Baekduia soli gen. nov., sp. nov., a novel bacterium isolated from the soil of Baekdu Mountain and proposal of a novel family name, Baekduiaceae fam. nov.

A taxonomic study was conducted on BR7-21T, a bacterial strain isolated from the soil of a ginseng field in Baekdu Mountain. Comparative studies of the 16S rRNA gene sequence showed that the isolate was most closely related to Conexibacter woesei DSM 14684T, Solirubrobacter pauli ATCC BAA-492T, Patulibacter minatonensis JCM 12834T, with 93.8%, 92.4%, and 91.5% sequence similarity, respectively; each genus represented a family in the order Solirubrobacterales. Strain BR7-21T was Gram-reaction positive, non-spore forming, aerobic, non-motile, and short rod-shaped. It grew well on half-strength R2A medium. The G + C content of the genomic DNA was 73.9%. It contained meso-diaminopimelic acid in the cell wall and the major menaquinones were MK-7(H4) and MK-8(H4). The major fatty acids were summarized as (C16:1ω7c/iso-C15:0 2-OH), iso-C16:0, and C17:0 cyclo. On the basis of polyphasic evidence, it was proposed that strain BR7-21T should be placed in a new genus and species, for which the name Baekduia soli gen. nov., sp. nov. was proposed with the type strain BR7-21T (= KCTC 22257T = LMG 24797T). The family Baekduiaceae fam. nov. is proposed to encompass the genus Baekduia gen. nov.

Gram-Scale Production of Ginsenoside F1 Using a Recombinant Bacterial ß-Glucosidase.

Naturally occurring ginsenoside F1 (20-O-ß-D-glucopyranosyl-20(S)-protopanaxatriol) is rare. Here, we produced gram-scale quantities of ginsenoside F1 from a crude protopanaxatriol saponin mixture comprised mainly of Re and Rg1 through enzyme-mediated biotransformation using recombinant ß-glucosidase (BgpA) cloned from a soil bacterium, Terrabacter ginsenosidimutans Gsoil 3082T. In a systematic step-by-step process, the concentrations of substrate, enzyme, and NaCl were determined for maximal production of F1. At an optimized NaCl concentration of 200 mM, the protopanaxatriol saponin mixture (25 mg/ml) was incubated with recombinant BgpA (20 mg/ml) for 3 days in a 2.4 L reaction. Following octadecylsilyl silica gel column chromatography, 9.6 g of F1 was obtained from 60 g of substrate mixture at 95% purity, as assessed by chromatography. These results represent the first report of gramscale F1 production via recombinant enzyme-mediated biotransformation.

[Corynebacterium aquaticum infection: one case report and literature review].

OBJECTIVE: To study the diagnosis and treatment of Corynebacterium aquaticum infection. METHODS: A retrospective analysis of one case of Corynebacterium aquaticum infection and literature review were conducted. RESULTS: A 39-year old male patient was admitted because of cough, sputum production, fever and right chest pain for 10 days. Broad-spectrum antibiotic therapy had been given in another hospital, but the patient's condition had deteriorated.Nuclear magnetic resonance-guided percutancous transthoracic needle aspiration and lung tissue, pleural fluid and blood culture were performed after admission to our hospital. Corynebacterium aquaticum was grown from the lung tissue, the blood and the pleural effusion. Therefore the diagnosis of Corynebacterium aquaticum pneumonia complicated with pyothorax and septicemia was confirmed. After draining of pleural pus and intravenous vancomycin therapy, the patient recovered and was discharged from hospital. After literature search, we did not find reports on Corynebacterium aquaticum pneumonia complicated with pyothorax and septicemia. CONCLUSIONS: Corynebacterium aquaticum pneumonia complicated with pyothorax and septicemia is rare. The diagnosis could be confirmed by bacterial culture of lung tissue, pleural fluid and blood. Thoracic cavity draining and intravenous vancomycin are effective therapies for the disease.

Sphingomonas ginsengisoli sp. nov. and Sphingomonas sediminicola sp. nov.

