Sung-Geun Woo

Stenotrophomonas daejeonensis sp. nov., isolated from sewage.

A Gram-stain-negative, motile, aerobic bacterial strain, designated MJ03(T), was isolated from sewage and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ03(T) belongs to the family Xanthomonadaceae, class Gammaproteobacteria, and was related most closely to Stenotrophomonas acidaminiphila AMX 19(T) (97.9  % sequence similarity), Stenotrophomonas humi R-32729(T) (97.1  %), Stenotrophomonas nitritireducens L2(T) (96.9  %), Stenotrophomonas maltophila ATCC 13637(T) (96.8  %) and Stenotrophomonas terrae R-32768(T) (96.7  %). The G+C content of the genomic DNA of strain MJ03(T) was 64.7 mol%. The detection of a quinone system with ubiquinone Q-8 as the predominant component and a fatty acid profile with iso-C₁₅:₀, iso-C₁₁:₀, iso-C₁₄:₀, iso-C₁₇:₁ω9c, iso-C₁₁:₀ 3-OH and iso-C₁₃:₀ 3-OH as major components supported the affiliation of strain MJ03(T) to the genus Stenotrophomonas. However, levels of DNA-DNA relatedness between strain MJ03(T) and the type strains of five closely related species of the genus Stenotrophomonas ranged from 11 to 34  %, showing clearly that the isolate represents a novel genospecies. Strain MJ03(T) could be differentiated clearly from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ03(T) is considered to represent a novel species of the genus Stenotrophomonas, for which the name Stenotrophomonas daejeonensis sp. nov. is proposed. The type strain is MJ03(T) (=KCTC 22451(T) =JCM 16244(T)).

Comparison of fatty acid analysis methods for assessing biorefinery applicability of wastewater cultivated microalgae

In this study, we compared the performances of four different gas chromatography (GC) based microalgal fatty acid analysis methods that are typically applied to biorefinery research using wastewater-adapted microalgae. Compared with the HP-5-type non-polar column, WAX-type polar columns exhibited excellent abilities to quantitatively separate C(16)-C(18) polyunsaturated fatty acids (PUFAs) from selected wastewater-adapted microalgae (Chlorella vulgaris, Ankistrodesmus gracilis and Scenedesmus quadricauda) isolates. GC-mass spectroscopy (MS) using the WAX-type polar column provided the strongest detection sensitivity among the tested methods by lowest detection limit, and GC-flame ionized detector (FID) with the same polar column exhibited nearly consistent results to GC-MS analysis. Our statistical comparison of microalgal fatty acid composition profiles generated using various GC methods, microalgal resources and culture media (wastewater, BG11 and nitrogen limitation) suggested that an appropriate GC method and algal resource choice are more important than the optimization of culture conditions to evaluate the applicability of microalgal biorefinery using wastewater resources.

Dyadobacter soli sp. nov., a starch-degrading bacterium isolated from farm soil

A Gram-negative, non-motile, aerobic bacterial strain, designated MJ20(T), was isolated from farm soil near Daejeon (South Korea) and was characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ20(T) belongs to the family Cytophagaceae, class Sphingobacteria, and was related most closely to Dyadobacter fermentans DSM 18053(T) (98.9 % sequence similarity), Dyadobacter beijingensis JCM 14200(T) (98.0 %) and Dyadobacter ginsengisoli KCTC 12589(T) (96.4 %). The G+C content of the genomic DNA of strain MJ20(T) was 48.5 mol%. The detection of MK-7 as the predominant menaquinone and a fatty acid profile with summed feature 4 (C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH), iso-C(15 : 0), C(16 : 0) and C(16 : 1)ω5c as major components supported the affiliation of strain MJ20(T) to the genus Dyadobacter. The new isolate exhibited relatively low levels of DNA-DNA relatedness with respect to D. fermentans DSM 18053(T) (mean±SD of three determinations, 47±7 %) and D. beijingensis JCM 14200(T) (38±8 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ20(T) (=KCTC 22481(T) =JCM 16232(T)) should be classified in the genus Dyadobacter as the type strain of a novel species, for which the name Dyadobacter soli sp. nov. is proposed.

Rhodanobacter caeni sp. nov., isolated from sludge from a sewage disposal plant

Two Gram-reaction-negative, motile bacteria, designated strains MJ01(T) and MJ14, were isolated from sludge collected from the Daejeon sewage disposal plant in South Korea. The taxonomic positions of both strains were determined using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strains MJ01(T) and MJ14 appeared indistinguishable and to be most closely related to members of the genus Rhodanobacter in the family Xanthomonadaceae of the Gammaproteobacteria (96.4-98.8% sequence similarity). Strain MJ01(T) exhibited a relatively high level of DNA-DNA relatedness with strain MJ14 (89.3 %) but relatively low DNA-DNA relatedness values with established species in the genus Rhodanobacter (<60 %). The genomic DNA G+C contents of strains MJ01(T) and MJ14 were 65.3 and 64.8 mol%, respectively. The major respiratory quinone of both novel strains was the ubiquinone Q-8. The major fatty acids of both strains were iso-C(15 : 0), iso-C(16 : 0), iso-C(17:0) and iso-C(17 : 1)ω9c, and the polar lipid profiles of the two strains contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and minor amounts of unidentified aminophospholipids and phospholipids. Based on the phenotypic, genotypic and phylogenetic evidence, strains MJ01(T) and MJ14 represent a single novel species in the genus Rhodanobacter, for which the name Rhodanobacter caeni sp. nov. is proposed. The type strain is MJ01(T) ( = KCTC 22449(T) = JCM 16242(T)), with MJ14 ( = KCTC 22460 = JCM 16243) as a reference strain.

