scholarly journals Pseudoxanthomonas spadix sp. nov., isolated from oil-contaminated soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1823-1827 ◽  
Author(s):  
Chiu Chung Young ◽  
Mann-Jing Ho ◽  
A. B. Arun ◽  
Wen-Ming Chen ◽  
Wei-An Lai ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Contaminated Soil ◽  
Sequence Divergence ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Hydroxylated Fatty Acids ◽  
Phyletic Line ◽  
Taxonomic Approach

A bacterial isolate from a sample of oil-contaminated soil was characterized using a polyphasic taxonomic approach. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constituted a distinct phyletic line within the genus Pseudoxanthomonas, displaying >3.7 % sequence divergence with respect to recognised Pseudoxanthomonas species. The genus assignment was confirmed by a chemotaxonomic analysis, which revealed the presence of a fatty acid profile characteristic of members of the genus Pseudoxanthomonas (straight-chain saturated, unsaturated and branched-chain fatty acids of the iso/anteiso type and 3-hydroxylated fatty acids) and the presence of a ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The novel isolate was distinguishable from other members of the genus Pseudoxanthomonas on the basis of a combination of phenotypic properties. The genotypic and phenotypic data show that the strain represents a novel species of the genus Pseudoxanthomonas, for which the name Pseudoxanthomonas spadix sp. nov. is proposed. The type strain is IMMIB AFH-5T (=DSM 18855T=CCUG 53828T).

scholarly journals Lysobacter defluvii sp. nov., isolated from municipal solid waste

2007 ◽  
Vol 57 (5) ◽  
pp. 1131-1136 ◽  
Author(s):  
A. F. Yassin ◽  
Wen-Ming Chen ◽  
H. Hupfer ◽  
C. Siering ◽  
R. M. Kroppenstedt ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Sequence Divergence ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Branched Chain Fatty Acids ◽  
Phyletic Line ◽  
Profile Characteristic ◽  
Taxonomic Approach ◽  
Branched Chain

A bacterial isolate obtained from soil from a municipal landfill site in India was characterized using a polyphasic taxonomic approach. The colonies of the isolate were found to be yellow and highly mucoid. Comparative analysis of the 16S rRNA gene sequence showed that this isolate constitutes a distinct phyletic line within the genus Lysobacter, displaying >3 % sequence divergence with respect to recognized Lysobacter species. The generic assignment was confirmed by chemotaxonomic data, which revealed the presence of a fatty acid profile characteristic of members of the genus Lysobacter and consisting of saturated, unsaturated, straight-chain and branched-chain fatty acids as well as iso-C11 : 0 3-OH as hydroxylated fatty acid, and the presence of an ubiquinone with eight isoprene units (Q-8) as the predominant respiratory quinone. The genotypic and phenotypic data show that strain IMMIB APB-9T merits classification as representing a novel species of the genus Lysobacter, for which the name Lysobacter defluvii sp. nov. is proposed. The type strain is IMMIB APB-9T (=CCUG 53152T=DSM 18482T).

scholarly journals Chryseobacterium treverense sp. nov., isolated from a human clinical source

2010 ◽  
Vol 60 (9) ◽  
pp. 1993-1998 ◽  
Author(s):  
A. F. Yassin ◽  
H. Hupfer ◽  
C. Siering ◽  
H.-J. Busse
Keyword(s):  
Fatty Acids ◽  
Sequence Divergence ◽  
Taxonomic Status ◽  
Biochemical Properties ◽  
Rrna Gene ◽  
Respiratory Quinone ◽  
Hydroxylated Fatty Acids ◽  
Phyletic Line ◽  
Branched Chain ◽  
Clinical Source

