scholarly journals Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas

2020 ◽  
Author(s):  
Hideomi Itoh ◽  
Zhenxing Xu ◽  
Yoko Masuda ◽  
Natsumi Ushijima ◽  
Chie Hayakawa ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Strictly Anaerobic ◽  
Bacterial Strains ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae . Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas , were 96.3–98.5 %. The genome-related indexes, average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity, among the three strains and G. oryza e S43T were 74.7–86.8 %, 21.2–33.3 % and 70.4–89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas , for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.

scholarly journals Erythrobacter pelagi sp. nov., a member of the family Erythrobacteraceae isolated from the Red Sea

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1348-1353 ◽  
Author(s):  
Hui-xian Wu ◽  
Pok Yui Lai ◽  
On On Lee ◽  
Xiao-jian Zhou ◽  
Li Miao ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Red Sea ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A novel Gram-negative, aerobic, catalase- and oxidase-positive, non-sporulating, non-motile, rod-shaped bacterium, designated strain UST081027-248T, was isolated from seawater of the Red Sea. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UST081027-248T fell within the genus Erythrobacter . Levels of 16S rRNA gene sequence similarity between the novel strain and the type strains of Erythrobacter species ranged from 95.3 % (with Erythrobacter gangjinensis ) to 98.2 % (with Erythrobacter citreus ). However, levels of DNA–DNA relatedness between strain UST081027-248T and the type strains of closely related species were below 70 %. Optimal growth of the isolate occurred in the presence of 2.0 % NaCl, at pH 8.0–9.0 and at 28–36 °C. The isolate did not produce bacteriochlorophyll a. The predominant cellular fatty acids were C17 : 1ω6c, summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C15 : 0 2-OH. The genomic DNA G+C content of strain UST081027-248T was 60.4 mol%. Phenotypic properties and phylogenetic distinctiveness clearly indicated that strain UST081027-248T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter pelagi sp. nov. is proposed. The type strain is UST081027-248T ( = JCM 17468T = NRRL 59511T).

scholarly journals Rhizobium flavum sp. nov., a triazophos-degrading bacterium isolated from soil under the long-term application of triazophos

2014 ◽  
Vol 64 (Pt_6) ◽  
pp. 2017-2022 ◽  
Author(s):  
Tao Gu ◽  
Li Na Sun ◽  
Jun Zhang ◽  
Xin Hua Sui ◽  
Shun Peng Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Degrading Bacterium ◽  
Type Strains

A Gram-stain-negative, non-motile, pale yellow, rod-shaped bacterial strain, YW14T, was isolated from soil and its taxonomic position was investigated by a polyphasic study. Strain YW14T did not form nodules on three different legumes, and the nodD and nifH genes were not detected by PCR. Strain YW14T contained Q-10 as the predominant ubiquinone. The major cellular fatty acid was C18 : 1ω7c. Phylogenetic analyses based on 16S rRNA gene sequences and seven housekeeping gene sequences (recA, atpD, glnII, gyrB, rpoB, dnaK and thrC) showed that strain YW14T belonged to the genus Rhizobium . Strain YW14T showed 16S rRNA gene sequence similarity of 93.4–97.3 % to the type strains of recognized species of the genus Rhizobium . DNA–DNA relatedness between strain YW14T and the type strains of Rhizobium sullae IS123T and Rhizobium yanglingense CCBAU 71623T was 19.6–25.7 %, indicating that strain YW14T was distinct from them genetically. Strain YW14T could also be differentiated from these phylogenetically related species of the genus Rhizobium by various phenotypic properties. On the basis of phenotypic properties, phylogenetic distinctiveness and genetic data, strain YW14T is considered to represent a novel species of the genus Rhizobium , for which the name Rhizobium flavum sp. nov. is proposed. The type strain is YW14T ( = KACC 17222T = CCTCC AB2013042T).

