Chryseobacterium phosphatilyticum sp. nov., a phosphate-solubilizing endophyte isolated from cucumber (Cucumis sativus L.) root.

A bacterial strain, designated as ISE14T, with Gram-stain-negative and non-motile rod-shaped cells, was isolated from the root of a cucumber plant collected in a field in Iksan, Republic of Korea and was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISE14T represented a member of the genus Chryseobacterium and was closely related to Chryseobacterium viscerum 687B-08T (16S rRNA gene sequence similarity of 98.50 %), Chryseobacterium lactis NCTC 11390T (98.49 %), Chryseobacterium ureilyticum F-Fue-04IIIaaaaT (98.49 %) and Chryseobacterium oncorhynchi 701B-08T (98.04 %). Average nucleotide identity values between genome sequences of strain ISE14T and the closely related species ranged from 81.44 to 83.15 %, which were lower than the threshold of 95 % (corresponding to a DNA-DNA hybridization value of 70 %). The DNA G+C content of strain ISE14T was 36.3 mol%. The dominant fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c) and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three unidentified aminolipids and eight unidentified lipids; the predominant respiratory quinone was MK-6. On the basis of the evidence presented in this study, strain ISE14T can be distinguished from closely related species belonging to the genus Chryseobacterium. Thus, strain ISE14T is a novel species of the genus Chryseobacterium, for which the name Chryseobacteriumphosphatilyticum sp. nov. is proposed. The type strain is ISE14T (=KACC 19820T=JCM 32876T).

Serinicoccus sediminis sp. nov., isolated from tidal flat sediment.

A novel Gram-strain-positive, non-spore-forming bacterial strain, designated GP-T3-3T, was isolated from sediment sampled at a tidal flat in Gopado, Republic of Korea. Cells were aerobic, catalase-negative, oxidase-positive, non-motile cocci that occurred singly, in pairs or in clusters. Strain GP-T3-3T grew at 4-45 °C (optimum, 28-37 °C), at pH 4.0-12.0 (pH 8.0-9.0) and in the presence of 0-15 % (w/v) NaCl (3-5 %). Colonies of strain GP-T3-3T were deep-yellow, circular, smooth and pulvinate. The results of the phylogenetic analyses based on 16S rRNA gene sequences indicated that strain GP-T3-3T was closely related to Serinicoccus profundi MCCC 1A05965T (99.1 %), Serinicoccus chungangensis CAU 9536T (99.0 %) and Serinicoccus marinus JC1078T (98.0 %). The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-8(H4) and the major fatty acids were anteiso-C17 : 0, iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0. The polar lipid profile consisted of diphosphadidylglycerol, phosphadidylglycerol, phosphatidylcholine, phosphatidylinositol and two unidentified phospholipids. The DNA G+C content was 72.9 mol%. DNA-DNA relatedness values between strain GP-T3-3T and type strains of the genus Serinicoccus ranged from 28.9 to 50.5 %. On the basis of the phenotypic differences and DNA-DNA relatedness data, the isolate represents a new species of the genus Serinicoccus, for which the name Serinicoccussediminis sp. nov. is proposed. The type strain is GP-T3-3T (=KCTC 49173T=JCM 32825T=KCCM 43309T=KACC 19850T).

Gemmobacter lutimaris sp. nov., a marine bacterium isolated from a tidal flat.

