Sphingobacterium oryzagri sp. nov., isolated from rice paddy soil.

An aerobic, Gram-stain-negative and short rod-shaped bacterial strain, designated M6-31T, was isolated from rice paddy soil sampled in Miryang, Republic of Korea. Growth was observed at 4-35 °C (optimum, 28 °C), pH 6.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 0-4 % (w/v) NaCl (optimum, 0 % w/v). Phylogenetic analysis based on 16S rRNA gene sequences grouped strain M6-31T with Sphingobacterium bambusae IBFC2009T, Sphingobacterium griseoflavum SCU-B140T and Sphingobacterium solani MLS-26-JM13-11T in the same clade, with the 16S rRNA gene sequence similarities ranging from 95.8 to 96.6 %. A genome-based phylogenetic tree reconstructed by using all publicly available Sphingobacterium genomes placed strain M6-31T with S. bambusae KACC 22910T, 'Sphingobacterium deserti' ACCC 05744T, S. griseoflavum CGMCC 1.12966T and Sphingobacterium paludis CGMCC 1.12801T. Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain M6-31T and its closely related strains were lower than 74.6 and 22.0 %, respectively. The respiratory quinone was menaquinone-7, and the major polar lipid was phosphatidylethanolamine. The major fatty acids (>10 %) were C15 : 0 iso, C17 : 0 iso 3OH and summed feature 3. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that strain M6-31T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium oryzagri sp. nov. (type strain M6-31T=KACC 22765T=JCM 35893T) is proposed.

Lacticaseibacillus pabuli sp. nov., isolated from fermented cattle feed.

Strain BSF-3MT is a Gram-stain-positive, non-flagellated, facultative anaerobic and rod-shaped bacterium that was isolated from fermented feed collected at a cattle farm in the Daejeon region of the Republic of Korea. It was studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strain was primarily identified as a member of the genus Lacticaseibacillus. Strain BSF-3MT contained a chromosome of 2.5 Mbp and a plasmid of 33.4 kbp. The G+C content of genomic DNA was 51.3 mol%. Strain BSF-3MT had the highest ortho-average nucleotide identity value of 73.7 % with Lacticaseibacillus songhuajiangensis 7-19T, its closest relative in the phylogenetic tree based on the 16S rRNA gene sequences and the phylogenomic tree based on up-to-date bacterial core genes. Based on the results of a polyphasic taxonomic study, strain BSF-3MT represents a novel species in the genus Lacticaseibacillus, for which the name Lacticaseibacillus pabuli sp. nov. is proposed. The type strain is BSF-3MT (=KACC 23028T=NBRC 116014T).

Brevibacillus ruminantium sp. nov., isolated from cow faeces.

An aerobic, Gram-stain-positive, rod-shaped, endospore-forming bacterial strain, designated BB3-R1T, was isolated from cow faeces sampled in Daejeon, Republic of Korea. Growth was observed at 25-45 °C (optimum, 35-40 °C) and pH 7.0-9.0 (optimum, pH 8.0), with up to 3 % (w/v) NaCl (optimum, 0 % NaCl). blast analysis of 16S rRNA gene sequences revealed the highest sequence similarity of strain BB3-R1T to Brevibacillus borstelensis NRRL NRS-818T (98.8 %) followed by Brevibacillus panacihumi JCM 15085T (97.5 %). According to 16S rRNA gene and whole-genome based phylogenetic trees, strain BB3-R1T clustered with Brevibacillus composti FJAT-54423T and B. borstelensis NRRL NRS-818T. OrthoANI and dDDH values of strain BB3-R1T with the closely related strains were lower than 77.5 and 26.8 %, respectively. The major menaquinones and polar lipids of the strain were MK-7 and phosphatidylmonomethylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, respectively. The major fatty acids (>10 %) were C14 : 0 iso, C15 : 0 iso, C15 : 0 anteiso and C16 : 1 ω7c alcohol. The cell-wall peptidoglycan contained cross-linked meso-diaminopimelic acid (type A1 gamma). The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strain represents a novel species of the genus Brevibacillus, for which the name Brevibacillus ruminantium sp. nov. (type strain BB3-R1T=KACC 22663T=NBRC 115962T) is proposed.

