Nocardioides alpinus sp. nov., a psychrophilic actinomycete isolated from alpine glacier cryoconite

2012 ◽  
Vol 62 (2) ◽  
pp. 445-450 ◽  
Author(s):  
De-Chao Zhang ◽  
Peter Schumann ◽  
Mersiha Redzic ◽  
Yu-Guang Zhou ◽  
Hong-Can Liu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Alpine Glacier ◽  
Diamino Acid ◽  
Lipid Pattern ◽  
Type Strains

A Gram-positive, non-motile, rod-shaped, psychrophilic actinomycete, designated strain Cr7-14T, was isolated from alpine glacier cryoconite. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Cr7-14T was related to members of the genus Nocardioides and shared highest 16S rRNA gene sequence similarities with the type strains of Nocardioides furvisabuli (98.6 %), Nocardioides ganghwensis (98.2 %), Nocardioides oleivorans (98.1 %) and Nocardioides exalbidus (97.6 %). The predominant cellular fatty acids of strain Cr7-14T were C17 : 1ω8c (39.5 %) and iso-C16 : 0 (32.4 %). The major menaquinone was MK-8(H4). The diagnostic diamino acid in the cell-wall peptidoglycan was ll-2,6-diaminopimelic acid. The predominant cell-wall sugars were galactose and rhamnose. The polar lipid pattern contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, four unknown glycolipids and two unknown polar lipids. The genomic DNA G+C content was 71.9 mol%. On the basis of phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness data, a novel species, Nocardioides alpinus sp. nov., is proposed, with Cr7-14T ( = DSM 23325T = LMG 26053T = CGMCC 1.10697T) as the type strain.

scholarly journals Aeromicrobium camelliae sp. nov., isolated from Pu′er tea

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4369-4373 ◽  
Author(s):  
Lili Niu ◽  
Mengjie Xiong ◽  
Tianyi Tang ◽  
Lei Song ◽  
Xing Hu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Closely Related Species ◽  
Hybridization Data ◽  
Diamino Acid ◽  
Type Strains

A novel Gram-reaction-positive, aerobic and non-spore-forming rod-shaped bacterial strain, YS17T, was isolated from ripened Pu′er tea. Growth of the strain was observed at 15–50 °C (optimum 30–37 °C) and at pH 5.5–10.5 (optimum 6.0–9.5). Phylogenetic analysis of 16S rRNA gene sequences indicated that the strain represented a member of the genus Aeromicrobium. The strains most closely related to YS17T were Aeromicrobium erythreum DSM 8599T, Aeromicrobium alkaliterrae JCM 13518T and Aeromicrobium ginsengisoli JCM 14732T, with 16S rRNA gene sequence similarities of 96.8, 96.8 and 96.7 %, respectively. DNA–DNA hybridization of YS17T with the type strains of the most closely related species, A. erythreum DSM 8599T, A. alkaliterrae JCM 13518T and A. ginsengisoli JCM 14732T, yielded reassociation values of 10.9, 16.8 and 10.9 %, respectively. The diagnostic diamino acid of the cell wall peptidoglycan was ll-diaminopimelic acid. The predominant menaquinones were menaquinone MK-9(H4) (76 %) and MK-8(H4) (17 %). The major fatty acids were C16 : 0, 10-methyl C18 : 0 and C18 : 1ω9c. The DNA G+C content of YS17T was 66 mol%. YS17T could be differentiated from recognized species of the genus Aeromicrobium on the basis of phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of evidence from the polyphasic analyses performed as part of this study a novel species, Aeromicrobium camelliae sp. nov., is proposed, with strain YS17T ( = CGMCC 1.12942T = JCM 30952T) as the type strain.

scholarly journals Paenibacillus wooponensis sp. nov., isolated from wetland freshwater

2011 ◽  
Vol 61 (11) ◽  
pp. 2763-2768 ◽  
Author(s):  
Keun Sik Baik ◽  
Han Na Choe ◽  
Seong Chan Park ◽  
Eun Mi Kim ◽  
Chi Nam Seong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Diamino Acid ◽  
Type Strains