scholarly journals Gramella aestuariivivens sp. nov., isolated from a tidal flat

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1262-1267 ◽  
Author(s):  
Ji-Min Park ◽  
Sooyeon Park ◽  
Sung-Min Won ◽  
Yong-Taek Jung ◽  
Kee-Sun Shin ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-flagellated and rod-shaped or ovoid bacterial strain, designated BG-MY13T, was isolated from a tidal flat sediment on the South Sea, South Korea. Strain BG-MY13T grew optimally at 30–35 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain BG-MY13T falls within the cluster comprising the type strains of species of the genus Gramella . Strain BG-MY13T exhibited 16S rRNA gene sequ4ence similarity values of 96.9–97.8 % to the type strains of Gramella echinicola , Gramella gaetbulicola , Gramella portivictoriae and Gramella marina and of 94.6–96.5 % to the type strains of other species of the genus Gramella with validly published names. Strain BG-MY13T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain BG-MY13T was 38.9 mol% and DNA–DNA relatedness values with the type strains of G. echinicola , G. gaetbulicola , G. portivictoriae and G. marina were 12–23 %. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain BG-MY13T is separated from other species of the genus Gramella . On the basis of the data presented, strain BG-MY13T is considered to represent a novel species of the genus Gramella , for which the name Gramella aestuariivivens sp. nov. is proposed. The type strain is BG-MY13T ( = KCTC 42285T = NBRC 110677T).

scholarly journals Alteromonas ponticola sp. nov., a gammaproteobacterium isolated from seawater

2020 ◽  
Vol 70 (12) ◽  
pp. 6396-6401 ◽  
Author(s):  
Young-Ok Kim ◽  
In-Suk Park ◽  
Sooyeon Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-spore-forming, non-motile and ovoid or rod-shaped bacterial strain, MYP5T, was isolated from seawater in Jeju island of South Korea. MYP5T grew optimally at 30–35 °C and in the presence of 2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences revealed that MYP5T fell within the clade enclosed by the type strains of species of the genus Alteromonas , clustering with the type strains of Alteromonas confluentis and Alteromonas halophila . MYP5T exhibited the highest 16S rRNA gene sequence similarity value (98.0 %) to the type strain of A. confluentis and similarities of 95.1–97.9 % to the type strains of the other species of the genus Alteromonas . ANI and dDDH values of genomic sequences between MYP5T and the type strains of 22 species of the genus Alteromonas were 66.8–70.5 % and 18.6–27.5 %, respectively. The DNA G+C content of MYP5T, determined from the genome sequence, was 46.1 %. MYP5T contained Q-8 as the predominant ubiquinone and C18 : 1 ω7c, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and 10-methyl C17 : 0 as the major fatty acids. The major polar lipids of MYP5T were phosphatidylethanolamine and phosphatidylglycerol. Distinguishing phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that MYP5T is separated from species of the genus Alteromonas . On the basis of the data presented, MYP5T is considered to represent a novel species of the genus Alteromonas , for which the name Alteromonas ponticola sp. nov. is proposed. The type strain is MYP5T (=KCTC 82144T=NBRC 114354T).

scholarly journals Erythrobacter insulae sp. nov., isolated from a tidal flat

2020 ◽  
Vol 70 (3) ◽  
pp. 1470-1477 ◽  
Author(s):  
Sooyeon Park ◽  
Siyu Chen ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Species ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus Erythrobacter . JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of Erythrobacter longus , Erythrobacter aquimaris , Erythrobacter nanhaisediminis , Erythrobacter vulgaris , Erythrobacter seohaensis , Erythrobacter litoralis and Erythrobacter citreus and 93.7–96.6 % to the type strains of the other species of the genus Erythrobacter . The ANI and dDDH values between JBTF-M21T and the type strains of E. longus , E. nanhaisediminis , E. seohaensis and E. litoralis were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of E. aquimaris , E. vulgaris and E. citreus were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus Erythrobacter with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus Erythrobacter , for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).

scholarly journals Thalassotalea ponticola sp. nov., isolated from seawater, reclassification of Thalassomonas fusca as Thalassotalea fusca comb. nov. and emended description of the genus Thalassotalea

