, summed feature 3 (comprising iso-C15:0 2-OH and/or C16:1 ω7c) and iso-C15:1 as predominant fatty acids. The major isoprenoid quinone was MK-7. The DNA G+C content of strain RIB1-6T was 47.3 mol%. On the basis of the genotypic and phenotypic data, strain RIB1-6T represents a new species in the genus Terrimonas, for which the name Terrimonas aquatica sp. nov. is proposed. The type strain is RIB1-6T (= BCRC 17941T = LMG 24825T). A bacterial strain designated NAA16T was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomic approach. Strain NAA16T was aerobic, Gram-staining-negative, rod-shaped, non-spore forming and motile by means of a single polar flagellum. Growth occurred at 20-40 oC, at pH 7.0-8.0 and with 0-1 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain NAA16T were Solimonas soli DCY12T, Sinobacter flavus CW-KD4T and Singularimonas variicoloris MN28T, with sequence similarities of 96.2, 96.6 and 96.7%, respectively. Strain NAA16T contained C16:0, C18:1 ω7c and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) as predominant fatty acids. The major isoprenoid quinone was Q-8. The DNA G+C content of the strain NAA16T was 66.2 mol%. Phylogenetic evidences, supported by chemotaxonomic and phenotypic data, assigned strain NAA16T to the genus Solimonas as Solimonas aquatica sp. nov. (type strain NAA16T = BCRC 17835T = LMG 24500T). The reclassification of Sinobacter flavus as Solimonas flava comb. nov. and Singularimonas variicoloris as Solimonas variicoloris comb. nov. is proposed. Two Gram-negative, aerobic, pale pink/rose-coloured, rod-shaped, non-motile bacterial strains, designated GFA-11T and RG-4, were isolated from a freshwater fish culture pond and a freshwater spring sample, respectively. Based on characterization by using a polyphasic approach, the two strains showed highly similar phenotypic, physiological and genetic characteristics. They shared 99.9% 16S rRNA gene sequence similarity and 89–94% DNA–DNA relatedness, suggesting that they represent a single genomic species. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains GFA-11T and RG-4 formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Flectobacillus within the family Flexibacteraceae. Their closest neighbours were Flectobacillus major DSM 103T (97.7% 16S rRNA gene sequence similarity) and Flectobacillus lacus CLGP79T (95.9%). Levels of DNA–DNA relatedness between the two novel strains and the type strains of F. major and F. lacus were less than 70 %. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strains GFA-11T and RG-4 from recognized members of the genus Flectobacillus. The predominant fatty acid constituents of strain GFA-11T were C16:1 ω5c (40.2% of the total) and iso-C15:0 (15.0 %). The DNA G+C content of strain GFA-11T was 39.7 mol%. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and physiological data, strains GFA-11T and RG-4 are considered to represent a novel species of the genus Flectobacillus, for which the name Flectobacillus roseus sp. nov. is proposed. The type strain is GFA-11T (= BCRC 17834T = LMG 24501T). A white to yellowish pigmented bacterial strain designated JS-43T was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Strain JS-43T was aerobic, Gram-staining-negative, rod-shaped, non-motile and non-spore forming. Growth occurred at 10-30 oC, at pH 7.0-10.0 and with 0-0.5 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain JS-43T belonged to the genus Catellibacterium and its two closest neighbours were Catellibacterium aquatile A1-9T and Catellibacterium nectariphilum AST4T with sequence similarities of 97.7% and 94.5%, respectively. Strain JS-43T contained Sum in feature 8（C18:1 ω7c and/or C18:1 ω6c）as predominant fatty acids. The major isoprenoid quinone was Q-10. The DNA G+C content of strain JS-43T was 69.3 mol%. On the basis of the genotypic and phenotypic data, strain JS-43T represents a new species in the genus Catellibacterium, for which the name Catellibacterium aquatilis sp. nov. is proposed. The type strain is JS-43T (= BCRC 80082T = LMG 25376T). A white pigmented bacterial strain designated ABP-4T was isolated from a freshwater spring in Taiwan and was characterized using the polyphasic taxonomy approach. Strain ABP-4T was aerobic, Gram-staining-negative, rod-shaped, non-motile and non-spore forming. Growth occurred at 25-40 oC, at pH 7.0-11.0 and with 0-3 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ABP-4T belonged to the genus Aquabacterium; its closest neighbours were Aquabacterium fontiphilum CS-6T (96.4% similarity), Aquabacterium commune B8T (96.1% similarity), Aquabacterium citratiphilum B4T (95.5 % similarity) and Aquabacterium parvum B6T (94.7% similarity). Strain ABP-4T contained C16:0, C18:1ω7c and summed feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c) as predominant fatty acids. The DNA G+C content of strain ABP-4T was 68.6 mol%. On the basis of the genotypic and phenotypic data, strain ABP-4T represents a new species in the genus Aquabacterium, for which the name Aquabacterium imneticum sp. nov. is proposed. The type strain is ABP-4T (= BCRC 80167T).