Two novel bacteria, designated strains Gsoil 634(T) and Dae 20(T), were isolated in South Korea from soil of a ginseng field and freshwater sediment, respectively and were characterized by a polyphasic approach to clarify their taxonomic positions. Phylogenetic analysis based on 16S rRNA gene sequences indicated that, although they probably represented two distinct species (indicated by a sequence similarity of 96.6 %), both strain Gsoil 634(T) and strain Dae 20(T) belonged to the genus Sphingomonas and were most closely related to 'Sphingomonas humi' PB323 (97.8 % and 96.7 % sequence similarity, respectively), Sphingomonas kaistensis PB56(T) (96.8 % and 96.7 %), Sphingomonas astaxanthinifaciens TDMA-17(T) (96.6 % and 95.4 %) and Sphingomonas jaspsi TDMA-16(T) (95.6 % and 95.8 %). For both novel strains, the major ubiquinone was Q-10, the major polyamine was homospermidine, the major cellular fatty acids included summed feature 7 (C(18 : 1)ω7c, C(18 : 1)ω9t and/or C(18 : 1)ω12t), C(17 : 1)ω6c and C(16 : 0), and the polar lipids included sphingoglycolipid. These chemotaxonomic data supported the affiliation of both strains to the genus Sphingomonas. However, the DNA-DNA relatedness value between strain Gsoil 634(T) and 'Sphingomonas humi' PB323(T) was 31 %. Moreover, the results of physiological and biochemical tests allowed the phenotypic differentiation of strains Gsoil 634(T) and Dae 20(T) from established members of the genus Sphingomonas. Based on these data, the two isolates represent two novel species in the genus Sphingomonas, for which the names Sphingomonas ginsengisoli sp. nov. (type strain Gsoil 634(T) = KCTC 12630(T) = DSM 18094(T) = LMG 23739(T)) and Sphingomonas sediminicola sp. nov. (type strain Dae 20(T)  = KCTC 12629(T) = DSM 18106(T) = LMG 23592(T)) are proposed.

Ramlibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity.

A novel beta-proteobacterium, designated BXN5-27(T), was isolated from soil of a ginseng field of Baekdu Mountain in China, and was characterized using a polyphasic approach. The strain was Gram-staining-negative, aerobic, motile, non-spore-forming, and rod shaped. Strain BXN5-27(T) exhibited beta-glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to compound Rd. Phylogenetic analysis based on 16S rRNA gene sequences showed that this strain belonged to the family Comamonadaceae; it was most closely related to Ramlibacter henchirensis TMB834(T) and Ramlibacter tataouinensis TTB310(T) (96.4% and 96.3% similarity, respectively). The G+C content of the genomic DNA was 68.1%. The major menaquinone was Q-8. The major fatty acids were C16:0, summed feature 4 (comprising C16:1 omega7c and/or iso-C15:0 2OH), and C17:0 cyclo. Genomic and chemotaxonomic data supported the affiliation of strain BXN5-27(T) to the genus Ramlibacter. However, physiological and biochemical tests differentiated it phenotypically from the other established species of Ramlibacter. Therefore, the isolate represents a novel species, for which the name Ramlibacter ginsenosidimutans sp. nov. is proposed, with the type strain being BXN5-27(T) (= DSM 23480(T) = LMG 24525(T) = KCTC 22276(T)).

Kinetics of a cloned special ginsenosidase hydrolyzing 3-O-glucoside of multi-protopanaxadiol-type ginsenosides, named ginsenosidase type III.

In this paper, the kinetics of a cloned special glucosidase, named ginsenosidase type III hydrolyzing 3-O-glucoside of multi-protopanaxadiol (PPD)-type ginsenosides, were investigated. The gene (bgpA) encoding this enzyme was cloned from a Terrabacter ginsenosidimutans strain and then expressed in E. coli cells. Ginsenosidase type III was able to hydrolyze 3-O-glucoside of multi-PPD-type ginsenosides. For instance, it was able to hydrolyze the 3-O-ß-D-(1-->2)-glucopyranosyl of Rb1 to gypenoside XVII, and then to further hydrolyze the 3-O-ß-D-glucopyranosyl of gypenoside XVII to gypenoside LXXV. Similarly, the enzyme could hydrolyze the glucopyranosyls linked to the 3-O- position of Rb2, Rc, Rd, Rb3, and Rg3. With a larger enzyme reaction Km value, there was a slower enzyme reaction speed; and the larger the enzyme reaction Vmax value, the faster the enzyme reaction speed was. The Km values from small to large were 3.85 mM for Rc, 4.08 mM for Rb1, 8.85 mM for Rb3, 9.09 mM for Rb2, 9.70 mM for Rg3(S), 11.4 mM for Rd and 12.9 mM for F2; and Vmax value from large to small was 23.2 mM/h for Rc, 16.6 mM/h for Rb1, 14.6 mM/h for Rb3, 14.3 mM/h for Rb2, 1.81mM/h for Rg3(S), 1.40 mM/h for Rd, and 0.41 mM/h for F2. According to the Vmax and Km values of the ginsenosidase type III, the hydrolysis speed of these substrates by the enzyme was Rc>Rb1>Rb3>Rb2>Rg3(S)>Rd>F2 in order.

