scholarly journals Paenibacillus dongdonensis sp. nov., isolated from rhizospheric soil of Elymus tsukushiensis

2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2865-2870 ◽  
Author(s):  
Jin-Soo Son ◽  
Hyun-Uk Kang ◽  
Sa-Youl Ghim
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gram Staining

A Gram-staining-positive, endospore-forming and rod-shaped bacterial strain, designated KUDC0114T, was isolated from rhizospheric soil of Elymus tsukushiensis from Dongdo Island, one of the largest of the Dokdo Islands, South Korea. The strain displayed optimal growth at 37 °C, pH 8.5 in the absence of NaCl. Based on phylogenetic analysis of 16S rRNA gene sequences, strain KUDC0114T represented a member of the genus Paenibacillus and was most closely related to Paenibacillus taichungensis BCRC 17757T (98.46 %). The cell-wall peptidoglycan was A1γ type, and the predominant quinone was menaquinone-7 (MK-7). The major cellular fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA–DNA hybridization of strain KUDC0114T with nine other strains indicated less than 23 % relatedness, and its DNA G+C content was 44.30 mol%. Based on genomic, phenotypic and phylogenetic analyses, KUDC0114T should be classified as representing novel species within the genus Paenibacillus . The name Paenibacillus dongdonensis sp. nov. is proposed. The type strain is KUDC0114T ( = DSM27607T = KCTC33221T).

scholarly journals Novosphingobium ovatum sp. nov., isolated from a freshwater mesocosm

2020 ◽  
Vol 70 (10) ◽  
pp. 5243-5254 ◽  
Author(s):  
Wen-Ming Chen ◽  
Cheng-Ye Cai ◽  
Der-Shyan Sheu ◽  
Jyh-Ming Tsai ◽  
Shih-Yi Sheu
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph

A bacterial strain, designated FSY-8T, was isolated from a freshwater mesocosm in Taiwan and characterized using the polyphasic taxonomy approach. Cells of strain FSY-8T were aerobic, Gram-stain-negative, rod-shaped, non-motile and formed yellow coloured colonies on Reasoner's 2A agar. Growth occurred at 20–40 °C (optimum, 30–37 °C) and pH 5–7 (optimum, pH 6) and in the presence of 0–0.5 % NaCl (optimum, 0 %, w/v). The major fatty acids (>10 %) of strain FSY-8T were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c). The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, diphosphatidylglycerol, an uncharacterized aminophospholipid, an uncharacterized glycolipid and an uncharacterized lipid. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 64.8 mol %. Phylogenetic analyses based on 16S rRNA gene sequences and coding sequences of 92 protein clusters indicated that strain FSY-8T formed a phylogenetic lineage in the genus Novosphingobium . Strain FSY-8T showed 71.6–77.2 % average nucleotide identity and 19.9–22.8 % digital DNA–DNA hybridization identity with the strains of other Novosphingobium species. On the basis of phenotypic and genotypic properties and phylogenetic inference, strain FSY-8T should be classified in a novel species of the genus Novosphingobium , for which the name Novosphingobium ovatum sp. nov. is proposed. The type strain is FSY-8T (=BCRC 81051T=LMG 30053T=KCTC 52812T).

scholarly journals Enterococcus diestrammenae sp. nov., isolated from the gut of Diestrammena coreana

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4540-4545 ◽  
Author(s):  
Joon Yong Kim ◽  
Na-Ri Shin ◽  
Hong-Kyung Na ◽  
Dong-Wook Hyun ◽  
Tae Woong Whon ◽  
...  
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Gram Stain ◽  
16S Rrna Gene Sequences ◽  
Sequence Analyses ◽  
Content Type ◽  
Link Type