Halobacillus salinarum sp. nov., Halobacillus shinanisalinarum sp. nov. and Halobacillus amylolyticus sp. nov., isolated from saltern soil.

Three bacterial strains, designated SSBR10-3T, SSTM10-2T and SSHM10-5T, were isolated from saltern soil sampled in Jeollanam-do, Republic of Korea. Cells were aerobic, Gram-stain-positive, flagellated and rod-shaped. The strains grew optimally at 28°C and at pH 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains SSBR10-3T, SSTM10-2T and SSHM10-5T were placed within the genus Halobacillus, showing the highest similarity to Halobacillus alkaliphilus FP5T (98.6 %), 'Halobacillus ihumii' Marseille-Q1234T (98.5 %) and Halobacillus locisalis MSS-155T (98.6 %), respectively. The genomic similarity values between strains SSBR10-3T, SSTM10-2T and SSHM10-5T and their related species were 17.6-22.6 % for digital DNA-DNA hybridization (dDDH) and 69.6-78.5 % for orthologous average nucleotide identity (OrthoANI), which were lower than the thresholds recommended for species delineation. The dDDH and OrthoANI values among the three strains were below 38.3 and 89.4 %, respectively. Besides the differences in genomic features, strains SSBR10-3T, SSTM10-2T and SSHM10-5T were distinct from each other and from members of the genus in terms of phenotypic traits related to substrate assimilation. The cell-wall peptidoglycan contained meso-diaminopimelic acid, the major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, and the predominant menaquinone was MK-7 for all three strains. Diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid were present in their polar lipid profiles. Based on a polyphasic approach incorporating genomic data, strains SSBR10-3T, SSTM10-2T and SSHM10-5T represent novel species, for which the names Halobacillus salinarum sp. nov. (SSBR10-3T=DSM 114353T=KACC 21935T=NBRC 115504T), Halobacillus shinanisalinarum sp. nov. (SSTM10-2T=DSM 114354T=KACC 21936T=NBRC 115505T) and Halobacillus amylolyticus sp. nov. (SSHM10-5T=DSM 114355T= KACC 21937T=NBRC 115506T) are proposed.

Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment.

Two aerobic, Gram-stain-positive, spore-forming motile bacterial strains, designated SSPM10-3T and SSWR10-1T, were isolated from salterns in Jeollanam province of South Korea. Both strains were halotolerant and grew well in 5 % NaCl but not in 20 and 25% NaCl, respectively. Optimal growth was observed with 5 % NaCl, at 30 °C and at pH 7.0-8.0. On the basis of the results of phylogenetic analysis using 16S rRNA gene sequence, both the strains were placed within the genus Gracilibacillus with Gracilibacillus massiliensis (98.65 % similarity) as their nearest neighbour. Menaquinone-7 (MK-7) (97 %) was the major isoprenoid quinone in both strains and major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Orthologous average nucleotide identity with usearch (OrthoANIu) and digital DNA-DNA hybridisation (dDDH) percentage comparison indicated that SSPM10-3T and SSWR10-1T exhibited highest similarity with G. massiliensis Awa-1T at 74.27 % and 21.0 and 74.23 % and 20.0 %, respectively. The DNA G+C contents of the strains were 39.1 % (SSPM10-3T) and 38.5 % (SSWR10-1T). Members of the genus Gracilibacillus, both strains were distinct from each other with respect to their ability to produce urease, ß-glucosidase, assimilation of inulin and methyl-α-d-glucopyranoside and degradation of casein. Compared with each other, ANI and d4 dDDH calculations were only 88.2 % and 36.3 %, well below the cut-off values for species delineation for each index. On the basis of their phenotypic, physiological, biochemical and phylogenetic characteristics,SSPM10-3T and SSWR10-1T represent distinct novel species for which names Gracilibacillus salinarum SSPM10-3T and Gracilibacillus caseinilyticus SSWR10-1T are proposed. The type strains are SSPM10-3T (=KACC 21933T =NBRC 115502T) and SSWR10-1T (=KACC 21934T =NBRC 115503T).

