Jae-Chan Lee

Terriglobus tenax sp. nov., an exopolysaccharide-producing acidobacterium isolated from rhizosphere soil of a medicinal plant.

An exopolysaccharide-producing bacterium, designated strain DRP 35(T), was isolated from the rhizosphere soil of a medicinal herb, Angelica sinensis, at Geumsan in Korea. Cells were Gram-staining-negative, non-motile, catalase-positive and oxidase-negative short rods. The isolate grew aerobically from 15 to 45 °C (optimum 30 °C), pH 3.5-7.0 (optimum pH 5.0) and in the presence of 0-1.0% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain DRP 35(T) belongs to the genus Terriglobus in the phylum Acidobacteria with a sequence similarity of 97.2% and 97.0% to Terriglobus saanensis SP1PR4(T) and Terriglobus roseus KBS63(T), respectively. The genomic DNA G+C content was 62.1 mol%. DNA-DNA relatedness between strain DRP 35(T) and the type strains of the other species of the genus Terriglobus, T. saanensis SP1PR4(T) and T. roseus KBS63(T), were 24.6 and 17.2%, respectively. The predominant menaquinone was MK-8. Major fatty acids were iso-C(15 : 0), C(16 : 1)ω7c and C(16 : 0). The polar lipids were phosphatidylethanolamine, unidentified aminophospholipid and unknown phospholipids. On the basis of polyphasic analysis from this study, strain DRP 35(T) represents a novel species of the genus Terriglobus for which the name Terriglobus tenax sp. nov. is proposed. The type strain is DRP 35(T) ( = KACC 16474(T) = NBRC 109677(T)).

Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil

Strains Y-12(T) and Y-47(T) were isolated from mountain forest soil and strain WR43(T) was isolated from rhizosphere soil, at Daejeon, Korea. The three strains grew at 10-55 °C (optimal growth at 28-30 °C), at pH 3.0-8.0 (optimal growth at pH 6.0) and in the presence of 0-4.0% (w/v) NaCl, growing optimally in the absence of added NaCl. On the basis of 16S rRNA gene sequence analysis, the three strains were found to belong to the genus Burkholderia, showing the closest phylogenetic similarity to Burkholderia diazotrophica JPY461(T) (97.2-97.7%); the similarity between the three sequences ranged from 98.3 to 98.7%. Additionally, the three strains formed a distinct group in phylogenetic trees based on the housekeeping genes recA and gyrB. The predominant ubiquinone was Q-8, the major fatty acids were C16 : 0 and C17  : 0 cyclo and the DNA G+C content of the novel isolates was 61.6-64.4 mol%. DNA-DNA relatedness among the three strains and the type strains of the closest species of the genus Burkholderia was less than 50%. On the basis of 16S rRNA, recA and gyrB gene sequence similarities, chemotaxonomic and phenotypic data, the three strains represent three novel species within the genus Burkholderia, for which the names Burkholderia humisilvae sp. nov. (type strain Y-12(T)= KACC 17601(T) = NBRC 109933(T) = NCAIM B 02543(T)), Burkholderia solisilvae sp. nov. (type strain Y-47(T) = KACC 17602(T)= NBRC 109934(T) = NCAIM B 02539(T)) and Burkholderia rhizosphaerae sp. nov. (type strain WR43(T) = KACC 17603(T) = NBRC 109935(T) = NCAIM B 02541(T)) are proposed.

