Ying-Shun Cui

Paenibacillus sediminis sp nov., a xylanolytic bacterium isolated from a tidal flat

A Gram-positive, rod-shaped, xylanolytic, spore-forming bacterium, strain GTH-3(T), was isolated from a tidal flat adjacent to Ganghwa Island, Republic of Korea, and was characterized to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain GTH-3(T) was shown to belong to the family Paenibacillaceae, being most closely related to the type strains of Paenibacillus ginsengisoli (94.9 %), Paenibacillus anaericanus (94.8 %), Paenibacillus urinalis (94.4 %), Paenibacillus cookii (94.2 %), Paenibacillus alvei (94.1 %) and Paenibacillus chibensis (94.0 %). The G+C content of the genomic DNA of strain GTH-3(T) was 45.9±0.2 mol% (mean±sd). The major menaquinone was MK-7. The major fatty acids were anteiso-C(15:0) and iso-C(16:0). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. Phenotypic and chemotaxonomic data supported the affiliation of strain GTH-3(T) to the genus Paenibacillus. The results of physiological and biochemical tests allowed strain GTH-3(T) to be distinguished genotypically and phenotypically from recognized species of the genus Paenibacillus. Strain GTH-3(T) is therefore considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sediminis sp. nov. is proposed. The type strain is GTH-3(T) ( = DSM 23491(T) = LMG 25635(T)).

Tumebacillus ginsengisoli sp. nov., isolated from soil of a ginseng field

A gram-reaction-positive, rod-shaped, spore-forming bacterium, designated Gsoil 1105(T), was isolated from soil of a ginseng field in Pocheon Province in South Korea and characterized in order to determine its taxonomic position. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the order Bacillales, showing the highest level of sequence similarity with respect to Tumebacillus permanentifrigoris Eur1 9.5(T) (94.6 %). The phylogenetic distances from other described species with validly published names within the order Bacillales were greater than 9.0 %. Strain Gsoil 1105(T) had a genomic DNA G+C content of 55.6 mol% and menaquinone 7 (MK-7) as the major respiratory quinone. The major fatty acids were iso-C(15 : 0) and anteiso-C(15 : 0). On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 1105(T) represents a novel species of the genus Tumebacillus, for which the name Tumebacillus ginsengisoli sp. nov. is proposed. The type strain is Gsoil 1105(T) ( = KCTC 13942(T)  = DSM 18389(T)).

Nocardioides ginsengisoli sp. nov., isolated from soil of a ginseng field

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 1124(T)) was isolated from soil of a ginseng field of Pocheon province in South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 1124(T) was shown to belong to the family Nocardioidaceae and related to Nocardioides simplex (98.2 % 16S rRNA gene sequence similarity), Nocardioides aromaticivorans (98.1 %), Nocardioides nitrophenolicus (97.7 %) and Nocardioides kongjuensis (97.5 %). The sequence similarity with any other species with validly published names within the genus Nocardioides was less than 94.5 %. Strain Gsoil 1124(T) was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H(4)) as the predominant menaquinone and iso-C(16 : 0), C(18 : 0), C(16 : 0), and C(18 : 1)omega9c as the major fatty acids. The G+C content of the genomic DNA was 70.2 mol%. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 1124(T) to the genus Nocardioides. The results of physiological and biochemical tests, and the low level of DNA-DNA relatedness allowed genotypic differentiation of strain Gsoil 1124(T) from recognized Nocardioides species. Therefore, strain Gsoil 1124(T) is considered to represent a novel species, for which the name Nocardioides ginsengisoli sp. nov. is proposed, with the type strain Gsoil 1124(T) (=KCTC 19135(T)=CCUG 52478(T)=DSM 17921(T)).

Brevibacterium daeguense sp. nov., a nitrate-reducing bacterium isolated from a 4-chlorophenol enrichment culture

