Humibacter ginsenosidimutans sp. nov., with ginsenoside-converting activity isolated from activated sludge.

A novel Gram-stain-positive, thin rod-shaped, non-motile, aerobic and creamy-white pigmented bacterium (designated strain WJ7-1T) was isolated from activated sludge sampled in Suwon, Republic of Korea. 16S rRNA gene sequence analysis indicated that the isolate belongs to the genus Humibacter, family Microbacteriaceae, with a sequence similarity of 97.9 % to its nearest neighbour Humibacter albus KACC 20986T. Strain WJ7-1T contained menaquinone (MK)-10 (16.0 %), 11 (48.5 %) and 12 (35.5 %) as major respiratory quinones. The predominant cellular fatty acids (>15 %) were anteiso-C17 : 0, iso-C16 : 0 and anteiso-C15 : 0. The peptidoglycan of strain WJ7-1T contained the diagnostic diamino acid ornithine and 2,4-diaminobutyric acid alanine. Alanine, glutamic acid and glycine were also present in the cell wall. The characteristic whole-cell sugars present were glucose, galactose, xylose and rhamnose. The polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, an unidentified glycolipid and two unidentified phospholipids. Strain WJ7-1T possessed ginsenoside-converting (ß-glucosidase) activity, which enabled it to transform ginsenoside protopanaxadiol-type Rb1 (one of the dominant active components of ginseng) to compound K. The genome size of strain WJ7-1T has 4.2 Mbp and the G+C content is 68.3 mol%. Average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values between strain WJ7-1T and the closely related strain were 79.8, 36.1 and 23.5 %, respectively, indicating that strain WJ7-1T represents a novel species of the genus Humibacter. Strain WJ7-1T could be distinguished from the other members of the genus Humibacter by a number of chemotaxonomic and phenotypic characteristics. Based on polyphasic taxonomic analysis, strain WJ7-1T (=KACC 19729T=LMG 30802T) represents a novel species within the genus Humibacter, for which the name Humibacter ginsenosidimutans sp. nov. is proposed.

Paludibacterium denitrificans sp. nov., a Novel Denitrifying Bacterium Isolated from Activated Sludge.

A Gram-reaction-negative, facultatively aerobic, motile, non-spore-forming, rod-shaped, and denitrifying bacterium, designated dN18-1T, was isolated from activated sludge, Republic of Korea. This bacterium was investigated via a polyphasic approach to reveal its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain dN18-1T belongs to the genus Paludibacterium and is most closely related to P. purpuratum KCTC 42852T (96.2% sequence similarity), P. yongneupense KACC 11601T (96.1%), and P. paludis BCRC 80514T (95.2%). The average nucleotide identity values and digital DNA-DNA hybridization values calculated between strain dN18-1T and the closely related strains were 72.5-73.1% and 19.0-19.6%. The genome comprises of 3,347,996 bp with a G + C content of 57.3 mol%. Strain dN18-1T possesses ubiquinone Q-8 as a predominant respiratory quinone, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), summed feature 8 (C18:1 ω6c/C18:1 ω7c), C16:0 and C12:0, as its major fatty acids (>5%). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified aminophospholipids. The results of ANI calculation, digital DNA-DNA hybridization, physiological and biochemical tests allowed phenotypic differentiation of strain dN18-1T from rephrase other genus Paludibacterium species with validly published names. Therefore, this isolate represents a novel species, for which the name Paludibacterium denitrificans sp. nov. (type strain dN18-1T = KACC 19537T = CGMCC 1.16961T) is proposed.

Hanamia caeni gen. nov., sp. nov., a Member of the Family Chitinophagaceae Isolated from Activated Sludge in Korea.

A novel Gram-stain-negative, aerobic, yellowish-pigmented, non-motile, rod-shaped bacterial strain, designated strain BO-59T, was isolated from the activated sludge of a wastewater treatment plant in Hanam City, South Korea. Phylogenetic study based on the 16S rRNA gene sequence positioned BO-59T in a distinct lineage in the family Chitinophagaceae, sharing less than 92.8% sequence similarity with members of the closely related genera Ferruginibacter, Flavitalea, Pseudoflavitalea, Flavisolibacter, Niastella, and Terrimonas. Phylogenomic- and genomic relatedness analyses revealed that strain BO-59T is clearly distinguished from other genera in the family Chitinophagaceae by average nucleotide identity < 66.9%) and the genome-to-genome distance (< 29.5%) values. The strain BO-59T contained MK-7 as the predominant quinone, and iso-C15:0, iso-C17:0 3OH, and iso-C15:1 G as major fatty acids (> 10%). The DNA G + C content was 39.1 mol% based on genome sequence analysis. The polar lipids of strain BO-59T were phosphatidylethanolamine, an unidentified aminophospholipid and three unidentified polar lipids. 16S rRNA gene sequence similarity, physiological, and biochemical characteristics indicated that strain BO-59T represents a novel species of a new genus, for which the name Hanamia caeni gen. nov., sp. nov. is proposed. The type strain is BO-59T (= KACC 19646T = LMG 30865 T).

