scholarly journals Terrimonas rubra sp. nov., isolated from a polluted farmland soil and emended description of the genus Terrimonas

2012 ◽  
Vol 62 (Pt_11) ◽  
pp. 2593-2597 ◽  
Author(s):  
Jing Zhang ◽  
Tao Gu ◽  
Yu Zhou ◽  
Jie He ◽  
Liu-Qiang Zheng ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Farmland Soil ◽  
Emended Description

A salmon-red-pigmented bacterial strain, designated M-8T, was isolated from a polluted farmland soil sample in China and was characterized in a taxonomic study using a polyphasic approach. Strain M-8T was Gram-stain-negative, rod-shaped, non-motile and non-spore-forming. Growth occurred at 20–37 °C, at pH 5.0–10.0 and with 0–2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain M-8T belonged to the genus Terrimonas .16S rRNA gene sequence similarity values between strain M-8T and the type strains of the three recognized species of the genus Terrimonas , Terrimonas ferruginea KACC 11310T, Terrimonas aquatica LMG 24825T and Terrimonas lutea KACC 13047T, were 97.1, 96.3 and 95.3 %, respectively. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The DNA G+C content of strain M-8T was 47.0 mol%. On the basis of genotypic and phenotypic data, strain M-8T is considered to represent a novel species of the genus Terrimonas , for which the name Terrimonas rubra sp. nov. is proposed. The type strain is M-8T ( = CCTCC AB 2010401T = KCTC 23299T). An emended description of the genus Terrimonas is also presented.

scholarly journals Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil

2015 ◽  
Vol 65 (Pt_6) ◽  
pp. 1786-1793 ◽  
Author(s):  
Wallace Rafael Souza ◽  
Rafael Eduardo Silva ◽  
Michael Goodfellow ◽  
Kanungnid Busarakam ◽  
Fernanda Sales Figueiro ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Gene Tree ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

Strain SB026T was isolated from Brazilian rainforest soil and its taxonomic position established using data from a polyphasic study. The organism showed a combination of chemotaxonomic and morphological features consistent with its classification in the genus Amycolatopsis and formed a branch in the Amycolatopsis 16S rRNA gene tree together with Amycolatopsis bullii NRRL B-24847T, Amycolatopsis plumensis NRRL B-24324T, Amycolatopsis tolypomycina DSM 44544T and Amycolatopsis vancoresmycina NRRL B-24208T. It was related most closely to A. bullii NRRL B-24847T (99.0 % 16S rRNA gene sequence similarity), but was distinguished from this strain by a low level of DNA–DNA relatedness (~46 %) and discriminatory phenotypic properties. Based on the combined genotypic and phenotypic data, it is proposed that the isolate should be classified in the genus Amycolatopsis as representing a novel species, Amycolatopsis rhabdoformis sp. nov. The type strain is SB026T ( = CBMAI 1694T = CMAA 1285T = NCIMB 14900T).

Mariniflexile jejuense sp. nov., isolated from the junction between seawater and a freshwater spring, and emended description of the genus Mariniflexile

2013 ◽  
Vol 63 (Pt_4) ◽  
pp. 1329-1334 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Hoon Yoon
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Freshwater Spring

A Gram-negative, non-spore-forming, non-flagellated, motile-by-gliding rod, designated SSK2-3T, was isolated from the junction between seawater and a freshwater spring at Jeju island, South Korea. Strain SSK2-3T grew optimally at 25–30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SSK2-3T clustered with type strains of species of the genus Mariniflexile , with which it exhibited 97.2–97.8 % 16S rRNA gene sequence similarity. Sequence similarity between the isolate and the other strains used in the phylogenetic analysis was <95.6 %. Strain SSK2-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15 : 1 G and C15 : 0 as the major fatty acids. The major polar lipids of strain SSK2-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain SSK2-3T was 32.4 mol%. DNA–DNA relatedness between the isolate and Mariniflexile gromovii KCTC 12570T, Mariniflexile fucanivorans DSM 18792T and Mariniflexile aquimaris HWR-17T was 19, 15 and 20 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK2-3T is separate from other members of the genus Mariniflexile . On the basis of the data presented, strain SSK2-3T is considered to represent a novel species of the genus Mariniflexile , for which the name Mariniflexile jejuense sp. nov. is proposed. The type strain is SSK2-3T ( = KCTC 23958T  = CCUG 62414T). An emended description of the genus Mariniflexile is given.

