Arthrobacter terricola sp. nov., isolated from forest soil

Author(s):  
Ngoc Hoang Trinh ◽  
Jaisoo Kim

A Gram-stain-positive, aerobic and rod-shaped bacterial strain, designated JH1-1T, was isolated from a forest soil sample collected in Suwon, Gyeonggi-do, Republic of Korea. Strain JH1-1T could grow at 10–35 °C (optimum, 28–30 °C), pH 4.5–8.5 and tolerated 5 % (w/v) NaCl. Strain JH1-1T was most closely related to members of the genus Arthrobacter , namely Arthrobacter alkaliphilus LC6T (98.5 % similarity), Arthrobacter methylotrophus TGAT (98.4 %), Arthrobacter ramosus CCM 1646T (97.8 %), Arthrobacter bambusae THG-GM18T (97.5 %) and Arthrobacter pokkalii P3B162T (97.3 %). The strain grew well on Reasoner's 2A agar, tryptone soya agar, nutrient agar, Mueller–Hinton agar and Luria–Bertani agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, unidentified phospholipid and unidentified glycolipids. The major respiratory quinone was MK-9(H2). The main fatty acids were C15 : 0 anteiso, C15 : 0 iso, C16 : 0 iso and C17 :0 anteiso. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain JH1-1T and its reference type strains ranged from 81.3 to 85.4 % and from 21.1 to 29.1 %, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain JH1-1T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Arthrobacter . Therefore, strain JH1-1T is considered to represent a novel species, for which the name Arthrobacter terricola sp. nov. is proposed. The type strain is JH1-1T (=KACC 21385T=JCM 33641T).

2020 ◽  
Vol 70 (4) ◽  
pp. 2509-2514 ◽  
Author(s):  
Ngoc Hoang Trinh ◽  
Jaisoo Kim

A Gram-stain-negative, aerobic and short rod-shaped bacterial strain, designated LD6T, was isolated from a forest soil sample in Suwon, Gyeonggi-do, Republic of Korea. Strain LD6T grew at 10–37 °C (optimal temperature, 28 °C), and tolerated pH 8.0 and 2 % (w/v) NaCl. Strain LD6T was related most closely to members of the genus Paraburkholderia , namely Paraburkholderia azotifigens NF2-5-3T (98.2 % 16S rRNA gene sequence similarity), P. megapolitana A3T (97.9 %), P. ginsengiterrae DCY85T (97.9 %) and P. caribensis MWAP64T (97.7 %). The strain grew well on R2A agar, tryptone soya agar, Mueller-Hinton agar and nutrient agar. The major polar lipid profile comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminophospholipid and glycolipid. The major respiratory quinone was ubiquinone 8 (Q-8). The main fatty acids were C17 : 0 cyclo, C16 : 0, C16 : 0 3-OH, C19 : 0 cyclo ω8c and C12 : 0. The DNA G+C content of the isolated strain based on the whole genome sequence was 63.4 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between strain LD6T and its reference type strains ranged from 80.3 to 82.4%, and from 23.7 to 33.7%, respectively. Based on phenotypic, chemotypic and genotypic evidence, strain LD6T could be differentiated phylogenetically and phenotypically from the recognized species of the genus Paraburkholderia . Therefore, strain LD6T is considered to represent a novel species, for which the name Paraburkholderia flava sp. nov. is proposed. The type strain is LD6T (=KACC 21387T=JCM 33640T).