Ochrobactrum soli sp. nov., Isolated from a Korean Cattle Farm.

A Gram stain negative, motile, non-spore-forming, rod-shaped, strictly aerobic, beige-pigmented bacterium, designated strain BO-7T, was isolated from soil of cattle farm, in Seosan, Republic of Korea. On the basis of 16S rRNA gene sequencing, strain BO-7T clustered with species of the genus Ochrobactrum and appeared closely related to O. haematophilum CCUG 38531T (98.9%), O. daejeonense KCTC 22458T (98.1%), O. rhizosphaerae DSM 19824T (98.1%), O. pituitosum DSM 22207T (98.0%), and O. pecoris DSM 23868T (98.0%). The digital DNA-DNA hybridization and average nucleotide identity between strain BO-7T and the closely related strains were 21.9-39.1%, 78.5-89.5%, respectively, indicating that BO-7T is a novel species of the genus Ochrobactrum. The DNA G + C content of the genomic DNA was 57.1 mol%, and ubiquinone Q-10 was the predominant respiratory quinone. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethyl-ethanolamine, di-phosphatidylglycerol, the major polyamines were spermidine, putrescine, and sym-homospermidine. The major cellular fatty acids (> 5%) were C16:0, C19:0 cycle ω7c, and C18:1ω7c and/or C18:1ω6c (summed feature 8). ANI calculation, digital DNA-DNA hybridization, physiological and biochemical characteristics indicated that strain BO-7T represents a novel species of the genus Ochrobactrum, for which the name Ochrobactrum soli sp. nov. is proposed. The type strain is BO-7T (= KACC 19676T = LMG 30809T).

Hydrogenophaga borbori sp. nov., isolated from activated sludge.

A novel Gram-stain-negative, yellowish-pigmented bacterial strain, designated LA-38T, was isolated from activated sludge of wastewater treatment plants in Hanam city, South Korea. Cell of LA-38T were rod-shaped, aerobic, motile and non-spore-forming. In phylogenetic analyses based on 16S rRNA genes, LA-38T clustered with species of the genus Hydrogenophaga and appeared closely related to Hydrogenophaga intermedia DSM 5680T (99.2 % similarity), Hydrogenophaga palleronii DSM 63T (98.2 %), Hydrogrenophaga laconesensis KCTC 42478T (98.1 %), Hydrogenophaga. atypica DSM 15342T (98.1 %), Hydrogenophaga defluvii DSM 15341T (98.0 %) and Hydrogenophaga taeniospiralis DSM 2082T (97.2 %). The average nucleotide identities between LA-38T and the closely related strains were 79.3-88.5 %, indicating that LA-38T represents a novel species of the genus Hydrogenophaga. The DNA G+C content of the genomic DNA was 69.9 mol% and ubiquinone Q-8 was the predominant respiratory quinone. The major cellular fatty acids (>5 %) were C16 : 0, cyclo-C19 : 0, C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), and C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8). The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine, the major polyamines were 2-hydroxyputrescine and putrescine. ANI calculation, physiological and biochemical characteristics indicated that LA-38T represents a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga borbori sp. nov. is proposed. The type strain is LA-38T (=KACC 19730T=LMG 30805T).

Polaromonas ginsengisoli sp. nov., isolated from ginseng field soil.

