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

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.

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1684-1689 ◽  
Author(s):  
Sooyeon Park ◽  
Jung-Hoon Yoon

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.


2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1696-1701 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
Yong-Taek Jung

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.


2012 ◽  
Vol 62 (Pt_9) ◽  
pp. 2187-2193 ◽  
Author(s):  
Srinivasan Krishnamurthi ◽  
A. Bhattacharya ◽  
P. Schumann ◽  
Syed G. Dastager ◽  
Shu-Kun Tang ◽  
...  

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.


2014 ◽  
Vol 64 (Pt_9) ◽  
pp. 3215-3221 ◽  
Author(s):  
Manziram Rozahon ◽  
Nurimangul Ismayil ◽  
Buayshem Hamood ◽  
Raziya Erkin ◽  
Mehfuzem Abdurahman ◽  
...  

An endophytic bacterium, designated K-38T, was isolated from the storage liquid in the stems of Populus euphratica trees at the ancient Ugan River in Xinjiang, PR China. Strain K-38T was found to be rod-shaped, Gram-stain-negative, aerobic, non-motile and non-spore-forming. Strain K-38T grew at temperatures of 25–37 °C (optimum, 28 °C), at pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0–3 % (w/v) NaCl with 1 % as the optimum concentration for growth. According to phylogenetic analysis based on 16S rRNA gene sequences, strain K-38T was assigned to the genus Rhizobium with highest 16S rRNA gene sequence similarity of 97.2 % to Rhizobium rosettiformans W3T, followed by Rhizobium nepotum 39/7T (96.5 %) and Rhizobium borbori DN316T (96.2 %). Phylogenetic analysis of strain K-38T based on the protein coding genes recA, atpD and nifH confirmed (similarities were less than 90 %) it to be a representative of a distinctly delineated species of the genus Rhizobium . The DNA G+C content was determined to be 63.5 mol%. DNA–DNA relatedness between K-38T and R. rosettiformans W3T was 48.4 %, indicating genetic separation of strain K-38T from the latter strain. The major components of the cellular fatty acids in strain K-38T were revealed to be summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c; 57.2 %), C16 : 0 (13.6 %) and summed feature 2 (comprising C12 : 0 aldehyde, C14 : 0 3-OH/iso-C16 : 1 I and/or unknown ECL 10.928; 11.0 %). Polar lipids of strain K-38T include phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified aminophospholipids and two unidentified phospholipids. Q-10 was the major quinone in strain K-38T. Based on phenotypic, chemotaxonomic and phylogenetic properties, strain K-38T represents a novel species of the genus Rhizobium , for which the name Rhizobium populi sp. nov. is proposed. The type strain is K-38T ( = CCTCC AB 2013068T = NRRL B-59990T = JCM 19159T).


2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 1952-1957 ◽  
Author(s):  
Ji Hee Lee ◽  
Keun Sik Baik ◽  
Duwoon Kim ◽  
Chi Nam Seong

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.


2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1561-1566 ◽  
Author(s):  
Jin-Hua Chen ◽  
Xiang-Rong Tian ◽  
Ying Ruan ◽  
Ling-Ling Yang ◽  
Ze-Qiang He ◽  
...  

A novel Gram-stain-positive, motile, catalase- and oxidase-positive, endospore-forming, facultatively anaerobic rod, designated strain JSM 100118T, was isolated from an oyster (Crassostrea hongkongensis) collected from the tidal flat of Naozhou Island in the South China Sea. Strain JSM 100118T 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 100118T belonged to the genus Bacillus , and was most closely related to Bacillus litoralis SW-211T (98.9 % 16S rRNA gene sequence similarity), Bacillus halosaccharovorans E33T (98.3 %), Bacillus niabensis 4T19T (97.8 %) and Bacillus herbersteinensis D-1,5aT (97.1 %). The combination of results from the phylogenetic analysis, DNA–DNA hybridization, and phenotypic and chemotaxonomic characterization supported the conclusion that strain JSM 100118T represents a novel species of the genus Bacillus , for which the name Bacillus crassostreae sp. nov. is proposed. The type strain is JSM 100118T ( = CCTCC AB 2010452T = DSM 24486T = JCM 17523T).