A yellow-pigmented, Gram-reaction-negative bacterium isolated from a human clinical source was investigated using a polyphasic approach in order to clarify its taxonomic status. Comparative 16S rRNA gene sequence analysis showed that the new isolate constituted a distinct phyletic line within the genus Chryseobacterium, displaying >2.8 % sequence divergence with recognized species of this genus. The generic assignment was confirmed by chemotaxonomic data which revealed a fatty acid profile consisting of straight-chain saturated, monounsaturated and branched-chain fatty acids of iso-/anteiso-types as well as 3-hydroxylated fatty acids; a menaquinone with six isoprene units (MK-6) as the predominant respiratory quinone and sym-homospermidine as the predominant polyamine. The novel isolate could be distinguished from other members of the genus Chryseobacterium by a set of distinct biochemical properties. On the basis of phenotypic and phylogenetic evidence, it is proposed that the new isolate represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium treverense sp. nov. is proposed. The type strain is IMMIB L-1519T (=DSM 22251T=CCUG 57657T).

scholarly journals Sphingobium olei sp. nov., isolated from oil-contaminated soil

2007 ◽  
Vol 57 (11) ◽  
pp. 2613-2617 ◽  
Author(s):  
C. C. Young ◽  
M.-J. Ho ◽  
A. B. Arun ◽  
W.-M. Chen ◽  
W.-A. Lai ◽  
...  
Keyword(s):  
Contaminated Soil ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Phyletic Line ◽  
Lipid Pattern ◽  
Taxonomic Approach

The taxonomic status of a yellow-coloured bacterial isolate from an oil-contaminated soil sample was determined using a polyphasic taxonomic approach. Comparative analysis of 16S rRNA gene sequences showed that the novel isolate formed a distinct phyletic line within the genus Sphingobium. The generic assignment was confirmed by chemotaxonomic data, which revealed: a fatty acid profile that is characteristic of the genus Sphingobium consisting of straight-chain saturated and unsaturated as well as 2-OH fatty acids; a ubiquinone with ten isoprene units (Q-10) as the predominant respiratory quinone; a polar lipid pattern consisting of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid, and spermidine as the major polyamine component. Genotypic and phenotypic data show that the new isolate merits classification as a representative of a novel species of the genus Sphingobium, for which the name Sphingobium olei sp. nov. is proposed. The type strain is IMMIB HF-1T (=DSM 18999T=CCUG 54329T).

scholarly journals Cloacibacterium rupense sp. nov., isolated from freshwater lake sediment

2010 ◽  
Vol 60 (9) ◽  
pp. 2023-2026 ◽  
Author(s):  
Shu-Juan Cao ◽  
Chun-Ping Deng ◽  
Bao-Zhen Li ◽  
Xiu-Qin Dong ◽  
Hong-Li Yuan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Respiratory Quinone ◽  
The Family ◽  
Taxonomic Approach

A Gram-negative, yellow-pigmented bacterium, designated strain R2A-16T, was isolated from sediment of Rupa Lake in Nepal and analysed using a polyphasic taxonomic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain R2A-16T is affiliated to the genus Cloacibacterium of the family Flavobacteriaceae; 16S rRNA gene sequence similarity between strain R2A-16T and Cloacibacterium normanense CCUG 46293T was 98.07 %. The isolate contained iso-C15 : 0 (35.6 %) as the major fatty acid and menaquinone MK-6 as the predominant respiratory quinone. The G+C content of the genomic DNA was 33.3 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain R2A-16T represents a novel species of the genus Cloacibacterium, for which the name Cloacibacterium rupense sp. nov. is proposed; the type strain is R2A-16T (=CGMCC 1.7656T =NBRC 104931T).

scholarly journals Arcicella rigui sp. nov., isolated from water of a wetland, and emended descriptions of the genus Arcicella , Arcicella aquatica , Arcicella rosea and Arcicella aurantiaca