A Gram-reaction-negative, strictly aerobic, milky-white and rod-shaped bacterium (designated Gsoil 115T) isolated from ginseng field soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain Gsoil 115T grew optimally at 30 °C and at pH 7.0 on Reasoner's 2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Gsoil 115T belongs to the genus Polaromonas and was most closely related to Polaromonaseurypsychrophila B717-2T (98.6 %), Polaromonasvacuolata 34-PT (98.3 %), Polaromonasjejuensis NBRC 106434T (98.1 %), Polaromonas aquatic CCUG 39402T (97.7 %) and Polaromonascryoconiti Cr4-35T (97.5 %). The DNA G+C content was 60.9 mol%. The DNA-DNA hybridization relatedness between strain Gsoil 115T and P. eurypsychrophila B717-2T, P. vacuolata 34-PT, P. jejuensis NBRC 106434T, P. aquatic CCUG 39402T and P. cryoconiti Cr4-35T were 31.2, 21.6, 16.9, 8.7 and 10.1 %, respectively. The major polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE). The sole respiratory quinone was Q-8. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), which supported the affiliation of strain Gsoil 115T to the genus Polaromonas. Moreover, the physiological, biochemical and low level of DNA-DNA relatedness value allowed the phenotypic and genotypic differentiation of strain Gsoil 115T from the recognized species of the genus Polaromonas. Therefore, strain Gsoil 115T represents a novel species of the genus Polaromonas, for which the name Polaromonas ginsengisoli sp. nov. is proposed, with the type strain Gsoil 115T (LMG 23393T=KCTC 12577T).

Ciceribacter azotifigens sp. nov., a nitrogen-fixing bacterium isolated from activated sludge.

A Gram-reaction-negative, catalase- and oxidase-positive, aerobic, transparent, motile and rod-shaped bacterium that was capable of fixing dinitrogen (designated strain A.slu09T), isolated from activated sludge, was characterized by a polyphasic approach to clarify its taxonomic position. Strain A.slu09T was observed to grow optimally at 30 °C and at pH 7.0 on R2A agar medium. Strain A.slu09T showed ß-glucosidase activity, converting the major ginsenoside Rd to ginsenoside F2. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain A.slu09T belongs to the genus Ciceribacter of the family Rhizobiaceae and was most closely related to Ciceribacter lividus MSSRFBL1T (97.8 % similarity). The DNA G+C content was 67.2 mol%. The DNA-DNA hybridization value between strain A.slu09T and C. lividus KCTC 32403T was 16.9±1.17 %. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine, aminophospholipid and two glycolipids, and one unknown phospholipid as a minor lipid. The predominant quinone was ubiquinone-10 (Q-10). The major fatty acids were C19 : 0 cyclo ω8c, C18 : 1 ω7c and/or C18 : 1ω6c (summed feature 8) and C18 : 0, a profile that supported the affiliation of A.slu09T to the genus Ciceribacter. Moreover, the physiological and biochemical characteristics and low level of DNA-DNA relatedness allowed the phenotypic and genotypic differentiation of strain A.slu09T from the recognized species of the genus Ciceribacter. Therefore, strain A.slu09T represents a novel species of the genus Ciceribacter, for which the name Ciceribacter azotifigens sp. nov. is proposed. The type strain is A.slu09T (=KACC 19080T=LMG 29962T).

Paraburkholderia azotifigens sp. nov., a nitrogen-fixing bacterium isolated from paddy soil.

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterial strain, designated NF2-5-3T, was isolated from a paddy soil in Anseong city, Republic of Korea. This bacterium was characterized to determine its taxonomic position using a polyphasic approach. On the basis of 16S rRNA gene sequence analysis, strain NF2-5-3T had a close relationship with, and was related most closely to, members of the genus Paraburkholderia, namely Paraburkholderia caribensis MWAP64T (98.8 % similarity), P. sabiae Br3407T (98.8 %), P. hospita LMG 20598T (98.5 %), P. terrae NBRC 100964T (98.3 %) and P. phymatum STM815T (98.1 %). Growth of strain NF2-5-3T occurred at 15-37 °C, at pH 6.0-8.0 and at NaCl concentrations of 0-2 % (w/v). The major respiratory quinone was ubiquinone 8 (Q-8) and the major fatty acids were C16 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C17 : 0 cyclo and C16 : 0 3-OH. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, an unidentified phospholipid, unidentified aminophospholipids, unidentified aminolipids and unidentified polar lipids. The G+C content of the genomic DNA was 64.2 mol%. DNA-DNA relatedness values between strain NF2-5-3T and its closest phylogenetic neighbours were much lower than 70 %. Strain NF2-5-3T could be differentiated phylogenetically and phenotypically from recognized species of the genus Paraburkholderia. The isolate therefore represents a novel species, for which the name Paraburkholderia azotifigens sp. nov. is proposed, with NF2-5-3T (=KACC 18968T=LMG 29961T) as the type strain.

Phenylobacterium hankyongense sp. nov., isolated from ginseng field soil.