A novel cream-pigmented marine bacterium, designated strain YJ-T1-11T, was isolated from a tidal flat at Yeongjong-do, Republic of Korea. Cells were rod-shaped, non-motile, aerobic, Gram-reaction-negative, oxidase-positive and catalase-positive. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain YJ-T1-11T clustered with Gemmobacter fontiphilus JS43T (98.3 %) within the genus Gemmobacter and its closest neighbours were G.emmobacter aquatilis DSM 3857T (98.5 %), Gemmobacter aquaticus A1-9T (98.4 %), Gemmobacterlanyuensis Orc-4T (98.4 %), Gemmobacterfontiphilus JS43T (98.3 %), Gemmobactercaeni DCA-1T (98.2 %), Gemmobacternanjingensis Y12T (97.5 %) and Gemmobactertilapiae Ruye-53T (97.2 %). Average nucleotide identity values between the genome sequences of strain YJ-T1-11T and the related type strains ranged from 77.08 to 90.48 %. The predominant fatty acid of strain YJ-T1-11T was summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c). The major isoprenoid quinone was Q-10 and the DNA G+C content was 65.6 mol%. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, diphosphatidylglycerol and three unidentified lipids. The DNA-DNA relatedness values between strain YJ-T1-11T and the type strains of the 12 phylogenetically related species of the genus Gemmobacter were 23.6-53.7 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain YJ-T1-11T is considered to represent a novel species of the genus Gemmobacter, for which the name Gemmobacter lutimaris sp. nov. is proposed. The type strain is YJ-T1-11T (=KCTC 62715T=JCM 32828T).

Blastococcus litoris sp. nov., isolated from sea-tidal flat sediment.

A novel Gram-strain-positive, non-spore-forming bacterial strain, designated GP-S2-8T, was isolated from a sea-tidal flat sediment sample from Gopado, Republic of Korea. Cells were aerobic, catalase-negative, oxidase-positive, non-motile and cocci, occurring singly, in pairs or in tetrads, and often tending to form aggregates. The strain grew at 4-45 °C (optimum, 28-37 °C), at pH 4.0-11.0 (pH 7.0-9.0) and in the presence of 0-11 % (w/v) NaCl (0-3 %). Phylogenetic analyses based on 16S rRNA gene sequences represented that the isolate belongs to the genus Blastococcus. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. Whole-cell sugar analysis of strain GP-S2-8T revealed rhamnose, glucose and mannose as characteristic sugars. The predominant respiratory quinone was MK-9(H4) and the major fatty acids were iso-C16 : 0, iso-C16 : 1 H, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C14 : 0. The polar lipid profile included diphosphadidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol, one unidentified glycophospholipid, two unidentified phospholipids and five unidentified lipids. The DNA G+C content was 74.2 mol%. DNA-DNA relatedness values between strain GP-S2-8T and type strains of the genus Blastococcus ranged from 14.6 to 48.6 %. On the basis of the phenotypic differences and DNA-DNA relatedness data, the isolate represents a new species of the genus Blastococcus, for which the name Blastococcuslitoris sp. nov. is proposed. The type strain is GP-S2-8T (=KCCM 43275T=JCM 32354T=DSM 106127T=KCTC 49078T).

Zobellella maritima sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium, isolated from beach sediment.

A novel Gram-stain-negative, motile, rod-shaped bacterium, designated strain 102-Py4T, was isolated from Sinduri beach sediment in Taean, Republic of Korea. Cells were aerobic, oxidase-positive and catalase-positive. The isolate grew optimally with 1-3 % (w/v) NaCl, but NaCl is not an absolute requirement for growth. 16S rRNA gene sequence analysis revealed that strain 102-Py4T clustered together with Zobellella aerophila and fell within the clade formed by recognized species of the genus Zobellella. Its closest phylogenetic neighbours were Z. aerophila JC2671T (98.1 % 16S rRNA gene sequence similarity), Zobellella denitrificans ZD1T (96.4 %) and Zobellella taiwanensis ZT1T (96.0 %). The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C12 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C16 : 0. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 62.1 mol%. The DNA-DNA relatedness value between strain 102-Py4T and Z. aerophila JC2671T was 12.4±1.3 %. The phenotypic properties of 102-Py4T demonstrated that this strain could be distinguished from other Zobellella species. On the basis of the data presented, strain 102-Py4T (=KCTC 62272T=JCM 32359T=DSM 106043T) is considered to represent a novel species of the genus Zobellella, for which the name Zobellella maritima sp. nov. is proposed.

Oceanimonas marisflavi sp. nov., a polycyclic aromatic hydrocarbon-degrading marine bacterium.