Characterization of a novel ginsenoside-hydrolyzing α-L-arabinofuranosidase, AbfA, from Rhodanobacter ginsenosidimutans Gsoil 3054T.

The gene encoding an α-L-arabinofuranosidase that could biotransform ginsenoside Rc {3-O-[ß-D-glucopyranosyl-(1-2)-ß-D-glucopyranosyl]-20-O-[α-L-arabinofuranosyl-(1-6)-ß-D-glucopyranosyl]-20(S)-protopanaxadiol} to ginsenoside Rd {3-O-[ß-D-glucopyranosyl-(1-2)-ß-D-glucopyranosyl]-20-O-ß-D-glucopyranosyl-20(S)-protopanaxadiol} was cloned from a soil bacterium, Rhodanobacter ginsenosidimutans strain Gsoil 3054(T), and the recombinant enzyme was characterized. The enzyme (AbfA) hydrolyzed the arabinofuranosyl moiety from ginsenoside Rc and was classified as a family 51 glycoside hydrolase based on amino acid sequence analysis. Recombinant AbfA expressed in Escherichia coli hydrolyzed non-reducing arabinofuranoside moieties with apparent K (m) values of 0.53 ± 0.07 and 0.30 ± 0.07 mM and V (max) values of 27.1 ± 1.7 and 49.6 ± 4.1 µmol min(-1) mg(-1) of protein for p-nitrophenyl-α-L-arabinofuranoside and ginsenoside Rc, respectively. The enzyme exhibited preferential substrate specificity of the exo-type mode of action towards polyarabinosides or oligoarabinosides. AbfA demonstrated substrate-specific activity for the bioconversion of ginsenosides, as it hydrolyzed only arabinofuranoside moieties from ginsenoside Rc and its derivatives, and not other sugar groups. These results are the first report of a glycoside hydrolase family 51 α-L-arabinofuranosidase that can transform ginsenoside Rc to Rd.

Bioconversion of ginsenosides Rb(1), Rb(2), Rc and Rd by novel ß-glucosidase hydrolyzing outer 3-O glycoside from Sphingomonas sp. 2F2: cloning, expression, and enzyme characterization.

A new ß-glucosidase gene (bglSp) was cloned from the ginsenoside converting Sphingomonas sp. strain 2F2 isolated from the ginseng cultivating filed. The bglSp consisted of 1344 bp (447 amino acid residues) with a predicted molecular mass of 49,399 Da. A BLAST search using the bglSp sequence revealed significant homology to that of glycoside hydrolase superfamily 1. This enzyme was overexpressed in Escherichia coli BL21 (DE3) using a pET21-MBP (TEV) vector system. Overexpressed recombinant enzymes which could convert the ginsenosides Rb(1), Rb(2), Rc and Rd to the more pharmacological active rare ginsenosides gypenoside XVII, ginsenoside C-O, ginsenoside C-Mc(1) and ginsenoside F(2), respectively, were purified by two steps with Amylose-affinity and DEAE-Cellulose chromatography and characterized. The kinetic parameters for ß-glucosidase showed the apparent K(m) and V(max) values of 2.9±0.3 mM and 515.4±38.3 µmol min(-1)mg of protein(-1) against p-nitrophenyl-ß-d-glucopyranoside. The enzyme could hydrolyze the outer C3 glucose moieties of ginsenosides Rb(1), Rb(2), Rc and Rd into the rare ginsenosides Gyp XVII, C-O, C-Mc(1) and F(2) quickly at optimal conditions of pH 5.0 and 37°C. A little ginsenoside F(2) production from ginsenosides Gyp XVII, C-O, and C-Mc(1) was observed for the lengthy enzyme reaction caused by the side ability of the enzyme.

Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.

