scholarly journals Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor

2005 ◽  
Vol 55 (6) ◽  
pp. 2543-2549 ◽  
Author(s):  
Zhe-Xue Quan ◽  
Hee-Sung Bae ◽  
Jong-Hwan Baek ◽  
Wen-Feng Chen ◽  
Wan-Taek Im ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Pcr Amplification ◽  
Growth Conditions ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Gene Encoding ◽  
Phenotypic Properties ◽  
Type Strains

A polyphasic study was carried out to determine the taxonomic position of two aerobic, cyanide-degrading bacterial strains, designated L61T and L22, which had been isolated from a bioreactor for the treatment of nickel-complexed cyanide. The two isolates exhibited almost identical taxonomic characteristics. Phylogenetic analysis inferred from comparative 16S rRNA gene sequences indicated that the isolates fall in a sublineage of the genus Rhizobium comprising the type strains of Rhizobium giardinii, Rhizobium radiobacter, Rhizobium rubi, Rhizobium larrymoorei, Rhizobium vitis, Rhizobium undicola, Rhizobium loessense, Rhizobium galegae and Rhizobium huautlense. Cells of the two isolates are Gram-negative, aerobic, motile and non-spore-forming rods (0·6–0·7×1·1–1·3 μm), with peritrichous flagella. The DNA G+C content is 60·1–60·9 mol%. Cellular fatty acids are C16 : 0 (2·2–3·3 %), C18 : 0 (2·1–3·2 %), C19 : 0 cyclo ω8c (9·9–16·8 %), C20 : 3 ω6,9,12c (2·7–3·3 %), summed feature 3 (7·2–7·7 %) and summed feature 7 (67·8–73·7 %). The strains formed nodules on a legume plant, Medicago sativa. A nifH gene encoding denitrogenase reductase, the key component of the nitrogenase enzyme complex, was detected in L61T by PCR amplification by using a nifH-specific primer system. Strains L61T and L22 were distinguished from the type strains of recognized Rhizobium species in the same sublineage based on low DNA–DNA hybridization values (2–4 %) and/or a 16S rRNA gene sequence similarity value of less than 96 %. Moreover, some phenotypic properties with respect to substrate utilization as a carbon or nitrogen source, antibiotic resistance and growth conditions could be used to discriminate L61T and L22 from Rhizobium species in the same sublineage. Based on the results obtained in this study, L61T and L22 are considered to be representatives of a novel species of Rhizobium, for which the name Rhizobium daejeonense sp. nov. is proposed. The type strain is L61T (=KCTC 12121T=IAM 15042T=CCBAU 10050T).

scholarly journals Psychrobacter cibarius sp. nov., isolated from jeotgal, a traditional Korean fermented seafood

2005 ◽  
Vol 55 (2) ◽  
pp. 577-582 ◽  
Author(s):  
Seo-Youn Jung ◽  
Mi-Hwa Lee ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Phenotypic Properties ◽  
Phenotypic Data ◽  
Dna Relatedness ◽  
The Mean ◽  
Type Strains

Two novel Psychrobacter-like bacterial strains, JG-219T and JG-220, were isolated from jeotgal, a traditional Korean fermented seafood. Cells of strains JG-219T and JG-220 were Gram-negative, non-motile coccobacilli. Growth of the two strains was observed at 4–32 °C. They grew optimally in the presence of 2–5 % (w/v) NaCl. Strains JG-219T and JG-220 contained C18 : 1 ω9c and C17 : 1 ω8c as the major fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains JG-219T and JG-220 were 43·5 and 43·0 mol%, respectively. The two strains showed no difference in their 16S rRNA gene sequences but exhibited minor differences in their phenotypic properties. Strains JG-219T and JG-220 exhibited levels of 16S rRNA gene sequence similarity of 95·2–98·7 % to the type strains of recognized Psychrobacter species. The mean level of DNA–DNA relatedness between strains JG-219T and JG-220 was 84·4 %. The two strains exhibited levels of DNA–DNA relatedness of 1·5–32·9 % to the type strains of eight phylogenetically related Psychrobacter species. On the basis of phenotypic data and phylogenetic and genetic distinctiveness, the two strains were classified as representing a novel species within the genus Psychrobacter, Psychrobacter cibarius sp. nov. The type strain is JG-219T (=KCTC 12256T=DSM 16327T).