A Gram-stain-negative, strictly aerobic, motile and rod-shaped bacterial strain, designated 102-Na3T, was isolated from sediment of Sinduri beach in Taean, Republic of Korea. Strain 102-Na3T grew optimally at 28-37 °C, at pH 7.0-11.0 and in the presence of 1-3 % (w/v) NaCl, but NaCl was not an absolute requirement for growth. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain 102-Na3T joined the clade comprising the type strains of Oceanimonasspecies. Strain 102-Na3T exhibited 16S rRNA gene sequence similarity values of 98.8, 98.3 and 98.0 % to the type strains of Oceanimonas doudoroffii MBIC1298T, Oceanimonas baumannii GB6T and Oceanimonas smirnovii 31-13T, respectively. Strain 102-Na3T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c), C16 : 0 and C12 : 0 as major fatty acids. The major quinone was ubiquinone-8. The polar lipids were composed of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified amino lipids. The DNA G+C content was 56.8 mol%. Strain 102-Na3T exhibited DNA-DNA relatedness values of 25.7, 21.7 and 14.8 % to the type strains of O. doudoroffii, O. baumannii and O. smirnovii, respectively. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain 102-Na3T is separated from recognized species of the genus Oceanimonas. On the basis of the data presented, strain 102-Na3T (=KCTC 62271T=JCM 32358T=DSM 106032T) is considered the type strain of a novel species of the genus Oceanimonas, for which the name Oceanimonas marisflavi sp. nov. is proposed.

Maribacter litoralis sp. nov. a marine bacterium isolated from seashore.

A novel Gram-stain-negative, moderately halophilic and aerobic bacterium, designated strain SDRB-Phe2T, was isolated from coastal sediment of the yellow sea in Sindu-ri, Republic of Korea. Cells were oxidase-positive, catalase-positive, rod-shaped and surrounded by a capsule with gliding motility. Colonies were yellow-coloured, circular, pulvinate with entire margins. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SDRB-Phe2T formed a distinct lineage within the genus Maribacter of the family Flavobacteriaceae. Stain SDRB-Phe2T exhibited 16S rRNA gene sequence similarity values of 97.1-98.9 % to the type strains of Maribacterstanieri, Maribacterspongiicola, Maribacter forsetii, Maribacter dokdonensis, Maribacter aquivivus, Maribactercaenipelagi, Maribacterlitorisediminis, Maribactersedimenticola, Maribacterulvicola, Maribacter confluentis and Maribacter orientalis, and of 94.8-96.7 % to the type strains of the other species of the genus Maribacter. Strain SDRB-Phe2T contained MK-6 as the predominant respiratory quinone and iso-C15 : 1 G, iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The polar lipids of strain SDRB-Phe2T were phosphatidylethanolamine, one unidentified amino lipid and two unidentified lipids. The DNA G+C content was 36.2 mol%. DNA-DNA relatedness values of strain SDRB-Phe2T to the type strains of the 11 phylogenetically related species of the genus Maribacter were 21.9-38.6 %. On the basis of the phenotypic features, phylogenetic and DNA-DNA hybridization analyses presented here, strain SDRB-Phe2T (=JCM 32373T=KCTC 62273T=DSM 106042T) represents a novel species of the genus Maribacter, for which the name Maribacterlitoralis sp. nov. is proposed.

Pseudokineococcus basanitobsidens sp. nov., isolated from volcanic rock.