Pusillimonas soli sp. nov., isolated from farm soil

A Gram-negative, motile, non-spore-forming bacterial strain, designated MJ07(T), was isolated from a farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ07(T) belongs to the family Alcaligenaceae, class Betaproteobacteria, and is related most closely to Pusillimonas ginsengisoli KCTC 22046(T) (98.6 % sequence similarity) and Pusillimonas noertemannii BN9(T) (96.9 %). The levels of 16S rRNA gene sequence similarity between strain MJ07(T) and members of all other recognized species of the family Alcaligenaceae were below 95.2 %. The G+C content of the genomic DNA of strain MJ07(T) was 59.4 mol%. The detection of a quinone system with ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine, phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unknown aminolipids as major polar lipids and a fatty acid profile with C₁₆:₀ (32.0 %), C₁₇:₀cyclo (24.7 %) and C₁₉:₀cyclo ω8c (11.5 %) as the major components supported the affiliation of strain MJ07(T) to the genus Pusillimonas. Strain MJ07(T) exhibited relatively low levels of DNA-DNA relatedness with respect to P. ginsengisoli KCTC 22046(T) (50 ± 8 %) and P. noertemannii KACC 13183(T) (18 ± 7 %). On the basis of its phenotypic and genotypic properties together with its phylogenetic distinctiveness, strain MJ07(T) (=KCTC 22455(T) =JCM 16386(T)) should be classified in the genus Pusillimonas as the type strain of a novel species, for which the name Pusillimonas soli sp. nov. is proposed.

Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant.

Strain MJ31(T), a gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31(T) belonged to the genus Nocardioides, appearing most closely related to Nocardioides dubius KSL-104(T) (98.6 % sequence similarity), Nocardioides jensenii DSM 20641(T) (97.6 %), Nocardioides daedukensis MDN22(T) (97.2 %) and Nocardioides mesophilus MSL-22(T) (97.0 %). The chemotaxonomic properties of strain MJ31(T) were consistent with those of the genus Nocardioides: MK-8(H(4)) was the predominant menaquinone, iso-C(16 : 0), iso-C(17 : 0) and C(18 : 1)ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on LL-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31(T) was 71.2 mol%. Some differential phenotypic properties and low DNA-DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31(T) represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31(T) ( = KCTC 19772(T) = JCM 16922(T)).

Luteolibacter yonseiensis sp. nov., isolated from activated sludge using algal metabolites.

A Gram-negative, rod-shaped, aerobic bacterial strain, designated EBTL01(T), was isolated from activated sludge by using metabolites of microalgae Ankistrodesmus gracilis SAG278-2. Phylogenetic analyses based on 16S rRNA gene sequence showed that strain EBTL01(T) belongs to the family Verrucomicrobiaceae, class Verrucomicrobiae, and is related most closely to Luteolibacter pohnpeiensis A4T-83(T) (95.5 % sequence similarity) and Luteolibacter algae A5J-41-2(T) (95.2 %). The G+C content of the genomic DNA of strain EBTL01(T) was 56.3 mol% and the menaquinone MK-9 was detected as the predominant quinone. Major fatty acid components were iso-C14 : 0, C16 : 1ω7c and C16 : 0. The amino acids of the cell-wall peptidoglycan contained muramic acid and meso-diaminopimelic acid. These profile results supported the affiliation of strain EBTL01(T) to the genus Luteolibacter. On the other hand, based on chemotaxonomic properties and phenotypic characteristics, strain EBTL01(T) could be clearly differentiated from its phylogenetic neighbours. Therefore, strain EBTL01(T) represents a novel species of the genus Luteolibacter, for which the name Luteolibacter yonseiensis sp. nov. is proposed. The type strain is EBTL01(T) ( = KCTC 23678(T) = JCM 18052(T)).

