scholarly journals Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai–Tibet Plateau

2020 ◽  
Vol 70 (5) ◽  
pp. 3234-3240 ◽  
Author(s):  
Sihui Zhang ◽  
Xiaoxia Wang ◽  
Jing Yang ◽  
Shan Lu ◽  
Xin-He Lai ◽  
...  

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144T and 4053, were isolated from leaves of Lamiophlomis rotata on the Qinghai–Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner’s 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144T belonged to the genus Nocardioides and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were Nocardioides litoris DSM 103718T (98.4 %), Nocardioides rubriscoriae DSM 23986T (98.2%) and Nocardioides plantarum DSM 11054T (97.8 %). The genome of strain S-1144T showed less than 70 % digital DNA–DNA hybridization and < 95–96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144T was 73.5 mol%. MK-8(H4) was the predominant respiratory quinone (96.0 %) and llLL-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1  ω8c, C17 : 0 and C18 : 1  ω9c. On the basis of obtained data, strain S-1144T represented a novel species of the genus Nocardioides , for which the name Nocardioides dongxiaopingii sp. nov. is proposed. The type strain is S-1144T (=CGMCC 4.7568T=JCM 33469T).

2012 ◽  
Vol 62 (Pt_12) ◽  
pp. 2997-3002 ◽  
Author(s):  
Neha Niharika ◽  
Swati Jindal ◽  
Jasvinder Kaur ◽  
Rup Lal

A bacterial strain, designated Dd16T, was isolated from a hexachlorocyclohexane (HCH) dumpsite at Lucknow, India. Cells of strain Dd16T were Gram-stain-negative, non-motile, rod-shaped and yellow-pigmented. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Sphingomonas in the family Sphingomonadaceae , as it showed highest sequence similarity to Sphingomonas asaccharolytica IFO 15499T (95.36 %), Sphingosinicella vermicomposti YC7378T (95.30), ‘Sphingomonas humi’ PB323 (95.20 %), Sphingomonas sanxanigenens NX02T (95.14 %) and Sphingomonas desiccabilis CP1DT (95.00 %). The major fatty acids were summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) C14 : 0 2-OH, summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipid profile of strain Dd16T also corresponded to those reported for species of the genus Sphingomonas (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, and a sphingoglycolipid), again supporting its identification as a member of the genus Sphingomonas . The predominant respiratory quinone was ubiquinone Q10, and sym-homospermidine was the major polyamine observed. The total DNA G+C content of strain Dd16T was 65.8 mol%. The results obtained on the basis of phenotypic characteristics and phylogenetic analysis and after biochemical and physiological tests, clearly distinguished strain Dd16T from closely related members of the genus Sphingomonas . Thus, strain Dd16T represents a novel species of the genus Sphingomonas for which the name Sphingomonas indica sp. nov. is proposed. The type strain is Dd16T ( = DSM 25434T = CCM 7882T).


Author(s):  
Jiao Huang ◽  
Ying Huang

A novel filamentous Actinobacterium, designated strain FXJ1.1311T, was isolated from soil collected in Ngari (Ali) Prefecture, Qinghai-Tibet Plateau, western PR China. The strain showed antimicrobial activity against Gram-positive bacteria and Fusarium oxysporum. Results of phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FXJ1.1311T belonged to the genus Lentzea and showed the highest sequence similarity to Lentzea guizhouensis DHS C013T (98.04%). Morphological and chemotaxonomic characteristics supported its assignment to the genus Lentzea . The genome-wide average nucleotide identity between strain FXJ1.1311T and L. guizhouensis DHS C013T as well as other Lentzea type strains was <82.2 %. Strain FXJ1.1311T also formed a monophyletic line distinct from the known Lentzea species in the phylogenomic tree. In addition, physiological and chemotaxonomic characteristics allowed phenotypic differentiation of the novel strain from L. guizhouensis . Based on the evidence presented here, strain FXJ1.1311T represents a novel species of the genus Lentzea , for which the name Lentzea tibetensis sp. nov. is proposed. The type strain is FXJ1.1311T (=CGMCC 4.7383T=DSM 104975T).