Author(s):  
Hye Su Jung ◽  
Byung Hee Chun ◽  
Hyung Min Kim ◽  
Che Ok Jeon

Two Gram-stain-negative, yellow-pigmented and strictly aerobic bacteria, designated strains SE-s27T and SE-s28T, were isolated from forest soil. Both strains were non-motile rods that were catalase-positive and oxidase-negative and grew optimally at 25–30 °C, pH 8.0 and with 0 % (w/v) NaCl. Strain SE-s28T produced flexirubin-type pigments, but strain SE-s27T did not produce them. Both strains contained menaquinone-6 as the sole respiratory quinone and phosphatidylethanolamine as a major polar lipid. As the major cellular fatty acids (>10 %), SE-s27T contained iso-C15 : 1 and iso-C15 : 1G, whereas SE-s28T contained iso-C15 : 0 and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c and/or iso-C15 : 0 2-OH. The DNA G+C contents of strains SE-s27T and SE-s28T were 33.1 and 44.3 mol%, respectively. The results of phylogenetic analysis based on 16S rRNA gene sequences revealed that SE-s27T and SE-s28T formed respective distinct phylogenetic lineages within the genus Flavobacterium . Strains SE-s27T and SE-s28T were most closely related to Flavobacterium macrobrachii an-8T and Flavobacterium piscinae ICH-30T with 98.0 and 94.5 % 16S rRNA gene sequence similarities, respectively. In conclusion, strains SE-s27T and SE-s28T represent novel species of the genus Flavobacterium , for which the names Flavobacterium solisilvae sp. nov. and Flavobacterium silvaticum sp. nov. are proposed. The type strains of F. solisilvae and F. silvaticum are SE-s27T (=KACC 18802T=JCM 31544T) and SE-s28T (=KACC 18803T=JCM 31545T), respectively.


2020 ◽  
Vol 70 (4) ◽  
pp. 2901-2906 ◽  
Author(s):  
Guang-Da Feng ◽  
Wendi Chen ◽  
Jun Zhang ◽  
Yong-Hong Wang ◽  
Yang Liu ◽  
...  

A novel bacterial strain, designated FGD1T, was isolated from subtropical forest soil of the Nanling National Forest Park located in Guangdong Province, P.R. China. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain FGD1T was most closely related to Novosphingobium lindaniclasticum DSM 25049T (98.8 %), followed by N. barchaimii DSM 25411T (98.7 %), N. guangzhouense DSM 32207T (98.2 %), N. panipatense DSM 22890T (98.1 %) and other species of Novosphingobium (<98 %). The draft genome sequence was 4.58 Mb in length with a G+C content of 65.1 mol%. The calculated average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain FGD1T and closely related type strains were 77.7‒79.6 % and 21.7–22.9 %, respectively. Major fatty acids were summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C14 : 0 2-OH and C16 : 0. The predominant respiratory quinone was ubiquinone 10 and the major polyamine was spermidine. Polar lipids were composed of sphingoglycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, diphosphatidylglycerol, an unidentified phospholipid and lipid. The polyphasic taxonomic results indicated that strain FGD1T represents a novel species of the genus Novosphingobium , for which the name Novosphingobium silvae sp. nov. is proposed. The type strain is FGD1T (=GDMCC 1.1761T=KACC 21283T).


2019 ◽  
Vol 69 (4) ◽  
pp. 909-913 ◽  
Author(s):  
Chunling Wang ◽  
Yingying Lv ◽  
Anzhang Li ◽  
Guangda Feng ◽  
Gegen Bao ◽  
...  

A Gram-stain-negative, rod-shaped and aerobic bacterium, designated K20C18050901T, was isolated from forest soil collected on 11 September 2017 from Dinghushan Biosphere Reserve, Guangdong Province, PR China (23° 10′ 24′′ N; 112° 32′ 10′′ E). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain K20C18050901T belongs to the genus Chitinophaga , and showed the highest similarities to Chitinophaga sancti NBRC 15057T (98.6 %) and Chitinophaga oryziterrae JCM 16595T (96.9 %). The major fatty acids (>10 %) were iso-C15 : 0, C16 : 1ω5c, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone-7. The major polar lipid was phosphatidylethanolamine. The draft genome size of strain K20C18050901T was 8.36 Mb with a DNA G+C content of 44.7 mol%. The digital DNA–DNA hybridization and average nucleotide identity values between strain K20C18050901T and C. sancti NBRC 15057T were 31.40 and 85.82 %, respectively. On the basis of phenotypic, genotypic and phylogenetic analysis, strain K20C18050901T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga silvisoli sp. nov. is proposed. The type strain is K20C18050901T (=GDMCC 1.1411T=KCTC 62860T).