Five novel Hymenobacter species isolated from air: Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov.

Five Hymenobacter strains isolated from air samples collected from the Suwon and Jeju regions of the Republic of Korea were studied using polyphasic taxonomic methods. Using 16S rRNA gene sequences and the resulting phylogenetic tree, the strains were primarily identified as members of the genus Hymenobacter. Digital DNA-DNA hybridization values and average nucleotide identities values for species delineation (70 and 95-96 %, respectively) between the five strains and their nearest type strains indicated that each strain represented a novel species. All strains were aerobic, Gram-stain-negative, mesophilic, rod-shaped and catalase- and oxidase-positive, with red to pink coloured colonies. The genome sizes of the five strains varied from 4.8 to 7.1 Mb and their G+C contents were between 54.1 and 59.4 mol%. Based on their phenotypic, chemotaxonomic and genotypic characteristics, we propose to classify these isolates into five novel species within the genus Hymenobacter for which we propose the names, Hymenobacter cellulosilyticus sp. nov., Hymenobacter cellulosivorans sp. nov., Hymenobacter aerilatus sp. nov., Hymenobacter sublimis sp. nov. and Hymenobacter volaticus sp. nov., with strains 5116 S-3T (=KACC 21925T=JCM 35216T), 5116 S-27T (=KACC 21926T=JCM 35217T), 5413 J-13T (=KACC 21928T=JCM 35219T), 5516 S-25T (=KACC 21931T=JCM 35222T) and 5420 S-77T (=KACC 21932T=JCM 35223T) as the type strains, respectively.

Agromyces larvae sp. nov., a novel actinobacterium isolated from gut of larvae of Protaetia brevitarsis seulensis.

A novel actinobacterium strain, designated CFWR-12T, was isolated from the larval gut of Protaetia brevitarsis seulensis grown at the National Institute of Agricultural Sciences, Wanju-gun, Republic of Korea, and its taxonomic position was evaluated. Strain CFWR-12T was aerobic, Gram-stain-positive and non-motile. Growth occurred at 10-40 °C, pH 6.0-9.0 and 0-4 % (w/v) NaCl, with optimal growth at 28-30 °C, pH 7.0 and in the absence of NaCl. Strain CFWR-12T showed high 16S rRNA gene sequence similarity to Agromyces intestinalis KACC 19306T (99.0 %) and Agromyces protaetiae FW100M-8T (97.9 %). The genome sequence of strain CFWR-12T was 4.01 Mb in size with a high G+C content of 71.2 mol%. The values of average nucleotide identity and digital DNA-DNA hybridization between strain CFWR-12T and A. intestinalis KACC 19306T were 89.8 and 39.1 %, respectively, which were the highest among the closely related Agromyces species. The predominant cellular fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0, and the major respiratory quinones (>10 %) were MK-11 and MK-12. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipid while the peptidoglycan type was identified to be B1. Data based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strain CFWR-12T represents a novel species of the genus Agromyces, for which the name Agromyces larvae sp. nov. is proposed. The type strain is strain CFWR-12T (=KACC 19307T= NBRC 113047T).

Production of a New Biosurfactant by a New Yeast Species Isolated from Prunus mume Sieb. et Zucc.