A novel gammaproteobacterium, designated LnR5-47(T), was isolated from soil of a ginseng field in Liaoning province, China. The isolate was a Gram-negative, aerobic, non-motile, non-spore-forming rod. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain LnR5-47(T) belonged to the genus Rhodanobacter. The isolate was most closely related to Rhodanobacter ginsengisoli GR17-7(T), Rhodanobacter terrae GP18-1(T), Dyella ginsengisoli Gsoil 3046(T), Rhodanobacter soli DCY45(T), Dyella soli JS12-10(T) and Dyella japonica IAM 15069(T) (98.0, 97.9, 97.7, 97.3, 97.2 and 97.1% 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data (Q-8 as the predominant ubiquinone, and iso-C(16:0), iso-C(17:1)ω9c and iso-C(15:0) as the major fatty acids) also supported the affiliation of strain LnR5-47(T) with the genus Rhodanobacter. However, DNA-DNA relatedness between strain LnR5-47(T) and its closest phylogenetic neighbours was <25.8%. Moreover, physiological and biochemical tests phenotypically differentiated the isolate from other members of the genus Rhodanobacter. Therefore, strain LnR5-47(T) represents a novel species, for which the name Rhodanobacter panaciterrae sp. nov. is proposed; the type strain is LnR5-47(T) (=KACC 12826(T)=KCTC 22232(T)=LMG 24460(T)).

Solirubrobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field.

A Gram-reaction-positive, non-motile, non-spore-forming, aerobic rod, designated BXN5-15(T), was isolated from the soil of a ginseng field on Baekdu Mountain in China. Strain BXN5-15(T) grew optimally at 30 °C and pH 6.0-7.0 in the absence of NaCl on R2A agar. Strain BXN5-15(T) displayed ß-glucosidase activity, which allowed it to transform ginsenoside Rb(1) (one of the dominant active components of ginseng) via Rd to minor ginsenoside F(2). On the basis of 16S rRNA gene sequence analysis, strain BXN5-15(T) was shown to belong to the genus Solirubrobacter. The closest phylogenetic relatives were Solirubrobacter soli Gsoil 355(T) (98.4 % 16S rRNA gene sequence similarity) and Solirubrobacter pauli B33D1(T) (96.4 %). Lower sequence similarities (<96.0 %) were found with all of the other recognized members of the order Solirubrobacterales. The predominant quinone was MK-7(H(4)). The major fatty acids (>10 %) were C(18 : 1)ω9c, iso-C(16 : 0) and C(18 : 3)ω6,9,12c. The G+C content of the genomic DNA was 70.6 mol%. DNA-DNA relatedness between strain BXN5-15(T) and S. soli KCTC 12628(T) was 23.3 %. On the basis of genotypic, phenotypic and chemotaxonomic data, strain BXN5-15(T) represents a novel species within the genus Solirubrobacter, for which the name Solirubrobacter ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-15(T) ( = KACC 20671(T) = LMG 24459(T)).

Phycicoccus ginsenosidimutans sp. nov., isolated from soil of a ginseng field.

A Gram-positive, non-motile, non-spore-forming, aerobic, coccoid-shaped bacterium, designated BXN5-13(T), was isolated from the soil of a ginseng field from Baekdu Mountain in Jilin district, China. Strain BXN5-13(T) grew optimally at 30 °C and pH 6.5-7.5 with 0-2  % (w/v) NaCl. Strain BXN5-13(T) had ß-glucosidase activity that was connected with ginsenoside-converting ability, so that it was able to convert ginsenoside Rb(1) to ginsenoside F2. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic relatives of strain BXN5-13(T) were Phycicoccus aerophilus 5516T-20(T) (98.4  % 16S rRNA gene sequence similarity), P. bigeumensis MSL-03(T) (98.3  %), P. dokdonensis DS-8(T) (97.9  %) and P. jejuensis KSW2-15(T) (96.9  %). Lower sequence similarity (<97.0  %) was found with the type strains of other recognized species of the family Intrasporangiaceae. The predominant quinone was MK-8(H4). The major fatty acids (>10  %) were iso-C15:0, C17:0, anteiso-C15:0 and iso-C16:0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The chemotaxonomic data and the high genomic DNA G+C content of strain BXN5-13(T) (70.8l %) supported its affiliation with the genus Phycicoccus. DNA-DNA relatedness between strain BXN5-13(T) and its closest phylogenetic neighbours was below 16  %. Strain BXN5-13(T) represents a novel species within the genus Phycicoccus, for which the name Phycicoccus ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-13(T) (=KCTC 19419(T)=DSM 21006(T)=LMG 24462(T)).