A novel Gram-stain-positive, facultatively anaerobic, non-motile and lactic-acid-producing bacterium, designated strain ORL-24T, was isolated from the gut of the camel cricket, Diestrammena coreana. Optimal growth occurred at 37 °C, pH 8 and with 0 % (w/v) NaCl. The ratio of l-lactate to d-lactate in strain ORL-24T was 96 : 4. Lancefield antigen D was not detected. The strain was negative for oxidase activity and catalase activity. According to a phylogenetic analysis based on 16S rRNA gene sequences, strain ORL-24T was most closely related to the type strain of Enterococcus asini (96.9 % similarity). Comparative pheS and rpoA sequence analyses of strain ORL-24T indicated that the strain belonged to the genus Enterococcus . The major fatty acids were C16 : 0 and C18 : 1ω9c. The DNA G+C content was 41.3 mol%. Based on phenotypic, genotypic and phylogenetic analyses, strain ORL-24T represents a novel species of the genus Enterococcus , for which the name Enterococcus diestrammenae is proposed. The type strain is ORL-24T ( = KACC 16708T = JCM 18359T).

Flavobacterium jumunjinense sp. nov., isolated from a lagoon, and emended descriptions of Flavobacterium cheniae , Flavobacterium dongtanense and Flavobacterium gelidilacus

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3937-3943 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Polar Lipids ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Distinct Lineage ◽  
Motile By Gliding

A Gram-staining-negative, yellow-pigmented bacterial strain, motile by gliding, designated HME7102T, was isolated from lagoon water in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain HME7102T formed a distinct lineage within the genus Flavobacterium . Strain HME7102T was closely related to Flavobacterium cheniae NJ-26T (94.5 %), Flavobacterium dongtanense LW30T (94.4 %) and Flavobacterium gelidilacus LMG 21477T (94.2 %). The major fatty acids of strain HME7102T were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polyamine was homospermidine and the major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and two unidentified polar lipids. The DNA G+C content of strain HME7102T was 36.5 mol%. On the basis of the evidence presented in this study, strain HME7102T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium jumunjinense sp. nov. is proposed. The type strain is HME7102T ( = KCTC 23618T = CECT 7955T). Emended descriptions of F. cheniae , F. dongtanense and F. gelidilacus are also proposed.

scholarly journals Chitinimonas viridis sp. nov., isolated from a mesotrophic artificial lake

2014 ◽  
Vol 64 (Pt_4) ◽  
pp. 1123-1126 ◽  
Author(s):  
Yochan Joung ◽  
Beom-Il Lee ◽  
Heeyoung Kang ◽  
Haneul Kim ◽  
Kiseong Joh
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Artificial Lake ◽  
Content Type ◽  
Link Type ◽  
Gram Staining ◽  
Bacterium Strain

A Gram-staining-negative, rod-shaped bacterium, strain HMD2169T, was isolated from a mesotrophic artificial lake in Korea. Strain HMD2169T grew in the presence of 0–3.0 % (w/v) NaCl, at pH 5–10 and at 20–37 °C. The predominant quinone of strain HMD2169T was ubiquinone (UQ)-8. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, two unidentified aminolipids and two unidentified lipids. The DNA G+C content was 59.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD2169T was a representative of a lineage within the genus Chitinimonas . Strain HMD2169T was closely related to Chitinimonas taiwanensis (95.8 % sequence similarity) and Chitinimonas koreensis (94.6 %). On the basis of the evidence presented in this study, strain HMD2169T is a representative of a novel species of the genus Chitinimonas , for which the name Chitinimonas viridis sp. nov. is proposed with the type strain HMD2169T ( = KCTC 22839T = CECT 7703T).

scholarly journals Gilvimarinus polysaccharolyticus sp. nov., an agar-digesting bacterium isolated from seaweed, and emended description of the genus Gilvimarinus

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 562-569 ◽  
Author(s):  
Hong Cheng ◽  
Shun Zhang ◽  
Ying-Yi Huo ◽  
Xia-Wei Jiang ◽  
Xin-Qi Zhang ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Hydrolysis Of ◽  
Sequence Similarities

