scholarly journals Flavobacterium aquidurense sp. nov. and Flavobacterium hercynium sp. nov., from a hard-water creek

2007 ◽  
Vol 57 (2) ◽  
pp. 243-249 ◽  
Author(s):  
Sylvie Cousin ◽  
Orsola Päuker ◽  
Erko Stackebrandt
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Hard Water ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phylogenetic Groups ◽  
Type Strains

Ten new Flavobacterium-like strains were isolated from freshwater of the hard-water creek Westerhöfer Bach, northern Germany. These strains formed two phylogenetic groups: strains WB 1.1-56T, WB 1.1-04, WB 1.1-14, WB 1.1-57 and WB 1.1-63; and strains WB 4.2-33T, WB 4.1-86, WB 4.2-34, WB 4.2-32 and WB 4.2-78. Cells were Gram-negative, yellow-pigmented, chemoheterotrophic rods. Their major fatty acid profiles were similar, consisting of iso-C15 : 0, iso-C15 : 0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). DNA G+C contents for strains WB 1.1-56T and WB 4.2-33T were 33.5 and 37.5 mol%, respectively. Phylogenetic analysis based on almost complete 16S rRNA gene sequences indicated that strain WB 1.1-56T was phylogenetically most closely related to Flavobacterium frigidimaris KUC-1T, and that strain WB 4.2-33T was related most closely to F. frigidimaris KUC-1T and Flavobacterium saccharophilum DSM 1811T. Levels of 16S rRNA gene sequence similarity between strains WB 1.1-56T and WB 4.2-33T and the type strains of recognized members of the genus Flavobacterium were below 98 %. DNA–DNA hybridization experiments confirmed the separate genomic status of strains WB 1.1-56T and WB 4.2-33T. Strains WB 1.1-56T and WB 4.2-33T and their respective relatives differed from phylogenetically related Flavobacterium species based on several phenotypic characteristics. On the basis of their phenotypic and phylogenetic distinctiveness, the two groups of strains are considered to represent two novel species, for which the names Flavobacterium aquidurense sp. nov. (type strain WB 1.1-56T=DSM 18293T=CIP 109242T) and Flavobacterium hercynium sp. nov. (type strain WB 4.2-33T=DSM 18292T=CIP 109241T) are proposed.

Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat

2020 ◽  
Vol 367 (9) ◽  
Author(s):  
Sooyeon Park ◽  
Siyu Chen ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Type Strains

ABSTRACT A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.

scholarly journals Thalassobius maritimus sp. nov., isolated from seawater

2012 ◽  
Vol 62 (1) ◽  
pp. 8-12 ◽  
Author(s):  
Sooyeon Park ◽  
Mi-Hwa Lee ◽  
Jung-Sook Lee ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
The Mean ◽  
Type Strains

A Gram-stain-negative, aerobic, motile, rod-shaped bacterial strain, GSW-M6T, was isolated from seawater of Geoje island, Korea, and was subjected to a polyphasic taxonomic study. Strain GSW-M6T grew optimally at pH 7.0–8.0, at 30 °C and in the presence of 2 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain GSW-M6T clustered with Thalassobius aestuarii, Thalassobius gelatinovorus and Thalassobius mediterraneus. Strain GSW-M6T exhibited 96.2–96.9 % 16S rRNA gene sequence similarity to the type strains of these three Thalassobius species. Strain GSW-M6T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The polar lipid profiles of strain GSW-M6T and the type strains of the three Thalassobius species were similar, with phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid as common major components. The DNA G+C content of strain GSW-M6T was 57 mol%. The mean level of DNA–DNA relatedness between strain GSW-M6T and the type strain of Thalassobius gelatinovorus was 17 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, enabled strain GSW-M6T to be differentiated from recognized species of the genus Thalassobius. On the basis of the data presented, strain GSW-M6T is considered to represent a novel species of the genus Thalassobius, for which the name Thalassobius maritimus sp. nov. is proposed. The type strain is GSW-M6T ( = KCTC 23347T  = CCUG 60021T).

scholarly journals Loktanella atrilutea sp. nov., isolated from seawater in Japan

2007 ◽  
Vol 57 (9) ◽  
pp. 1966-1969 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sanriku Coast ◽  
Type Strains

A Gram-negative, rod-shaped bacterium, IG8T, was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8T represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA–DNA hybridization values between strain IG8T and the type strains of L. salsilacus (27.9–36.1 %) and L. fryxellensis (11.3–31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8T was 66.3 mol%. On the basis of DNA–DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8T (=IAM 15450T=NCIMB 14280T).

scholarly journals Glaciecola arctica sp. nov., isolated from Arctic marine sediment

2011 ◽  
Vol 61 (10) ◽  
pp. 2338-2341 ◽  
Author(s):  
Yan-Jiao Zhang ◽  
Xi-Ying Zhang ◽  
Zi-Hao Mi ◽  
Chun-Xiao Chen ◽  
Zhao-Ming Gao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Marine Sediment ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Hybridization Data ◽  
Gene Sequence Analysis ◽  
Curved Rods ◽  
Type Strains