Biosurfactants reduce surface and interfacial tension due to their amphiphilic properties and are an eco-friendly alternative for chemical surfactants. In this study, a new yeast strain JAF-11 that produces a biosurfactant was selected using drop collapse method, and the properties of the extracts were investigated. The nucleotide sequences of the strain were compared with closely related strains and identified based on the D1/D2 domain of the large subunit ribosomal DNA (LSU) and internal transcribed spacer (ITS) regions. Neodothiora populina CPC 39399T, the closest species with strain JAF-11, showed a sequence similarity of 97.75% for LSU and 94.27% for ITS, respectively. The result suggests that the strain JAF-11 represents a distinct species that cannot be assigned to any existing genus or species in the family Dothideaceae. Strain JAF-11 produced a biosurfactant reducing the surface tension of water from 72 mN/m to 34.5 mN/m on the sixth day of culture and the result of measuring the critical micelle concentration (CMC) by extracting the crude biosurfactant was found to be 24 mg/l. The molecular weight 502 of the purified biosurfactant was confirmed by measuring the fast atom bombardment mass spectrum. The chemical structure was analyzed by measuring 1H nuclear magnetic resonance (NMR), 13C NMR, and two-dimensional NMRs of the compound. The molecular formula was C26H46O9, and it was composed of one octanoyl group and two hexanoyl groups to myo-inositol moiety. The new biosurfactant is the first report of a compound produced by a new yeast strain, JAF-11.

Whole-Genome Sequence of Mucilaginibacter jinjuensis Strain KACC 16571T.

We report the whole-genome sequence of Mucilaginibacter jinjuensis type strain KACC 16571, which was isolated from rotten wood in South Korea. The genome of Mucilaginibacter jinjuensis KACC 16571T consists of a 6.16-Mb circular chromosome, with a G+C content of 42.1% and 5,262 total predicted coding genes.

Leucobacter allii sp. nov. and Leucobacter rhizosphaerae sp. nov., isolated from rhizospheres of onion and garlic, respectively.

Three bacterial strains, H21R-40T and H21R-36 from garlic (Allium sativum) and H25R-14T from onion (Allium cepa), were isolated from plant rhizospheres sampled in the Republic of Korea. Results of 16S rRNA gene sequence analysis revealed the highest sequence similarity of strain H21R-40T to Leucobacter celer subsp. astrifaciens CBX151T (97.3 %) and Leucobacter triazinivorans JW-1T (97.2 %), and strain H25R-14T to Leucobacter insecticola HDW9BT (98.8 %) and Leucobacter humi Re6T (98.4 %), while the sequence similarity between strains H21R-40T and H21R-36 was 99.8 %. According to the phylogenomic tree, strains H21R-40T with H21R-36 formed an independent clade separable from other Leucobacter species within the genus Leucobacter and strain H25R-14T clustered with Leucobacter insecticola HDW9BT, Leucobacter coleopterorum HDW9AT and Leucobacter viscericola HDW9CT. Strains H21R-40T and H21R-36 had orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values (98.1 % and 86.9 %, respectively) higher than the threshold ranges for species delineation (95-96 % and 70 %, respectively). The OrthoANI and dDDH values between two strains (H21R-40T and H25R-14T) and the type strains of species of the genus Leucobacter were lower than 81 and 24 %, respectively. The peptidoglycan type of three strains was type B1. The major menaquinones and major polar lipids of the strains were MK-11 and MK-10, and diphosphatidylglycerol, phatidylglycerol and an unidentified glycolipid, respectively. The major fatty acids (more than 10 % of the total fatty acids) of strains H21R-40T and H21R-36 were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0, and those of strain H25R-14T were anteiso-C15 : 0 and iso-C16 : 0. The phenotypic, chemotaxonomic and genotypic data obtained in this study showed that the strains represent two novel species of the genus Leucobacter, named Leucobacter allii sp. nov. (H21R-40T and H21R-36) and Leucobacter rhizosphaerae sp. nov. (H25R-14T). The respective type strains are H21R-40T (=DSM 114348T=JCM 35241T=KACC 21839T=NBRC 115481T) and H25R-14T (=DSM 114346T=JCM 35239T=KACC 21837T=NBRC 115479T).

