Microbacterium karelineae sp. nov. isolated from a halophyte plant in the Taklamakan desert

Author(s):  
Qi-hui Zhu ◽  
Cai-ling Yang ◽  
Xiao-xia Luo ◽  
Li-li Zhang ◽  
Zhan-feng Xia

A bacterial strain, designated TRM 80801T, was isolated from the Karelinea in Taklamakan desert, Xinjiang Uygur Autonomous Region, north-west China. Cells were Gram-stain-positive, aerobic, non-motile, short rods. Strain TRM 80801T grew at 4–50 °C, with optimum growth at 28 °C, and grew at pH 6.0–11.0 and 1–15 % (w/v) NaCl. Phylogenetic analyses of the 16S rRNA gene sequences placed strain TRM 80801T within the genus Microbacterium with the highest similarities to Microbacterium suaedae YZYP 306T (98.97 %) and Microbacterium indicum BBH6T (98.17 %), respectively. The DNA G+C content of TRM 80801T is 69.38 mol%. The cell-wall peptidoglycan contained the amino acids ornithine, glutamic acid, glycine and alanine, the diagnostic diamino acid was ornithine. The acyl type of the peptidoglycan was glycolyl. Whole-cell sugars were ribose, mannose, glucose, rhamnose and galactose. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The predominant menaquinones were MK-10, MK-11 and MK-12. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol. The whole-genome average nucleotide identity (ANI) value between strain TRM 80801T and Microbacterium suaedae YZYP 306T is 70.2 %. On the basis of the evidence presented in this study, strain TRM 80801T is representative of a novel species in the genus Microbacterium , for which the name Microbacterium karelineae sp. nov. is proposed. The type strain is TRM 80801T (=CCTCC AB 2019248T=KCTC 49357T).

Author(s):  
Wan-Ni Lu ◽  
Yi-Zhuo Xu ◽  
Yuan-Guo Xie ◽  
Rui Gao ◽  
Jie-Qiong Song ◽  
...  

A Gram-stain-positive, non-motile and short rod-shaped actinobacterium, designated strain LNNU 22110T, was isolated from the rhizosphere soil of the halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze, which collected in Xinjiang, north-west China. Growth occurred at 10–45 °C, pH 6.0–10.0 and in the presence of 0–11 % NaCl (w/v). Based on the results of 16S rRNA gene sequence phylogenetic analyses, strain LNNU 22110T belonged to the genus Ruania and had 97.5 and 95.5 % sequence similarity to Ruania alba KCTC 19413T and Ruania albidiflava CGMCC 4.3142T, respectively. The digital DNA–DNA hybridization relatedness values between strain LNNU 22110T and R. alba KCTC 19413T and R. albidiflava CGMCC 4.3142T were 23.2 and 19.9 %, respectively. The highest average nucleotide identity value between strain LNNU 22110T and its closest related strain ( R. alba KCTC 19413T) was 80.2 %, much lower than the species delineation threshold of 95–96 %. The genome of strain LNNU 22110T was 4.4 Mb, with a genomic DNA G+C content of 68.4 mol%. The diagnostic diamino acids in the peptidoglycan layer of strain LNNU 22110T were lysine, alanine, glycine, glutamic acid and aspartic acid. The predominant menaquinone was MK-8(H4). The major fatty acid (>10 %) was anteiso-C15 : 0. The polar lipid profile of strain LNNU 22110T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, diacylated phosphatidyl dimannoside, one unidentified glycolipid and two unidentified phospholipids. According to the phenotypic, phylogenetic and chemotaxonomic results, strain LNNU 22110T is considered to represent a novel species of the genus Ruania , for which the name Ruania rhizosphaerae sp. nov. is proposed. The type strain is LNNU 22110T (=KCTC 39807T=CGMCC 1.17105T).


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1945-1951 ◽  
Author(s):  
Yong-Guang Zhang ◽  
Qing Liu ◽  
Hong-Fei Wang ◽  
Dao-Feng Zhang ◽  
Yuan-Ming Zhang ◽  
...  