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 134-140 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A bacterial strain, designated NSW-5T, was isolated from a water sample taken from Niao-Song Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain NSW-5T were strictly aerobic, Gram-stain-negative, non-motile and polymorphic, being straight, vibrioid, curved and spiral-shaped rods surrounded by a thick capsule and forming light pink-coloured colonies. Some rings consisting of several cells were present. Growth occurred at 10–40 °C (optimum, 25 °C), with 0–3.0 % NaCl (optimum, 0 %) and at pH 6.0–8.0 (optimum, pH 7.0). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain NSW-5T belonged to the genus Arcicella with sequence similarities of 98.6, 98.0 and 97.3 % with Arcicella aquatica NO-502T, Arcicella rosea TW5T and Arcicella aurantiaca TNR-18T, respectively. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.8 %), C16 : 0 (14.6 %), iso-C15 : 0 (13.8 %), C16 : 1ω5c (12.5 %) and C18 : 0 (11.4 %), and the only respiratory quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized glycolipids, aminolipids, phospholipids and aminophospholipids. The DNA G+C content of strain NSW-5T was 44.1 mol%. The DNA–DNA relatedness of strain NSW-5T with respect to recognized species of the genus Arcicella was less than 70 %. On the basis of phylogenetic inference and phenotypic data, strain NSW-5T should be classified as a representative of a novel species, for which the name Arcicella rigui sp. nov. is proposed. The type strain is NSW-5T ( = KCTC 23307T = BCRC 80260T). Emended descriptions of the genus Arcicella and of Arcicella aquatica , Arcicella rosea and Arcicella aurantiaca are also proposed.

scholarly journals Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2817-2823 ◽  
Author(s):  
Yang Liu ◽  
Su Yao ◽  
Yong-Jae Lee ◽  
Yanhua Cao ◽  
Lei Zhai ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Morinda Citrifolia ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Physiological And Biochemical Characteristics ◽  
Sphingomonas Wittichii ◽  
Taxonomic Approach

Two yellow bacterial strains, designated NBD5T and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6T (96.9  % similarity), Sphingomonas polyaromaticivorans B2-7T (95.8  %), Sphingomonas yantingensis 1007T (94.9  %), Sphingomonas sanguinis IFO 13937T (94.7  %), Sphingomonas ginsenosidimutans Gsoil 1429T (94.6  %), Sphingomonas wittichii RW1T (94.6  %) and Sphingomonas formosensis CC-Nfb-2T (94.5  %). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5T and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5T and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5T ( = DSM 29151T = KCTC 42183T = CICC 10879T).

scholarly journals Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4196-4201 ◽  
Author(s):  
Yang Liu ◽  
Lei Zhai ◽  
Su Yao ◽  
Yanhua Cao ◽  
Yu Cao ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Morinda Citrifolia ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Taxonomic Approach ◽  
Type Strains

A Gram-stain-positive bacterial strain, designated as NR2T, isolated from noni (Morinda citrifolia L.) branch was investigated using a polyphasic taxonomic approach. The cells were small coccoid to ovoid, non-spore-forming and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a representative of a member of the genus Brachybacterium, to which the most closely related neighbours were Brachybacterium squillarum M-6-3T (97.90 % similarity), Brachybacterium faecium DSM 4810T (97.50 %), Brachybacterium sacelli LMG 20345T (97.41 %), Brachybacterium phenoliresistens phenol-AT (97.36 %), Brachybacterium nesterenkovii DSM 9573T (97.36 %) and Brachybacterium rhamnosum LMG 19848T (97.32 %). The polar lipid profile of strain NR2T consisted of diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and unknown glycolipids. The predominant respiratory quinone was MK-8, with MK-9 and MK-7 as minor components. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Strain NR2T was clearly distinguishable from the type strains of related species on the basis of phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data analysis and a range of physiological and comparison of biochemical characteristics. It is evident from the genotypic and phenotypic data that strain NR2T represents a novel species of the genus Brachybacterium, for which the name Brachybacterium hainanense sp. nov. is proposed. The type strain is NR2T ( = DSM 29535T = CICC 10874T).

scholarly journals Streptomyces atacamensis sp. nov., isolated from an extreme hyper-arid soil of the Atacama Desert, Chile

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2680-2684 ◽  
Author(s):  
Rakesh Santhanam ◽  
Chinyere K. Okoro ◽  
Xiaoying Rong ◽  
Ying Huang ◽  
Alan T. Bull ◽  
...  
Keyword(s):  
Type Strain ◽  
Gene Tree ◽  
Atacama Desert ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Content Type ◽  
Arid Soil ◽  
Link Type ◽  
Phyletic Line

