20 results on '"Yang, Ling-Ling"'
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2. Paenibacillus paridis sp. nov., an endophytic bacterial species isolated from the root of Paris polyphylla Smith var. yunnanensis .
- Author
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Wang M, Jiang XW, Tang SK, Zhi XY, and Yang LL
- Subjects
- Bacterial Typing Techniques, Base Composition, Cell Wall chemistry, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Endophytes classification, Endophytes isolation & purification, Fatty Acids chemistry, Nucleic Acid Hybridization, Paenibacillus isolation & purification, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Melanthiaceae microbiology, Paenibacillus classification, Phylogeny, Plant Roots microbiology
- Abstract
A Gram-reaction-positive, endospore-forming and rod-shaped bacterial strain, designated py1325
T , was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan Province, PR China, and subjected to a polyphasic taxonomic characterization. It grew optimally with 0-1 % NaCl (w/v), at pH 7 and at 30 °C. The major respiratory quinone was MK-7 and the diagnostic diamino acid in the cell-wall peptidoglycan was meso -diaminopimelic acid. The major cellular fatty acid was anteiso-C15 : 0 . The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two unidentified aminophospholipids, two unidentified phospholipids and two unidentified lipids. The results of 16S rRNA gene sequence analysis revealed the highest levels of sequence similarity with respect to Paenibacillus luteus R-3T (99.0 %), Paenibacillus sinopodophylli CCTCC AB 2016047T (97.9 %), Paenibacillus castaneae DSM 19417T (97.5 %) and Paenibacillus endophyticus LMG 27297T (97.2 %). The digital DNA-DNA hybridization and average nucleotide identity values between py1325T and these species ranged 20.6-53.3 % and 79.9-93.6 %. The G+C content of the genomic DNA was 47.7 mol%. According to the phylogenetic, phenotypic and chemotaxonomic evidence, strain py1325T clearly represents a novel species of the genus Paenibacillus , for which the name Paenibacillus paridis sp. nov. is proposed. The type strain is py1325T (=CCTCC AB 2015220T =LMG 29068T ).- Published
- 2020
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3. Sediminibacillus terrae sp. nov., a moderate halophile isolated from non-saline farm soil.
- Author
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Wu QL, Chen JH, Deng LY, Liu ZX, He JW, Liu ZX, Yang LL, Tang SK, and Chen YG
- Subjects
- Bacillaceae isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacillaceae classification, Farms, Phylogeny, Soil Microbiology
- Abstract
A Gram-stain-positive, moderately halophilic, strictly aerobic, endospore-forming, rod-shaped bacterium, strain JSM 102062
T , was isolated from a non-saline farm soil sample collected from Dehang Canyon in Hunan, PR China. Growth occurred with 0.5-20 % (w/v) NaCl (optimum 4-7 %) at pH 5.5-11.0 (optimum pH 8.0) and at 20-50 °C (optimum 30-35 °C). Contained cell-wall peptidoglycan based on meso -diaminopimelic acid and possessed menaquinone-7 (MK-7) as the major respiratory isoprenoid quinone. The major cellular fatty acids were anteiso-C15 : 0 , anteiso-C17 : 0 and iso-C16 : 0 . The polar lipid pattern consisted of diphosphatidylglycerol, phosphatidylglycerol, five unidentified phospholipids and an unidentified glycolipid. The DNA G+C content was 44.1 mol%. Phylogeny based on 16S rRNA gene sequences indicated that strain JSM 102062T belonged to the genus Sediminibacillus , sharing high 16S rRNA gene sequence similarities to Sediminibacillus halophilus EN8dT (99.4 %) and Sediminibacillus albus NHBX5T (98.3 %). The whole genomic analysis showed that strain JSM 102062T constituted a different taxon separated from the recognized Sediminibacillus species. Combined data from phenotypic and genotypic studies demonstrated that strain JSM 102062T represents a noval species of the genus Sediminibacillus , for which the name Sediminibacillus terrae sp. nov. is proposed; the type strain is JSM 102062T (=CCTCC AB 2014166T = CGMCC 1.12957T =DSM 28949T =KCTC 33541T ).- Published
- 2020
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4. Bailinhaonella thermotolerans gen. nov., sp. nov., a new member of the order Streptosporangiales.