A facultatively alkaliphilic actinomycete strain, designated EGI 80088T, was isolated from a saline-alkali soil sample from Xinjiang province, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80088T formed fragmented aerial hyphae and short spore chains, and rod-like spores aggregated at maturity. Whole-cell hydrolysates of the isolate contained ll-diaminopimelic acid as the diagnostic diamino acid, and glucosamine, mannose, galactose, glucose and rhamnose as the marker sugars. The major fatty acids identified (>5 %) were anteiso-C15 : 0, iso-C15 : 0, summed feature 4 (iso-C17 : 1I/anteiso-C17 : 1B), iso-C16 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA of strain EGI 80088T was 70.6 mol%. EGI 80088T showed the highest 16S rRNA gene sequence similarity to its closest phylogenetic neighbour Haloactinopolyspora alba YIM 93246T (98.5 %). The DNA–DNA relatedness value of the strain EGI 80088T and H. alba YIM 93246T was 59.3±5.2 %. On the basis of morphological, chemotaxonomic and phylogenetic characteristics and DNA–DNA hybridization data, strain EGI 80088T represents a novel species of the genus Haloactinopolyspora , for which the name Haloactinopolyspora alkaliphila sp. nov. (type strain EGI 80088T = BCRC 16946T = JCM 19128T) is proposed. The description of the genus Haloactinopolyspora has also been emended.


Author(s):  
Qing Liu ◽  
Hong-Can Liu ◽  
Lei-Lei Yang ◽  
Yu-Hua Xin

The genus Flavobacterium (family Flavobacteriaceae ) can be found in diverse environments. In this study, seven novel strains were isolated from glaciers in PR China and subjected to taxonomic research. Phylogenetic analyses based on the 16S rRNA gene revealed that the strains belonged to the genus Flavobacterium . None of the seven strains grew at temperatures above 22 °C, indicating that they are psychrophilic. Furthermore, the average nucleotide identity (ANI) values of the seven strains were calculated and indicated that they represented two novel species in Flavobacterium . Strain LB3P56T was most closely related to Flavobacterium soyangense IMCC26223T (97.70 %) and strain GSP16T was most closely related to Flavobacterium sinopsychrotolerans 0533T (98.03 %). The ANI values between the two Flavobacterium strains and their closest relatives were less than 83.47 %, which was much lower than the threshold for species delineation of 95–96 %. Therefore, we propose two novel species, Flavobacterium franklandianum sp. nov. (LB3P56T=CGMCC 1.11934T=NBRC 113651T) and Flavobacterium gawalongense sp. nov. (GSP16T=CGMCC 1.24642T=NBRC 113664T).


2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3143-3147 ◽  
Author(s):  
Yuto Yamauchi ◽  
Hiroaki Minegishi ◽  
Akinobu Echigo ◽  
Yasuhiro Shimane ◽  
Masahiro Kamekura ◽  
...  

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).


2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3404-3408 ◽  
Author(s):  
Atsuko Matsumoto ◽  
Hiroaki Kasai ◽  
Yoshihide Matsuo ◽  
Yoshikazu Shizuri ◽  
Natsuko Ichikawa ◽  
...  

Bacterial strains YM16-303T and YM16-304T were isolated from a sample of seashore sand using a medium with an artificial seawater base. Both isolates grew slowly on marine agar, and were found to be Gram-reaction-positive, aerobic, non-motile and rod-shaped. The cell-wall peptidoglycan contained ll-diaminopimelic acid, glycine, alanine and hydroxyglutamic acid, and the acyl type of the muramic acid was glycolyl. The predominant menaquinone was MK-9(H8). The 16S rRNA gene sequences of strains YM16-303T and YM16-304T were most similar to that of Ilumatobacter fluminis YM22-133T, and phylogenetic analyses also indicated that they belong to the genus Ilumatobacter . Ilumatobacter fluminis YM22-133T and strains YM16-303T and YM16-304T should be classified as distinct species in the genus Ilumatobacter , however, since the 16S rRNA gene sequence similarity between them was low and the major cellular fatty acids and some physiological properties were different. Moreover, average nucleotide identity and maximal unique exact matches index values also supported the conclusion that they represent different species. On the basis of the above analyses, two novel species, Ilumatobacter nonamiense sp. nov. (type strain YM16-303T = NBRC 109120T = KCTC 29139T) and Ilumatobacter coccineum sp. nov. (type strain YM16-304T = NBRC 103263T = KCTC 29153T), are proposed. The order Acidimicrobiales , which contains the genus Ilumatobacter , currently includes six genera and only six species, and they are phylogenetically very far from each other. Phylogenetic analyses revealed that strains YM16-303T and YM16-304T clustered with closely related uncultured actinobacteria but not Ilumatobacter fluminis YM22-133T, suggesting that many uncultured bacteria related to these isolates exist in the environment. This is the first report on interspecies relationships in the order Acidimicrobiales .


2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1068-1072 ◽  
Author(s):  
Hui-Jing Du ◽  
Yu-Zhen Wei ◽  
Jing Su ◽  
Hong-Yu Liu ◽  
Bai-Ping Ma ◽  
...  

