scholarly journals Rhodobacter ruber sp. nov., isolated from a freshwater pond

2021 ◽  
Author(s):  
Wen-Ming Chen ◽  
Ting-Hsuan Chang ◽  
Der-Shyan Sheu ◽  
Li-Cheng Jheng ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Rrna Gene ◽  
Freshwater Pond ◽  
Average Amino Acid Identity

Abstract Strain CCP-1T, isolated from a freshwater pond in Taiwan, is characterized using a polyphasic taxonomy approach. Cells of strain CCP-1T are Gram-stain-negative, aerobic, non-motile, rod-shaped and form dark red colored colonies. Growth occurs at 20–40 oC, at pH 6.5-9 and with 0-0.5% NaCl. Strain CCP-1T contains bacteriochlorophyll a, and shows optimum growth under anaerobic condition by photoheterotrophy, but not by photoautotrophy. 16S rRNA gene sequence similarity indicates that strain CCP-1T is closely related to species within the genus Rhodobacter (93.9–96.2% sequence similarity), Haematobacter (96.3%) and Xinfangfangia (95.5–96.2%). Phylogenetic analyses based on 16S rRNA gene sequences and based on up-to-date bacterial core gene set (92 protein clusters) reveal that strain CCP-1T is affiliated with species in the genus Rhodobacter. The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization identity between strain CCP-1T and Rhodobacter species are 71.3–76.3%, 70.4–77.9% and 21.4–23.2%, respectively, supporting that strain CCP-1T is a novel species of the genus Rhodobacter. The DNA G + C content is 66.2%. The predominant fatty acid is C18:1ω7c and the major isoprenoid quinone is Q-10. The polar lipids have phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two uncharacterized aminophospholipids and two uncharacterized phospholipids. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain CCP-1T should represent a novel species of the genus Rhodobacter, for which the name Rhodobacter ruber sp. nov. is proposed. The type strain is CCP-1T (= BCRC 81189T = LMG 31335T).

scholarly journals Rhizobium lacunae sp. nov., Isolated From a Freshwater Pond

2021 ◽  
Author(s):  
Wen-Ming Chen ◽  
Che-Chia Yang ◽  
Chiu-Chung Young ◽  
Shih-Yao Lin ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Analyses ◽  
Amino Acid Identity ◽  
Core Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Principal Fatty Acid ◽  
Freshwater Pond

Abstract Bacterial strain designated CSW-27T was isolated from a freshwater pond in Taiwan. Cells were Gram-stain-negative, aerobic, oxidase-positive, catalase-negative, rod-shaped and motile by flagella. Strain CSW-27T grew at 20-40 oC (optimum, 30-37 oC), at pH 5-9 (optimum, pH 6-7) and in the presence of 0-4% NaCl (optimum, 0%). Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set revealed that strain CSW-27T was affiliated with species in the genus Rhizobium. Analysis of 16S rRNA gene sequences showed that strain CSW-27T had the highest similarity to Rhizobium straminoryzae CC-LY845T (98.5%) followed by Rhizobium capsici CC-SKC2T (96.9%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain CSW-27T and the closely related Rhizobium species were 73.4-86.5, 66.0-88.8 and 13.3-22.1%, respectively. The principal fatty acid was summed feature 8 (C18:1ω7c and/or C18:1ω6c). The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, one uncharacterized aminophospholipid, three uncharacterized aminolipids and two uncharacterized lipids. The predominant polyamine was spermidine. The major isoprenoid quinone was Q-10. Genomic DNA G+C content of strain CSW-27T was 63.3%. These polyphasic taxonomic data indicited that strain CSW-27T should be considered as representing a novel species in the genus Rhizobium, for which the name Rhizobium lacunae sp. nov. is proposed with strain CSW-27T (=BCRC 81244T =LMG 31684T) as the type strain.

scholarly journals Chryseobacterium caeni sp. nov., isolated from bioreactor sludge

2007 ◽  
Vol 57 (1) ◽  
pp. 141-145 ◽  
Author(s):  
Zhe-Xue Quan ◽  
Kwang Kyu Kim ◽  
Myung-Kyum Kim ◽  
Long Jin ◽  
Sung-Taik Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Bacterium Strain