Identification and characterization of a novel Terrabacter ginsenosidimutans sp. nov. beta-glucosidase that transforms ginsenoside Rb1 into the rare gypenosides XVII and LXXV.

A new beta-glucosidase from a novel strain of Terrabacter ginsenosidimutans (Gsoil 3082(T)) obtained from the soil of a ginseng farm was characterized, and the gene, bgpA (1,947 bp), was cloned in Escherichia coli. The enzyme catalyzed the conversion of ginsenoside Rb1 {3-O-[beta-D-glucopyranosyl-(1-2)-beta-D-glucopyranosyl]-20-O-[beta-D-glucopyranosyl-(1-6)-beta-D-glucopyranosyl]-20(S)-protopanaxadiol} to the more pharmacologically active rare ginsenosides gypenoside XVII {3-O-beta-D-glucopyranosyl-20-O-[beta-D-glucopyranosyl-(1-6)-beta-D-glucopyranosyl]-20(S)-protopanaxadiol}, gypenoside LXXV {20-O-[beta-v-glucopyranosyl-(1-6)-beta-D-glucopyranosyl]-20(S)-protopanaxadiol}, and C-K [20-O-(beta-D-glucopyranosyl)-20(S)-protopanaxadiol]. A BLAST search of the bgpA sequence revealed significant homology to family 3 glycoside hydrolases. Expressed in E. coli, beta-glucosidase had apparent K(m) values of 4.2 +/- 0.8 and 0.14 +/- 0.05 mM and V(max) values of 100.6 +/- 17.1 and 329 +/- 31 micromol x min(-1) x mg of protein(-1) against p-nitrophenyl-beta-D-glucopyranoside and Rb1, respectively. The enzyme catalyzed the hydrolysis of the two glucose moieties attached to the C-3 position of ginsenoside Rb1, and the outer glucose attached to the C-20 position at pH 7.0 and 37 degrees C. These cleavages occurred in a defined order, with the outer glucose of C-3 cleaved first, followed by the inner glucose of C-3, and finally the outer glucose of C-20. These results indicated that BgpA selectively and sequentially converts ginsenoside Rb1 to the rare ginsenosides gypenoside XVII, gypenoside LXXV, and then C-K. Herein is the first report of the cloning and characterization of a novel ginsenoside-transforming beta-glucosidase of the glycoside hydrolase family 3.

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

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 346(T)) was isolated from the soil of a ginseng field in South Korea and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequences, strain Gsoil 346(T) was shown to belong to the genus Nocardioides in the family Nocardioidaceae, with the most closely related species being Nocardioides aquiterrae GW-9(T) (96.6 % 16S rRNA gene sequence similarity); however, the strain clustered in a distinct branch of the phylogenetic tree with Nocardioides kongjuensis A2-4(T) (96.2 %), Nocardioides aromaticivorans H-1(T) (96.1 %), Nocardioides nitrophenolicus NSP41(T) (96.1 %) and Nocardioides simplex ATCC 15799(T) (95.9 %). Strain Gsoil 346(T) was characterized chemotaxonomically and found to have ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, phosphatidylinositol and phosphatidylglycerol as the major polar lipids, MK-8(H(4)) as the predominant menaquinone and iso-C(16 : 0), C(18 : 1)omega9c and C(17 : 1)omega8c as the major fatty acids. The G+C content of the genomic DNA of the novel strain was 73.0 mol%. These chemotaxonomic properties supported the placement of strain Gsoil 346(T) in the genus Nocardioides. The results of physiological and biochemical tests, along with the phylogenetic analysis, allowed strain Gsoil 346(T) to be differentiated genotypically and phenotypically from recognized species of the genus Nocardioides. Therefore, strain Gsoil 346(T) represents a novel species, for which the name Nocardioides panacisoli sp. nov. is proposed, with Gsoil 346(T) (=KCTC 19470(T)=DSM 21348(T)) as the type strain.

Mucilaginibacter daejeonensis sp. nov., isolated from dried rice straw.

