scholarly journals Sphingomonas lacunae sp. nov., isolated from a freshwater pond

2020 ◽  
Vol 70 (11) ◽  
pp. 5899-5910 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Che-Chia Yang ◽  
Der-Shyan Sheu ◽  
Jyh-Ming Tsai ◽  
Wen-Ming Chen

A novel bacterial strain, designated CSW-10T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed yellow-coloured colonies. Optimal growth occurred at 30 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain CSW-10T formed a phylogenetic lineage in the genus Sphingomonas . The 16S rRNA gene sequence similarity indicated that strain CSW-10T was most closely related to Sphingomonas fonticola TNR-2T (97.6%). Strain CSW-10T showed 69.8–70.7% average nucleotide identity and 19.0–23.0% digital DNA–DNA hybridization identity with the strains of other related Sphingomonas species. The major fatty acids of strain CSW-10T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) and C17:1 ω6c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized sphingoglycolipid, five uncharacterized aminophospholipids, one uncharacterized phospholipid and one uncharacterized lipid. The predominant polyamines were homospermidine and spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-10T was 62.0 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CSW-10T should represent a novel species of the genus Sphingomonas , for which the name Sphingomonas lacunae sp. nov. is proposed. The type strain is CSW-10T (=BCRC 81190T =LMG 31340T).

2020 ◽  
Vol 70 (5) ◽  
pp. 3145-3153 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Tzu-Ying Chen ◽  
Wen-Ming Chen

A bacterial strain designated CAR-16T was isolated from a freshwater lake in Taiwan and characterized using the polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, motile by gliding, rod-shaped and formed rose-colored colonies. Optimal growth occurred at 30 °C, pH 7 and with 0 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that CAR-16T represented a member of the family Cytophagaceae and formed a phylogenetic lineage in the genus Aquirufa . CAR-16T was most closely related to Aquirufa nivalisilvae 59G-WUEMPELT with a 99.7 % 16S rRNA gene sequence similarity. CAR-16T showed 71.2–79.5 % average nucleotide identity and 17.8–21.7 % digital DNA–DNA hybridization identity with the strains of other species of the genus Aquirufa . The major fatty acids of strain CAR-16T were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c and/or iso-C15 : 0 2-OH). The polar lipid profile consisted of a mixture of phosphatidylethanolamine and several uncharacterized aminophospholipids, phospholipids and lipids. The major isoprenoid quinone was MK-7. The genomic DNA G+C content of CAR-16T was 38.8 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, CAR-16T should be classified as representing a novel species of the genus Aquirufa , for which the name Aquirufa rosea sp. nov. is proposed. The type strain is CAR-16T (=BCRC 81153T=LMG 30923T=KCTC 62869T).


2020 ◽  
Vol 70 (4) ◽  
pp. 2888-2895 ◽  
Author(s):  
Wen-Ming Chen ◽  
Tzu-Ying Chen ◽  
Soon-Wo Kwon ◽  
Shih-Yi Sheu

A novel bacterial strain, designated KMB7T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, motile by means of a single polar flagellum, rod-shaped and formed cream colonies. Optimal growth occurred at 25 °C, pH 7, and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain KMB7T is affiliated with species in the genus Aquabacterium . The 16S rRNA gene sequence similarity indicated that strain KMB7T is closely related to species within the genus Aquabacterium (95.2–97.6 % sequence similarity) and is most similar to A. fontiphilum CS-6T (97.6 %), followed by A. parvum B6T (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization identity between strain KMB7T and the closely related strains were 74.6–78.0 % and 19.0–21.2 %, respectively. The major fatty acids of strain KMB7T were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C18 : 1  ω7c and C16 : 0. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, diphosphatidylglycerol and four unidentified phospholipids. The sole isoprenoid quinone was ubiquinone-8 (Q-8). Genomic DNA G+C content of strain KMB7T was 65.4 %. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain KMB7T should be classified in a novel species of the genus Aquabacterium , for which the name Aquabacterium lacunae sp. nov. is proposed. The type strain is KMB7T (=BCRC 81156T=LMG 30924T=KCTC 62867T).


Author(s):  
Chih-Horng Kuo ◽  
Pin-Yun Huang ◽  
Shih-Yi Sheu ◽  
Der-Shyan Sheu ◽  
Li-Cheng Jheng ◽  
...  