- Author
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Feng YZ, Yang LL, Gao S, Ji Y, Yin M, Zhao YR, Chunyu WX, Li P, Zhi XY, and Tang SK
- Subjects
- Actinomycetales isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall chemistry, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 chemistry, Actinomycetales classification, Phylogeny, Soil Microbiology
- Abstract
A Gram-positive, aerobic, non-motile actinobacterium, designated YIM 75507
T , that was isolated from a soil sample collected from a dry-hot valley, was subjected to a polyphasic taxonomic study. The isolate formed branched hyphae and no fragmentation was found. Clustered spore chains were borne from aerial mycelium. The cell-wall peptidoglycan contained glutamic acid, alanine and meso-diaminopimelic acid. Whole-cell sugars were galactose, mannose, glucosamine, glucose and ribose. The major menaquinones were MK-9(H6), MK-9(H8) and MK-10(H6). The polar phospholipids contained phosphatidylmethylethanolamine, phosphatidylethanolamine and ninhydrin-positive phosphoglycolipid. Major fatty acids were iso-C16 : 0 and 10-methyl-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 75507T formed a stable and distinct lineage clustered with the genus Sinosporangium in the family Streptosporangiaceae. The draft genome sequence of strain YIM 75507T exhibited low average nucleotide identity to the closest related strain, Sinosporangium album CPCC 201354T (83.97 %), well below the 95-96 % species circumscription threshold. The G+C content of the genomic DNA was 73.8 mol%. On the basis of morphological, chemotaxonomic and phylogenetic evidence, strain YIM 75507T is assigned to a novel species of a new genus, for which the name Bailinhaonella thermotolerans gen. nov., sp. nov. is proposed. The type strain of Bailinhaonella thermotolerans is YIM 75507T (=KCTC 49229T =CGMCC 4.7547T ).- Published
- 2019
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5. Genome-based taxonomic classification within the family Thermoactinomycetaceae.
- Author
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Jiang Z, Xiao M, Yang LL, Zhi XY, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Nucleic Acid Hybridization, Peptidoglycan chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacillales classification, Phylogeny
- Abstract
The family Thermoactinomycetaceaecomprises 43 validly published species, which were identified by a polyphasic taxonomic study based on molecular phylogenetics, physiological and biochemical characteristics. However, phylogenetic analysis merely based on 16S rRNA gene sequences cannot infer a robust and reliable phylogeny. For disentangling the phylogenetic relationships among members of this family, we used a large collection of genome data and the approach of phylogenomics, to re-examine their taxonomy. The topologies of phylogenomic trees are different from those of the 16S rRNA gene sequences. In addition, based on the average nucleotide identity, digital DNA-DNA hybridization, phenotypic and biochemical characteristics, we found that Laceyella sediminis should be reclassified as a later heterotypic synonym of Laceyella tengchongensis; and reclassified Thermoactinomyces guangxiensis as Paenactinomyces guangxiensis gen. nov., comb. nov.; and establish Novibacillaceae fam. nov. to accommodate the genus Novibacillus as the type genus. In addition, compared to values calculated directly from genome sequences, the genomic DNA G+C contents mentioned in some species descriptions are too imprecise; and the corrected G+C content values have a significantly better fit to the phylogeny. Thus, the corresponding emendations of species descriptions are also proposed. In this paper, phylogenomics has been used to resolve the classification of the family Thermoactinomycetaceae.
- Published
- 2019
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6. Bacillus endozanthoxylicus sp. nov., an endophytic bacterium isolated from Zanthoxylum bungeanum Maxim leaves.
- Author
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Ma L, Xi JQ, Cao YH, Wang XY, Zheng SC, Yang CG, Yang LL, Mi QL, Li XM, Zhu ML, and Mo MH
- Subjects
- Bacillus genetics, Bacillus isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall chemistry, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Nucleic Acid Hybridization, Peptidoglycan chemistry, Phosphatidylglycerols chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Soil Microbiology, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacillus classification, Phylogeny, Plant Leaves microbiology, Zanthoxylum microbiology
- Abstract
A Gram-stain-positive, rod-shaped, motile bacterium, designated as 1404
T , was isolated from leaves of Chinese red pepper (Huajiao) (Zanthoxylum bungeanum Maxim) collected from Gansu, north-west China. Spores were not observed under a range of conditions. Strain 1404T was observed to grow at 15-45 °C and pH 6.0-10.0 and in presence of 0-5 % (w/v) NaCl concentration. The cell wall of strain 1404T was found to contain meso-diaminopimelic acid, and the predominant respiratory quinone was identified as MK-7. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as well as three unidentified polar lipids. The major fatty acids profile of strain 1404T consisted of iso-C15 : 0 (25.6 %), anteiso-C15 : 0 (18.4 %) and iso-C14 : 0 (12.1 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 1404T was affiliated to the genus Bacillus and was closely related to Bacillusoryzisoli 1DS3-10T , Bacillusbenzoevorans DSM 5391T and Bacilluscirculans DSM 11T with sequence similarity of 98.3, 98.2 and 96.9 %, respectively. The G+C content of the genomic DNA was determined to be 39.4 mol%. DNA-DNA hybridization values indicated that relatedness between strain 1404T and the type strains of closely related species of the genus Bacillus was below 41 %. Therefore, on the basis of the data from the polyphasic taxonomic study presented, strain 1404T represents a novel species of the genus Bacillus, for which the name proposed is Bacillus endozanthoxylicus sp. nov. The type strain is 1404T (=CCTCC AB 2017021T =KCTC 33827T ).- Published
- 2017
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7. The underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.