Author(s):  
Ram Hari Dahal ◽  
Dhiraj Kumar Chaudhary ◽  
Dong-Uk Kim ◽  
Jaisoo Kim

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and yellow-coloured bacterium designated strain G-6-1-13T was isolated from Gwanggyo mountain forest soil. Strain G-6-1-13T could grow at 15–40 °C (optimum, 20–32 °C), pH 4.5–10.5 (optimum, pH 6.0–9.0), at 2 % (w/v) NaCl concentration, and produced flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain G-6-1-13T formed a lineage within the genus Chitinophaga that was distinct from other species of the genus. Closest member was Chitinophaga varians 10–7 W-9003T (98.6 % sequence similarity) followed by C. eiseniae DSM 22224T (98.4 %), C. qingshengii JN246T (97.6 %) and C. terrae KP01T (97.4%). The major cellular fatty acids were iso-C15 : 0, C16 : 1  ω5c, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1  ω6c). MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content of strain G-6-1-13T was 48.7 mol%. Average nucleotide identity and in silico DNA–DNA hybridization were below the species threshold. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characterization, G-6-1-13T represents a novel species in the genus Chitinophaga , for which the name Chitinophaga fulva sp. nov. is proposed. The type strain is G-6-1-13T (=KACC 21624T=NBRC 114361T).


2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4533-4539 ◽  
Author(s):  
Asif Hameed ◽  
Mariyam Shahina ◽  
Shih-Yao Lin ◽  
Wei-An Lai ◽  
Yi-Han Hsu ◽  
...  

A novel, Gram-staining-negative, non-flagellated, oval or short-rod-shaped, strictly aerobic and non-spore-forming marine bacterium, designated strain CC-AMW-CT, was isolated from coastal surface seawater in Kending County, Taiwan. Cells of strain CC-AMW-CT displayed unusual morphology and formed colourless or beige colonies on marine agar. The isolate shared pairwise 16S rRNA gene sequence similarities of 97.2 and 97.1 % with Shimia marina BCRC 80068T and Shimia isoporae BCRC 80085T, respectively, and established a discrete phyletic lineage closely associated with the members of the genus Shimia . DNA–DNA hybridization values indicated <18.2 % genomic relatedness with species of the genus Shimia . The polar lipid profile of strain CC-AMW-CT comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, four unidentified lipids and an unidentified phospholipid. The predominant fatty acids were C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8; 75.5 %). The DNA G+C content was 61.2 mol%. The predominant respiratory quinone was ubiquinone Q-10 and the major polyamine was cadaverine. The chemotaxonomic evidence, including extraordinary amounts of C18 : 1ω7c and/or C18 : 1ω6c, major polar lipids, polyamine, quinone and DNA G+C contents of CC-AMW-CT, was in line with that of the members of the genus Shimia . Thus, strain CC-AMW-CT should be classified as a novel species of the genus Shimia , for which the name Shimia biformata sp. nov. is proposed. The type strain is CC-AMW-CT ( = JCM 18818T = BCRC 80548T). An emended description of the genus Shimia is also proposed.


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 321-326 ◽  
Author(s):  
Dong-Heon Lee ◽  
Sun Ja Cho ◽  
Suk Min Kim ◽  
Sun Bok Lee

A novel bacterium, designated F081-2T, isolated from seawater from Damupo beach in Pohang, Korea, was investigated using a polyphasic taxonomic approach. Cells were yellow-pigmented, strictly aerobic, motile by gliding, Gram-negative-staining and rod-shaped. The temperature, pH and NaCl ranges for growth were 4–35 °C, pH 5.5–9.5 and 1.0–5.0 %, respectively. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain F081-2T belonged to a distinct lineage in the genus Winogradskyella of the family Flavobacteriaceae , sharing 93.7–98.1 % similarity with recognized members of the genus. Low levels of DNA–DNA relatedness values were found between strain F081-2T and Winogradskyella eximia KCTC 12219T (61.1 %), Winogradskyella thalassocola KCTC 12221T (47.0 %), Winogradskyella echinorum KCTC 22026T (39.3 %), Winogradskyella rapida CCUG 56098T (34.3 %) and Winogradskyella arenosi JCM 17633T (33.4 %). The major cellular fatty acids were iso-C15 : 0 (25.3 %), iso-C15 : 1 G (14.6 %), iso-C17 : 0 3-OH (9.3 %), anteiso-C15 : 0 (7.8 %) and iso-C15 : 0 3-OH (7.6 %). The polar lipid profile was composed of phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid, one unidentified aminophospholipid and six unidentified lipids. The major respiratory quinone was menaquinone-6 and the DNA G+C content of the strain was 32.3 mol%. On the basis of phenotypic, phylogenetic and genotypic data, strain F081-2T represents a novel species within the genus Winogradskyella , for which the name Winogradskyella damuponensis sp. nov. is proposed. The type strain is F081-2T ( = KCTC 23552T = JCM 17633T).


Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).


Author(s):  
Shan Jiang ◽  
Feng-Bai Lian ◽  
You-Yang Sun ◽  
Xiao-Kui Zhang ◽  
Zong-Jun Du

A Gram-stain-negative, rod-shaped and facultatively aerobic bacterial strain, designated F7430T, was isolated from coastal sediment collected at Jingzi Wharf in Weihai, PR China. Cells of strain F7430T were 0.3–0.4 µm wide, 2.0–2.6 µm long, non-flagellated, non-motile and formed pale-beige colonies. Growth was observed at 4–40 °C (optimum, 30 °C), pH 6.0–9.0 (optimum, pH 7.5–8.0) and at NaCl concentrations of 1.0–10.0 % (w/v; optimum, 1.0 %). The sole respiratory quinone of strain F7430T was ubiquinone 8 and the predominant cellular fatty acids were summed feature 8 (C18 : 1  ω7c / C18 : 1  ω6c; 60.7 %), summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c; 30.2 %) and C15 : 0 iso (13.9 %). The polar lipids of strain F7430T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, one unidentified phospholipid and three unidentified lipids. Results of 16S rRNA gene sequences analyses indicated that this strain belonged to the family Halieaceae and had high sequence similarities to Parahaliea aestuarii JCM 51547T (95.3 %) and Halioglobus pacificus DSM 27932T (95.2 %) followed by 92.9–95.0 % sequence similarities to other type species within the aforementioned family. The rpoB gene sequences analyses indicated that the novel strain had the highest sequence similarities to Parahaliea aestuarii JCM 51547T (82.2 %) and Parahaliea mediterranea DSM 21924T (82.2 %) followed by 75.2–80.5 % sequence similarities to other type species within this family. Phylogenetic analyses showed that strain F7430T constituted a monophyletic branch clearly separated from the other genera of family Halieaceae . Whole-genome sequencing of strain F7430T revealed a 3.3 Mbp genome size with a DNA G+C content of 52.6 mol%. The genome encoded diverse metabolic pathways including the Entner–Doudoroff pathway, assimilatory sulphate reduction and biosynthesis of dTDP-l-rhamnose. Based on results from the current polyphasic study, strain F7430T is proposed to represent a novel species of a new genus within the family Halieaceae , for which the name Sediminihaliea albiluteola gen. nov., sp. nov. is proposed. The type strain of the type species is F7430T (=KCTC 72873T=MCCC 1H00420T).


2019 ◽  
Vol 69 (4) ◽  
pp. 1075-1080 ◽  
Author(s):  
Leni Sun ◽  
Yan Chen ◽  
Wei Tian ◽  
Lunguang Yao ◽  
Zhaojin Chen ◽  
...  

A Gram-stain-positive, rod-shaped, motile bacterial strain, designated 3-2-2T, was isolated from field topsoil collected from a western suburb of Nanyang city, Henan province, China. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 3-2-2T was a member of the genus Bacillus and most closely related to Bacillus fortis R-6514T (98.9 % similarity), Bacillus terrae RA9T (98.0 %) and Bacillus fordii R-7190T (97.7 %). A draft genome sequence determined for strain 3-2-2T revealed a DNA G+C content of 42.2 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between 3-2-2T and the closely related Bacillus species ranged 79.4–84.2 % and 23.4–24.6 %. The major fatty acids of strain 3-2-2T were iso-C15 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. meso-Diaminopimelic acid was detected in the peptidoglycan. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid and an unidentified lipid. The results of phylogenetic analyses, in silico genomic comparisons, and chemotaxonomic and phenotypic analyses clearly indicated that strain 3-2-2T represents a novel species within the genus Bacillus , for which the name Bacillus acidinfaciens sp. nov. is proposed. The type strain is 3-2-2T (=CGMCC 1.13685T=LMG 30839T).


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