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3676-3682 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Chul-Hyung Kang ◽  
Ja-Min Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
South Sea ◽  
Type Strains

A Gram-stain-negative, aerobic, non-flagellated and rod-shaped or ovoid bacterial strain, designated GJSW-36T, was isolated from seawater at Geoje island in the South Sea, South Korea. Strain GJSW-36T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain GJSW-36T fell within the clade comprising the type strains of species of the genus Thalassotalea and Thalassomonas fusca . Strain GJSW-36T exhibited 16S rRNA gene sequence similarity values of 94.2–96.0 % to the type strains of species of the genus Thalassotalea and Thalassomonas fusca and of 93.8–94.5 % to the type strains of the other species of the genus Thalassomonas . Strain GJSW-36T contained ubiquinone-8 (Q-8) as the predominant ubiquinone and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω8c and C16 : 0 as the major fatty acids. The major polar lipids of strain GJSW-36T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain GJSW-36T was 45.1 mol%. Differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain GJSW-36T is separated from species of the genus Thalassotalea and Thalassomonas fusca . On the basis of the data presented, strain GJSW-36T is considered to represent a novel species of the genus Thalassotalea , for which the name Thalassotalea ponticola sp. nov. is proposed. The type strain is GJSW-36T ( = KCTC 42155T = CECT 8656T). From this study, it is also proposed that Thalassomonas fusca should be reclassified as a member of the genus Thalassotalea and the description of the genus Thalassotalea is emended.

scholarly journals Litoreibacter ponti sp. nov., isolated from seawater

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3810-3815 ◽  
Author(s):  
Sooyeon Park ◽  
Ji-Min Park ◽  
Doo-Sang Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated GJSW-31T, was isolated from seawater from the South Sea, South Korea. The novel strain 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 GJSW-31T clustered with the type strains of species of the genus Litoreibacter . Strain GJSW-31T exhibited 16S rRNA gene sequence similarity values of 95.2–98.5 % to the type strains of species of the genus Litoreibacter and sequence similarities of less than 96.18 % to type strains of the other species with validly published names. Strain GJSW-31T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. The major polar lipids of strain GJSW-31T were phosphatidylcholine, phosphatidylglycerol, one unidentified lipid and one unidentified aminolipid. The DNA G+C content of strain GJSW-31T was 62.5 mol% and its DNA–DNA relatedness values with the type strains of Litoreibacter albidus , Litoreibacter janthinus , Litoreibacter meonggei and Litoreibacter ascidiaceicola were 13–23 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GJSW-31T is separate from other species of the genus Litoreibacter . On the basis of the data presented, strain GJSW-31T is considered to represent a novel species of the genus Litoreibacter , for which the name Litoreibacter ponti sp. nov. is proposed. The type strain is GJSW-31T ( = KCTC 42114T = NBRC 110379T).

scholarly journals Pedobacter silvilitoris sp. nov., isolated from wood falls

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1284-1289 ◽  
Author(s):  
Sooyeon Park ◽  
Yong-Taek Jung ◽  
Ji-Min Park ◽  
Sung-Min Won ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
South Sea ◽  
Type Strains

A Gram-stain-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterium, designated W-WS1T, was isolated from wood falls collected around Wando, an island located in the South Sea, Republic of Korea. Strain W-WS1T grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 0–3.0 % (w/v) NaCl. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain W-WS1T belonged to the genus Pedobacter , clustering coherently with the type strains of Pedobacter daechungensis , Pedobacter lentus , Pedobacter terricola , Pedobacter arcticus and Pedobacter glucosidilyticus , showing 94.3–96.3 % sequence similarity. Strain W-WS1T exhibited 16S rRNA gene sequence similarity values of 91.2–94.0 % to the type strains of other species of the genus Pedobacter . Strain W-WS1T contained MK-7 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids detected in strain W-WS1T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain W-WS1T was 37.7 mol%. The differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain W-WS1T is separated from recognized species of the genus Pedobacter . On the basis of the data presented, strain W-WS1T is considered to represent a novel species of the genus Pedobacter , for which the name Pedobacter silvilitoris sp. nov. is proposed. The type strain is W-WS1T ( = KCTC 42174T = CECT 8669T).