- Author
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Zhi XY, Jiang Z, Yang LL, and Huang Y
- Subjects
- Animals, Gene Transfer, Horizontal, Genetic Variation, Metabolic Networks and Pathways genetics, Actinomycetales classification, Actinomycetales genetics, Genetic Speciation, Genome, Bacterial, Genomics, Phylogeny
- Abstract
The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations., (Copyright © 2016 Elsevier Inc. All rights reserved.)
- Published
- 2017
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8. Yimella radicis sp. nov., an endophytic actinobacterium isolated from the root of Paris polyphylla Smith var. yunnanensis.
- Author
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Yang LL, Jiang Z, Tang SK, Chu X, Xu LH, and Zhi XY
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall chemistry, China, DNA, Bacterial genetics, DNA, Ribosomal genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Actinomycetales classification, Melanthiaceae microbiology, Phylogeny, Plant Roots microbiology
- Abstract
An endophytic actinobacterial strain, designated py1292T, was isolated from the root of Paris polyphylla Smith var. yunnanensis collected from Yunnan province, China, and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate in the family Dermacoccaceae and clustered with Yimella lutea (showing the highest similarity of 99.1 %). DNA-DNA relatedness between strain py1292T and Y. lutea YIM 45900T was 45.6±3.2 % (reciprocal 47.8±3.6 %). The novel isolate was found to be a Gram-staining-positive rod, catalase- and oxidase-positive. It grew at pH 6.0-8.0, with 0-9 % NaCl and at 20-45 ºC, optimally at pH 7.0, with 0-3 % NaCl and at 28 ºC. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, two unknown phospholipids and two unknown polar lipids. The major cellular fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The whole-cell hydrolysates contained mannose, ribose, rhamnose, glucose and galactose. The peptidoglycan contained alanine, glycine, serine, aspartic acid, glutamic acid and lysine. The genomic DNA G+C content was determined to be 65.6 mol%. Phylogenetic, phenotypic and chemotaxonomic data (especially the same peptidoglycan type) showed that strain py1292T should be classified as a representative of a novel species of the genus Yimella, for which the name Yimella radicis sp. nov. is proposed. The type strain is py1292T (=KCTC 39612T=LMG 29070T).
- Published
- 2016
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9. Ornithinicoccus halotolerans sp. nov., and emended description of the genus Ornithinicoccus.
- Author
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Zhang YG, Wang HF, Yang LL, Guo JW, Xiao M, Huang MJ, Nabil Hozzein W, and Li WJ
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Desert Climate, Fatty Acids chemistry, Glycolipids chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Actinomycetales classification, Phylogeny, Soil Microbiology
- Abstract
A halotolerant actinobacterial strain, designated EGI 80423T, was isolated from a desert soil of Xinjiang, north-west China, and subjected to a polyphasic taxonomic characterization. Strain EGI 80423T grew at pH 7.0-10.0 and with 0-14.0% (w/v) NaCl, optimally at pH 8.0-9.0 and with 2.0-4.0% (w/v) NaCl. Cells of strain EGI 80423T were Gram-stain-positive, non-motile cocci with diameters of 0.6-0.8 μm. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was Orn ← Glu. The major fatty acids identified were iso-C17:1ω9c, iso-C15:0 and iso-C17:0. The predominant menaquinone was MK-8(H4), while the polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unknown phospholipids, two unknown glycolipids, six unknown phosphoglycolipids and five unknown polar lipids. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain EGI 80423T clustered with the single member of the genus Ornithinicoccus. Sequence similarity between strain EGI 80423T and Ornithinicoccus hortensis NBRC 16434T. Because the type strain has been provided by NBRC, Japan was 97.7%. The DNA-DNA relatedness value between strain EGI 80423T and O. hortensis NBRC 16434T was 36.84%. Based on morphological, chemotaxonomic and phylogenetic characteristics, and DNA-DNA hybridization data, strain EGI 80423T represents a novel species of the genus Ornithinicoccus, for which the name Ornithinicoccus halotolerans sp. nov. is proposed. The type strain is EGI 80423T (=CGMCC 1.14989T=KCTC 39700T). The description of the genus Ornithinicoccus has also been emended.