A rod-shaped, endospore-forming, Gram-reaction-positive bacterium, designated strain WPCB018T, was isolated from a fresh water sample collected from Woopo wetland, Korea. The isolate was identified as a member of the genus Paenibacillus on the basis of phenotypic characteristics and phylogenetic inference based on 16S rRNA gene sequence analysis. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and unknown aminophospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acids were anteiso-C15 : 0 (32.2 %), C16 : 0 (20.1 %) and C18 : 0 (18.1 %). The DNA G+C content was 56.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB018T belongs to a cluster comprising species of the genus Paenibacillus, its closest neighbours being Paenibacillus humicus PC-147T (97.5 %) and Paenibcillus pasadenensis SAFN-007T (96.2 %). Genomic DNA–DNA hybridizations performed with strain WPCB018T and type strains of the species P. humicus, P. pinihumi, P. phyllosphaerae, P. pasadenensis and P. tarimensis showed relatedness values of only 10, 17, 18, 19 and 20 %, respectively. On the basis of phenotypic, molecular and genetic evidence, strain WPCB018T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus wooponensis sp. nov. is proposed. The type strain of the novel species is WPCB018T ( = KCTC 13280T  = JCM 16350T).

scholarly journals Streptomonospora halotolerans sp. nov., an actinomycete isolated from soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3183-3189 ◽  
Author(s):  
Junwei Zhao ◽  
Lifeng Guo ◽  
Chongxi Liu ◽  
Pengyu Sun ◽  
Jiansong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Northern China ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain NEAU-Jh2-17T, was isolated from muddy soil collected from a riverbank in Jilin Province, northern China, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain NEAU-Jh2-17T showed highest similarity to those of Streptomonospora nanhaiensis 12A09T (99.26 %), Nocardiopsis rosea YIM 90094T (97.31 %), Streptomonospora halophila YIM 91355T (97.24 %) and Streptomonospora arabica S186T (97.02 %). Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-Jh2-17T fell within a cluster consisting of the type strains of species of the genus Streptomonospora and formed a stable clade with S. nanhaiensis 12A09T in trees generated with two algorithms. Key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-Jh2-17T to the genus Streptomonospora. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained glucose, ribose and galactose. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylinositol mannoside (PIM), two unknown phospholipids (PLs) and two unknown glycolipids (GLs). The predominant menaquinones were MK-10(H2), MK-10(H8), MK-10(H6) and MK-10(H4). Major fatty acids were C18 : 0 10-methyl, anteiso-C17 : 0, C16 : 0 10-methyl, iso-C15 : 0, C17 : 0 10-methyl and C18 : 0. The DNA G+C content was 71.82 mol%. However, a combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-Jh2-17T could be distinguished from its closely related relatives. Therefore, strain NEAU-Jh2-17T is considered to represent a novel species of the genus Streptomonospora, for which the name Streptomonospora halotolerans sp. nov. is proposed. The type strain is NEAU-Jh2-17T ( = CGMCC 4.7218T = JCM 30347T).

scholarly journals Humicoccus flavidus gen. nov., sp. nov., isolated from soil

2007 ◽  
Vol 57 (1) ◽  
pp. 56-59 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Seo-Youn Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Polar Lipid Profile ◽  
Diamino Acid

A Gram-positive, non-motile, spherical, non-spore-forming bacterial strain, DS-52T, was isolated from soil from Dokdo, Korea, and its taxonomic position was investigated by using a polyphasic approach. It grew optimally at 25 °C and pH 6.0–7.0. Strain DS-52T had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan, and galactose, mannose, xylose and rhamnose as whole-cell sugars. It contained MK-8(H4) and MK-9(H4) as the predominant menaquinones and anteiso-C15 : 0, iso-C15 : 0 and C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyldimethylethanolamine. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain DS-52T is most closely related to the genus Nakamurella of the suborder Frankineae. Strain DS-52T exhibited 16S rRNA gene sequence similarity values of 96.5 % to Nakamurella multipartita JCM 9543T and 92.0–93.9 % to other members of the suborder Frankineae. The diagnostic diamino acid type and polar lipid profile of strain DS-52T were the same as those of the genus Nakamurella. However, strain DS-52T could be clearly distinguished from the genus Nakamurella by differences in predominant menaquinones, major fatty acids and cell-wall sugars. Accordingly, based on combined phenotypic, chemotaxonomic and phylogenetic data, strain DS-52T (=KCTC 19127T=CIP 108919T) is proposed as the type strain of a novel species in a new genus, Humicoccus flavidus gen. nov., sp. nov.

scholarly journals Pseudonocardia artemisiae sp. nov., isolated from surface-sterilized Artemisia annua L.