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4191-4197 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon

A Gram-stain-negative, coccoid- or short-rod-shaped and non-gliding bacterial strain, designated CDM-7T, was isolated from the zone where the ocean meets a freshwater spring at Jeju island, South Korea, and was subjected to a polyphasic taxonomic study. Strain CDM-7T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain CDM-7T falls within the clade comprising species of the genus Defluviimonas, clustering with the type strain of Defluviimonas aestuarii , with which it exhibited the highest 16S rRNA gene sequence similarity value (98.4 %). The 16S rRNA gene sequence similarity values between strain CDM-7T and the type strains of Defluviimonas denitrificans and Defluviimonas indica were 97.1 and 96.2 %, respectively. The genomic DNA G+C content was 66.8 mol% and the mean DNA–DNA relatedness values between strain CDM-7T and the type strains of D. aestuarii and D. denitrificans were 15.6±2.5 and 6.7±3.2 %, respectively. Strain CDM-7T contained Q-10 as the predominant ubiquinone and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) as the major fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified aminolipid, an unidentified phospholipid and an unidentified lipid. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, demonstrated that strain CDM-7T is distinguishable from other species of the genus Defluviimonas . On the basis of the data presented, strain CDM-7T is considered to represent a novel species of the genus Defluviimonas , for which the name Defluviimonas aquaemixtae sp. nov. is proposed. The type strain is CDM-7T ( = KCTC 42108T = CECT 8626T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 755-760 ◽  
Author(s):  
Dong-Heon Lee ◽  
Jae Seoun Hur ◽  
Hyung-Yeel Kahng

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.


2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 657-662 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Jung-Hoon Yoon

A Gram-staining-negative, aerobic, non-spore-forming, non-flagellated, non-gliding and rod-shaped bacterial strain, SSK3-3T, was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK3-3T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK3-3T clustered with the type strains of species of the genus Kordia , with which it exhibited 96.5–97.2 % 16S rRNA gene sequence similarity. Sequence similarities to the type strains of other recognized species were less than 92.2 %. Strain SSK3-3T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids of strain SSK3-3T were phosphatidylethanolamine, one unidentified lipid and one unidentified glycolipid. The DNA G+C content of strain SSK3-3T was 34.9 mol% and the mean DNA–DNA relatedness with Kordia periserrulae KACC 14311T was 12 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain SSK3-3T is separate from other species of the genus Kordia . On the basis of the data presented, strain SSK3-3T is considered to represent a novel species of the genus Kordia , for which the name Kordia jejudonensis sp. nov. is proposed. The type strain is SSK3-3T ( = KCTC 32426T = CECT 8368T). An emended description of the genus Kordia is also provided.


2014 ◽  
Vol 64 (Pt_12) ◽  
pp. 4115-4119 ◽  
Author(s):  
Parisa Zarparvar ◽  
Mohammad Ali Amoozegar ◽  
Mahdi Moshtaghi Nikou ◽  
Peter Schumann ◽  
Antonio Ventosa

A halophilic actinomycete, strain R4S8T, was isolated from soil of Inche-Broun hypersaline wetland in the north of Iran. The isolate grew aerobically at temperatures of 30–50 °C (optimum 40 °C), pH 6–10 (optimum pH 7.0) and in the presence of 1–15 % (w/v) NaCl (optimum 3–5 %). It formed short and straight to moderately flexuous aerial mycelium without motile elements. The cell wall of strain R4S8T contained meso-diaminopimelic acid as the diamino acid without any diagnostic sugars. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylmonomethylethanolamine two unknown phospholipids and one unknown aminophospholipid. It synthesized anteiso-C15 : 0 (44.8 %), iso-C15 : 0 (28.8 %) and iso-C14 : 0 (8.5 %) as major fatty acids. MK-6 was the predominant respiratory quinone. The G+C content of the genomic DNA was 52.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R4S8T belongs to the family Thermoactinomycetaceae and showed the closest 16S rRNA gene sequence similarity with Desmospora activa IMMIB L-1269T (95.5 %) and Marininema mesophilum SCSIO 10219T (95.3 %). On the basis of phylogenetic analysis and phenotypic characteristics, strain R4S8T represents a novel species in a new genus within the family Thermoactinomycetaceae , for which the name Salinithrix halophila gen. nov., sp. nov. is proposed. The type strain of the type species is R4S8T ( = IBRC-M 10813T = CECT 8506T).


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