2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 230-235 ◽  
Author(s):  
P. Kämpfer ◽  
K. Martin ◽  
W. Dott

Two Gram-stain-positive, non-endospore-forming actinobacteria (Ca8Tand Ca14) were isolated from a bioreactor with extensive phosphorus removal. Based on 16S rRNA gene sequence similarity comparisons, strains Ca8T and Ca14 were shown to belong to the genus Gordonia and were most closely related to Gordonia hirsuta DSM 44140T (98.0 % sequence similarity) and Gordonia hydrophobica DSM 44015T (97.2 %). In comparison with the sequences of the type strains of all other species of the genus Gordonia tested, similarities were below 97 %. The quinone systems of the strains were determined to consist predominantly of MK-9H2. The polar lipid profile for both organisms consisted of diphosphatidylglycerol, phosphatidylglycerol, phospatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. Whole-organism hydrolysates contained meso-diaminopimelic acid as the diamino acid of the peptidoglycan; mycolic acids were detected as well. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis-9, C16 : 0 and C18 : 1 and tuberculostearic acid strongly supported the grouping of strains Ca8T and Ca14 into the genus Gordonia . The two strains showed a DNA–DNA similarity of 96 %. DNA–DNA hybridizations of strain Ca8T with G. hirsuta DSM 44140T and G. hydrophobica DSM 44015T resulted in values of 26.3 and 25.0 %, respectively. These results and those of the physiological and biochemical tests allowed a clear phenotypic differentiation of strains Ca8T and Ca14 from the most closely related species of the genus Gordonia . It is concluded that strains Ca8T and Ca14 represent a novel species, for which the name Gordonia phosphorivorans sp. nov. is proposed, with the type strain Ca8T ( = DSM 45630T = CCUG 61533T = CCM 7957T = LMG 26648T).


2020 ◽  
Vol 70 (5) ◽  
pp. 3323-3327 ◽  
Author(s):  
Qian Wang ◽  
Sheng-Dong Cai ◽  
Jie Liu ◽  
De-Chao Zhang

The Gram-strain-negative, rod-shaped, facultatively anaerobic, non-motile bacterial strain, designated S1-10T, was isolated from marine sediment. Strain S1-10T grew at 4–42 °C (optimally at 30–35 °C), at pH 7.0–10 (optimally at pH 9) and in the presence of 0.5–8 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S1-10T was related to the genus Aequorivita and had highest 16S rRNA gene sequence similarity to Aequorivita viscosa 8-1bT (97.7%). The predominant cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The main respiratory quinone was menaquinone 6 (MK-6). The genomic DNA G+C content of strain S1-10T was 34.6 mol%. The polar lipid profile of strain S1-10T contained phosphatidylethanolamine, two aminolipids, two glycolipids, one phosphoglycolipid and three unidentified polar lipids. In addition, the maximum values of in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI) between strain S1-10T and A. viscosa CGMCC 1.11023T were 15.4 and 75.7 %, respectively. Combined data from phenotypic, phylogenetic, isDDH and ANI analyses demonstrated that strain S1-10T is the representative of a novel species of the genus Aequorivita , for which we propose the name Aequorivita sinensis sp. nov. (type strain S1-10T=CGMCC 1.12579T=JCM 19789T). We also propose that Vitellibacter todarodis and Vitellibacter aquimaris should be transferred into genus Aequorivita and be named Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov., respectively. The type strain of Aequorivita todarodis comb. nov. is MYP2-2T (= KCTC 62141T= NBRC 113025T) and the type strain of Aequorivita aquimaris comb. nov. is D-24T (=KCTC 42708T=DSM 101732T).


2020 ◽  
Vol 70 (11) ◽  
pp. 5627-5633 ◽  
Author(s):  
Yong Li ◽  
Shengkun Wang ◽  
Ju-pu Chang ◽  
Dan-ran Bian ◽  
Li-min Guo ◽  
...  