Sphingomonas oligoaromativorans sp. nov., an oligotrophic bacterium isolated from a forest soil

A halo- and organo-sensitive oligotrophic bacterium, designated strain SY-6T, was isolated from humus forest soil at Gyeryong mountain in Korea. Cells of the strain were Gram-negative, strictly aerobic, non-motile rods and the strain formed yellow-pigmented colonies on 100-fold-diluted nutrient broth. Strain SY-6T grew at pH 6.0-7.0 (optimal growth at pH 7.0), at 10-37 °C (optimal growth at 28 °C) and at salinities of 0-0.5% (w/v) NaCl, growing optimally at 0.01% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain SY-6T was shown to belong to the genus Sphingomonas and showed the closest phylogenetic similarity to Sphingomonas polyaromaticivorans B2-7T (96.7%). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone and polyamine were Q-10 and sym-homospermidine, respectively. The major fatty acids were C18:1ω7c and C16:0. The DNA G+C content of the novel isolate was 65.3 mol%. On the basis of the evidence from this polyphasic study, strain SY-6T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas oligoaromativorans sp. nov. is proposed. The type strain is SY-6T (=KACC 12948T=NBRC 105508T).

Halobacillus sediminis sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.

A Gram-staining-positive, moderately halophilic bacterium, designated strain NGS-2T, was isolated from sediment of a solar saltern pond located in Shinan, Korea. Strain NGS-2T was a strictly aerobic, non-motile rod that grew at pH 5.0-10.0 (optimum, pH 8.0), at 10-30 °C (optimum, 28 °C) and in the presence of 1-20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain NGS-2T belonged to the genus Halobacillus, with sequence similarity of 98.4-95.8 % to existing type strains, showing the highest sequence similarity to Halobacillus dabanensis D-8T (98.4 %), H. litoralis SL-4T (98.4 %), H. trueperi SL-5T (98.2 %), H. faecis IGA7-4T (98.2 %), H. profundi IS-Hb4T (98.1 %) and H. mangrovi MS10T (98.0 %). The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidyl-N-methylethanolamine and an unknown glycolipid. The cell-wall peptidoglycan was based on l-Orn-d-Asp, the predominant isoprenoid quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C15: 0 and anteiso-C17: 0. The DNA G+C content of the novel isolate was 45.0 mol%. Levels of DNA-DNA relatedness between strain NGS-2T and the type strains of 12 other species of the genus ranged from 32 to 3 %. On the basis of the polyphasic analysis conducted in this study, strain NGS-2T represents a novel species of the genus Halobacillus, for which the name Halobacillus sediminis sp. nov. is proposed. The type strain is NGS-2T ( = KACC 18263T = NBRC 110639T).

Planifilum composti sp. nov., a thermophile isolated from compost

Two thermophilic bacteria, designated strains P8(T) and P12, were isolated from compost in Korea. The isolates grew aerobically from 50 to 75 °C (optimum at 55 °C) and at pH 4.0-9.0 (optimum pH 6.5). Aerial mycelia were not observed. Single spores were produced along the substrate hypha. The predominant menaquinone was MK-7. Major fatty acids were iso-C17 : 0, iso-C15 : 0 and iso-C16 : 0. The cell wall contained meso-diaminopimelic acid and the polar lipids were phosphatidylethanolamine, an aminophospholipid and sphingoglycolipid. The DNA G+C contents were 55.9-56.5 mol%. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strains P8(T) and P12 belonged to the genus Planifilum in the family Thermoactinomycetaceae with sequence similarities of 96.1-97.2 %. Levels of DNA-DNA relatedness between strain P8(T) and the type strains of recognized species of the genus Planifilum ranged from 28.9 to 38.2 %. On the basis of data from the present polyphasic study, strains P8(T) and P12 are considered to represent a novel species of the genus Planifilum, for which the name Planifilum composti sp. nov. is proposed. The type strain is P8(T) ( = KACC 16581(T) = NBRC 108858(T)).