A Gram-negative, non-spore-forming, yellow-pigmented bacterium, strain N4T, was isolated from a nickel-complexed cyanide-degrading bioreactor and subjected to a polyphasic taxonomic study. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain N4T is affiliated to the genus Chryseobacterium of the family Flavobacteriaceae. The levels of 16S rRNA gene sequence similarity between strain N4T and the type strains of all known Chryseobacterium species were 93.2–95.8 %, suggesting that strain N4T represents a novel species within the genus Chryseobacterium. The strain contained iso-C15 : 0 and summed feature 4 as the major fatty acids and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 38.2 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain N4T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium caeni sp. nov. is proposed. The type strain is N4T (=KCTC 12506T=CCBAU 10201T=DSM 17710T).

scholarly journals Bacillus seohaeanensis sp. nov., a halotolerant bacterium that contains l-lysine in its cell wall

2006 ◽  
Vol 56 (8) ◽  
pp. 1893-1898 ◽  
Author(s):  
Jae-Chan Lee ◽  
Jee-Min Lim ◽  
Dong-Jin Park ◽  
Che Ok Jeon ◽  
Wen-Jun Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Positive Bacterium

A halotolerant, round-endospore-forming, aerobic, Gram-positive bacterium, designated BH724T, was isolated from a solar saltern at Taean in Korea. Cells of this strain were rod-shaped and found to be non-motile. Strain BH724T grew at salinities of 0–10 % (w/v) NaCl with an optimum of 3 % (w/v) NaCl and at temperatures of 15–50 °C with an optimum of 40 °C. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain BH724T belonged to the genus Bacillus and that Bacillus aquimaris TF-12T, Bacillus marisflavi TF-11T and Bacillus vietnamensis JCM 11124T were its closest neighbours, sharing 97.3, 97.2 and 97.0 % 16S rRNA gene sequence similarity, respectively. The genomic DNA G+C content was 39 mol% and the predominant menaquinone was MK-7. Its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and iso-C14 : 0. The peptidoglycan type was A1α, linked directly through l-lysine. On the basis of morphological, chemotaxonomic, physiological and phylogenetic properties, strain BH724T represents a novel species of the genus Bacillus, for which the name Bacillus seohaeanensis sp. nov. is proposed. The type strain is BH724T (=KCTC 3913T=DSM 16464T).

scholarly journals Mucilaginibacter boryungensis sp. nov., isolated from soil

2011 ◽  
Vol 61 (7) ◽  
pp. 1549-1553 ◽  
Author(s):  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Ki-Hoon Oh ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-stain-negative, non-motile, non-spore-forming bacterial strain, BDR-9T, was isolated from soil collected from Boryung on the west coast of the Korean peninsula, and its taxonomic position was investigated by using a polyphasic study. Strain BDR-9T grew optimally at 25 °C, at pH 6.0–7.5 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain BDR-9T fell within the clade comprising species of the genus Mucilaginibacter within the phylum Bacteroidetes. 16S rRNA gene sequence similarity values between strain BDR-9T and the type strains of species of the genus Mucilaginibacter were in the range 94.0–95.6 %. Strain BDR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The DNA G+C content was 44.3 mol%. Differential phenotypic properties and phylogenetic distinctiveness of strain BDR-9T demonstrated that this strain is distinguishable from species of the genus Mucilaginibacter. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain BDR-9T is considered to represent a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter boryungensis sp. nov. is proposed. The type strain is BDR-9T ( = KCTC 23157T  = CCUG 59599T).

scholarly journals Terrimonas aquatica sp. nov., isolated from a freshwater spring

2010 ◽  
Vol 60 (12) ◽  
pp. 2705-2709 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Nian-Tsz Cho ◽  
A. B. Arun ◽  
Wen-Ming Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Freshwater Spring

A yellow-pigmented bacterial strain, designated RIB1-6T, was isolated from a freshwater spring in Taiwan. Strain RIB1-6T was aerobic, Gram-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 10–37 °C, at pH 7–8 and with 0–1 % (w/v) 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 ATCC 13524T and Terrimonas lutea DYT (16S rRNA gene sequence similarity 97.4 % and 93.5 %, respectively). Strain RIB1-6T contained iso-C15 : 0 (33.4 %), iso-C17 : 0 3-OH (18.2 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 14.7 %) and iso-C15 : 1 (11.5 %) as the 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 novel 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).