Draft Genome Sequences of Three Type Strains, Acetobacter farinalis KACC 21251, Acetobacter suratthaniensis KACC 21252, and Acetobacter thailandicus KACC 21253.

As part of a genome database construction of type strains, we report the draft genome sequences of three strains of acetic acid bacteria, i.e., Acetobacter farinalis KACC 21251T, Acetobacter suratthaniensis KACC 21252T, and Acetobacter thailandicus KACC 21253T.

Spirosoma oryzicola sp. nov., isolated from dried rice husk.

Strain RHs26T is an aerobic, Gram-stain-negative, non-flagellated and rod- or filamentous-shaped (1.0-1.1×2.3-50 µm) bacterium that was isolated from dried rice husk. It was positive for oxidase and catalase, hydrolysed starch and Tween 80, and weakly hydrolysed CM-cellulose. The strain grew at temperatures between 10 and 37 °C (optimum, 28 °C), in 0-1 % NaCl (optimum, 0 %) and at pH 6.0-9.0 (optimum, pH 7.0-8.0). The predominant membrane fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 1 ω5c, iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, an unidentified aminolipid, two unidentified aminophospholipids and two unidentified lipids. The predominant quinone was menaquinone MK-7. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain RHs26T belongs to the genus Spirosoma, presenting the highest sequence similarity to Spirosoma agri S7-3-3T (95.8 %). The genomic DNA G+C content of strain RHs26T was 49.5 %. Strain RHs26T showed the highest orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values of 76.4 % and 20.0 % with S. agri KCTC 52727T while sharing OrthoANI and dDDH values of 74.6 % and 19.2 % with Spirosoma terrae KCTC 52035T, the closest relative in the phylogenomic tree. Based on the results of a polyphasic taxonomic study, strain RHs26T represents a novel species in the genus Spirosoma, for which the name Spirosoma oryzicola sp. nov. is proposed. The type strain is RHs26T (=JCM 35224T=KACC 17318T).

Frateuria soli sp. nov. and Frateuria edaphi sp. nov., isolated from greenhouse soil.

Two bacterial strains, designated 5GH9-11T and 5GH9-34T, were isolated from greenhouse soil sampled in Wanju-gun, Jeollabuk-do, Republic of Korea. Both strains formed yellow colonies and were aerobic, rod-shaped and flagellated. The 16S rRNA gene sequence similarity between 5GH9-11T and 5GH9-34T was 98.6 %. Strain 5GH9-11T showed the highest sequence similarities to Dyella thiooxydans ATSB10T (98.1 %) and Frateuria aurantia DSM 6220T (97.7 %) while strain 5GH9-34T revealed the highest sequence similarity to F. aurantia DSM 6220T (98.3 %) and D. thiooxydans ATSB10T (98.3 %). Phylogenetic analysis on the basis of the 16S rRNA gene sequence showed that strains 5GH9-11T and 5GH9-34T formed a robust cluster with Frateuria flava MAH-13T and Frateuria terrea NBRC 104236T. The phylogenomic tree also showed that strains 5GH9-11T and 5GH9-34T formed a robust cluster with F. terrea DSM 26515T and F. flava MAH-13T. Strain 5GH9-11T showed the highest orthologous average nucleotide identity (OrthoANI; 88.5 %) and digital DNA-DNA hybridization (dDDH) values (35.5 %) with F. flava MAH-13T, and strain 5GH9-34T revealed highest OrthoANI (88.1 %) and dDDH (34.2 %) values with F. flava MAH-13T. The orthoANI and dDDH values between strain 5GH9-11T and 5GH9-34T were 87.7 and 33.9 %, respectively. Their major respiratory quinone was ubiquinone 8, and the major cellular fatty acids were iso-C16 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The major polar lipids of both strains were composed of large or moderate amounts of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminolipid and an unidentified aminophospholipid. Based on these data, strains 5GH9-11T and 5GH9-34T should represent two independent novel species of Frateuria, for which the names Frateuria soli sp. nov. (type strain 5GH9-11T=KACC 16943T=JCM 35197T) and Frateuria edaphi sp. nov. (type strain 5GH9-34T=KACC 16945T=JCM 35198T) are proposed.