A novel strain, designated Jip 10(T), isolated from dried rice straw, was characterized by a polyphasic approach to clarify its taxonomic position. The isolate was Gram-negative, facultatively aerobic, heterotrophic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate clustered with the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities between strain Jip 10(T) and the type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis were 93.7 and 93.6 %, respectively. The G+C content of the genomic DNA was 48.1 mol%. Chemotaxonomic data [major menaquinone MK-7 and major fatty acids iso-C(15 : 0), iso-C(17 : 0) 3-OH and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c)] supported the affiliation of strain Jip 10(T) to the genus Mucilaginibacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of strain Jip 10(T) from other Mucilaginibacter species with validly published names. Therefore, strain Jip 10(T) (=KCTC 12639(T) =LMG 23488(T)) was classified in the genus Mucilaginibacter as the type strain of a novel species, for which the name Mucilaginibacter daejeonensis sp. nov. is proposed.

Rhodanobacter ginsenosidimutans sp. nov., isolated from soil of a ginseng field in South Korea.

A novel gammaproteobacterium, designated Gsoil 3054(T), was isolated from soil of a ginseng field in Pocheon province, South Korea, and was characterized using a polyphasic approach to determine its taxonomic position. The strain was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain belonged to the genus Rhodanobacter; it was most closely related to Rhodanobacter fulvus Jip2(T) and Rhodanobacter thiooxydans LCS2(T) (97.9 and 97.2 % 16S rRNA gene sequence similarity, respectively). Chemotaxonomic data, i.e. Q-8 as the predominant ubiquinone and iso-C(15 : 0), 10-methyl C(16 : 0) and iso-C(17 : 0) as major fatty acids, also supported classification of strain Gsoil 3054(T) in the genus Rhodanobacter. However, DNA-DNA hybridization values of Gsoil 3054(T) with R. fulvus Jip2(T) and R. thiooxydans LCS2(T) were 45 and 31 %, respectively. Moreover, physiological and biochemical tests enabled strain Gsoil 3054(T) to be differentiated phenotypically from other established species of Rhodanobacter. Therefore, the isolate represents a novel species, for which the name Rhodanobacter ginsenosidimutans sp. nov. is proposed; the type strain is Gsoil 3054(T) (=KACC 12822(T) =DSM 21013(T) =KCTC 22231(T) =LMG 24457(T)).

Dyella ginsengisoli sp. nov., isolated from soil of a ginseng field in South Korea.

A Gram-negative, aerobic, yellow-pigmented, non-spore-forming, motile, rod-shaped bacterium, designated strain Gsoil 3046(T), was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized taxonomically by using a polyphasic approach. A comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 3046(T) belongs to the family Xanthomonadaceae in the Gammaproteobacteria. The greatest sequence similarity was found with respect to Dyella koreensis KCTC 12359(T) (97.7 %), Dyella japonica IAM 15069(T) (97.4 %), Frateuria aurantia DSM 6220(T) (96.7 %), Fulvimonas soli LMG 19981(T) (96.2 %) and Luteibacter rhizovicinus DSM 16549(T) (96.0 %). The phylogenetic distances from other recognized species within the family Xanthomonadaceae, including Dyella yeojuensis KACC 11405(T), were greater than 4.0 % (i.e. the sequence similarities were less than 96.0 %). DNA-DNA hybridization experiments showed that the levels of DNA-DNA relatedness between strain Gsoil 3046(T) and its phylogenetically closest neighbours were below 25 %. The G+C content of the genomic DNA was 66.6 mol%. In addition, the presence of ubiquinone Q-8 as the predominant respiratory quinone, iso-C(17 : 1)omega9c, iso-C(16 : 0), iso-C(15 : 0) and iso-C(17 : 0) as the major cellular fatty acids and iso-C(13 : 0) 3-OH and iso-C(11 : 0) 3-OH as the major hydroxy fatty acids supported the affiliation of strain Gsoil 3046(T) to the genus Dyella. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 3046(T) represents a novel species in the genus Dyella, for which the name Dyella ginsengisoli sp. nov. is proposed. The type strain is Gsoil 3046(T) (=KCTC 12599(T)=DSM 18387(T)).

Pedobacter daechungensis sp. nov., from freshwater lake sediment in South Korea.