A novel Gram-strain-positive, non-spore-forming bacterial strain, designated SKC1-2T, was isolated from volcanic rock of the scoria cone of Seobjikoji, Jeju, Republic of Korea. Cells were aerobic, catalase-positive, oxidase-negative, motile and cocci. Colonies of cells were dark orange-coloured, circular, smooth and convex. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate was related to members of the genus Pseudokineococcus. Phylogenetic neighbours were P. marinus KCCM 42250T (98.2 %, 16S rRNA gene sequence similarity) and P. lusitanus DSM 23768T (98.0 %). The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant respiratory quinone was MK-9(H2). The predominant respiratory quinone was MK-9(H2) and the major fatty acid was anteiso-C15 : 0. The polar lipid profile included major amounts of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and two unidentified phosphoglycolipids. The DNA G+C content was 74.9 mol%. DNA-DNA relatedness values between strain SKC1-2T and P. lusitanus DSM 23768T or P. marinus KCCM 42250T were 37.5-38.1 % or 45.4-46.4 %, respectively. On the basis of the phenotypic differences and DNA-DNA relatedness data, the isolate represents a new species of the genus Pseudokineococcus, for which the name Pseudokineococcus basanitobsidens sp. nov. is proposed. The type strain is SKC1-2T (=DSM 103726T=KCCM 43221T).

Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae.

The Gram-stain-negative, yellow-pigmented, rod-shaped bacterial strain GSE06T, isolated from the surface-sterilized root of a cucumber plant grown in a field in Gunsan, Korea, was characterized by not only cultural and morphological features but also physiological, biochemical and molecular analyses. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GSE06T was most closely related to species of the genus Chryseobacterium. Furthermore, strain GSE06T exhibited the highest sequence similarities with the type strains Chryseobacterium indologenes ATCC 29897T (98.9 %), Chryseobacterium gleum ATCC 35910T (98.8 %), Chryseobacterium arthrosphaerae CC-VM-7T (98.7 %), Chryseobacterium contaminans C26T (98.5 %), Chryseobacterium artocarpi UTM-3T (98.3 %), and Chryseobacterium gallinarum 100T (97.9 %). Average nucleotide identity values between genome sequences of strain GSE06T and the above-mentioned reference strains ranged from 81.2 to 86.9 %, which were lower than the threshold of 95 % (corresponding to a DNA-DNA reassociation value of 70 %). The DNA G+C content of strain GSE06T was 36.1 mol%; the predominant respiratory quinone of the strain was MK-6. The major fatty acids were iso-C15 : 0, summed feature 9 (iso-C17 : 1ω9c), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, three aminolipids, one aminophospholipid, four glycolipids and one unidentified lipid. These results of phenotypic and genotypic characteristics could differentiate strain GSE06T from closely related type strains belonging to the genus Chryseobacterium. Thus, strain GSE06T is proposed as a representative of a novel species in the genus Chryseobacterium, Chryseobacterium cucumeris sp. nov. The type strain is GSE06T (=KACC 18798T=JCM 31422T).

Echinicola sediminis sp. nov., a marine bacterium isolated from coastal sediment.

A novel Gram-stain-negative, rod-shaped, gliding bacterium, designated strain 001-Na2T, was isolated from coastal sediment of the Yellow Sea in Sindu-ri, Republic of Korea. Cells were aerobic, oxidase-positive and catalase-positive. Colonies were dark salmon-coloured, circular, and pulvinate with entire margins. 16S rRNA gene sequence analysis revealed that strain 001-Na2T belonged to the genus Echinicola and these species formed a distinct lineage within the family Cyclobacteriaceae. The closest phylogenetic neighbours were 'Echinicola shivajiensis' AK12T (98.1 % 16S rRNA gene sequence similarity), Echinicola vietnamensis LMG 23754T (96.4 %), Echinicola jeungdonensis HMD 3054T (96.0 %), Echinicola pacifica KMM 6172T (96.0 %) and Echinicola rosea JL 3085T (95.8 %). The predominant respiratory quinone was menaquinone MK-7. The major fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C17 : 1ω6c and summed feature 9 (comprising iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The polar lipids were phosphatidylethanolamine, one unidentified aminophospholipid, one unidentified phospholipid and three unidentified lipids. The DNA G+C content was 44.6 mol%. DNA-DNA relatedness between strain 001-Na2T and 'E. shivajiensis' JCM 17847T was 20.8-21.1 %. On the basis of the phenotypic features, and phylogenetic and DNA-DNA hybridization analyses presented, strain 001-Na2T (=KCTC 52495T=JCM 31786T=DSM 103729T) is the type strain of a novel species of the genus Echinicola, for which the name Echinicola sediminis sp. nov. is proposed.