Hirschia litorea sp. nov., isolated from seashore sediment, and emended description of the genus Hirschia

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1684-1689 ◽  
Author(s):  
Sooyeon Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Type Strains

A Gram-negative, non-spore-forming, non-flagellated, coccoid-, oval- or rod-shaped strain, designated M-M23T, was isolated from seashore sediment at Geoje island, South Korea. Strain M-M23T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain M-M23T clustered with the type strains of the two species of the genus Hirschia , with which it exhibited 97.6–98.1 % 16S rRNA gene sequence similarity. Sequence similarity with the type strains of other recognized species was <90.8 %. Strain M-M23T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C16 : 0 as the major fatty acids. The major polar lipids of strain M-M23T were phosphatidylglycerol and two unidentified lipids. The DNA G+C content of strain M-M23T was 45.4 mol%. DNA–DNA relatedness between the isolate and Hirschia baltica DSM 5838T and Hirschia maritima JCM 14974T was 22±7.2 and 14±5.6 %, respectively. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain M-M23T is separate from the other described members of the genus Hirschia . On the basis of the data presented, strain M-M23T is considered to represent a novel species of the genus Hirschia , for which the name Hirschia litorea sp. nov. is proposed. The type strain is M-M23T ( = KCTC 32081T  = CCUG 62793T). An emended description of the genus Hirschia is also provided.

Pseudofulvibacter geojedonensis gen. nov., sp. nov., a polysaccharide-degrading member of the family Flavobacteriaceae isolated from seawater, and emended description of the genus Fulvibacter

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1696-1701 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
Yong-Taek Jung
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Emended Description

A Gram-negative, non-spore-forming, aerobic, non-flagellated, non-gliding rod, designated YCS-9T, was isolated from seawater in the South Sea, South Korea. Strain YCS-9T grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain YCS-9T fell within the family Flavobacteriaceae and formed a cluster with Fulvibacter tottoriensis MTT-39T with a bootstrap resampling value of 75.4 %. Strain YCS-9T showed 92.3 % 16S rRNA gene sequence similarity to F. tottoriensis MTT-39T and 89.0–93.7 % sequence similarity to the other strains used in the phylogenetic analysis. Strain YCS-9T contained MK-6 as the only menaquinone and iso-C15 : 1 G, iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were one unidentified lipid and one unidentified aminolipid. The DNA G+C content was 34.2 mol%. Strain YCS-9T could be differentiated from F. tottoriensis NBRC 102624T by differences in fatty acid composition, polar lipid profile and some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain YCS-9T represents a novel species in a new genus within the phylum Bacteroidetes , for which the name Pseudofulvibacter geojedonensis gen. nov., sp. nov. is proposed. The type strain of Pseudofulvibacter geojedonensis is YCS-9T ( = KCTC 23884T  = CCUG 62114T). An emended description of the genus Fulvibacter is also presented.

scholarly journals Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium

2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2187-2193 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
A. Bhattacharya ◽  
P. Schumann ◽  
Syed G. Dastager ◽  
Shu-Kun Tang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Surface Soil ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-positive, non-endospore-forming bacterium, designated strain SK 18T, was isolated from surface soil of a landfill site by dilution plating on trypticase soy broth agar. Preliminary characterization of strain SK 18T via biochemical tests, analysis of fatty acid methyl esters and partial 16S rRNA gene sequencing placed it within the genus Microbacterium . Analysis of the cell wall indicated that the peptidoglycan was of cross-linkage type B, containing the amino acids lysine and ornithine and with muramic acid in the N-glycolyl form. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The major fatty acids of the cell membrane were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. These data further strengthened placement of the strain within the genus Microbacterium . Strain SK 18T shared highest 16S rRNA gene sequence similarity (97.2 %) with Microbacterium ulmi DSM 16931T. Levels of similarity with the type strains of all other recognized Microbacterium species were less than 97.0 %. DNA–DNA hybridization experiments with strain SK 18T and its closest relative, M. ulmi DSM 16931T, revealed a low reassociation value of 39.0 % (σ = 3.8 %). Moreover, strain SK 18T showed a number of differences in phenotypic characteristics (colony colour, catalase activity, hydrolysis of polymers, acid production from sugars and oxidation of various substrates), and its DNA G+C content was also higher than that of M. ulmi DSM 16931T. These data indicated that strain SK 18T represents a novel species of the genus Microbacterium , for which the name Microbacterium immunditiarum sp. nov. is proposed. The type strain is SK 18T ( = MTCC 7185T = JCM 14034T). An emended description of the genus Microbacterium is also provided.