Melaminivora suipulveris sp. nov., isolated from pigpen dust.

A bacterial strain designated SC2-9T was isolated from the dust collector of a pigpen located in Wanju-gun, Jeollabuk-do, Republic of Korea. Cells were strictly aerobic, Gram-stain-negative, flagellated and rod-shaped. The strain was catalase- and oxidase-positive, and grew optimally 28-30 °C, pH 8.0 and 0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed 99.1 and 98.3 % similarities to Melaminivora jejuensis KBB12T and Melaminivora alkalimesophila CY1T, and revealing less than 97 % similarity to other validly named species. The genomic DNA G+C content of strain SC2-9T was 68.2 %. The orthologous average nucleotide identity and dDDH values of strain SC2-9T with the closest species Melaminivora jejuensis KCTC 32230T were 85.6 and 29.3 %, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids and one unidentified lipid. The major fatty acids (>10 %) were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω6c and/ or C18 : 1 ω7c). The predominant isoprenoid quinone was ubiquinone-8. Based on phenotypic, chemotaxonomic and phylogenetic data, strain SC2-9T should be assigned as a novel species of the genus Melaminivora, for which the name Melaminivora suipulveris sp. nov. is proposed. The type strain is SC2-9T (=KACC 19310T=NBRC 113103T).

Aristophania vespae gen. nov., sp. nov., isolated from wasps, is related to Bombella and Oecophyllibacter, isolated from bees and ants.

Acetic acid bacteria (family Acetobacteraceae) are found in the gut of most insects. Two clades are currently recognized: Commensalibacter-Entomobacter and Bombella-Oecophyllibacter. The latter group is only found in hymenopteran insects and the described species have been isolated from bees and ants. In this study, two new strains DDB2-T1T (=KACC 21507T=LMG 31759T) and DM15PD (=CCM 9165=DSM 112731=KACC 22353=LMG 32454) were isolated from wasps collected in the Republic of Korea and Germany, respectively. Molecular and phenotypic analysis revealed that the strains are closely related, with 16S rRNA gene sequences showing 100 % identity and genomic average nucleotide identity (ANI) values ≥99 %. The closest related species based on type strain 16S rRNA gene sequences are Swingsia samuiensis, Acetobacter peroxydans, Bombella favorum and Bombella intestini (94.8-94.7% identity), whereas the closest related species based on type strain genome analysis are Saccharibacter floricola and Bombella intestini (ANI values of 68.8 and 68.2 %, respectively). The reconstruction of a phylogenomic tree based on 107 core proteins revealed that the branch leading to DDB2-T1T and DM15PD is localized between Oecophyllibacter and Saccharibacter-Bombella. Further genomic distance metrics such as ANI, percentage of conserved proteins and alignment fraction values were consistent with these strains belonging to a new genus. The key phenotypic characteristics were one MALDI-TOF-MS peak (m/z=4601.9±2.0) and the ability to produce acid from d-arabinose. Based on this polyphasic approach, including phylogenetics, phylogenomics, genome distance calculations, ecology and phenotypic characteristics, we propose to name the novel strains Aristophania vespae gen. nov., sp. nov., with the type strain DDB2-T1T (=KACC 21507T=LMG 31759T).

Neodothiora pruni sp. nov., a Biosurfactant-Producing Ascomycetous Yeast Species Isolated from Flower of Prunus mume.