Nocardioides litoris sp. nov., isolated from the Taean seashore.

A novel Gram-stain-positive, irregularly rod-shaped actinomycete, designated strain 002-2T, was isolated from sand beach sediment collected from the Taean seashore, Republic of Korea. Cells were aerobic, oxidase-negative and catalase-positive. Colonies of cells were bright yellow, circular, smooth and convex. The diagnostic diamino acid in the cell wall was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H4). The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid and two unknown amino phospholipids. The major fatty acids were iso-C16 : 0 and C17 : 1ω8c. The DNA G+C content was 68.8 mol%. 16S rRNA gene sequence analysis revealed that strain 002-2T belongs to the family Nocardioidaceae and formed a cluster with Nocardioides rubroscoriae Sco-A25T (98.1 % sequence similarity) and Nocardioides plantarum NCIMB 12834T (97.6 %). On the basis of the phenotypic and phylogenetic data, strain 002-2T (=KCTC 39838T=DSM 103718T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides litoris sp. nov. is proposed.

Increased valinomycin production in mutants of Streptomyces sp. M10 defective in bafilomycin biosynthesis and branched-chain α-keto acid dehydrogenase complex expression.

Streptomyces sp. M10 is a valinomycin-producing bacterial strain that shows potent bioactivity against Botrytis blight of cucumber plants. During studies to increase the yield of valinomycin (a cyclododecadepsipeptide) in strain M10, additional antifungal metabolites, including bafilomycin derivatives (macrolide antibiotics), were identified. To examine the effect of bafilomycin biosynthesis on valinomycin production, the bafilomycin biosynthetic gene cluster was cloned from the genome of strain M10, as were two branched-chain α-keto acid dehydrogenase (BCDH) gene clusters related to precursor supply for bafilomycin biosynthesis. A null mutant (M10bafm) of one bafilomycin biosynthetic gene (bafV) failed to produce bafilomycin, but resulted in a 1.2- to 1.5-fold increase in the amount of valinomycin produced. In another null mutant (M10bkdFm) of a gene encoding a subunit of the BCDH complex (bkdF), bafilomycin production was completely abolished and valinomycin production increased fourfold relative to that in the wild-type M10 strain. The higher valinomycin yield was likely the result of redistribution of the metabolic flux from bafilomycin to valinomycin biosynthesis, because the two antibiotics share a common precursor, 2-ketoisovaleric acid, a deamination product of valine. The results show that directing precursor flux toward active ingredient biosynthesis could be used as a prospective tool to increase the competence of biofungicides.

Nocardioides rubroscoriae sp. nov., isolated from volcanic ash.

A rod-shaped actinobacterium, designated Sco-A25(T), was isolated from a red-coloured layer of scoria (volcanic ash) in the Republic of Korea and subjected to a polyphasic taxonomic characterization. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain Sco-A25(T) is a member of the genus Nocardioides and formed a tight monophyletic unit with the type strain of Nocardioides plantarum (98.7 % gene similarity). LL-Diaminopimelic acid was detected in the cell wall. The predominant menaquinone is MK-8(H4). The polar lipids found were phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, and an unknown phospholipid. The fatty acid profile was represented by large amounts of saturated, unsaturated and iso-branched fatty acids. The DNA G+C content was 71.6 mol %. Genomic DNA similarity between strain Sco-A25(T) and N. plantarum KCTC 9577(T) was 47.8 %. On the basis of the results of phenotypic, genetic and phylogenetic analyses presented here, strain Sco-A25(T) is considered to represent a novel species of the genus Nocardioides, for which the name Nocardioides rubroscoriae sp. nov. is proposed. The type strain is Sco-A25(T) (=KCTC 19805(T) = DSM 23986(T) = NBRC 107916(T)).

Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash.

A novel actinomycete, designated strain Sco-B14(T), was isolated from volcanic ash collected near Darangshi Oreum (a parasitic or satellite volcano) in Jeju, Republic of Korea. The organism formed well-developed, branched substrate mycelium, on which short chains of non-motile spores were arranged singly or in clusters. Aerial mycelium was not produced. Globose bodies were observed. The reverse colour of colonies was light brown to brown. Diffusible pigments were produced on ISP medium 3 and oatmeal-nitrate agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Sco-B14(T) formed a lineage within the family Micromonosporaceae and was distinct from established genera. The 16S rRNA gene sequence similarity of strain Sco-B14(T) to members of related genera of the family was 95.0-95.7 % to type strains of Catellatospora species, 94.7 % to Hamadaea tsunoensis IMSNU 22005(T), 94.7 % to Longispora albida K97-0003(T) and 94.0 % to Catelliglobosispora koreensis LM 042(T). 3-Hydroxydiaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Whole-cell sugars were glucose, rhamnose, ribose, xylose, arabinose, galactose and mannose. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The menaquinone profile contained MK-10(H(4)) (49 %), MK-9(H(4)) (24 %), MK-10(H(6)) (18 %) and MK-9(H(6)) (9 %). The predominant fatty acids were iso-C(15 : 0) and C(17 : 0). The DNA G+C content was 70.1 mol%. The combination of chemotaxonomic and phylogenetic data clearly separated the isolate from the type strains of all genera in the family Micromonosporaceae. On the basis of the phylogenetic and chemotaxonomic data presented in this paper, strain Sco-B14(T) is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Allocatelliglobosispora scoriae gen. nov., sp. nov. is proposed. The type strain of Allocatelliglobosispora scoriae is Sco-B14(T) (=KCTC 19661(T) =DSM 45362(T)).

Marmoricola korecus sp. nov.

A novel actinomycete, designated strain Sco-A36(T), was isolated from volcanic ash. Cells were aerobic, Gram-stain-positive, oxidase-negative, catalase-positive, non-motile cocci; colonies were yellow-coloured, smooth, entire and convex. Phylogenetic analysis showed that the organism formed a distinct phyletic line within the radiation of the genus Marmoricola. Its closest phylogenetic neighbours were Marmoricola aurantiacus DSM 12652(T) (97.9 % 16S rRNA gene sequence similarity), Marmoricola scoriae Sco-D01(T) (97.9 %), Marmoricola aequoreus SST-45(T) (97.4 %) and Marmoricola bigeumensis MSL-05(T) (96.3 %). The diagnostic diamino acid in the cell walls was ll-diaminopimelic acid. The predominant menaquinone was MK-8(H(4)). The polar lipids contained phosphatidylinositol, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine and an unknown phospholipid. The predominant fatty acids were C(16 : 0), C(17 : 1)ω8c, C(18 : 1)ω9c and C(16 : 1)ω7c and/or iso-C(15 : 0) 2-OH. The DNA G+C content of strain Sco-A36(T) was 71.0 mol%. Levels of DNA-DNA relatedness between the new isolate and the type strains of recognized species of the genus Marmoricola were 4.9-29.2 %. The phenotypic and DNA-DNA hybridization data presented here strongly suggest that strain Sco-A36(T) represents a novel species of the genus Marmoricola, for which the name Marmoricola korecus sp. nov. is proposed. The type strain is Sco-A36(T) ( = KCTC 19596(T) = DSM 22128(T)).

Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil.