Pontibacillus salicampi sp. nov., a moderately halophilic bacterium isolated from saltern soil

A Gram-stain-positive, moderately halophilic bacterium, designated BH043(T), was isolated from saltern soil of Gomso in Korea. Cells were motile rods, producing ellipsoidal endospores at a terminal position in swollen sporangia. Strain BH043(T) was strictly aerobic, grew at pH 6.0-10.0 (optimal growth at pH 7.5), at 10-55 °C (optimal growth at 30 °C) and at salinities of 1-20 % (w/v) NaCl, growing optimally with 7 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain BH043(T) belongs to the family Bacillaceae and was most closely related to the type strains of the five recognized species of the genus Pontibacillus, showing sequence similarity to Pontibacillus yanchengensis Y32(T) (97.5 % similarity), Pontibacillus marinus BH030004(T) (97.4 %), Pontibacillus chungwhensis BH030062(T) (97.0 %), Pontibacillus litoralis JSM 072002(T) (96.4 %) and Pontibacillus halophilus JSM 076056(T) (96.2 %). The major cellular fatty acids of strain BH043(T) were iso-C15 : 0 and anteiso-C15 : 0. The genomic DNA G+C content was 42.5 mol%. The major isoprenoid quinone was MK-7 and meso-diaminopimelic acid was present in the cell-wall peptidoglycan as the diagnostic diamino acid. The major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. DNA-DNA relatedness between strain BH043(T) and the type strains of other species of the genus Pontibacillus, P. yanchengensis CGMCC 1.10680(T) and P. marinus KCTC 3917(T) and P. chungwhensis KCTC 3890(T), was 35, 24 and 18 %, respectively. On the basis of polyphasic analysis from this study, strain BH043(T) represents a novel species of the genus Pontibacillus for which the name Pontibacillus salicampi sp. nov. is proposed. The type strain is BH043(T) ( = KACC 17607(T) = NBRC 109831(T) = NCAIM B.02529(T)).

Idiomarina halophila sp. nov., isolated from a solar saltern sediment.

A Gram-stain-negative, halophilic bacterium, designated strain BH195(T), was isolated from the sediment of the solar saltern pond located in Gomso, Republic of Korea. Strain BH195(T) was a strictly aerobic, non-motile rod, which grew at pH 3.5-10.5 (optimum, pH 7.5), at 4-55 °C (optimum, 30 °C) and at salinities of 0.5-11% (w/v) NaCl [optimum, 2-3% (w/v) NaCl]. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain BH195(T) belongs to the genus Idiomarina , showing the highest sequence similarity to Idiomarina salinarum ISL-52(T) (97.4%), Idiomarina homiensis PO-M2(T) (96.8%), Idiomarina aestuarii KYW314(T) (96.7%), and Idiomarina tainanensis PIN1(T) (96.7%). The major cellular fatty acids of strain BH195(T) were iso-C(11 : 0) 3-OH, iso-C(15 : 0) and iso-C(11 : 0). The DNA G+C content was 51.3 mol% and the major respiratory quinone was ubiquinone 8. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. DNA-DNA relatedness between strain BH195(T) and I. salinarum KCTC 12971(T) was 33%. On the basis of this polyphasic analysis, strain BH195(T) represents a novel species of the genus Idiomarina for which the name Idiomarina halophila sp. nov. is proposed. The type strain is BH195(T) ( = KACC 17610(T) = NCAIM B 02544(T)).

Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment.

A Gram-stain-negative, moderately halophilic bacterium, designated strain CPS11T, was isolated from the sediment of a solar pond located in Shinan, Korea. Strain CPS11T was a strictly aerobic, motile, straight rod-shaped bacterium that grew at pH 5.0-9.0 (optimum, pH 7.0-8.0), at 10-37 °C (optimum, 28 °C) and at salinities of 1-20 % (w/v) NaCl (optimum, 10 % NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain CPS11T belonged to the genus Halomonas, with sequence similarity of 98.5-94.3 % to existing type strains, showing highest sequence similarity to Halomonasfontilapidosi 5CRT (98.5 %), Halomonasventosae Al12T (98.5 %), Halomonascampaniensis 5AGT (98.2 %), Halomonas huangheensis BJGMM-B45T (98.0 %), Halomonas alimentaria YKJ-16T (98.0 %), Halomonas mongoliensis Z-7009T (97.8 %), Halomonas shengliensis SL014B-85T (97.5 %) and Halomonas cupida DSM 4740T (97.5 %). The predominant ubiquinone was Q-9. The major fatty acids were C19 : 0 cyclo ω8c, C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0, C17 : 0 cyclo, C12 : 0 3-OH and C18 : 1ω7c. The polar lipids were phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, an unknown phospholipid and unknown lipids. The DNA G+C content of this novel isolate was 64.3 mol%. Levels of DNA-DNA relatedness between strain CPS11T and the type strains of ten other species of the genus ranged from 50 to 21 %. On the basis of the polyphasic analysis conducted in this study, strain CPS11T represents a novel species of the genus Halomonas, for which the name Halomonas sediminicola sp. nov. is proposed. The type strain is CPS11T(=KACC 18262T=NBRC 110636T).