A Gram-stain-negative, aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain, designated HKS-05T, was isolated from ginseng field soil. This bacterium was characterized to determine its taxonomic position by using the polyphasic approach. HKS-05T grew at 10-37 °C and at pH 6.0-8.0 on R2A agar. On the basis of 16S rRNA gene sequence similarity, HKS-05T was shown to represent a member of the family Caulobacteraceaeand to be related to Phenylobacterium lituiforme FaiI3T (98.1 % sequence similarity), 'Phenylobacterium zucineum' HLK1 (97.9 %), Phenylobacterium muchangponense A8T (97.7 %), Phenylobacteriumcomposti 4T-6T (97.2 %) and Phenylobacterium immobile ET (97.1 %). The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids were phosphatidylglycerol, unidentified glycolipids and unidentified polar lipids. The G+C content of the genomic DNA was 70.4 mol%. DNA-DNA relatedness values between HKS-05T and its closest phylogenetically neighbours were low. HKS-05T could be differentiated genotypically and phenotypically from the species of the genus Phenylobacterium with validly published names. The isolate therefore represents a novel species, for which the name Phenylobacteriumhankyongense sp. nov. is proposed, with the type strain HKS-05T (=KACC 18628T=LMG 30081T).

Paenibacillus azotifigens sp. nov., a novel nitrogen-fixing bacterium isolated from paddy soil.

A nitrogen-fixing bacterium, designated NF2-4-5T, was isolated from a paddy soil in Anseong City, Korea. Cells of strain NF2-4-5T were Gram-staining-positive, motile rods and aerobic. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Paenibacillus and was closely related to Paenibacillus graminis RSA19T (98.7 %), Paenibacillus jilunlii Be17T (98.6 %), Paenibacillus salinicaeni LAM0A28T (98.6 %) and Paenibacillus riograndensis SBR5T (98.6 %). Growth of strain NF2-4-5T occurs at temperatures of 18-37 °C, at pH 6.0-8.5 and between 0.5% and 2 % NaCl (w/v). The only respiratory quinone was MK-7. The cell wall peptidoglycan of strain NF2-4-5T contained meso-diaminopimelic acid. The main cellular fatty acids were C16 : 0 and anteiso-C15 : 0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). The DNA G+C content was 56.36 mol%. The DNA-DNA hybridization relatedness between strain NF2-4-5T and four reference strains, Paenibacillus graminis RSA19T, Paenibacillus jilunlii Be17T, Paenibacillus sonchi X19-5T and Paenibacillus riograndensis SBR5T, was 22.0±0.3, 20.1±0.7, 18.3±0.3 and 12.6±0.5 %, respectively. The phenotypic, phylogenetic and chemotaxonomic results indicate that the strain NF2-4-5T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus azotifigens sp. nov. is proposed. The type strain is NF2-4-5T (=KACC 18967T=LMG 29963T).

Sphingomonas agri sp. nov., a bacterium isolated from soil.

A Gram-reaction-negative, aerobic, non-motile, white (translucent) and rod-shaped bacterium (designated HKS-06T) isolated from soil was characterized by a polyphasic approach to clarify its taxonomic position. Strain HKS-06T was observed to grow optimally at 30 °C and at pH 6.5-7.0 on R2A agar medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HKS-06T belongs to the genus Sphingomonas and is most closely related to Sphingomonas lutea JS5T (97.4 % similarity). The G+C content of the genomic DNA was 64.1 mol%. Chemotaxonomic data [major quinone (Q-10), major polar lipids (phosphatidylethanolamine, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine, unknown polar lipid) and major fatty acids (summed feature 8, comprising C18 : 1ω7c/ω6c and/or C18 : 1ω6c, C18 : 0 3-OH and C16 : 0)] supported the affiliation of strain HKS-06T to the genus Sphingomonas. Moreover, the physiological and biochemical results and low level of DNA-DNA relatedness [between strain HKS06T and S. lutea JS5T (20.24±1.2 %)] allowed the phenotypic and genotypic differentiation of strain HKS-06T from recognized species of the genus Sphingomonas. The new isolate therefore represents a novel species, for which the name Sphingomonas agri sp. nov. is proposed. The type strain is HKS-06T (=KACC 18880T=LMG 29563T).

Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water.