A Gram-stain-positive, rod-shaped actinobacterium, designated strain I10A-01402T, was isolated from surface-sterilized roots of a medicinal plant, Perilla frutescens, collected in a suburb of Beijing, China. Chemotaxonomically, the strain contained ll-diaminopimelic acid as the diagnostic diamino acid and MK-8(H4) as the predominant menaquinone. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The major fatty acids were C17 : 1ω9c, C18 : 1ω9c, C17 : 0, C16 : 0 and iso-C16 : 0. The genomic DNA G+C content was 70.4 mol%. 16S rRNA gene sequence analysis indicated that strain I10A-01402T belonged to the genus Nocardioides . Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolate formed a robust cluster with Nocardioides ginsengisegetis Gsoil 485T, N. koreensis MSL-09T and N. alkalitolerans KSL-1T. On the basis of the evidence from our polyphasic taxonomic study, a novel species, Nocardioides perillae sp. nov., is proposed. The type strain is I10A-01402T ( = CPCC 203382T  = DSM 24552T  = KCTC 29022T).


Author(s):  
Dan-Feng Liu ◽  
Shao-Qi Chen ◽  
Hong-Fei Wang ◽  
Yuan-Guo Xie ◽  
Rui Gao ◽  
...  

A Gram-stain-positive, non-motile and coccus-shaped bacterium, designated strain LNNU 331112T, was isolated from the composite rhizosphere soil of the halophyte Suaeda aralocaspica (Bunge) Freitag and Schütze, which was collected in Xinjiang, north-west China. Growth occurred at 10–45 °C, pH 6.0–11.0 and in the presence of 0–10 % NaCl (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence suggested that strain LNNU 331112T belonged to the genus Hoyosella and showed 95.6, 95.5 and 95.4 % sequence similarities to Hoyosella altamirensis DSM 45258T, Hoyosella subflava CGMCC 4.3532T and Hoyosella rhizosphaerae CGMCC 1.15478T, respectively. The estimated digital DNA–DNA hybridization relatedness values between strain LNNU 331112T and the type strains of H. altamirensis DSM 45258T, H. subflava CGMCC 4.3532T and H. rhizosphaerae CGMCC 1.15478T were 18.9, 19.3 and 18.3 %, respectively. The average nucleotide identity values between strain LNNU 331112T and H. altamirensis DSM 45258T, H. subflava CGMCC 4.3532T and H. rhizosphaerae CGMCC 1.15478T were 72.6, 72.7 and 72.3 %, respectively. The genome sequence of strain LNNU 331112T showed 69.0–72.3 % average amino acid identity values in comparison with the related genome sequences of three validly published Hoyosella species. The genome of strain LNNU 331112T was 3.47 Mb, with a DNA G+C content of 68.4 mol%. A total of 3182 genes were identified as protein-coding in strain LNNU 331112T. Genomic analysis revealed that a number of genes involved in osmotic pressure regulation, intracellular pH homeostasis and potassium (K+) uptake protein were found in strain LNNU 331112T. The predominant menaquinones were MK-8 (44.6 %) and MK-7 (55.4 %), which differentiated strain LNNU 331112T from other three recognized Hoyosella species. Major fatty acids (>10 %) were C17 : 1 ω8c (33.8 %), C16 : 0 (23.3 %), C17 : 0 (12.8 %) and summed feature 3 (12.9 %), which also clearly separated strain LNNU 331112T from three recognized Hoyosella species. The polar lipid profile of strain LNNU 331112T included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, one unidentified glycolipid, one unidentified phospholipid and two unidentified lipids. According to the results of phenotypic, chemotaxonomic and phylogenetic analyses, strain LNNU 331112T is considered to represent a novel species of the genus Hoyosella , for which the name Hoyosella suaedae sp. nov. is proposed. The type strain is LNNU 331112T (=KCTC 39808T=CGMCC 1.17107T=DSM 103463T).


2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2192-2196 ◽  
Author(s):  
Bing-Bing Liu ◽  
Shu-Kun Tang ◽  
Heng-Lin Cui ◽  
Yong-Guang Zhang ◽  
Li Li ◽  
...  