Two Gram-stain-negative, aerobic, non-motile bacterial strains, 36D10-4-7T and 30C10-4-7T, were isolated from bark canker tissue of Populus × euramericana, respectively. 16S rRNA gene sequence analysis revealed that strain 36D10-4-7T shows 98.0 % sequence similarity to Sphingomonas adhaesiva DSM 7418T, and strain 30C10-4-7T shows highest sequence similarity to Sphingobacterium arenae H-12T (95.6 %). Average nucleotide identity analysis indicates that strain 36D10-4-7T is a novel member different from recognized species in the genus Sphingomonas . The main fatty acids and respiratory quinone detected in strain 36D10-4-7T are C18 : 1  ω7c and/or C18 : 1  ω6c and Q-10, respectively. The polar lipids are diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, aminolipid, phosphatidylethanolamine, sphingoglycolipid, two uncharacterized phospholipids and two uncharacterized lipids. For strain 30C10-4-7T, the major fatty acids and menaquinone are iso-C15 : 0, C16 : 1  ω7c and/or C16 : 1  ω6c and iso-C17 : 0 3-OH and MK-7, respectively. The polar lipid profile includes phosphatidylethanolamine, phospholipids, two aminophospholipids and six unidentified lipids. Based on phenotypic and genotypic characteristics, these two strains represent two novel species within the genera Sphingomonas and Sphingobacterium . The name Sphingomonas corticis sp. nov. (type strain 36D10-4-7T=CFCC 13112T=KCTC 52799T) and Sphingobacterium corticibacterium sp. nov. (type strain 30C10-4-7T=CFCC 13069T=KCTC 52797T) are proposed.


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3010-3015 ◽  
Author(s):  
Avinash Sharma ◽  
Sunil Kumar Dhar ◽  
Om Prakash ◽  
Venkata Ramana Vemuluri ◽  
Vishal Thite ◽  
...  

A novel Gram-stain-positive, spore-forming, aerobic, non-motile, rod-shaped bacterium designated strain SD111T that forms red-pigmented colonies was isolated from a marine sediment sample (collected from 5 m depth) from Lakshadweep, India. Strain SD111T grew well on seawater agar at pH 6–10 (optimum pH 7.5±0.2). It showed maximum (97.6 %) 16S rRNA gene sequence similarity and formed a monophyletic clade with Domibacillus robiginosus WS 4628T ( = DSM 25058T). The genomic DNA G+C content was 37.4 mol% and the strain showed 37.7 % DNA–DNA relatedness to D. robiginosus DSM 25058T. The major fatty acids were anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and iso-C16 : 0 and MK-6 was the predominant quinone. The polar lipid profile of strain SD111T consisted of unidentified phospholipids (PL1 and PL2), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG). The cell wall contained meso-diaminopimelic acid and the peptidoglycan was of A1γ type. Glucose and ribose were detected as major cell-wall sugars. Results from polyphasic studies indicated that SD111T represents a novel species of the genus Domibacillus for which the name Domibacillus indicus sp. nov. is proposed. The type strain is SD111T ( = MCC 2255T = DSM 28032T).


Author(s):  
Wentao Zhu ◽  
Kui Dong ◽  
Jing Yang ◽  
Shan Lu ◽  
Xin-He Lai ◽  
...  

Six aerobic, non-motile, non-haemolytic, Gram-stain-negative, oxidase-negative strains (185T, 187, 323-1T, 194, dk386T and dk771) were recovered from different faecal samples of Equus kiang on the Qinghai–Tibet Plateau. In the 16S rRNA gene sequences, one strain pair, 185T/187, shared highest similarity to Acinetobacter equi 114T (97.9 %), and the other two (323-1T/194 and dk771T/dk386) to Acinetobacter harbinensis CGMCC 1.12528T (98.6 and 97.0 %, respectively). Phylogenomic tree analysis showed that these six strains formed three separate clades in the genus Acinetobacter . Digital DNA–DNA hybridization values of each pair of the isolates with all members of the genus Acinetobacter were far below 70 %. The main cellular fatty acids of all six strains were C18 : 1  ω9c, C16 : 0 and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c). Q-9 was the predominant respiratory quinone for strains 185T, 323-1T and dk386T. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on the genotypic, phenotypic and biochemical analyses, these six strains represent three novel species of the genus Acinetobacter , for which the names Acinetobacter lanii sp. nov., Acinetobacter shaoyimingii sp. nov. and Acinetobacter wanghuae sp. nov. are proposed. The type strains are 185T (=CGMCC 1.13636T=JCM 33607T), 323-1T (=CGMCC 1.13940T=JCM 33608T) and dk386T (=CGMCC 1.16589T=JCM 33592T), respectively.