A novel bacterial strain, designated IPMB12T, isolated from the gut of the superworm Zophobas morio in Taiwan, was characterized using a polyphasic taxonomic approach. Cells were Gram-stain-negative, facultatively anaerobic, non-motile, coccoid or rod-shaped and formed translucent colonies. Optimal growth occurred at 25–37 °C, pH 9–10, and with 0–2 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain IPMB12T is affiliated with genus in the the family Orbaceae in the class Gammaproteobacteria . Strain IPMB12T was most closely related to Gilliamella mensalis LMG 29880T with a 94.6 % 16S rRNA gene sequence similarity. Strain IPMB12T showed less than 71.6 % average nucleotide identity, less than 71.5 % average amino acid identity and less than 21.2 % digital DNA–DNA hybridization identity compared to the strains of related genera within the family Orbaceae . The major fatty acids of strain IPMB12T were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized phosphoaminoglycolipid and one uncharacterized aminophospholipid. The major isoprenoid quinone was Q-8. Genomic DNA G+C content of strain IPMB12T was 39.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain IPMB12T represents a novel species of a new genus in the family Orbaceae , for which the name Zophobihabitans entericus gen. nov., sp. nov. is proposed. The type strain is IPMB12T (=BCRC 80908T =LMG 32079T=KCTC 82347T=KACC 22323T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3440-3448 ◽  
Author(s):  
Wen-Ming Chen ◽  
Tzu-Ying Chen ◽  
Che-Chia Yang ◽  
Shih-Yi Sheu

Bacterial strain TWA-58T, isolated from irrigation water in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain TWA-58T formed a phylogenetic lineage in the genus Oleiharenicola of the family Opitutaceae . Strain TWA-58T was most closely related to Oleiharenicola alkalitolerans NVTT with a 96.7 % 16S rRNA gene sequence similarity. Strain TWA-58T showed 75.2 % average nucleotide identity, 70.9 % average amino acid identity and 21.0 % digital DNA–DNA hybridization identity with O. alkalitolerans NVTT. Cells were Gram-stain-negative, aerobic, motile, coccoid-shaped and formed transparent colonies. Optimal growth occurred at 25 °C, pH 6, and 0 % NaCl. The major fatty acids of strain TWA-58T were iso-C15 : 0 and anteiso-C15 : 0. The predominant hydroxy fatty acid was iso-C13 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified aminophospholipids. The major isoprenoid quinone was MK-7. Genomic DNA G+C content of strain TWA-58T was 65.3 mol%. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain TWA-58T should be classified in a novel species of the genus Oleiharenicola , for which the name Oleiharenicola lentus sp. nov. is proposed. The type strain is TWA-58T (=BCRC 81161T=LMG 31019T=KCTC 62872T).


2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1479-1484 ◽  
Author(s):  
Mi-Hwa Lee ◽  
Soo-Young Lee ◽  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Hoon Yoon

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated WT-MW11T, was isolated from wood falls on the coast of Wando, an island of South Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain WT-MW11T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2.0–3.0 % (w/v) NaCl. Bacteriochlorophyll a was not produced. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain WT-MW11T clustered with Pseudorhodobacter ferrugineus IAM 12616T and Pseudorhodobacter aquimaris HDW-19T, with which it exhibited 16S rRNA gene sequence similarity values of 97.9 and 95.5 %, respectively. Strain WT-MW11T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profile of strain WT-MW11T was similar to those of P. ferrugineus JCM 20687T and P. aquimaris HDW-19T. The DNA G+C content of strain WT-MW11T was 61.6 mol% and its mean DNA–DNA relatedness value with P. ferrugineus JCM 20687T was 12.3 %. The phylogenetic and genetic distinctiveness and differential phenotypic properties revealed that strain WT-MW11T was distinguishable from the two recognized species of the genus Pseudorhodobacter . On the basis of the data presented, strain WT-MW11T is considered to represent a novel species of the genus Pseudorhodobacter , for which the name Pseudorhodobacter wandonensis sp. nov. is proposed. The type strain is WT-MW11T ( = KCTC 23672T = CCUG 61506T). The description of the genus Pseudorhodobacter is emended.


2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1086-1091 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Wei-Cheng Huang ◽  
Chih-Yu Cheng ◽  
Shih-Yi Sheu

A facultatively anaerobic, chitinolytic bacterium, strain KL-9T, was isolated from a freshwater lake in Taiwan and characterized by using a polyphasic taxonomic approach. Cells of strain KL-9T were Gram-negative, rod-shaped, motile by means of a single polar flagellum and non-spore-forming. Growth occurred at 15–40 °C (optimum, 30–37 °C), at pH 7.0–9.0 (optimum, pH 8.0) and with 0–1.0 % NaCl (optimum, 0 %). The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8. The DNA G+C content of strain KL-9T was 64.6 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidyldimethylethanolamine and several uncharacterized phospholipids and aminolipids. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KL-9T formed a distinct lineage with respect to closely related genera within the class Betaproteobacteria , being most closely related to members of the genera Leeia , Chitinimonas , Silvimonas and Andreprevotia . Levels of 16S rRNA gene sequence similarity with respect to the type strains of type species of these genera were below 91 %. On the basis of genotypic and phenotypic data, strain KL-9T is thus considered to represent a novel species of a new genus within the class Betaproteobacteria , for which the name Chitinivorax tropicus gen. nov., sp. nov. is proposed. The type strain of Chitinivorax tropicus is KL-9T ( = BCRC 80168T = LMG 25530T).