- Published
- 2016
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10. Egicoccus halophilus gen. nov., sp. nov., a halophilic, alkalitolerant actinobacterium and proposal of Egicoccaceae fam. nov. and Egicoccales ord. nov.
- Author
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Zhang YG, Chen JY, Wang HF, Xiao M, Yang LL, Guo JW, Zhou EM, Zhang YM, and Li WJ
- Subjects
- Actinobacteria genetics, Actinobacteria isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids chemistry, Nucleic Acid Hybridization, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Actinobacteria classification, Phylogeny, Soil Microbiology
- Abstract
A novel Gram-stain-positive, non-motile, moderately halophilic and alkalitolerant actinobacterium, designated EGI 80432T, was isolated from a saline-alkaline soil of Xinjiang province, north-west China. Cells were non-endospore-forming cocci with a diameter of 0.5-0.8 μm. Strain EGI 80432T grew in the presence of 0-9 % (w/v) NaCl (optimum at 3-5 %), and also grew within the pH range 6.0-10.0 (optimum at pH 8.0-9.0) on marine 2216E medium. The peptidoglycan type was A1γ. The whole-cell hydrolysates contained glucose, galactose, mannose and three unknown sugars as major sugars. The predominant menaquinone was MK-9(H4). The major fatty acids were C17 : 1ω8c, summed feature 3 (C16 : 1ω7c/C16 : 1ω6c), C18 : 1ω9c and iso-C15 : 0 The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, one unknown phosphoglycolipid, three unknown phospholipids and four unknown polar lipids. The genomic DNA G+C content was 75.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain EGI 80432T clustered within the radius of the class Nitriliruptoria. Levels of sequence similarity between strain EGI 80432T and its phylogenetic neighbours Nitriliruptor alkaliphilus ANL-iso2T and Euzebya tangerina F10T were 94.1 and 88.1 %, respectively. Based on morphological, physiological and chemotaxonomic characteristics and phylogenetic analysis, a novel species of a new genus, Egicoccus halophilus gen. nov., sp. nov., is proposed, within the new family and new order Egicoccaceae fam. nov. and Egicoccales ord. nov. in the class Nitriliruptoria. The type strain of Egicoccus halophilus is EGI 80432T ( = CGMCC 1.14988T = KCTC 33612T).
- Published
- 2016
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11. Egibacter rhizosphaerae gen. nov., sp. nov., an obligately halophilic, facultatively alkaliphilic actinobacterium and proposal of Egibaceraceae fam. nov. and Egibacterales ord. nov.
- Author
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Zhang YG, Wang HF, Yang LL, Zhou XK, Zhi XY, Duan YQ, Xiao M, Zhang YM, and Li WJ
- Subjects
- Actinobacteria genetics, Actinobacteria isolation & purification, Base Composition, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Molecular Sequence Data, Peptidoglycan chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Tamaricaceae microbiology, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Actinobacteria classification, Phylogeny, Rhizosphere, Soil Microbiology
- Abstract
A novel obligately halophilic, facultatively alkaliphilic actinobacterium, designated EGI 80759T, was isolated from the rhizosphere of Tamarix hispida Willd, Karamay, Xinjiang province, north-west China. Cells of strain EGI 80759T were Gram-stain-positive, non-motile and non-endospore-forming rods. Strain EGI 80759T showed obligately halophilic growth with a tolerance to 8-25 % (w/v) NaCl (optimum growth at 10-12 %, w/v) and facultatively alkaliphilic growth within the pH range 7.0-11.0 (optimum growth at pH 9.0-10.0). Cell-wall hydrolysates of the isolate contained meso-diaminopimelic acid (peptidoglycan type A1γ), with glucose, glucosamine, ribose and mannose as the major sugars. The major fatty acids identified were 10-methyl-C17 : 0, C17 : 1ω8c and C17 : 0. The predominant menaquinone was MK-9(H4). The G+C content of the genomic DNA was 72.1 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain EGI 80759T clustered with members of the class Nitriliruptoria and showed highest 16S rRNA gene sequence similarities with Euzebya tangerina F10T (90.3 %) and Nitriliruptor alkaliphilus ANL-iso2T (88.1 %). On the basis of the data obtained from phenotypic and chemotaxonomic studies and the phylogenetic analysis, the isolate is proposed to be a representative of a novel genus and a novel species, Egibacter rhizosphaerae gen. nov., sp. nov., of a proposed novel family, Egibacteraceae fam. nov., and order, Egibacterales ord. nov., within the class Nitriliruptoria. The type strain of the type species, Egibacter rhizosphaerae, is EGI 80759T ( = CGMCC 1.14997T = KCTC 39588T).