2020 ◽  
Vol 70 (4) ◽  
pp. 2493-2498 ◽  
Author(s):  
Yajun Ge ◽  
Jing Yang ◽  
Xin-He Lai ◽  
Gui Zhang ◽  
Dong Jin ◽  
...  

A Gram-stain-positive, coccus-shaped, non-motile bacterium, designated CF-49T, was isolated from the cloacal content of a snow finch, which was incidentally captured in a plateau pika burrow on the Qinghai–Tibet Plateau, PR China. Analysis of the 16S rRNA gene sequence showed that strain CF-49T was closely related to Vagococcus elongatus CCUG 51432T (96.5 % similarity), Vagococcus fluvialis NCFB 2497T (96.0 %) and Vagococcus lutrae CCUG 39187T (95.9 %), whereas the similarity to another isolate (CF-210) was 99.9 %. Strains CF-49T and CF-210 grew optimally at 37 °C and pH 7.0 and in the presence of 0.5 % (w/v) NaCl. Acid was produced from N-acetylglucosamine, cellobiose, d-fructose, d-glucose, d-mannose, d-mannitol, maltose, d-ribose and salicin. The cell-wall peptidoglycan type was A4α (l-Lys–d-Asp). The major cellular fatty acids (>10 %) were C16 : 0 (35.6 %), C14 : 0 (17.3 %), C18 : 1 ω9c (16.2 %) and C16 : 1 ω9c (10.6 %). The predominant respiratory quinone was menaquinone MK-7 (68.8 %). The G+C content of the genomic DNA was 35.9 mol%. Digital DNA–DNA hybridization of strain CF-49T with V. fluvialis DSM 5731T, V. elongatus CCUG 51432Tand V. lutrae CCUG 39187T resulted in relatedness values of 21.4, 23.3 and 24.6 %, respectively. Based on results from polyphasic analyses, our two isolates are proposed to represent a novel species in the genus Vagococcus , with the name Vagococcus xieshaowenii. The type strain is CF-49T (=CGMCC 1.6436T=GDMCC 1.1588T=JCM 33477T).


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).


2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1259-1264 ◽  
Author(s):  
Ming-Hui Chen ◽  
Shih-Yi Sheu ◽  
Chaolun Allen Chen ◽  
Jih-Terng Wang ◽  
Wen-Ming Chen

A bacterial strain, isolated from a sample of reef-building coral (Isopora palifera) collected off the coast of southern Taiwan, was characterized using a polyphasic taxonomic approach. The strain, designated sw-2T, was Gram-staining-negative, aerobic, rod-shaped and motile, with subpolar flagella, and formed greyish pink colonies. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain sw-2T was most closely related to Roseivivax halodurans Och 239T (97.4 % sequence similarity) and Roseivivax halotolerans Och 210T (96.4 %). The novel strain did not require NaCl for growth and exhibited optimal growth at 35–40 °C, at pH 7.5–8.0 and with 3–7 % (w/v) NaCl. It produced bacteriochlorophyll a under aerobic conditions. Summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 63.7 %) predominated in the cellular fatty acid profile. The novel strain’s major respiratory quinone was ubiquinone Q-10 and its genomic DNA G+C content was 68.8 mol%. The polar lipid profile consisted of a mixture of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol, phosphatidyldimethylethanolamine, sulfo-quinovosyl diacylglycerol and three uncharacterized phospholipids. The level of DNA–DNA relatedness between strain sw-2T and Roseivivax halodurans Och 239T was only 15.0 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from all established species of the genus Roseivivax . Based on the genotypic, phenotypic and chemotaxonomic data, strain sw-2T represents a novel species in the genus Roseivivax , for which the name Roseivivax isoporae sp. nov. is proposed. The type strain is sw-2T ( = LMG 25204T = BCRC 17966T).


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