2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2497-2502 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Zih-Han Chen ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen

A bacterial strain, designated KBP-21T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain KBP-21T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile rods that formed yellow colonies. Growth occurred at 15–40 °C (optimum, 30 °C), at pH 5.0–8.0 (optimum, pH 8.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-21T belonged to the genus Paludibacterium within the family Neisseriaceae of the class Betaproteobacteria and the closest related neighbour was Paludibacterium yongneupense 5YN8-15T with a 16S rRNA gene sequence similarity value of 96.4 %. Strain KBP-21T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 1ω7c as the predominant fatty acids. The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 62.1 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one uncharacterized aminophospholipid and several uncharacterized phospholipids. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain KBP-21T represents a novel species in the genus Paludibacterium , for which the name Paludibacterium paludis sp. nov. is proposed. The type strain is KBP-21T ( = BCRC 80514T = LMG 27230T = KCTC 32182T).


2020 ◽  
Vol 70 (9) ◽  
pp. 5141-5148 ◽  
Author(s):  
Wen-Ming Chen ◽  
Yi-Ru Xie ◽  
Der-Shyan Sheu ◽  
Jyh-Ming Tsai ◽  
Shih-Yi Sheu

Bacterial strain CCP-6T, isolated from a freshwater pond in Taiwan, was characterized using a polyphasic taxonomy approach. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set (92 protein clusters) indicated that strain CCP-6T is affiliated with species in the genus Rhodovarius . Strain CCP-6T was most closely related to Rhodovarius lipocyclicus CCUG 44693T with a 98.9% 16S rRNA gene sequence similarity. Cells were Gram-stain-negative, aerobic, non-motile, rod-shaped and formed light pink-coloured colonies. Optimal growth occurred at 30 °C, pH 6 and in the absence of NaCl. The major fatty acids of strain CCP-6T were C18 : 1 ω7c, C16 : 0 and C19 : 0 cyclo ω8c. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, three unidentified aminophospholipids and an unidentified phospholipid. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content of the genomic DNA was 69.3 mol%. Strain CCP-6T showed 85.8% average nucleotide identity and 14.5% digital DNA–DNA hybridization identity with Rhodovarius lipocyclicus CCUG 44693T. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain CCP-6T represents a novel species in the genus Rhodovarius , for which the name Rhodovarius crocodyli sp. nov. is proposed. The type strain is CCP-6T (=BCRC 81095T=LMG 30310T=KCTC 62188T).


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3341-3345 ◽  
Author(s):  
Jia-Fa Wu ◽  
Jie Li ◽  
Zhi-Qing You ◽  
Si Zhang

A novel Gram-stain-positive actinobacterium, designated strain SCSIO 11529T, was isolated from tissues of the stony coral Galaxea fascicularis, and characterized by using a polyphasic approach. The temperature range for growth was 22–50 °C (optimum 28–45 °C), the pH range for growth was 6.0–8.0 (optimum pH 7.0), and the NaCl concentration range for growth was 0–7 % (w/v) NaCl. The polar lipid profile contained diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and an unknown polar lipid. The predominant menaquinone was MK-9(H4). The major fatty acids (>10 %) were iso-C16 : 0, iso-C17 : 1ω6c, iso-C16 : 1 H and C16 : 1ω7c/iso-C15 : 0 2-OH. The DNA G+C content of strain SCSIO 11529T was 70.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SCSIO 11529T belongs to the genus Prauserella , with the closest neighbours being Prauserella marina MS498T (97.0 % 16S rRNA gene sequence similarity), Prauserella rugosa DSM 43194T (96.4 %) and Prauserella flava YIM 90630T (95.9 %). Based on the evidence of the present study, strain SCSIO 11529T is considered to represent a novel species of the genus Prauserella , for which the name Prauserella coralliicola sp. nov. is proposed. The type strain is SCSIO 11529T ( = DSM 45821T = NBRC 109418T).


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2163-2168 ◽  
Author(s):  
Yong-Taek Jung ◽  
Ji-Hoon Kim ◽  
So-Jung Kang ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon

A Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T  = CCUG 61485T).


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