Reyranella graminifolii sp. nov., isolated from bamboo (Phyllostachys bambusoides) litter.

A novel strain designated Wo-34(T) was isolated from bamboo (Phyllostachys bambusoides) litter. Cells were Gram-stain-negative, non-motile, catalase-negative and oxidase-positive rods. The isolate grew aerobically at 15-35 °C (optimum 28 °C), pH 4.0-9.0 (optimum pH 7.0) and in the presence of 0-1.0% (w/v) NaCl (optimum 0.1% NaCl). Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain Wo-34(T) belonged to the genus Reyranella with the sequence similarities of 97.9% and 97.3% to the other species of the genus Reyranella, Reyranella massiliensis 521(T) and Reyranella soli KIS14-15(T), respectively. The predominant ubiquinone was Q-10. Major fatty acids were C18 : 1ω7c, C18 : 1 2-OH and C19 : 0 cyclo ω8c. The polar lipids contained phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unknown aminolipid, unidentified phospholipids and unknown lipids. DNA-DNA relatedness values between strain Wo-34(T) and R. massiliensis DSM 23428(T) and R. soli KACC 13034(T) were 35% and 29%, respectively. On the basis of polyphasic analysis from this study, strain Wo-34(T) represents a novel species of the genus Reyranella for which the name Reyranella graminifolii sp. nov. is proposed. The type strain is Wo-34(T) ( = KACC 17605(T) = NBRC 109813(T)).

Sphingobium subterraneum sp. nov., isolated from ground water

A Gram-stain-negative, strictly aerobic, non-motile, non-spore-forming, yellow, rod-shaped bacterium, designated S-II-13(T), was isolated from ground water at Daejeon in Korea. Strain S-II-13(T) grew between 15 and 30 °C (optimal growth at 28 °C), between pH 6.0 and 9.0 (optimal growth at pH 7.5) and at salinities of 0.3-1.5 % (w/v) NaCl, growing optimally with 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, strain S-II-13(T) was found to belong to the genus Sphingobium, showing closest phylogenetic similarity to Rhizorhapis suberifaciens CA1(T) (97.0 % 16S rRNA gene sequence similarity), Sphingobium sufflavum HL-25(T) (96.9 %) and Sphingobium vulgare HU1-GD12(T) (96.6 %). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine and sphingoglycolipid. The predominant ubiquinone was Q-10. The major fatty acids were C18 : 1ω7c, C14 : 0 2-OH, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The DNA G+C content of strain S-II-13(T) was 63.5 mol%. DNA-DNA relatedness between strain S-II-13(T) and Rhizorhapis suberifaciens LMG 17323(T), Sphingobium sufflavum KCTC 23953(T) and Sphingobium vulgare KCTC 22289(T) was 24, 52 and 55 %, respectively. On the basis of evidence from this taxonomic study using a polyphasic approach, strain S-II-13(T) represents a novel species of the genus Sphingobium for which the name Sphingobium subterraneum sp. nov. is proposed. The type strain is S-II-13(T) ( = KACC 17606(T) = NBRC 109814(T)).