A taxonomic study was carried out on strain YN3T, which was isolated from a seaweed sample taken from the coast of Weihai, China. The bacterium was Gram-stain-negative, rod-shaped, and could grow at pH 5.0–10.0 and 4–32 °C in the presence of 0–9.0 % (w/v) NaCl. Strain YN3T was positive for the hydrolysis of polysaccharides, such as agar, starch and xylan. The predominant respiratory quinone was ubiquinone-8. The major fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0 and C18 : 1ω7c. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and two unidentified glycolipids. The genomic DNA G+C content was 49.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YN3T should be assigned to the genus Gilvimarinus . ‘Gilvimarinus agarilyticus’ KCTC 23325 and Gilvimarinus chinensis QM42T had the closest phylogenetic relationship to strain YN3T, and showed 97.9 % and 95.8 % sequence similarities, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data and DNA–DNA hybridization studies, we propose that strain YN3T represents a novel species of the genus Gilvimarinus , for which the name Gilvimarinus polysaccharolyticus sp. nov. is proposed. The type strain is YN3T ( = KCTC 32438T = JCM 19198T). An emended description of the genus Gilvimarinus is also presented.

Chitinibacter bivalviorum sp. nov., isolated from the gut of the freshwater mussel Anodonta arcaeformis

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Jee-Won Choi ◽  
Jae-Yun Lee ◽  
Dong-Wook Hyun ◽  
June-Young Lee ◽  
Pil Soo Kim ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Freshwater Mussel ◽  
Optimal Growth ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Republic ◽  
Genotypic Characteristics

A novel Gram-stain-negative, aerobic, rod-shaped bacterium with a single polar flagellum, designated strain 2T18T, was isolated from the gut of the freshwater mussel Anodonta arcaeformis collected in the Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain belonged to the genus Chitinibacter . Strain 2T18T formed a monophyletic clade with Chitinibacter fontanus KCTC 42982T, C. tainanensis KACC 11706T and C. alvei KCTC 23839T, with sequence similarities of 98.5, 98.4 and 95.9 %, respectively. Strain 2T18T exhibited optimal growth at 30 °C, at pH 8 and with 0.5 % (w/v) NaCl. The major isoprenoid quinone was ubiquinone-8 (Q-8). The predominant fatty acids were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified lipid, three unidentified phospholipids and two unidentified aminophospholipids. The G+C content of the genomic DNA was 50.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strains 2T18T and C. fontanus KCTC 42982T were below the thresholds used for the delineation of a novel species. Based on the phylogenetic, phenotypic, chemotaxonomic and genotypic characteristics, strain 2T18T represents a novel species of the genus Chitinibacter , for which the name Chitinibacter bivalviorum sp. nov. is proposed. The type strain is 2T18T (=KCTC 72821T=CCUG 74764T).

Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Antonio Castellano-Hinojosa ◽  
David Correa-Galeote ◽  
Martha-Helena Ramírez-Bahena ◽  
Germán Tortosa ◽  
Jesús González-López ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Dna Hybridization ◽  
Type Species ◽  
Novel Species ◽  
Pcr Amplification ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to ‘ A. deltaense ’ YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium . Whole genome average nucleotide identity and digital DNA–DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10–42 °C, pH 5.0–10.0 and with 0.0–0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium , for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).

Halarchaeum rubridurum sp. nov., a moderately acidophilic haloarchaeon isolated from commercial sea salt samples

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3143-3147 ◽  
Author(s):  
Yuto Yamauchi ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  
Keyword(s):  
Type Species ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
The Philippines ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Optimum Ph ◽  
The 16S Rrna Gene