- Published
- 2016
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12. Bacillus crassostreae sp. nov., isolated from an oyster (Crassostrea hongkongensis).
- Author
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Chen JH, Tian XR, Ruan Y, Yang LL, He ZQ, Tang SK, Li WJ, Shi H, and Chen YG
- Subjects
- Animals, Bacillus genetics, Bacillus isolation & purification, Base Composition, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan chemistry, Phospholipids chemistry, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Bacillus classification, Crassostrea microbiology, Phylogeny
- Abstract
A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118(T), was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118(T) was able to grow with 0-13% (w/v) NaCl (optimum 2-5%), at pH 5.5-10.0 (optimum pH 7.5) and at 5-50 °C (optimum 30-35 °C). The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant respiratory quinone was menaquinone-7 and the major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C16 : 0 and C16 : 1ω11c. The polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown glycolipid and an unknown phospholipid. The genomic DNA G+C content was 35.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 100118(T) belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211(T) (98.9% 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33(T) (98.3%), Bacillus niabensis 4T19(T) (97.8%) and Bacillus herbersteinensis D-1,5a(T) (97.1%). The combination of results from the phylogenetic analysis, DNA-DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118(T) represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118(T) ( = CTCC AB 2010452(T) =DSM 24486(T) =JCM 17523(T))., (© 2015 IUMS.)
- Published
- 2015
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13. Actinophytocola sediminis sp. nov., an actinomycete isolated from a marine sediment.
- Author
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Zhang DF, Jiang Z, Zhang XM, Yang LL, Tian XP, Long LJ, Zhang S, and Li WJ
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Base Composition, China, DNA, Bacterial genetics, Diaminopimelic Acid chemistry, Fatty Acids chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Seawater microbiology, Vitamin K 2 chemistry, Actinomycetales classification, Geologic Sediments microbiology, Phylogeny
- Abstract
A novel actinomycete strain, designated YIM M13705(T), was isolated from a marine sediment sample of the South China Sea and its characteristics were determined by a polyphasic approach. The slowly growing, Gram-stain-positive, aerobic strain produced branched substrate mycelium and aerial hyphae, and no diffusible pigment was produced on the media tested. At maturity, spore chains were formed on aerial hyphae and substrate mycelium was not fragmented. Whole-cell hydrolysates of the strain contained meso-diaminopimelic acid and galactose, glucose, ribose and rhamnose. The predominant menaquinones were MK-9(H4) and MK-10(H2). The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyphosphatidylethanolamine, phosphatidylinositol and ninhydrin-positive phosphoglycolipids. The major fatty acid was iso-C(16 : 0). The G+C content of the genomic DNA was 68.2 mol%. On the basis of 16S rRNA gene sequence, the strain was shown to be most closely related to species of the genus Actinophytocola. DNA-DNA hybridization relatedness values (<70%) of the isolate with its closest neighbour Actinophytocola xinjiangensis QAIII60(T) supported classification of the isolate as a representative of a novel species. On the basis of phylogenetic analysis, and phenotypic and genotypic data, it is concluded that the new isolate belongs to a novel species of the genus Actinophytocola, for which the name Actinophytocola sediminis sp. nov. (type strain YIM M13705(T) = DSM 45939(T) = BCRC 16956(T)) is proposed., (© 2014 IUMS.)
- Published
- 2014
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14. Rhodococcus canchipurensis sp. nov., an actinomycete isolated from a limestone deposit site.