The taxonomic position of a Streptomyces strain isolated from an extreme hyper-arid soil sample collected from the Atacama Desert was determined using a polyphasic approach. The strain, isolate C60T, had chemical and morphological features typical of members of the genus Streptomyces and formed a distinct phyletic line in the Streptomyces 16S rRNA gene tree, together with the type strain of Streptomyces radiopugnans . The two strains were distinguished readily using a combination of phenotypic properties and by a DNA–DNA relatedness value of 23.17 (±0.95) %. On the basis of these genotypic and phenotypic data, it is proposed that isolate C60T ( = CGMCC 4.7018T = KACC 15492T) be classified in the genus Streptomyces as Streptomyces atacamensis sp. nov.

scholarly journals Sphingopyxis baekryungensis sp. nov., an orange-pigmented bacterium isolated from sea water of the Yellow Sea in Korea

2005 ◽  
Vol 55 (3) ◽  
pp. 1223-1227 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Choong-Hwan Lee ◽  
Soo-Hwan Yeo ◽  
Tae-Kwang Oh
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Yellow Sea ◽  
Sea Water ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Orange Pigment ◽  
Taxonomic Approach

A Gram-negative, motile, slightly halophilic bacterial strain, SW-150T, was isolated from sea water of the Yellow Sea, Korea, and was characterized by a polyphasic taxonomic approach. Strain SW-150T grew optimally at 25–30 °C and in the presence of 2 % (w/v) NaCl. The isolate could be distinguished from other Sphingopyxis species in producing an orange pigment. It contained ubiquinone-10 as the predominant respiratory lipoquinone and C18 : 1 ω7c and C17 : 1 ω6c as the major fatty acids. No 3-hydroxy fatty acids were detected. Major polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63 mol%. Comparative 16S rRNA gene sequence analyses showed that strain SW-150T was phylogenetically affiliated to the genus Sphingopyxis of the family Sphingomonadaceae. Similarity values between the 16S rRNA gene sequences of strain SW-150T and the type strains of Sphingopyxis species ranged from 91·6 to 94·2 %, making it possible to categorize strain SW-150T as a species that is separate from previously described Sphingopyxis species. On the basis of phenotypic properties and phylogenetic distinctiveness, SW-150T (=KCTC 12231T=DSM 16222T) should be classified as the type strain of a novel Sphingopyxis species, for which the name Sphingopyxis baekryungensis sp. nov. is proposed.

Rheinheimera tilapiae sp. nov., isolated from a freshwater culture pond

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1457-1463 ◽  
Author(s):  
Wen-Ming Chen ◽  
Shwu-Harn Yang ◽  
Chiu-Chung Young ◽  
Shih-Yi Sheu
Keyword(s):  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Cichlid Fish ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Respiratory Quinone ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type ◽  
Taxonomic Approach

A bacterial strain designated Ruye-90T was isolated from a freshwater tilapiine cichlid fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Strain Ruye-90T was Gram-negative, aerobic, yellow-coloured, rod-shaped, and motile by means of a single polar flagellum. Growth occurred at 4–30 °C (optimum, 20–30 °C), at pH 7.0–9.0 (optimum, pH 8.0–9.0) and with 0–2 % NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Ruye-90T belonged to the genus Rheinheimera and its most closely related neighbour was Rheinheimera tangshanensis JA3-B52T with sequence similarity of 97.5 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 41.3 %), C16 : 0 (19.3 %), C18 : 1ω7c (8.4 %) and C12 : 0 3-OH (7.0 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 49.0 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, aminolipid and two uncharacterized phospholipids. The DNA–DNA relatedness of strain Ruye-90T with respect to recognized members of the genus Rheinheimera was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Ruye-90T represents a novel species in the genus Rheinheimera , for which the name Rheinheimera tilapiae sp. nov. is proposed. The type strain is Ruye-90T ( = LMG 26339T = BCRC 80263T = KCTC 23315T).

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