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).

scholarly journals Pedobacter boryungensis sp. nov., isolated from soil

2012 ◽  
Vol 62 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Yong-Taek Jung ◽  
Soo-Young Lee ◽  
Won-Chan Choi ◽  
Tae-Kwang Oh ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, non-sporulating, non-flagellated rod, designated BR-9T, was isolated from soil collected on the Korean peninsula. Strain BR-9T grew optimally at pH 6.0–7.0, at 30 °C and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BR-9T belonged to the genus Pedobacter and clustered with Pedobacter insulae DS-139T and Pedobacter koreensis WPCB189T. Strain BR-9T exhibited 98.2 and 97.5 % 16S rRNA gene sequence similarity with P. insulae DS-139T and P. koreensis WPCB189T, respectively, and <96.7 % sequence similarity with the type strains of other species in the genus Pedobacter. Strain BR-9T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content of strain BR-9T was 38.5 mol%. DNA–DNA relatedness between strain BR-9T and P. insulae DS-139T and P. koreensis KCTC 12536T was 3.4–4.2 %, which indicated that the isolate was genetically distinct from these type strains. Strain BR-9T was also distinguishable by differences in phenotypic properties. On the basis of the data presented, strain BR-9T is considered to represent a novel species of the genus Pedobacter, for which the name Pedobacter boryungensis sp. nov. is proposed. The type strain is BR-9T ( = KCTC 23344T  = CCUG 60024T).

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 Marinobacter salicampi sp. nov., isolated from a marine solar saltern in Korea

2007 ◽  
Vol 57 (9) ◽  
pp. 2102-2105 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Mi-Hwa Lee ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
The Novel ◽  
Solar Saltern ◽  
Marine Solar Saltern ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, motile, rod-shaped, Marinobacter-like bacterial strain, ISL-40T, was isolated from a marine solar saltern of the Yellow Sea in Korea. The taxonomic position of the novel strain was investigated using a polyphasic approach. Strain ISL-40T grew optimally at pH 7.0–8.0 and at 30 °C. It contained Q-9 as the predominant ubiquinone. The major fatty acids were C16 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH and 10-methyl C16 : 0. The DNA G+C content was 58.1 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-40T belongs to the genus Marinobacter. Strain ISL-40T exhibited 16S rRNA gene sequence similarity values of 93.5–96.4 % to the type strains of recognized Marinobacter species. The differential phenotypic properties and phylogenetic distinctiveness of strain ISL-40T revealed that it is separate from recognized Marinobacter species. On the basis of phenotypic, phylogenetic and genetic data, therefore, strain ISL-40T represents a novel species of the genus Marinobacter, for which the name Marinobacter salicampi sp. nov. is proposed. The type strain is ISL-40T (=KCTC 12972T=CCUG 54357T).

Winogradskyella litorisediminis sp. nov., isolated from coastal sediment

2013 ◽  
Vol 63 (Pt_5) ◽  
pp. 1793-1799 ◽  
Author(s):  
Chul-Hyung Kang ◽  
Soo-Young Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Coastal Sediment ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Content Type ◽  
Link Type ◽  
Type Strains

A Gram-staining-negative, non-flagellated, non-gliding, aerobic, rod-shaped bacterium, designated DPS-8T, was isolated from coastal sediment of Geoje island in the South Sea, South Korea, and subjected to a polyphasic study. Strain DPS-8T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain DPS-8T joined the clade comprising the type strains of Winogradskyella species with a high bootstrap resampling value of 93.5 %. Phylogenetic trees constructed using maximum-likelihood and maximum-parsimony algorithms revealed that strain DPS-8T belonged to the genus Winogradskyella . Strain DPS-8T exhibited 94.1–96.5 % 16S rRNA gene sequence similarity to the type strains of species of the genus Winogradskyella . Strain DPS-8T contained MK-6 as the predominant menaquinone and iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids of strain DPS-8T were phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain DPS-8T was 34.7 mol%. Differential phenotypic properties, together with its phylogenetic distinctiveness, revealed that strain DPS-8T is separate from recognized species of the genus Winogradskyella . On the basis of the data presented, strain DPS-8T is considered to represent a novel species of the genus Winogradskyella , for which the name Winogradskyella litorisediminis sp. nov. is proposed. The type strain is DPS-8T ( = KCTC 32110T = CCUG 62215T).