A Gram-reaction-positive, non-spore-forming, aerobic actinobacterial strain (2C6-41(T)) was isolated from the activated sludge from an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, closest phylogenetic relatives to strain 2C6-41(T) were Brevibacterium pityocampae DSM 21720(T) (97.2 %), Brevibacterium salitolerans KCTC 19616(T) (96.7 %), Brevibacterium album KCTC 19173(T) (96.2 %) and Brevibacterium samyangense KCCM 42316(T) (96.2 %). The DNA G+C content of strain 2C6-41(T) was 66.4 mol%. Chemotaxonomic data, which included MK-8(H(2)) as the major menaquinone; meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; ribose, mannose and glucose as major cell-wall sugars; and anteiso-C(15 : 0), anteiso-C(17 : 0), C(16 : 0) and iso-C(15 : 0) as major fatty acids, supported the affiliation of strain 2C6-41(T) to the genus Brevibacterium. The aromatic ring cleavage enzyme catechol 1,2-dioxygenase was not detected in strain 2C6-41(T), but catechol 2,3-dioxygenase was detected. The results of physiological and biochemical tests, and the low level of DNA-DNA relatedness to the closest phylogenetic relative enabled strain 2C6-41(T) to be differentiated genotypically and phenotypically from recognized species of the genus Brevibacterium. The isolate is therefore considered to represent a novel species in the genus Brevibacterium, for which the name Brevibacterium daeguense sp. nov. is proposed. The type strain is 2C6-41(T) (=KCTC 19800(T) = JCM 17458(T)).

Georgenia daeguensis sp nov., isolated from 4-chlorophenol enrichment culture

During screening for 4-chlorophenol-degrading micro-organisms in activated sludge from industrial wastewater treatment, a Gram-positive, rod-shaped, aerobic bacterial strain, designated 2C6-43(T), was isolated and characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 2C6-43(T) belongs to the family Bogoriellaceae, class Actinobacteria, and is related most closely to Georgenia soli CC-NMPT-T3(T) (98.8% sequence similarity), Georgenia muralis 1A-C(T) (97.6%), Georgenia thermotolerans TT02-04(T) (96.8%), Georgenia ruanii YIM 004(T) (96.6%) and Georgenia halophila YIM 93316(T) (96.0%). The G+C content of the genomic DNA of strain 2C6-43(T) was 66.2 mol%. Sugars from whole-cell hydrolysates found in strain 2C6-43(T) were rhamnose, ribose and galactose. The menaquinone MK-8(H(4)) was detected as the predominant quinone. Polar lipid analysis of 2C6-43(T) revealed diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and phosphatidylglycerol. An aromatic compound ring cleavage enzyme of catechol 1,2-dioxygenase was detected but catechol 2,3-dioxygenase was not detected in 2C6-43(T). A fatty acid profile with anteiso-C(15:0), iso-C(15:0) and C(16:0) as the major components supported the affiliation of strain 2C6-43(T) to the genus Georgenia. However, the DNA-DNA relatedness between strain 2C6-43(T) and the type strains of five species of the genus Georgenia ranged from 17 to 40%, clearly showing that the isolate constitutes a new genospecies. Strain 2C6-43(T) could be clearly differentiated from its phylogenetic neighbours on the basis of some phenotypic, genotypic and chemotaxonomic features. Therefore, strain 2C6-43(T) is considered to represent a novel species of the genus Georgenia, for which the name Georgenia daeguensis sp. nov. is proposed; the type strain is 2C6-43(T) (=KCTC 19801(T)=JCM 17459(T)).

Vagococcus acidifermentans sp. nov., isolated from an acidogenic fermentation bioreactor.

A Gram-staining-positive, coccus-shaped, non-spore-forming, facultatively anaerobic bacterium, designated AC-1(T), was isolated from an acidogenic fermentation bioreactor treating food wastewater. On the basis of 16S rRNA gene sequence analysis, strain AC-1(T) was shown to belong to the genus Vagococcus. The closest phylogenetic relatives were Vagococcus elongatus PPC9(T) (97.4 % 16S rRNA gene sequence similarity), Vagococcus penaei CD276(T) (96.7 %) and Vagococcus carniphilus ATCC BAA-640(T) (96.6 %). The major fatty acids were C(18 : 1)ω9c (24.8 %) and C(16 : 0) (19.5 %) and the G+C content of genomic DNA was 44.2 mol%, which supported the affiliation of strain AC-1(T) to the genus Vagococcus. Strain AC-1(T) and V. elongatus DSM 21480(T) exhibited 11 % DNA-DNA relatedness. Physiological and biochemical tests differentiated strain AC-1(T) from the type strains of recognized species of the genus Vagococcus. Therefore, strain AC-1(T) is considered to represent a novel species, for which the name Vagococcus acidifermentans sp. nov. is proposed. The type strain is AC-1(T) ( = KCTC 13418(T)  = LMG 24798(T)).