A Gram-negative, motile, psychrotolerant, oxidase- and catalase-positive bacterium, designated BSs20135T, was isolated from Arctic marine sediment. Cells were straight or slightly curved rods and formed circular, convex and yellowish-brown colonies. Buds and prosthecae could be produced. The strain grew at 4–28 °C (optimum 25 °C) and with 1–5 % (w/v) NaCl (optimum 2 %) and hydrolysed aesculin and DNA, but did not reduce nitrate to nitrite. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain BSs20135T belonged to the genus Glaciecola and shared 93.6–97.7 % sequence similarity with the type strains of known species of the genus Glaciecola. The major cellular fatty acids of strain BSs20135T were summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0, C17 : 1ω8c and C18 : 1ω7c. The genomic DNA G+C content was 40.3 mol%. Based on 16S rRNA gene sequence analysis, DNA–DNA hybridization data and phenotypic and chemotaxonomic characterization, strain BSs20135T represents a novel species, for which the name Glaciecola arctica sp. nov. is proposed. The type strain is BSs20135T ( = CCTCC AB 209161T  = KACC 14537T).

scholarly journals Polaribacter undariae sp. nov., isolated from a brown alga reservoir

2015 ◽  
Vol 65 (Pt_5) ◽  
pp. 1679-1685 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Yong-Taek Jung ◽  
Kang Hyun Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Brown Alga ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped or ovoid bacterial strain, designated W-BA7T, was isolated from a brown alga reservoir on the South Sea in South Korea. This strain grew optimally at 25 °C, at pH 7.0–8.0 and in the presence of approximately 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain W-BA7T belonged to the genus Polaribacter , clustering coherently with the type strain of Polaribacter sejongensis, showing 99.3 % sequence similarity. Strain W-BA7T exhibited 16S rRNA gene sequence similarity of 93.4–98.6 % to the type strains of the other species of the genus Polaribacter . Strain W-BA7T contained MK-6 as the predominant menaquinone and iso-C15 : 0 3-OH and anteiso-C15 : 0 as the major fatty acids. The major polar lipids of strain W-BA7T were phosphatidylethanolamine, three unidentified lipids, one unidentified glycolipid, one unidentified aminolipid and one unidentified aminophospholipid. The DNA G+C content of strain W-BA7T was 31.9 mol%, and the mean DNA–DNA relatedness with the type strains of four phylogenetically related species of the genus Polaribacter was 12–27 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain W-BA7T is separated from recognized species of the genus Polaribacter . On the basis of the data presented, strain W-BA7T is considered to represent a novel species of the genus Polaribacter , for which the name Polaribacter undariae sp. nov. is proposed. The type strain is W-BA7T ( = KCTC 42175T = CECT 8670T).

scholarly journals Paenibacillus sophorae sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Sophora japonica

2011 ◽  
Vol 61 (4) ◽  
pp. 767-771 ◽  
Author(s):  
Hao-Jie Jin ◽  
Jing Lv ◽  
San-Feng Chen
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Sophora Japonica ◽  
Type Strains

A nitrogen-fixing bacterium, designated strain S27T, was isolated from rhizosphere soil of Sophora japonica. Phylogenetic analysis based on a fragment of the nifH gene and the full-length 16S rRNA gene sequence revealed that strain S27T is a member of the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain S27T and Paenibacillus durus DSM 1735T (97.3 %), Paenibacillus sabinae DSM 17841T (96.9 %), Paenibacillus forsythiae DSM 17842T (96.7 %) and Paenibacillus zanthoxyli DSM 18202T (96.6 %). However, DNA–DNA hybridization values between strain S27T and the four type strains were 37.64 %, 23.12 %, 25.6 % and 34.99 %, respectively. Levels of 16S rRNA gene sequence similarity between strain S27T and the type strains of other recognized members of the genus Paenibacillus were below 96.5 %. The DNA G+C content of strain S27T was 46.0 mol%. The major fatty acids were anteiso-C15 : 0, C16 : 0 and iso-C16 : 0. The major isoprenoid quinone was MK-7. On the basis of its phenotypic characteristics and DNA–DNA hybridization results, strain S27T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sophorae sp. nov. is proposed. The type strain is S27T ( = CGMCC 1.10238T  = DSM 23020T).

scholarly journals Niastella koreensis gen. nov., sp. nov. and Niastella yeongjuensis sp. nov., novel members of the phylum Bacteroidetes, isolated from soil cultivated with Korean ginseng

2006 ◽  
Vol 56 (8) ◽  
pp. 1777-1782 ◽  
Author(s):  
Hang-Yeon Weon ◽  
Byung-Yong Kim ◽  
Seung-Hee Yoo ◽  
Seon-Young Lee ◽  
Soon-Wo Kwon ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Separate Species ◽  
Phenotypic Data ◽  
Species Type ◽  
Korean Ginseng