Six halo-acidophilic archaeal strains were isolated from four commercial salt samples obtained from seawater in the Philippines, Indonesia (Bali) and Japan (Okinawa) on agar plates at pH 4.5. Cells of the six strains were pleomorphic, and stained Gram-negative. Two strains were pink–red pigmented, while four other strains were orange–pink pigmented. Strain MH1-16-3T was able to grow at 9–30 % (w/v) NaCl [with optimum at 18 % (w/v) NaCl], at pH 4.5–6.8 (optimum, pH 5.5) and at 20–50 °C (optimum, 42 °C). The five other strains grew at slightly different ranges. The six strains required at least 1 mM Mg2+ for growth. The 16S rRNA gene sequences of the six strains were almost identical, sharing 99.9 (1–2 nt differences) to 100 % similarity. The closest relatives were Halarchaeum acidiphilum MH1-52-1T and Halarchaeum salinum MH1-34-1T with 97.7 % similarity. The DNA G+C contents of the six strains were 63.2–63.7 mol%. Levels of DNA–DNA relatedness amongst the six strains were 79–86 %, while those between MH1-16-3T and H. acidiphilum MH1-52-1T and H. salinum MH1-34-1T were both 43 and 45 % (reciprocally), respectively. Based on the phenotypic, genotypic and phylogenetic analyses, it is proposed that the six isolates represent a novel species of the genus Halarchaeum , for which the name Halarchaeum rubridurum sp. nov. is proposed. The type strain is MH1-16-3T ( = JCM 16108T = CECT 7535T).

scholarly journals Streptosporangium jomthongense sp. nov., an actinomycete isolated from rhizospheric soil and emendation of the genus Streptosporangium

2014 ◽  
Vol 64 (Pt_7) ◽  
pp. 2400-2406 ◽  
Author(s):  
Bungonsiri Intra ◽  
Atsuko Matsumoto ◽  
Yuki Inahashi ◽  
Satoshi Ōmura ◽  
Watanalai Panbangred ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Species ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type

A novel actinomycete, strain 30EHST, was isolated from the rhizospheric soil under an elephant ear plant (Caladium bicolor) in Jomthong district, Bangkok, Thailand. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 30EHST fell within the cluster of the genus Streptosporangium . Chemical composition analysis confirmed that the strain represented a member of the genus Streptosporangium even though this strain produced a tightly packed single spore on aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain 30EHST was most closely related to Streptosporangium fragile NBRC 14311T (98.1 %), Streptosporangium carneum NBRC 15562T (97.8 %) and Streptosporangium violaceochromogenes NBRC 15560T (97.4 %). The DNA–DNA hybridization relatedness values between strain 30EHST and the above three strains were below 70 %. Based on combined data for phylogenetic analysis, DNA–DNA hybridization relatedness and physiological characteristics, it was concluded that strain 30EHST should be classified as representing a novel species of the genus Streptosporangium . We propose the name Streptosporangium jomthongense sp. nov., with the type strain 30EHST ( = BCC 53154T = NBRC 110047T). An emended description of the genus Streptosporangium is also proposed.

Roseovarius lutimaris sp. nov., isolated from a marine tidal flat

2013 ◽  
Vol 63 (Pt_10) ◽  
pp. 3835-3840 ◽  
Author(s):  
Eun Jin Choi ◽  
Hyo Jung Lee ◽  
Jeong Myeong Kim ◽  
Che Ok Jeon
Keyword(s):  
Tidal Flat ◽  
Novel Species ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Aerobic Bacterium ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Cellular Fatty Acids ◽  
Link Type ◽  
Gram Staining

A novel Gram-staining-negative, moderately halophilic and strictly aerobic bacterium, designated strain 112T, was isolated from a tidal flat at Taean, Korea. Cells were catalase- and oxidase-positive ovoids to rods and did not produce bacteriochlorophyll a. Optimum growth of strain 112T was observed at 30 °C, at pH 6.5–7.5 and in the presence of 2–4 % (w/v) NaCl. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0 and Q-10 was detected as the predominant ubiquinone. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and three unidentified lipids. The genomic DNA G+C content of strain 112T was 58.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 112T formed a phyletic lineage within the genus Roseovarius of the class Alphaproteobacteria . Strain 112T was most closely related to Roseovarius mucosus DFL-24T, with 96.52 % similarity. On the basis of phenotypic, chemotaxonomic and molecular properties, strain 112T represents a novel species of the genus Roseovarius , for which the name Roseovarius lutimaris sp. nov. is proposed. The type strain is 112T ( = KACC 16185T = JCM 17743T).

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