scholarly journals Chitinophaga longshanensis sp. nov., a mineral-weathering bacterium isolated from weathered rock

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 418-423 ◽  
Author(s):  
Shan Gao ◽  
Wen-Bin Zhang ◽  
Xia-Fang Sheng ◽  
Lin-Yan He ◽  
Zhi Huang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Mineral Weathering ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Weathered Rock ◽  
Link Type ◽  
Type Strains

A Gram-stain-negative, aerobic, yellow-pigmented, non-motile, non-spore-forming, rod-shaped bacterial strain, Z29T, was isolated from the surface of weathered rock (potassic trachyte) from Nanjing, Jiangsu Province, PR China. Phylogenetic analysis based on 16S rRNA gene sequences suggested that strain Z29T belongs to the genus Chitinophaga in the family Chitinophagaceae . Levels of 16S rRNA gene sequence similarity between strain Z29T and the type strains of recognized species of the genus Chitinophaga ranged from 92.7 to 98.2 %. The main fatty acids of strain Z29T were iso-C15 : 0, C16 : 1ω5c and iso-C17 : 0 3-OH. It also contained menaquinone 7 (MK-7) as the respiratory quinone and homospermidine as the main polyamine. The polar lipid profile contained phosphatidylethanolamine, unknown aminolipids, unknown phospholipids and unknown lipids. The total DNA G+C content of strain Z29T was 51.3 mol%. Phenotypic properties and chemotaxonomic data supported the affiliation of strain Z29T with the genus Chitinophaga . The low level of DNA–DNA relatedness (ranging from 14.6 to 29.8 %) to the type strains of other species of the genus Chitinophaga and differential phenotypic properties demonstrated that strain Z29T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga longshanensis sp. nov. is proposed. The type strain is Z29T ( = CCTCC AB 2014066T = LMG 28237T).

Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov., isolated from a tidal flat

2021 ◽  
Vol 71 (6) ◽  
Author(s):  
Sooyeon Park ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Genomic Sequences ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

Two Gram-stain-negative and non-flagellated bacteria, YSTF-M3T and YSTF-M6T, were isolated from a tidal flat from Yellow Sea, Republic of Korea, and subjected to a polyphasic taxonomic study. Neighbour-joining phylogenetic tree of 16S rRNA gene sequences showed that strains YSTF-M3T and YSTF-M6T belong to the genera Kordia and Olleya of the family Flavobacteriaceae , respectively. The 16S rRNA gene sequence similarities between strain YSTF-M3T and the type strains of Kordia species and between strain YSTF-M6T and the type strains of Olleya species were 94.1–98.4 and 97.3–98.3 %, respectively. The ANI and dDDH values between genomic sequences of strain YSTF-M3T and the type strains of five Kordia species and between those of strain YSTF-M6T and the type strains of three Olleya species were in ranges of 77.0–83.2 and 20.7–27.1 % and 79.4–81.5 and 22.3–23.9 %, respectively. The DNA G+C contents of strain YSTF-M3T and YSTF-M6T from genomic sequences were 34.1 and 31.1 %, respectively. Both strains contained MK-6 as predominant menaquinone and phosphatidylethanolamine as only major phospholipid identified. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strains YSTF-M3T and YSTF-M6T are separated from recognized species of the genera Kordia and Olleya , respectively. On the basis of the data presented, strains YSTF-M3T (=KACC 21639T=NBRC 114499T) and YSTF-M6T (=KACC 21640T=NBRC 114500T) are considered to represent novel species of the genera Kordia and Olleya , respectively, for which the names Kordia aestuariivivens sp. nov. and Olleya sediminilitoris sp. nov. are proposed.

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