Two extremely halophilic archaea, designated YIM 94188T and YIM 94189, were isolated from Qijiaojing lake in Xinjiang province, north-west China and subjected to taxonomic characterization using a polyphasic approach. The cells of the two strains were coccoid, non-motile and Gram-stain-negative. Colonies were pink–white-pigmented and aerobic. Growth occurred at 10–30 % (w/v) NaCl, 20–55 °C and pH 6.0–8.0 (optimum: 20–25 % NaCl, 37–42 °C, pH 6.5–7.0). Magnesium was necessary for growth in the range of 0.2–1.2 M. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the two strains belonged to the genus Halopelagius showing 98.5 % sequence similarity to the closest phylogenetic neighbour, Halopelagius inordinatus RO5-2T. In addition, the DNA–DNA hybridization values of strains YIM 94188T and YIM 94189 to Halopelagius inordinatus RO5-2T were 35.7 % and 37.7 %, respectively. Polar lipid analyses revealed that the two strains contained phosphatidylglycerol (PG), phosphatidylglycerol phosphate methyl ester (PGP-Me), sulfated mannosyl glucosyl diether (S-DGD-1) and mannosyl glucosyl diether (DGD-1). The DNA G+C contents of strains YIM 94188T and YIM 94189 were 66.3 mol% and 64.6 mol%, respectively. On the basis of physiological and chemotaxonomic data, and phylogenetic analysis, strains YIM 94188T and YIM 94189 were classified as representing a novel species in the genus Halopelagius . The name Halopelagius fulvigenes sp. nov. is proposed, with YIM 94188T ( = CCTCC AB 2010456T = JCM 17506T) as the type strain.


2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1576-1580 ◽  
Author(s):  
Hai-Yu Huang ◽  
Jie Li ◽  
Guo-Zhen Zhao ◽  
Wen-Yong Zhu ◽  
Ling-Ling Yang ◽  
...  

A novel bacterium (strain YIM 65583T) belonging to the genus Sphingomonas was isolated from surface-sterilized tissue of Artemisia annua L., which was collected from Yunnan province, south-west China. Its morphology, physiology and biochemical features were consistent with those of members of the genus Sphingomonas . Analysis of the 16S rRNA gene sequence of strain YIM 65583T further confirmed that it should be classified as a member of the genus Sphingomonas and was most closely related to Sphingomonas phyllosphaerae FA2T (99.7 %) and Sphingomonas yunnanensis YIM 003T (98.3 %). The isolate was Gram-negative and formed yellow-pigmented colonies on ISP 2 medium. It grew optimally at pH 6.0–8.0, at 20–37 °C and in the presence of 0–1 % (w/v) NaCl. The major respiratory lipoquinone was ubiquinone-10; C18 : 1ω7c, anteiso-C16 : 1, C14 : 0-2OH, C17 : 1ω6c, C16 : 0 and C15 : 0 were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and sphingoglycolipid. The G+C content of the genomic DNA was 63.3 mol%. The DNA–DNA relatedness values of the isolate YIM 65583T with S. phyllosphaerae FA2T and S. yunnanensis YIM 003T were 43.1 % and 37.9 %, respectively. Based on these features, it is concluded that the strain represents a novel species of the genus Sphingomonas, for which the name Sphingomonas endophytica sp. nov. is proposed, with YIM 65583T ( = CCTCC AA 209035T = JCM 17394T) as the type strain.


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1859-1865 ◽  
Author(s):  
Dimitry Y. Sorokin ◽  
Dana Vejmelkova ◽  
Sebastian Lücker ◽  
Galina M. Streshinskaya ◽  
W. Irene C. Rijpstra ◽  
...  

A novel nitrite-oxidizing bacterium (NOB), strain LbT, was isolated from a nitrifying bioreactor with a high loading of ammonium bicarbonate in a mineral medium with nitrite as the energy source. The cells were oval (lancet-shaped) rods with pointed edges, non-motile, Gram-positive (by staining and from the cell wall structure) and non-spore-forming. Strain LbT was an obligately aerobic, chemolitoautotrophic NOB, utilizing nitrite or formate as the energy source and CO2 as the carbon source. Ammonium served as the only source of assimilated nitrogen. Growth with nitrite was optimal at pH 6.8–7.5 and at 40 °C (maximum 46 °C). The membrane lipids consisted of C20 alkyl 1,2-diols with the dominant fatty acids being 10MeC18 and C18 : 1ω9. The peptidoglycan lacked meso-DAP but contained ornithine and lysine. The dominant lipoquinone was MK-8. Phylogenetic analyses of the 16s rRNA gene sequence placed strain LbT into the class Thermomicrobia of the phylum Chloroflexi with Sphaerobacter thermophilus as the closest relative. On the basis of physiological and phylogenetic data, it is proposed that strain LbT represents a novel species of a new genus, with the suggested name Nitrolancea hollandica gen. nov., sp. nov. The type strain of the type species is LbT ( = DSM 23161T = UNIQEM U798T).


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