Two novel Gram-reaction-positive, rod-shaped actinobacterial strains, designated RP-B26(T) and RP-B30(T), were isolated from rhizosphere soil of a cliff-associated plant (Peucedanum japonicum Thunb.) which was collected from Mara Island, Republic of Korea. The colonies of the isolates were circular, smooth, convex and moderately yellow-light-yellow in colour. 16S rRNA gene sequence analysis revealed that the isolates belonged to the family Nocardioidaceae and formed two distinct sublineages within the radiation of the genus Nocardioides. 16S rRNA gene sequence similarity between the isolates was 98.2 %. The closest phylogenetic neighbours of strain RP-B26(T) were Nocardioides humi DCY24(T) and Nocardioides kongjuensis A2-4(T) with 97.4 and 97.0 % 16S rRNA gene sequence similarity, respectively, whereas 16S rRNA gene sequence similarities between strain RP-B30(T) and N. humi DCY24(T) and N. kongjuensis A2-4(T) were 96.5 and 96.0 %, respectively. Both of the isolates contained ll-diaminopimelic acid as the diagnostic diamino acid in the cell walls. The predominant menaquinone was MK-8(H(4)). The polar lipids were phosphatidylinositol and phosphatidylglycerol. The fatty acid profiles of the isolates were characterized by the presence of saturated, unsaturated, 10-methyl and hydroxyl fatty acids, with small amounts of branched fatty acids. The DNA G+C contents of strains RP-B26(T) and RP-B30(T) were 73.0 and 71.7 mol%, respectively. Levels of DNA-DNA relatedness between the isolates were 44.9 ± 1.5 % (thermal renaturation method) and 43.2 % (photobiotin-labelled method); the isolates showed low DNA-DNA relatedness values (<11 %) to the most closely related strain, N. humi KCTC 19265(T). On the basis of the phenotypic, genotypic and DNA-DNA hybridization data presented here, the isolates are considered to represent two novel species of the genus Nocardioides, for which the names Nocardioides ultimimeridianus sp. nov. (type strain RP-B26(T)  = KCTC 19368(T)  = DSM 19768(T)) and Nocardioides maradonensis sp. nov. (type strain RP-B30(T)  = KCTC 19384(T)  = DSM 19769(T)) are proposed.

Actinomadura scrupuli sp. nov., isolated from rock.

A novel actinomycete, designated strain R-Ac121(T), was isolated from a small stone collected from an agricultural field in Jeju, Republic of Korea. The organism formed abundant vegetative mycelium that was branched and twisted. The reverse colour of colonies was brownish-yellow. Non-motile, wrinkled arthrospores were produced directly on the substrate mycelium. Aerial mycelium and sporangia were not observed. A neighbour-joining tree based on 16S rRNA gene sequences indicated that the isolate formed a distinct clade within the radiation of the family Thermomonosporaceae. The highest 16S rRNA gene sequence identity was found with the type strain of Spirillospora rubra (97.3 % sequence similarity) followed by those of Actinoallomurus purpureus (97.0 %), Actinomadura alba (96.5 %), Actinomadura fibrosa (96.5 %) and Actinomadura echinospora (96.4 %). The cell wall contained meso-diaminopimelic acid. The whole-cell sugars were rhamnose, glucose, ribose, xylose and arabinose. The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The major menaquinone was MK-9(H(6)) and the predominant fatty acids were iso-C(16 : 0), C(16 : 0), C(17 : 1)ω8c and 10-methyl C(17 : 0). The DNA G+C content was 71.8 mol%. The combination of morphological, chemotaxonomic and phylogenetic data clearly supports the separation of the organism from recognized species of the genus Actinomadura and related genera. On the basis of the data presented here, strain R-Ac121(T) represents a novel species of the genus Actinomadura, for which the name Actinomadura scrupuli sp. nov. is proposed. The type strain is strain R-Ac121(T) (=KCTC 19488(T) =DSM 45225(T)).

Isolation and characterization of five novel probiotic strains from Korean infant and children faeces.