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 Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov., isolated from soil

2007 ◽  
Vol 57 (9) ◽  
pp. 2089-2095 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Sooyeon Park ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Bacterial Strains ◽  
Type Strains

Two Gram-negative, non-motile, pleomorphic bacterial strains, DS-40T and DS-45T, were isolated from a soil sample collected from Dokdo, Korea, and their exact taxonomic positions were investigated by using a polyphasic approach. Strains DS-40T and DS-45T grew optimally at 25 °C and pH 6.5–7.5 in the presence of 0–1.0 % (w/v) NaCl. They contained MK-7 as the predominant menaquinone and possessed iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C contents of strains DS-40T and DS-45T were 36.0 and 36.8 mol%, respectively. Strains DS-40T and DS-45T shared a 16S rRNA gene sequence similarity of 96.7 % and demonstrated a mean DNA–DNA relatedness level of 12 %. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains DS-40T and DS-45T were most closely phylogenetically affiliated with the genus Pedobacter of the family Sphingobacteriaceae. Strains DS-40T and DS-45T exhibited 16S rRNA gene sequence similarity values of 91.4–93.7 and 89.9–91.6 % with respect to the type strains of Pedobacter and Sphingobacterium species, respectively. Phenotypic and chemotaxonomic properties, together with the phylogenetic data, support the assignment of strains DS-40T and DS-45T as two distinct species within the genus Pedobacter. On the basis of phenotypic, phylogenetic and genetic data, strains DS-40T and DS-45T represent two novel species of the genus Pedobacter, for which the names Pedobacter lentus sp. nov. and Pedobacter terricola sp. nov. are proposed, respectively. The respective type strains are DS-40T (=KCTC 12875T=JCM 14593T) and DS-45T (=KCTC 12876T=JCM 14594T).

scholarly journals Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works

2007 ◽  
Vol 57 (6) ◽  
pp. 1355-1359 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
So-Jung Kang ◽  
Tae-Kwang Oh
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Textile Dye ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Properties ◽  
Type Strains

A Gram-negative, rod-shaped bacterial strain, K105T, was isolated from wastewater of a textile dye works in Korea and subjected to a polyphasic taxonomic study. Strain K105T grew optimally at pH 6.5–7.5 and 30–37 °C. It contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 1 ω9c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH) as the major fatty acids. The DNA G+C content was 36.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain K105T belonged to the genus Chryseobacterium. Strain K105T exhibited 16S rRNA gene sequence similarity values of less than 96.9 % to the type strains of recognized Chryseobacterium species. Strain K105T differed from phylogenetically related Chryseobacterium species in several phenotypic properties. On the basis of phenotypic and phylogenetic data, strain K105T (=KCTC 12841T=JCM 14362T) is placed in the genus Chryseobacterium as the type strain of a novel species, for which the name Chryseobacterium daeguense sp. nov. is proposed.

scholarly journals Algoriphagus aestuarii sp. nov., a member of the Cyclobacteriaceae isolated from a tidal-flat sediment of the Yellow Sea in Korea

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3439-3446 ◽  
Author(s):  
Yong-Taek Jung ◽  
Jung-Sook Lee ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
The Yellow Sea ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Tidal Flat Sediment ◽  
The Mean ◽  
Type Strains

A Gram-strain-negative, coccoid or oval-shaped, non-motile bacterial strain, designated MDM-1T, was isolated from a tidal-flat sediment on the Korean peninsula. Strain MDM-1T was found to grow optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain MDM-1T falls within the clade comprising species of the genus Algoriphagus, clustering with the type strains of Algoriphagus halophilus, A. lutimaris, A. chungangensis and A. machipongonensis, with which it exhibited 97.2–98.5 % 16S rRNA gene sequence similarity. Sequence similarities to the type strains of the other recognized species of the genus Algoriphagus were 92.8–97.6 %. Strain MDM-1T was found to contain MK-7 as the predominant menaquinone and iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the major fatty acids. The major polar lipids were identified as phosphatidylcholine, phosphatidylethanolamine and two unidentified lipids. The DNA G+C content of strain MDM-1T was determined to be 42.7 mol% and the mean DNA–DNA relatedness with A. halophilus KCTC 12051T, A. lutimaris S1-3T, A. chungangensis KCTC 23759T, A. machipongonensis DSM 24695T and A. ratkowskyi CIP 107452T was 19.7–5.2 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain MDM-1T is distinguishable from recognized species of the genus Algoriphagus. On the basis of the data presented, strain MDM-1T is proposed to represent a novel species of the genus Algoriphagus, for which the name Algoriphagus aestuarii sp. nov. is proposed. The type strain is MDM-1T ( = KCTC 42199T = NBRC 110552T).

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