- Author
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Nimaichand S, Sanasam S, Zheng LQ, Zhu WY, Yang LL, Tang SK, Ningthoujam DS, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, DNA, Bacterial genetics, Fatty Acids analysis, Molecular Sequence Data, Mycolic Acids analysis, Nucleic Acid Hybridization, RNA, Ribosomal, 16S genetics, Rhodococcus genetics, Rhodococcus isolation & purification, Sequence Analysis, DNA, Calcium Carbonate, Phylogeny, Rhodococcus classification, Soil Microbiology
- Abstract
A novel actinobacterial strain, MBRL 353(T), was isolated from a sample collected from a limestone quarry at Hundung, Manipur, India. Comparison of 16S rRNA gene sequences of strain MBRL 353(T) and other members of the genus Rhodococcus showed sequence similarities ranging from 95.5 to 98.2 %, with strain MBRL 353(T) showing closest sequence similarity to Rhodococcus triatomae IMMIB RIV-085(T) (98.2 %) and Rhodococcus equi DSM 20307(T) (97.2 %). DNA-DNA hybridization results, however, revealed that DNA-DNA relatedness values between strain MBRL 353(T) and R. triatomae DSM 44892(T) (43.4 %) and R. equi DSM 20307(T) (33.4 %) were well below the 70 % limit for species identification. Strain MBRL 353(T) contained meso-diaminopimelic acid as the diagnostic diamino acid and galactose and arabinose in the cell wall. Mycolic acids were present. The major fatty acids were C(16 : 0) (45.7 %), C(18 : 1)ω9c (18.2 %) and 10-methyl C(18 : 0) (11.3 %). The only menaquinone detected was MK-8(H(2)), while the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. The G+C content of the genomic DNA was 69.2 mol%. The phenotypic and genotypic data showed that strain MBRL 353(T) merits recognition as a representative of a novel species of the genus Rhodococcus for which the name Rhodococcus canchipurensis sp. nov. is proposed; the type strain is MBRL 353(T) (= KCTC 19851(T) = JCM 17578(T)).
- Published
- 2013
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15. Streptomyces glycovorans sp. nov., Streptomyces xishensis sp. nov. and Streptomyces abyssalis sp. nov., isolated from marine sediments.
- Author
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Xu Y, He J, Tian XP, Li J, Yang LL, Xie Q, Tang SK, Chen YG, Zhang S, and Li WJ
- Subjects
- Bacterial Typing Techniques, China, DNA, Bacterial genetics, Fatty Acids analysis, Molecular Sequence Data, Phospholipids analysis, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Streptomyces genetics, Streptomyces isolation & purification, Geologic Sediments microbiology, Phylogeny, Streptomyces classification
- Abstract
Strains YIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were isolated from marine sediments collected from the Xisha Islands in the South China Sea. All three isolates were able to grow optimally at pH 7.0, 28-37 °C and 0-3% (w/v) NaCl. Comparison of 16S rRNA gene sequences showed that these strains are members of the genus Streptomyces, exhibiting moderately high 16S rRNA gene sequence similarities of 97.0-98.8% to members of the most closely related Streptomyces species. Morphological characteristics, physiological characteristics and compositions of whole-cell sugars and phospholipids are consistent with the diagnostic characteristics of the genus Streptomyces, but still allowed differentiation amongst the three strains and their neighbours. Based on 16S rRNA gene sequence analysis, DNA-DNA relatedness, phenotypic characteristics and chemotaxonomic data, strains YIM M 10366(T), YIM M 10378(T) and YIM M 10400(T) were identified as members of three novel species of the genus Streptomyces, for which the names Streptomyces glycovorans sp. nov. (type strain YIM M 10366(T) =DSM 42021(T) =CCTCC AA2010005(T)), Streptomyces xishensis sp. nov. (type strain YIM M 10378(T) = DSM 42022(T) =CCTCC AA 2010006(T)) and Streptomyces abyssalis sp. nov. (type strain YIM M 10400(T) =DSM 42024(T) = CCTCC AA 2010008(T)) are proposed.
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- 2012
- Full Text
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16. Thermocatellispora tengchongensis gen. nov., sp. nov., a new member of the family Streptosporangiaceae.