Agromyces soli sp. nov., isolated from farm soil

A Gram-positive, aerobic to microaerophilic, non-motile bacterial strain, designated MJ21(T), was isolated from farm soil and was characterized to determine its taxonomic position by using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain MJ21(T) was placed within the genus Agromyces, and exhibited relatively high levels of similarity to Agromyces ulmi XIL01(T) (97.8 %), Agromyces aurantiacus YIM 21741(T) (97.1 %), Agromyces mediolanus JCM 3346(T) (96.7 %), A. mediolanus JCM 1376 (99.1 %), A. mediolanus JCM 9632 (99.1 %), A. mediolanus JCM 9633 (98.9 %) and A. mediolanus JCM 9631 (96.5 %). Chemotaxonomic data also supported the classification of strain MJ21(T) within the genus Agromyces. The new isolate contained MK-12 as the predominant menaquinone and rhamnose, galactose and xylose as cell-wall sugars. The major cellular fatty acids (>10 % of the total) were anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(16 : 0). Cell-wall amino acids were 2,4-diaminobutyric acid, glutamic acid, glycine and alanine. Diphosphatidylglycerol, phosphatidylglycerol, two unknown glycolipids and one unidentified phospholipid were detected as polar lipids. The DNA G+C content of strain MJ21(T) was 73.4 mol%. However, levels of DNA-DNA relatedness between strain MJ21(T) and the seven phylogenetically closest Agromyces strains ranged from 14 to 56 %, showing clearly that the new isolate represents a novel genomic species. Strain MJ21(T) could be differentiated clearly from its phylogenetic neighbours on the basis of phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ21(T) is considered to represent a novel species of the genus Agromyces, for which the name Agromyces soli sp. nov. is proposed. The type strain is MJ21(T) ( = KCTC 19549(T)  = JCM 16247(T)).

Shinella daejeonensis sp. nov., a nitrate-reducing bacterium isolated from sludge of a leachate treatment plant

A Gram-negative-staining, motile, rod-shaped, aerobic bacterial strain, designated MJ02(T), was isolated from sludge of a leachate treatment plant in Daejeon (South Korea) and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain MJ02(T) belonged to the family Rhizobiaceae, class Alphaproteobacteria, and was most closely related to Shinella yambaruensis MS4(T) (97.6 % sequence similarity) and Shinella fusca DC-196(T) (97.5 %). The G+C content of the genomic DNA of strain MJ02(T) was 64.3 mol%. The detection of a quinone system with ubiquinone Q-10 as the predominant respiratory lipoquinone and a fatty acid profile with C₁₈:₁ω7c (45.8 %) and C₁₆:₀ (21.8 %) as the major components supported the affiliation of strain MJ02(T) to the genus Shinella. However, strain MJ02(T) exhibited relatively low levels of DNA-DNA relatedness with respect to S. fusca DSM 21319(T) (17±7 %) and S. yambaruensis KACC 14483(T) (12±6 %), showing clearly that the isolate constituted a new genospecies. Strain MJ02(T) could be clearly differentiated from its phylogenetic neighbours on the basis of several phenotypic, genotypic and chemotaxonomic features. Therefore, strain MJ02(T) is considered to represent a novel species of the genus Shinella, for which the name Shinella daejeonensis sp. nov. is proposed. The type strain is MJ02(T) ( = KCTC 22450(T) = JCM 16236(T)).

Castellaniella daejeonensis sp. nov., isolated from soil

A Gram-negative, non-spore-forming, motile, facultatively anaerobic bacterium, designated strain MJ06(T), was isolated from oil-contaminated soil and was characterized taxonomically by using a polyphasic approach. Strain MJ06(T) contained ubiquinone Q-8 as the major respiratory lipoquinone, putrescine as the predominant polyamine and phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. The G+C content of the genomic DNA of strain MJ06(T) was 66.2 mol%. The major fatty acids were summed feature 4 (C(16 : 1)ω 7c and/or iso-C(15 : 0) 2-OH; 32.5 %), C(16 : 0) (22.8 %) and summed feature 7 (one or more of C(18 : 1)ω 7c, C(18 : 1)ω 9t and C(18 : 1)ω 12t; 14.9 %). Comparative 16S rRNA gene sequence analysis showed that strain MJ06(T) belonged to the family Alcaligenaceae, class Betaproteobacteria, and joined the evolutionary radiation enclosed by the genus Castellaniella. Levels of 16S rRNA gene sequence similarity between strain MJ06(T) and its phylogenetically closest relatives, Castellaniella denitrificans NKNTAU(T), Castellaniella defragrans 54Pin(T), Castellaniella ginsengisoli DCY36(T) and Castellaniella caeni Ho-11(T), were 98.6, 98.3, 97.8 and 97.3 %, respectively. Levels of similarity between strain MJ06(T) and the type strains of all other recognized species in the family Alcaligenaceae were below 95.0 %. Strain MJ06(T) exhibited relatively low levels of DNA-DNA relatedness with respect to C. defragrans DSM 12141(T) (52 %), C. denitrificans DSM 11046(T) (31 %), C. ginsengisoli KCTC 22398(T) (18 %) and C. caeni KCTC 12197(T) (15 %). On the basis of its phenotypic and genotypic properties together with phylogenetic distinctiveness, strain MJ06(T) is considered to represent a novel species of the genus Castellaniella, for which the name Castellaniella daejeonensis sp. nov. is proposed. The type strain is MJ06(T) (=KCTC 22454(T) =JCM 16240(T)).