scholarly journals Psychrosphaera aestuarii sp. nov. and Psychrosphaera haliotis sp. nov., isolated from the marine environment, and emended description of the genus Psychrosphaera

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1952-1957 ◽  
Author(s):  
Ji Hee Lee ◽  
Keun Sik Baik ◽  
Duwoon Kim ◽  
Chi Nam Seong
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type ◽  
Emended Description

Two motile, rod-shaped and agarolytic bacterial strains, designated PSC101T and KDW4T, were isolated from seawater and gut microflora of abalone, respectively, collected from the South Sea (Republic of Korea). Cells were Gram-stain-negative, aerobic, catalase- and oxidase-positive. Strains PSC101T and KDW4T showed high 16S rRNA gene sequence similarity to each other (98.6 %). Psychrosphaera saromensis SA4-48T was the nearest neighbour of strains PSC101T and KDW4T with 96.6 % and 97.0 % 16S rRNA gene sequence similarity, respectively. DNA–DNA relatedness among strains PSC101T, KDW4T and Psychrosphaera saromensis KCTC 23240T was less than 70 %. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates belonged to the genus Psychrosphaera and formed a distinct phyletic line from Psychrosphaera saromensis SA4-48T. The common major cellular fatty acids of the two novel isolates were C16 : 0, C17 : 1ω8c and summed feature 3 (C16 : 1ω6c/C16 : 1ω7c). Flexirubin-type pigments were absent. The main ubiquinone was UQ-8 and the DNA G+C content of strains PSC101T and KDW4T was 49.5 and 42.5 mol%, respectively. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified amino lipid. On the basis of the polyphasic characterization of the two strains, it is suggested that the two isolates represent two novel species of the genus Psychrosphaera , for which the names Psychrosphaera aestuarii sp. nov. (type strain, PSC101T = KCTC 32274T = JCM 19496T) and Psychrosphaera haliotis sp. nov. (type strain, KDW4T = KCTC 22500T = JCM 16340T) are proposed. An emended description of the genus Psychrosphaera is also proposed.

Marininema halotolerans sp. nov., a novel thermoactinomycete isolated from a sediment sample, and emended description of the genus Marininema Li et al. 2012

2013 ◽  
Vol 63 (Pt_12) ◽  
pp. 4562-4567 ◽  
Author(s):  
Xiao-Mei Zhang ◽  
Jie He ◽  
Dao-Feng Zhang ◽  
Wei Chen ◽  
Zhao Jiang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sediment Sample ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Polar Lipid Profile ◽  
Content Type ◽  
Link Type

A novel Gram-stain-positive bacterium, designated strain YIM M11385T, was isolated from a marine sediment sample collected from the South Bay, Little Andaman Island, India with a salinity of 35 p.p.m., pH 8.5. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM M11385T belongs to the genus Marininema , supported by a bootstrap value of 100 %. The taxonomic position of this organism was further established by using a polyphasic approach. Strain YIM M11385T grew optimally at 28 °C, pH 7.0 and in the presence of 0–5 % (w/v) NaCl. The 16S rRNA gene sequence similarity between strain YIM M11385T and Marininema mesophilum SCSIO 10219T was 98.3 %. Strain YIM M11385T exhibited a quinone system with only MK-7, the polar lipid profile included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major components, and the major fatty acids were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The level of DNA–DNA relatedness between strain YIM M11385T and M. mesophilum SCSIO 10219T was 59.36 %. On the basis of genotypic and phenotypic data, it is apparent that strain YIM M11385T represents a novel species of the genus Marininema , for which the name Marininema halotolerans sp. nov. is proposed. The type strain is YIM M11385T ( = CCTCC AB 2012052T = DSM 45789T). In addition, we propose that the description of the genus Marininema should be further emended based on the results of the present study.