- Author
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Zhou EM, Yang LL, Song ZQ, Yu TT, Nie GX, Ming H, Zhou Y, Tang SK, and Li WJ
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Bacterial Typing Techniques, Base Composition, Cell Wall chemistry, China, DNA, Bacterial genetics, Fatty Acids analysis, Molecular Sequence Data, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Spores, Bacterial, Vitamin K 2 analysis, Actinomycetales classification, Phylogeny, Soil Microbiology
- Abstract
A novel Gram-positive, aerobic, spore-forming, thermophilic actinomycete, designated strain YIM 77521(T), was isolated from a sandy soil sample collected at Rehai National Park, Tengchong, Yunnan province, south-west China. The strain formed branched substrate mycelia and no fragmentation was found. Masses of short, straight or irregular chains of three to eight warty ornamented spores were borne from aerial mycelia. The strain contained meso-diaminopimelic acid in the cell wall and the whole-cell sugars contained mannose, galactose, glucose and ribose. The predominant menaquinones were MK-9(H(4)), MK-9(H(6)) and MK-9(H(8)). The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxyphosphatidylmonomethylethanolamine and N-acetylglucosamine-containing phospholipids. The major fatty acids were iso-C(16 : 0), C(17 : 0) 10-methyl and C(18 : 0). The DNA G+C content of strain YIM 77521(T) was 73.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 77521(T) fell within the radiation of the suborder Streptosporangineae and formed a distinct monophyletic lineage adjacent to the family Streptosporangiaceae with a high bootstrap value. On the basis of combined data from the phenotypic and phylogenetic analyses, strain YIM 77521(T) represents a novel genus and species within the family Streptosporangiaceae, for which the name Thermocatellispora tengchongensis gen. nov., sp. nov. is proposed. The type strain is YIM 77521(T) ( = DSM 45615(T) = CCTCC AA 2011013(T)).
- Published
- 2012
- Full Text
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17. Salinisphaera halophila sp. nov., a moderately halophilic bacterium isolated from brine of a salt well.
- Author
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Zhang YJ, Tang SK, Shi R, Klenk HP, Chen C, Yang LL, Zhou Y, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids analysis, Gammaproteobacteria genetics, Gammaproteobacteria isolation & purification, Molecular Sequence Data, Quinones analysis, Salts analysis, Sequence Analysis, DNA, Gammaproteobacteria classification, Phylogeny, Water Microbiology
- Abstract
A Gram-stain-negative, moderately halophilic, strictly aerobic bacterium, designated YIM 95161(T), was isolated from brine of a salt well in Yunnan province, China, and subjected to a taxonomic study using a polyphasic approach. Cells of strain YIM 95161(T) were short rods, approximately 0.9-1.4 µm long and 0.4-0.6 µm wide. Strain YIM 95161(T) grew at 15-40 °C (optimum, 25-30 °C), 6-29 % (w/v) NaCl (optimum, 14-19 %) and at pH 5.0-8.0 (optimum, pH 7.0). The predominant isoprenoid quinone was Q-8. The major fatty acids (>10 %) were summed feature 8 (C(18 : 1)ω6c and/or C(18 : 1)ω7c) and C(14 : 0). The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unknown phosphoglycolipid and two unknown lipids. The DNA G+C content was 69.5 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 95161(T) was a member of the genus Salinisphaera and exhibited sequence similarities of 96.7 %, 95.6 % and 95.4 % to Salinisphaera shabanensis E1L3A(T), Salinisphaera dokdonensis CL-ES53(T) and Salinisphaera hydrothermalis EPR70(T), respectively. On the basis of phylogenetic, physiological and chemotaxonomic analysis, strain YIM 95161(T) represents a novel species of the genus Salinisphaera, for which the name Salinisphaera halophila sp. nov. is proposed. The type strain is YIM 95161(T) (= CCTCC AB 2011132(T) = JCM 17431(T)).
- Published
- 2012
- Full Text
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18. Actinokineospora soli sp. nov., a thermotolerant actinomycete isolated from soil, and emended description of the genus Actinokineospora.
- Author
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Tang X, Zhou Y, Zhang J, Ming H, Nie GX, Yang LL, Tang SK, and Li WJ
- Subjects
- Actinomycetales genetics, Actinomycetales isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids analysis, Molecular Sequence Data, Phospholipids analysis, Quinones analysis, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Soil analysis, Actinomycetales classification, Phylogeny, Soil Microbiology
- Abstract
A strain of thermotolerant actinomycete, designated YIM 75948(T), was isolated from a soil sample in Yunnan province, China. The strain grew at 25-55 °C (optimum 37 °C). The substrate mycelium and aerial mycelium produced on Czapek's agar were both pale yellow to white. The diagnostic diamino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid, and the whole-cell sugars were mannose, ribose, glucose, galactose and arabinose. The major fatty acids were iso-C(15:0), iso-C(16:0) and C(16:0) and the predominant respiratory quinone was MK-9(H(4))(.) The polar lipids consisted of phosphatidylethanolamine, phosphatidylethanolamine with hydroxy fatty acids, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 73.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 75948(T) belonged in the genus Actinokineospora and that its closest relative among recognized species was Actinokineospora fastidiosa DSM 43855(T) (97.6% sequence similarity). The mean level of DNA-DNA relatedness between the novel strain and A. fastidiosa DSM 43855(T) was, however, only 47.8%. Based on the phenotypic, chemotaxonomic and phylogenetic data and the results of the DNA-DNA hybridizations, strain YIM 75948(T) represents a novel species of the genus Actinokineospora for which the name Actinokineospora soli sp. nov. is proposed. The type strain is YIM 75948(T) ( =JCM 17695(T) =DSM 45613(T)). The description of the genus Actinokineospora is emended to reflect the fact that the genomic DNA G+C contents of A. fastidiosa DSM 43855(T) and the type strain of Actinokineospora soli sp. nov. recorded in the present study fell above the range given in previous descriptions of this genus.