A Gram-stain-negative, oxidase- and catalase-positive, strictly aerobic, non-gliding bacterial strain, designated as NPT, was isolated from lake water and subjected to a taxonomic study using a polyphasic approach. Colonies of strain NP5T were light-yellow-coloured, circular with regular margins, and opaque. Cells were rods, 0.2-0.5 µm wide and 1.2-3.0 µm long. Strain NP5T possessed ß-glycosidase activity, which was responsible for its ability to convert ginsenosides Rb1, Rc and Rd (three main active components of ginseng) to ginsenoside F2. Phylogenetic study based on the 16S rRNA gene sequence put strain NP5T in a distinct lineage in the family Flavobacteriaceae, sharing less than 96.0 % sequence similarity with members of the closely related genera Chryseobacterium, Bergeyella, Epilithonimonas and 'Candidatus Amoebinatus'. The novel isolate showed the highest sequence similarity with the genus Chryseobacterium. Strain NP5T contained MK-6 as predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, C18 : 0 3-OH, anteiso-C15 : 0 and C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3) as major fatty acids. The DNA G+C content was 44.8 mol%. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The physiological, biochemical and taxonomical characteristics allowed the phenotypic differentiation of strain NP5T from its closest phylogenetic neighbours. On the basis of the evidence of this polyphasic study, isolate NP5T represents a novel genus and species in the family Flavobacteriaceae for which the name Daejeonia ginsenosidivorans gen. nov., sp. nov. is proposed. The type strain is NP5T (=KACC 18626T=LMG 29198T).

Sphingomonas aquatica sp. nov., isolated from tap water.

A Gram-stain-negative, strictly aerobic, rod-shaped bacterium, designated W1-2-1T, was isolated from tap water in South Korea. The strain was characterized by a polyphasic approach to clarify its taxonomic position. Strain W1-2-1T grew at 18-42 °C and at pH 6.0-10.0 on R2A medium. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Sphingomonas and is most closely related to the Sphingomonas oligophenolica JCM 12082T (97.2 % similarity), Sphingomonas asaccharolyticaNBRC 15499T (96.8 %), Sphingomonas desiccabilis CP1DT (96.8 %), Sphingomonas pruniNBRC 15498T (96.8 %), Sphingomonas hankookensis ODN7T (96.4 %) and Sphingomonas yabuuchiae DSM 14562T (95.8 %). Chemotaxonomic data [major ubiquinone - Q10, major polyamine - homospermidine, major fatty acids - summed feature 8 (C18  : 1ω7c/ω6c), C16 : 0 and C14 : 0 2-OH and presence of sphingoglycolipid] supported the affiliation of the strain to the genus Sphingomonas. The G+C content of genomic DNA was 67.1 mol%. However, low level of DNA-DNA relatedness value between strain W1-2-1T and S. oligophenolica JCM 12082T and the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain W1-2-1T from other Sphingomonas species with validly published names. Therefore, the isolate represents a novel species, for which the name Sphingomonas aquatica sp. nov. (type strain W1-2-1T=KACC 18309T=LMG 28596T) is proposed.

Phenylobacterium aquaticum sp. nov., isolated from the reservoir of a water purifier.

A Gram-reaction-negative, strictly aerobic, non-motile, non-spore-forming, rod-shaped bacterial strain designated W2-3-4T was isolated from the reservoir of a water purifier. This bacterium was characterized to determine its taxonomic position by using a polyphasic approach. Strain W2-3-4T grew well at 25-30 °C on nutrient and R2A agars. On the basis of 16S rRNA gene sequence similarity, strain W2-3-4T was shown to belong to the family Caulobacteraceaeand to be related to Phenylobacterium conjunctumFWC21T (98.0 % sequence similarity) and Phenylobacterium haematophilum CCUG 26751T (97.2 %). Lower sequence similarities were found with the type strains of all other recognized members of the genus Phenylobacterium (95.7-97.1 %). The G+C content of the genomic DNA was 68.7 mol%. The major respiratory quinone was Q-10 and the major fatty acids were summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0, C18 : 1ω7c 11-methyl and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). The polar lipids were phosphatidylglycerol, an unknown phospholipid, four unknown glycolipids and three unidentified polar lipids. DNA-DNA relatedness values between strain W2-3-4Tand its closest phylogenetically neighbours were below 7 %. Strain W2-3-4T could be differentiated genotypically and phenotypically from recognized species of the genus Phenylobacterium. The isolate therefore represents a novel species, for which the name Phenylobacterium aquaticum sp. nov. is proposed, with the type strain W2-3-4T (=KACC 18306T=LMG 28593T).