2011 ◽  
Vol 61 (5) ◽  
pp. 1061-1065 ◽  
Author(s):  
Guo-Zhen Zhao ◽  
Jie Li ◽  
Hai-Yu Huang ◽  
Wen-Yong Zhu ◽  
Li-Xing Zhao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Artemisia Annua ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Actinomycete Strain ◽  
Diamino Acid ◽  
Unknown Phospholipid ◽  
Phosphatidylinositol Mannosides ◽  
Type Strains

A novel actinomycete strain, designated YIM 63587T, was isolated from surface-sterilized roots of Artemisia annua L. collected from Yunnan province, south-west China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 63587T was affiliated to the genus Pseudonocardia. 16S rRNA gene sequence similarities between strain YIM 63587T and type strains of species of the genus Pseudonocardia were 96.6–93.8 %. The diagnostic cell-wall diamino acid in the peptidoglycan layer of strain YIM 63587T was meso-diaminopimelic acid and the whole-cell sugars were arabinose, galactose, mannose and ribose. The predominant menaquinone was MK-8(H4) (97.7 %). The phospholipids were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol mannosides, phosphatidylinositol and an unknown phospholipid. The major cellular fatty acids (>5 %) were iso-C16 : 0 (44.7 %), iso-C14 : 0 (10.3 %), iso-C16 : 1 H (9.8 %) and iso-C15 : 0 (7.7 %). The G+C content of the genomic DNA was 68.2 mol%. On the basis of phylogenetic, physiological and chemotaxonomic data, strain YIM 63587T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia artemisiae sp. nov. is proposed. The type strain is YIM 63587T ( = DSM 45313T = CCTCC AA 208081T).

scholarly journals Alloactinosynnema album gen. nov., sp. nov., a member of the family Actinosynnemataceae isolated from soil

2010 ◽  
Vol 60 (1) ◽  
pp. 39-43 ◽  
Author(s):  
Li-Jie Yuan ◽  
Yu-Qin Zhang ◽  
Li-Yan Yu ◽  
Hong-Yu Liu ◽  
Yan Guan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
The Family ◽  
Distinct Lineage ◽  
Diamino Acid ◽  
Signature Pattern ◽  
The 16S Rrna Gene

The taxonomic position of a Gram-stain-positive, aerobic strain, designated 03-9939T, isolated from a soil sample collected from Xinjiang Province, China, was established using a polyphasic approach. Whole-cell hydrolysates of strain 03-9939T contained galactose and ribose as diagnostic sugars and meso-diaminopimelic acid as the diamino acid. The predominant menaquinone was MK-9(H4). The phospholipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. The major fatty acids were iso-C16 : 0 (61.5 %) and iso-C16 : 1 H (11.6 %). The genomic DNA G+C content was 68.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 03-9939T should be placed within the family Actinosynnemataceae, in which the strain formed a distinct lineage. Signature nucleotides in the 16S rRNA gene sequence showed that the strain contained a genus-specific diagnostic nucleotide signature pattern. The combination of phylogenetic analysis, phenotypic characteristics and chemotaxonomic data supported the conclusion that strain 03-9939T represents a novel species in a new genus of the family Actinosynnemataceae, for which the name Alloactinosynnema album gen. nov., sp. nov. is proposed. Strain 03-9939T (=DSM 45114T =KCTC 19294T =CCM 7461T) is the type strain of Alloactinosynnema album.

scholarly journals Pullulanibacillus pueri sp. nov., isolated from Pu'er tea

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2167-2171 ◽  
Author(s):  
Lili Niu ◽  
Tianyi Tang ◽  
Lei Song ◽  
Mengjie Xiong ◽  
Jianqing Tian ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Hybridization Data ◽  
The Family ◽  
A Cell ◽  
Diamino Acid

A novel Gram-stain-positive, aerobic, endospore-forming, rod-shaped bacterial strain YN3T was isolated from ripened Pu'er tea. Phylogenetic analysis of 16S rRNA gene sequences showed that the strain belonged to the family Sporolactobacillaceae and was closely related to Pullulanibacillus naganoensis DSM 10191T (95.8 % 16S rRNA gene sequence similarity) and Pullulanibacillus uraniitolerans DSM 19429T (95.4 %). Growth of the strain was observed at 20–50 °C (optimum 30–37 °C), at pH 4.0–8.0 (optimum pH 5.0–6.0). The strain had a cell-wall type A1γ peptidoglycan with meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinone was menaquinone-7 (MK-7). The major fatty acids were anteiso-C15:0, anteiso-C17:0 and C18:1ω7c. The DNA G+C content of strain YN3T was 38.7 mol%. Strain YN3T could be differentiated from recognized species of the genus Pullulanibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of polyphasic evidence from this study, Pullulanibacillus pueri sp. nov., is proposed, with strain YN3T ( = CGMCC 1.12777T = JCM 30075T) as the type strain.

scholarly journals Amycolatopsis halophila sp. nov., a halophilic actinomycete isolated from a salt lake