- Published
- 2012
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19. Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco.
- Author
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Liu J, Yang LL, Xu CK, Xi JQ, Yang FX, Zhou F, Zhou Y, Mo MH, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Fatty Acids analysis, Molecular Sequence Data, Quinones analysis, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sphingobacterium genetics, Sphingobacterium isolation & purification, Phylogeny, Sphingobacterium classification, Nicotiana microbiology
- Abstract
A novel Gram-negative strain, designated M-SX103(T), was isolated from a fresh leaf of Nicotiana tabacum Linn. collected at Yuxi City, Yunnan province, China, and subjected to a polyphasic taxonomic study. Growth occurred at 10-40 °C, at pH 6.0-9.0 and with 0-3% (w/v) NaCl. The predominant isoprenoid quinone was MK-7. The major cellular fatty acids of strain M-SX103(T) were iso-C(15:0), iso-C(17:0) 3-OH and summed feature 3 (C(16:1)ω7c and/or C(16:1)ω6c). The G+C content of the genomic DNA was 40.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Sphingobacterium, sharing 95.4-89.7% sequence similarity with type strains of members of the genus Sphingobacterium; it was most closely related to Sphingobacterium composti T5-12(T). On the basis of the taxonomic evidence, a novel species, Sphingobacterium nematocida sp. nov., is proposed. The type strain is M-SX103(T) ( = JCM 17339(T) = CCTCC AB 2010390(T)).
- Published
- 2012
- Full Text
- View/download PDF
20. Rhodococcus artemisiae sp. nov., an endophytic actinobacterium isolated from the pharmaceutical plant Artemisia annua L.
- Author
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Zhao GZ, Li J, Zhu WY, Tian SZ, Zhao LX, Yang LL, Xu LH, and Li WJ
- Subjects
- Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial genetics, Endophytes genetics, Endophytes isolation & purification, Fatty Acids chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan chemistry, Plants, Medicinal microbiology, RNA, Ribosomal, 16S genetics, Rhodococcus genetics, Rhodococcus isolation & purification, Sequence Analysis, DNA, Vitamin K 2 analogs & derivatives, Vitamin K 2 chemistry, Artemisia annua microbiology, Endophytes classification, Phylogeny, Rhodococcus classification
- Abstract
A Gram-positive, non-motile actinobacterium, designated YIM 65754T, was isolated from the stem of Artemisia annua L., collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YIM 65754T comprised an evolutionary lineage within the genus Rhodococcus. The isolate clustered with Rhodococcus pyridinivorans PDB9T, Rhodococcus gordoniae W 4937T and Rhodococcus rhodochrous DSM 43241T, with which it shared 98.4, 97.9 and 97.8 % 16S rRNA gene sequence similarities, respectively. However, DNA-DNA relatedness demonstrated that strain YIM 65754T was distinct from its closest phylogenetic neighbours. The cell-wall peptidoglycan contained meso-diaminopimelic acid, arabinose, galactose, mannose and glucose (cell-wall chemotype IV). The major menaquinone was MK-8(H2) and the predominant fatty acids were C16:0 (27.83 %), iso-C15:0 2-OH and/or C16:1ω7c (20.21 %) and 10-methyl C18:0 (17.50 %). The DNA G+C content was 66.2 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, the isolate represents a novel species of the genus Rhodococcus, for which the name Rhodococcus artemisiae sp. nov. is proposed; the type strain is YIM 65754T (=CCTCC AA 209042T=DSM 45380T).
- Published
- 2012
- Full Text
- View/download PDF
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