A novel bacterial strain, designated Dae 13T, was isolated from sediment from a freshwater lake in Daejeon, South Korea, and was characterized taxonomically by using a polyphasic approach. The isolate was Gram-negative, aerobic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Pedobacter in the family Sphingobacteriaceae but was clearly separate from established species of this genus. The 16S rRNA gene sequence similarities between strain Dae 13(T) and type strains of Pedobacter species with validly published names ranged from 91.6 to 97.5 %. The G+C content of the genomic DNA was 33.8 mol%. Chemotaxonomic data, i.e. the presence of MK-7 as the major menaquinone and iso-C(15 : 0), C(16 : 0) and summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)omega7c) as the major fatty acids, supported the affiliation of strain Dae 13T to the genus Pedobacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolate with respect to Pedobacter species with validly published names. Therefore, strain Dae 13T represents a novel species within the genus Pedobacter, for which the name Pedobacter daechungensis sp. nov. is proposed. The type strain is Dae 13T (=KCTC 12637T=LMG 23489T).

Microlunatus panaciterrae sp. nov., a beta-glucosidase-producing bacterium isolated from soil in a ginseng field.

A novel bacterial strain, designated Gsoil 954(T), showing beta-glucosidase activity was isolated from a soil sample from a ginseng field in Pocheon Province, South Korea. The isolate was a Gram-positive, aerobic, motile, coccus-shaped, non-endospore-forming bacterium. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 954(T) belonged to the family Propionibacteriaceae, the highest levels of sequence similarity being found with the type strains of Microlunatus ginsengisoli (96.4 %) and Microlunatus phosphovorus (96.2 %). The strain showed <95.9 % similarity with respect to other species within the family Propionibacteriaceae. In addition, the presence of ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-9(H(4)) as the major menaquinone and anteiso-C(15 : 0) and iso-C(15 : 0) as the major cellular fatty acids suggested its affiliation with the genus Microlunatus. The G+C content of the genomic DNA was 65.1 mol%. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 954(T) represents a novel species within the genus Microlunatus, for which the name Microlunatus panaciterrae sp. nov. is proposed. The type strain is Gsoil 954(T) (=KCTC 13058(T)=DSM 18662(T)).

Chitinophaga soli sp. nov. and Chitinophaga terrae sp. nov., isolated from soil of a ginseng field in Pocheon Province, Korea.

Two novel strains of the Cytophaga-Flexibacter-Bacteroides (CFB) group, designated Gsoil 219" and Gsoil 2381, were isolated from soil of a ginseng field of Pocheon Province in Korea. Both strains were Gram-negative, aerobic, nonmotile, nonspore-forming, and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that both isolates belong to the genus Chitinophaga but were clearly separated from established species of this genus. The sequence similarities between strain Gsoil 219T and type strains of the established species and between strain Gsoil 238T and type strains of the established species ranged from 91.4 to 94.7% and 91.6 to 94.2%, respectively. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15:0 and C(16:1) omega5c; major hydroxy fatty acid, iso-C(17:0) 3-OH; major polyamine, homospermidine) supported the affiliation of both strains Gsoil 219T and Gsoil 238T to the genus Chitinophaga. Furthermore, the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of both strains from the other validated Chitinophaga species. Therefore, the two isolates represent two novel species, for which the name Chitinophaga soli sp. nov. (type strain, Gsoil 219T=KCTC 12650T=DSM 18093T) and Chitinophaga terrae sp. nov. (type strain, Gsoil 238T=KCTC 12651T=DSM 18078T) are proposed.

Kaistia granuli sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor.

A Gram-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (designated strain Ko04(T)) was isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor, and was investigated using a polyphasic taxonomic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Ko04(T) belongs to the order Rhizobiales in the Alphaproteobacteria. Comparative 16S rRNA gene sequence analysis showed that strain Ko04(T) was most closely related to Kaistia adipata (97.5 %) and that sequence similarities with other species of Rhizobiales with validly published names were less than 92.5 %. The predominant ubiquinone was Q-10 and the major fatty acids were C(18 : 1)omega7c/omega9t/omega12t, C(19 : 0 )cyclo omega8c and C(18 : 0). The G+C content of the genomic DNA of strain Ko04(T) was 67.8 mol%. The level of DNA-DNA relatedness with K. adipata Chj404(T) was 15 %. The results of the genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Ko04(T) represents a novel species within the genus Kaistia, for which the name Kaistia granuli sp. nov. is proposed. The type strain is Ko04(T) (=KCTC 12575(T)=LMG 23410(T)).