Probiotics are dietary supplements containing viable, non-pathogenic microorganisms that interact with the gastrointestinal microflora and directly with the immune system. The possible health effects of probiotics include modulating the immune system and exerting antibacterial, anticancer, and anti-mutagenic effects. The purpose of this study was to isolate, identify, and characterize novel strains of probiotics from the faeces of Korean infants. Various assays were conducted to determine the physiological features of candidate probiotic isolates, including Gram staining, 16S rRNA gene sequencing, tolerance assays to stimulated gastric juice and bile salts, adherence ability assays, antibiotic susceptibility testing, and assays of immunomodulatory effects. Based on these morphological and biochemical characteristics, five potential probiotic isolates (Enterococcus faecalis BioE EF71, Lactobacillus fermentum BioE LF11, Lactobacillus plantarum BioE LPL59, Lactobacillus paracasei BioE LP08, and Streptococcus thermophilus BioE ST107) were selected. E. faecalis BioE EF71 and L. plantarum BioE LPL59 showed high tolerance to stimulated gastric juice and bile salts, and S. thermophilus BioE ST107 as well as these two strains exhibited stronger adherence ability than reference strain Lactobacillus rhamnosus GG. All five strains inhibited secretion of lipopolysaccharide-induced pro-inflammatory cytokines IL-6 and TNF-α in RAW264.7 macrophages in vitro. L. fermentum BioE LF11, L. plantarum BioE LPL59, and S. thermophilus BioE ST107 enhanced the production of anti-inflammatory cytokine IL-10. Overall, our findings demonstrate that the five novel strains have potential as safe probiotics and encouraged varying degrees of immunomodulatory effects.

Desorption and solubilization of anthracene by a rhamnolipid biosurfactant from Rhodococcus fascians.

The rhamnolipid biosurfactant-producing bacterium, strain SDRB-G7, was isolated from the sediment of Sindu-ri beach and identified as Rhodococcus fascians based on a phylogenetic analysis. Optimal activity, with the highest yield (2.441 g/L) and surface tension-reducing activity (24.38 mN/m), was observed when the cells were grown on olive oil as their sole source of carbon at pH 8.0. The rhamnolipid biosurfactant showed environmental stability at a variety of NaCl concentrations (2-20%) and pH values (2-12) even under acidic conditions. Of the initial anthracene, 66% was solubilized by 100% crude biosurfactant. Furthermore, 100% crude biosurfactant desorbed 81% of the anthracene in sediment into the aqueous phase. These results suggest that the rhamnolipid biosurfactant produced from R. fascians SDRB-G7 is a promising candidate for polycyclic aromatic hydrocarbon (PAH) removal from the sediment and can be an effective agent for processes that bioremediate PAHs such as surfactant-enhanced remediation. PRACTITIONER POINTS: Biosurfactants can accelerate desorption of PAHs and improve their solubility. BS-producing R. fascians SDRB-G7 was selected by screening of biochemical tests. Solubility of anthracene was enhanced by rhamnolipid produced by strain SDRB-G7. Microbial surfactant is a promising alternative for bioremediation of PAH-polluted sites.

Importance of functional diversity in assessing the recovery of the microbial community after the Hebei Spirit oil spill in Korea.

Over 10 years after the Hebei Spirit oil spill (HSOS), the concentrations of pollutants, such as TPH and PAHs, in spilled crude oil have recovered to background levels, but in some areas, the environment has not fully recovered. In particular, PAHs were more resistant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem. This study aimed to evaluate the microbial recovery of coastal sediments from the HSOS by analyzing the structure and diversity of the microbial community and its functional contribution to PAHs degradation. High-throughput sequencing on the MiSeq platform was conducted using tidal flat sediments collected in 2014 and 2016 from the area contaminated by the HSOS. The microbial recovery was evaluated by various diversity factors, including microbial composition and structure and functional diversity based on PICRUSt analysis. The abundance of microbial taxa associated with TPH degradation was higher in 2014 than that in 2016, but the taxa associated with PAHs degradation were similar between years. These results are consistent with the dynamics of microbes associated with the fate of pollutants, and they also showed similar tendency in functional profiles. That is, even if the pollutants are completely degraded, the microbial community has not yet completely recovered from the HSOS. The evaluation of microbial ecosystems in contaminated environments should consider both the fate of pollutants and the dynamics of microbial species that make functional contributions to the degradation of pollutants.