Parvularcula dongshanensis sp. nov., isolated from soft coral

2013 ◽  
Vol 63 (Pt_6) ◽  
pp. 2114-2117 ◽  
Author(s):  
Zhiwei Yu ◽  
Qiliang Lai ◽  
Guizhen Li ◽  
Zongze Shao
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Soft Coral ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Chromosomal Dna ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type

A taxonomic study was carried out on strain SH25T, which was isolated from soft coral collected from Dongshan Island, China. The isolate was a heterotrophic organism to the soft coral, and was a Gram-reaction-negative, short rod that was motile by a polar flagellum. Growth was observed at salinities from 0 to 12 % and at temperatures from 10 to 41 °C. It was unable to reduce nitrate to nitrite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SH25T belonged to the genus Parvularcula , with highest sequence similarity to Parvularcula lutaonensis CC-MMS-1T (96.1 %) and Parvularcula bermudensis HTCC2503T (94.3 %); 16S rRNA gene sequence similarities to other taxa were below 90.0 %. The dominant fatty acids were C16 : 0 and summed feature 8 (C18 : 1ω7c/ω6c,). The G+C content of the chromosomal DNA was 61.8 mol%. The major quinone was Q10. These combined genotypic and phenotypic data show that strain SH25T represents a novel species of the genus Parvularcula , for which the name Parvularcula dongshanensis sp. nov. is proposed. The type strain is SH25T ( = CCTCC AB 2010355T = LMG 26158T = MCCC 1A06534T).

Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense

2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 755-760 ◽  
Author(s):  
Dong-Heon Lee ◽  
Jae Seoun Hur ◽  
Hyung-Yeel Kahng
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Strictly Aerobic ◽  
Content Type ◽  
Link Type ◽  
Emended Description ◽  
Type Strains

A strictly aerobic, Gram-stain-negative bacterium, designated strain No.6T, was isolated from a lichen (Cladonia sp.) collected in Geogeum Island, Korea, and its taxonomic status was established by a polyphasic study. Cells of strain No.6T were non-motile, catalase- and oxidase-positive, non-spore-forming rods. Growth was observed at 15–35 °C (optimum, 25–30 °C), at pH 5.0–10.0 (optimum, pH 6.0–8.0) and with 0–3 % NaCl (optimum, 0–2 %). The predominant cellular fatty acids were summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1ω7c, 41.5 %), iso-C15 : 0 (26.7 %) and C16 : 0 (9.6 %), and menaquinone MK-7 was the only respiratory quinone. The G+C content of the genomic DNA of strain No.6T was 36.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain No.6T fell within the evolutionary group encompassed by the genus Sphingobacterium . Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of recognized Sphingobacterium species ranged from 92.1 to 99.1 %, the highest values being with Sphingobacterium siyangense SY1T (99.1 %) and Sphingobacterium multivorum IAM 14316T (98.5 %). DNA–DNA relatedness between strain No.6T and these two type strains were 32.0 and 5.7 %, respectively. The polar lipids found in strain No.6T were phosphatidylethanolamine, two unidentified phospholipids, three unidentified aminophospholipids, one glycolipid and four unidentified lipids. One unidentified sphingolipid was also found. On the basis of phenotypic and genotypic data, strain No.6T represents a novel species of the genus Sphingobacterium , for which the name Sphingobacterium cladoniae sp. nov. is proposed. The type strain is No.6T ( = KCTC 22613T = JCM 16113T). An emended description of Sphingobacterium siyangense is also proposed.

Paraperlucidibaca wandonensis sp. nov., isolated from seawater, and emended description of the genus Paraperlucidibaca Oh et al. 2011

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 4113-4117 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Sook Lee ◽  
Keun-Chul Lee
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Emended Description

A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated WT-RY4T, was isolated from wood falls in the South Sea, South Korea, and its taxonomic position was investigated using a polyphasic approach. Strain WT-RY4T grew optimally at 25 °C, at pH 7.0–7.5 and in the absence of NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain WT-RY4T clustered with the type strain of Paraperlucidibaca baekdonensis with a bootstrap resampling value of 100 %. Strain WT-RY4T exhibited 16S rRNA gene sequence similarity values of 98.8 % and 96.3 % to Paraperlucidibaca baekdonensis RL-2T and Perlucidibaca piscinae IMCC 1704T, respectively and less than 91.5 % to the type strains of other species used in the phylogenetic analysis. The DNA G+C content of strain WT-RY4T was 52.4 mol% and the mean DNA–DNA relatedness value with Paraperlucidibaca baekdonensis RL-2T was 25 %. Strain WT-RY4T contained Q-11 as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C12 : 0 3-OH as the major fatty acids. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain WT-RY4T was distinguishable from Paraperlucidibaca baekdonensis RL-2T. On the basis of the data presented, strain WT-RY4T is considered to represent a novel species of the genus Paraperlucidibaca , for which the name Paraperlucidibaca wandonensis sp. nov. is proposed. The type strain is WT-RY4T ( = KCTC 32216T = CCUG 63419T). An emended description of the genus Paraperlucidibaca is also provided.

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