2010 ◽  
Vol 60 (5) ◽  
pp. 1073-1078 ◽  
Author(s):  
Shu-Kun Tang ◽  
Yun Wang ◽  
Tong-Wei Guan ◽  
Jae-Chan Lee ◽  
Chang-Jin Kim ◽  
...  
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Salt Lake ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
North West ◽  
Halophilic Actinomycete ◽  
Type Strains

A novel halophilic actinomycete, designated strain YIM 93223T, was isolated from a salt lake in Xinjiang Province, north-west China, and was subjected to a polyphasic taxonomic study. The isolate grew at 25–45 °C, at pH 6–8 and in the presence of 1–15 % (w/v) NaCl; no growth was observed in the absence of NaCl. Strain YIM 93223T contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids, and glucose and galactose as major whole-cell-wall sugars. Major fatty acids were iso-C16 : 0, C16 : 0 and C16 : 1 ω7c/iso-C15 : 0 2-OH. MK-8(H4) was the predominant menaquinone. The genomic DNA G+C content was 66.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93223T belongs to the genus Amycolatopsis. It shared highest 16S rRNA gene sequence similarity with Amycolatopsis palatopharyngis 1BDZT (96.6 %) and Amycolatopsis marina Ms392AT (96.4 %), but lower values (94.5–96.2 %) with the type strains of other recognized species of the genus Amycolatopsis. On the basis of the data from this polyphasic study, strain YIM 93223T is considered to represent a novel species of the genus Amycolatopsis, for which the name Amycolatopsis halophila sp. nov. is proposed. The type strain is YIM 93223T (=DSM 45216T =KCTC 19403T).

scholarly journals Halobacillus campisalis sp. nov., containing meso-diaminopimelic acid in the cell-wall peptidoglycan, and emended description of the genus Halobacillus

2007 ◽  
Vol 57 (9) ◽  
pp. 2021-2025 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Yong-Taek Jung ◽  
Tae-Kwang Oh
Keyword(s):  
Cell Wall ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Diaminopimelic Acid ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Cell Wall Peptidoglycan ◽  
Type Strains

A Gram-positive or variable, motile and coccoid or oval-shaped bacterial strain, ASL-17T, was isolated from a marine solar saltern of the Yellow Sea in Korea and its exact taxonomic position was investigated by a polyphasic approach. Strain ASL-17T grew optimally at pH 7.0–8.0 and 37 °C. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ASL-17T is most closely affiliated phylogenetically to the genus Halobacillus. Strain ASL-17T exhibited 16S rRNA gene sequence similarity values of 97.7–98.6 % to the type strains of recognized Halobacillus species. Interestingly, strain ASL-17T had cell-wall peptidoglycan based on meso-diaminopimelic acid, unlike other Halobacillus species. It contained MK-7 as the predominant menaquinone. The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The DNA G+C content was 42.1 mol%. DNA–DNA relatedness data and differential phenotypic properties demonstrated that strain ASL-17T can be differentiated from recognized Halobacillus species. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strain ASL-17T represents a novel species of the genus Halobacillus, for which the name Halobacillus campisalis sp. nov. is proposed. The type strain is ASL-17T (=KCTC 13144T =CCUG 54360T).

scholarly journals Nocardioides marinus sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 775-779 ◽  
Author(s):  
Dong Han Choi ◽  
Hye Min Kim ◽  
Jae-Hoon Noh ◽  
Byung Cheol Cho
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Diamino Acid ◽  
Ph Range ◽  
Type Strains

A Gram-positive, slightly halophilic, rod-shaped bacterium, designated CL-DD14T, was isolated from seawater of the East Sea, Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CL-DD14T belongs to the genus Nocardioides. Levels of 16S rRNA gene sequence similarity between strain CL-DD14T and the type strains of recognized species of the genus Nocardioides were low (94.1–97.1 %). Strain CL-DD14 T grew over the pH range 6–9 and temperature range 10–40 °C. The strain grew at NaCl concentrations of 0.5–8 % (w/v) with optimum growth at 1–3 % and no growth was observed after 3 weeks on nutrient agar without any salts. It contained ll-diaminopimelic acid as the diamino acid in the cell wall. The major isoprenoid quinone was MK-8(H4) and the major cellular fatty acids were iso-C16 : 0 and 10-methyl C17 : 0. The DNA G+C content was 72.9 mol%. On the basis of phenotypic and phylogenetic data, strain CL-DD14T is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides marinus sp. nov. is proposed. The type strain is CL-DD14T (=KCCM 42321T=DSM 18248T).

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