Nocardioides daeguensis sp. nov., a nitrate-reducing bacterium isolated from activated sludge of an industrial wastewater treatment plant.

A Gram-reaction-positive, rod-shaped, non-spore-forming bacterium (strain 2C1-5(T)) was isolated from activated sludge of an industrial wastewater treatment plant in Daegu, South Korea. Its taxonomic position was investigated by using a polyphasic approach. On the basis of 16S rRNA gene sequence similarity, the closest phylogenetic relatives were the type strains of Nocardioides nitrophenolicus (98.6 % similarity), N. kongjuensis (98.5 %), N. caeni (98.4 %), N. simplex (98.3 %), N. aromaticivorans (98.1 %) and N. ginsengisoli (97.5 %); the phylogenetic distance from other species with validly published names within the genus Nocardioides was greater than 3 %. Strain 2C1-5(T) was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C16 : 0 and C17 : 1ω6c as the major fatty acids. The G+C content of the genomic DNA was 74.9 mol%. These chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain 2C1-5(T) to the genus Nocardioides. The results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 2C1-5(T) from existing species with validly published names. Therefore, strain 2C1-5(T) represents a novel species of the genus Nocardioides, for which the name Nocardioides daeguensis sp. nov. is proposed, with the type strain 2C1-5(T) ( = JCM 17460(T) = KCTC 19799(T)).

Streptomyces panacagri sp. nov., isolated from soil of a ginseng field

A Gram-positive, spore-forming, aerobic actinomycete, strain Gsoil 519T, was isolated from soil of a ginseng field of Pocheon province in South Korea. The closest phylogenetic relatives were Streptomyces marinus Sp080513GE-26T (97.94 % 16S rRNA gene sequence similarity), Streptomyces albiaxialis NRRL B-24327T (97.84 %), Streptomyces albus subsp. albus DSM 40313T (97.84 %), Streptomyces almquistii NBRC 13015T (97.81 %), Streptomyces gibsonii NBRC 15415T (97.81 %), Streptomyces rangoonensis NBRC 13078T (97.81 %), Streptomyces sodiiphilus YIM 80305T (97.77 %) and Streptomyces flocculus NBRC 13041T (97.67 %). The G+C content of the genomic DNA was 71.8 mol%. The chemotaxonomic data [MK-9(H6) and MK-9(H8) as the major menaquinones; ll-diaminopimelic acid as a component of the cell-wall peptidoglycan; ribose, xylose, mannose and glucose as the major cell-wall sugars; and anteiso-C15:0, iso-C15:0, iso-C17:0, anteiso-C17:0 and C16:0 as the major fatty acids] supported the affiliation of strain Gsoil 519T to the genus Streptomyces. The physiological and biochemical characteristics and the low level of DNA-DNA relatedness differentiated the isolate genotypically and phenotypically from recognized members of the genus Streptomyces. The isolate, therefore, represents a novel species, for which the name Streptomyces panacagri sp. nov. is proposed, with Gsoil 519T (=KCTC 19139T=DSM 41871T) as the type strain.

Kribbella ginsengisoli sp. nov., isolated from soil of a ginseng field

A Gram-positive, non-spore-forming, aerobic bacterium, designated Gsoil 001(T), was isolated from the soil of a ginseng field in Pocheon province, South Korea. On the basis of 16S rRNA gene sequence analysis, strain Gsoil 001(T) was shown to belong to the genus Kribbella. The closest phylogenetic relatives were Kribbella koreensis LM 161(T) (99.0 % 16S rRNA gene sequence similarity), Kribbella flavida KACC 20248(T) (98.8 %) and Kribbella alba (98.8%). Lower similarity (98.4-96.9 %) was found with the other recognized species of the genus Kribbella. The major quinone was MK-9(H(4)), the major fatty acids were anteiso-C(15 : 0) and iso-C(16 : 0) and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol and phosphatidylinositol. The cell-wall peptidoglycan contained ll-2,6-diaminopimelic acid. These chemotaxonomic data and the high genomic DNA G+C content (66.3 mol%) supported the affiliation of strain Gsoil 001(T) to the genus Kribbella. The results of physiological and biochemical tests differentiated strain Gsoil 001(T) genotypically and phenotypically from the Kribbella species with validly published names. Therefore, this isolate represents a novel species, for which the name Kribbella ginsengisoli sp. nov. is proposed, with the type strain Gsoil 001(T) (=KCTC 19134(T) =DSM 17941(T)).