Two novel strains, GR20-10T and GR20-13T, were isolated from soil using R2A medium. The soil sample was collected from a field in the Yeongju region of Korea that was cultivated with Korean ginseng. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains formed a cluster with several uncultured bacterial clones and with Flexibacter filiformis, Flexibacter sancti, Flexibacter japonensis, Cytophaga arvensicola and Flavobacterium ferrugineum (recently reclassified as Terrimonas ferruginea) in the phylum Bacteroidetes. The level of 16S rRNA gene sequence similarity between the two novel strains was 98.9 %. Isolates GR20-10T and GR20-13T showed the highest sequence similarities to Flexibacter japonensis IFO 16041T (91.8 and 91.9 %, respectively) and T. ferruginea ATCC 13524T (90.4 and 90.6 %, respectively). The whole-cell fatty acid profiles of the two isolates were similar and their major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. The major isoprenoid quinone of both strains was MK-7. The G+C contents of GR20-10T and GR20-13T were 45.8 and 44.3 mol%, respectively. DNA–DNA hybridization (57 % DNA–DNA hybridization value) and phenotypic data indicated that strains GR20-10T and GR20-13T each belong to a separate species. On the basis of phenotypic and phylogenetic data and genomic distinctiveness, strains GR20-10T and GR20-13T represent two novel species in a novel genus in the phylum Bacteroidetes; the names Niastella koreensis gen. nov., sp. nov. (the type species; type strain GR20-10T=KACC 11465T=DSM 17620T) and Niastella yeongjuensis sp. nov. (type strain GR20-13T=KACC 11466T=DSM 17621T) are proposed.

scholarly journals Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water

2007 ◽  
Vol 57 (11) ◽  
pp. 2629-2635 ◽  
Author(s):  
Margarita Gomila ◽  
Botho Bowien ◽  
Enevold Falsen ◽  
Edward R. B. Moore ◽  
Jorge Lalucat
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99 % with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3 % 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA–DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA–DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.

scholarly journals Demequina activiva sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2042-2047 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Sung-Min Won ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
South Sea ◽  
Type Strains

A Gram-stain-positive, facultatively anaerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated BS-12MT, was isolated from a tidal flat sediment on the South Sea, South Korea. Strain BS-12MT grew optimally at 35 °C, at pH 7.0–8.0 and in the presence of 2.0 % (w/v) NaCl. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain BS-12MT fell within the cluster comprising the type strains of species of the genus Demequina, joining the type strain of Demequina aestuarii with which it shared the highest sequence similarity (98.6 %). It exhibited 16S rRNA gene sequence similarity of 96.1–97.9 % to the type strains of other species of the genus Demequina. The peptidoglycan type of strain BS-12MT was A4β based on l-Orn − l-Ser − d-Glu. Strain BS-12MT contained demethylmenaquinone-9(H4) as the major menaquinone and anteiso-C15:0 and C16:0 as the major fatty acids. The major polar lipids of strain BS-12MT were phosphatidylinositol and phosphatidylinositolmannoside. The DNA G+C content of strain BS-12MT was 70.7 mol% and its DNA–DNA relatedness values with the type strains of five phylogenetically related species of the genus Demequina were 15–34 %. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain BS-12MT is separate from other species of the genus Demequina. On the basis of the data presented, strain BS-12MT is considered to represent a novel species of the genus Demequina, for which the name Demequina activiva sp. nov. is proposed. The type strain is BS-12MT ( = KCTC 29674T = NBRC 110675T).

scholarly journals Loktanella ponticola sp. nov., isolated from seawater

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3717-3723 ◽  
Author(s):  
Yong-Taek Jung ◽  
Sooyeon Park ◽  
Ji-Min Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
South Sea ◽  
Type Strains

A Gram-reaction-negative, aerobic, non-flagellated and coccoid, ovoid or rod-shaped bacterial strain, designated W-SW2T, was isolated from seawater in the South Sea of South Korea. The novel strain grew optimally at pH 7.0–8.0, at 25 °C and in the presence of approximately 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that strain W-SW2T fell within the clade comprising the type strains of species of the genus Loktanella , clustering and sharing the highest sequence similarity value (96.3 %) with the type strain of Loktanella koreensis . The 16S rRNA gene sequence similarity values between strain W-SW2T and the type strains of the other species of the genus Loktanella were in the range 93.1–96.0 %. The DNA G+C content of strain W-SW2T was 55.9 mol%. Strain W-SW2T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the predominant fatty acid. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. Differential phenotypic properties, together with the phylogenetic distinctiveness, revealed that strain W-SW2T is separated phylogenetically from other species of the genus Loktanella . On the basis of the data presented, strain W-SW2T is considered to represent a novel species of the genus Loktanella , for which the name Loktanella ponticola sp. nov. is proposed. The type strain is W-SW2T ( = KCTC 42133T = NBRC 110409T).

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