scholarly journals Stenotrophomonas dokdonensis sp. nov., isolated from soil

2006 ◽  
Vol 56 (6) ◽  
pp. 1363-1367 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Hyun Woo Oh ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, rod-shaped, Stenotrophomonas-like bacterial strain, DS-16T, was isolated from soil from Dokdo, Korea, and subjected to a polyphasic taxonomic study. Strain DS-16T grew optimally at pH 6.0–7.0 and 30 °C in the presence of 0.5 % (w/v) NaCl. It contained Q-8 as the predominant ubiquinone and iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c as the major fatty acids. The DNA G+C content was 65.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-16T joined the cluster comprising Stenotrophomonas species. The levels of 16S rRNA gene sequence similarity between strain DS-16T and the type strains of Stenotrophomonas species ranged from 95.5 to 97.5 %. DNA–DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness of strain DS-16T, demonstrated that this novel strain differs from Stenotrophomonas species with validly published names. On the basis of phenotypic, phylogenetic and genetic data, strain DS-16T (=KCTC 12543T=CIP 108839T) should be classified in the genus Stenotrophomonas as a member of a novel species, for which the name Stenotrophomonas dokdonensis sp. nov. is proposed.

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
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Freshwater Pond

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).

scholarly journals Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake

2011 ◽  
Vol 61 (2) ◽  
pp. 408-411 ◽  
Author(s):  
Ying Liu ◽  
Xue-Feng Song ◽  
Jia-Tong Jiang ◽  
Ying-Hao Liu ◽  
Cheng-Jun Xu ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
North East ◽  
Optimum Ph

A Gram-negative bacterium, designated B2-9T, was isolated from water of a slightly alkaline lake, Longhu Lake in Daqing, north-east China. Strain B2-9T was an aerobic rod, heterotrophic, catalase- and oxidase-positive and motile by means of a single polar flflagellum. The isolate grew well on n-alkanes C9–C17 and weakly on C6–C8, C18 and C19. Growth occurred at 10–37 °C (optimum 20–25 °C), at pH 5.5–9.5 (optimum pH 7.0) and with ≤1.0 % (w/v) NaCl. The major fatty acids were C18 : 1 ω7c (41.4 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 18.5 %) and C16 : 0 (10.9 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain B2-9T belonged to the genus Hydrocarboniphaga of the class Gammaproteobacteria and shared 97.0 % 16S rRNA gene sequence similarity with Hydrocarboniphaga effusa AP103T. DNA–DNA relatedness between strain B2-9T and H. effusa DSM 16095T was 24 %. The DNA G+C content of strain B2-9T was 66 mol%. Strain B2-9T is considered to represent a novel species of the genus Hydrocarboniphaga, for which the name Hydrocarboniphaga daqingensis sp. nov. is proposed. The type strain is B2-9T (=CGMCC 1.7049T =NBRC 104238T).

Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces

2012 ◽  
Vol 62 (Pt_5) ◽  
pp. 1145-1150 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Sayaka Tsuchida ◽  
Koh Kawasumi ◽  
Hiromi Amao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Distinct Line

Strains of Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces, and three strains, ST161T, ST33 and ST37T, were investigated taxonomically. Based on phylogenetic analyses and specific phenotypic characteristics, the three strains were allocated to the genus Bacteroides . Phylogenetic analyses of their 16S rRNA gene sequences revealed that strain ST161T formed a distinct line of descent, with highest sequence similarity to strain ST33 (98.7 %) and Bacteroides oleiciplenus JCM 16102T (97.7 %). High levels of DNA–DNA relatedness (79–89 %) were found between strains ST161T and ST33, but low levels were found between strain ST161T and B. oleiciplenus JCM 16102T (33–37 %) and between strain ST33 and B. oleiciplenus JCM 16102T (33–37 %). These data clearly indicated that strains ST161T and ST33 represent a single novel species. 16S rRNA gene sequence analyses showed that strain ST37T also formed a distinct line of descent, with highest sequence similarity to Bacteroides acidifaciens JCM 10556T (96.5 %) and Bacteroides caccae JCM 9498T (95.6 %). Analysis of hsp60 gene sequences also supported these relationships. Based on phenotypic and phylogenetic characteristics, two novel species, Bacteroides stercorirosoris sp. nov. and Bacteroides faecichinchillae sp. nov., are thus proposed. The type strains of B. stercorirosoris and B. faecichinchillae are ST161T ( = JCM 17103T = CCUG 60872T) and ST37T ( = JCM 17102T = CCUG 60873T), respectively. The DNA G+C contents of strains ST161T and ST37T were 45.7 and 41.0 mol%, respectively.

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

2020 ◽  
Vol 70 (4) ◽  
pp. 2888-2895 ◽  
Author(s):  
Wen-Ming Chen ◽  
Tzu-Ying Chen ◽  
Soon-Wo Kwon ◽  
Shih-Yi Sheu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Freshwater Pond

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).

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