A yeast strain, designated as JAF-11T, was isolated from flower of Prunus mume Sieb. et Zucc. in Gwangyang, Republic of Korea. Phylogenetic analysis showed that strain JAF-11T was closely related to Neodothiora populina CPC 39399T with 2.07 % sequence divergence (12 nucleotide substitutions and three gaps in 581 nucleotides) in the D1/D2 domain of the large subunit (LSU) rRNA gene, and Rhizosphaera macrospora CBS 208.79T with 4.66 % sequence divergence (25 nucleotide substitutions and five gaps in 535 nucleotides) in the internal transcribed spacer (ITS) region. Further analysis based on the concatenated sequences of the D1/D2 domain of the LSU rRNA gene and the ITS region confirmed that strain JAF-11T was well-separated from Neodothiora populina CPC 39399T. In addition to the phylogenetic differences, strain JAF-11T was distinguished from its closest species, Neodothiora populina CPC 39399T and Rhizosphaera macrospora CBS 208.79T belonging to the family Dothioraceae by its phenotypic characteristics, such as assimilation of carbon sources. Hence, the name Neodothiora pruni sp. nov. is proposed with type strain JAF-11T (KACC 48808T; MB 850034).

A New Approach Using the SYBR Green-Based Real-Time PCR Method for Detection of Soft Rot Pectobacterium odoriferum Associated with Kimchi Cabbage.

Pectobacterium odoriferum is the primary causative agent in Kimchi cabbage soft-rot diseases. The pathogenic bacteria Pectobacterium genera are responsible for significant yield losses in crops. However, P. odoriferum shares a vast range of hosts with P. carotovorum, P. versatile, and P. brasiliense, and has similar biochemical, phenotypic, and genetic characteristics to these species. Therefore, it is essential to develop a P. odoriferum- specific diagnostic method for soft-rot disease because of the complicated diagnostic process and management as described above. Therefore, in this study, to select P. odoriferum-specific genes, species-specific genes were selected using the data of the P. odoriferum JK2.1 whole genome and similar bacterial species registered with NCBI. Thereafter, the specificity of the selected gene was tested through blast analysis. We identified novel species-specific genes to detect and quantify targeted P. odoriferum and designed specific primer sets targeting HAD family hydrolases. It was confirmed that the selected primer set formed a specific amplicon of 360 bp only in the DNA of P. odoriferum using 29 Pectobacterium species and related species. Furthermore, the population density of P. odoriferum can be estimated without genomic DNA extraction through SYBR Green-based real-time quantitative PCR using a primer set in plants. As a result, the newly developed diagnostic method enables rapid and accurate diagnosis and continuous monitoring of soft-rot disease in Kimchi cabbage without additional procedures from the plant tissue.

Chryseobacterium oryzae sp. nov. and Chryseobacterium suipulveris sp. nov., isolated from Andong sikhye and pigpen dust, respectively.

Two Gram-stain-negative, aerobic, mesophilic, rod-shaped bacteria, ADR-1T and SC2-2T, were isolated from Andong sikhye and dust in a pigpen, respectively. The phylogenetic tree on the basis of 16S rRNA gene sequences showed that strains ADR-1T and SC2-2T were members of the genus Chryseobacterium and revealed the highest sequence similarities to Chryseobacterium binzhouense LM2T (97.6 %) and Chryseobacterium koreense Chj707T (94.9 %), respectively. Phylogenomic treeing using 92 core genes clearly indicated that strain ADR-1T clustered with Chryseobacterium echinoideorum CC-CZW010T, Chryseobacterium binzhouense LM2T and Chryseobacterium taihuense CGMCC 1.10941T, and strain SC2-2T formed a compact cluster with Chryseobacterium koreense CCUG 49689T. The digital DNA-DNA hybridization (dDDH) and orthologous average nucleotide identity (ANI) values of strain ADR-1T with the closely related species of the genus Chryseobacterium were ≤24.4 % and ≤80.7 %, and those of strain SC2-2T were ≤24.0 % and ≤77.8 %, respectively, which are well below the cut-off values of species discrimination (>70 % dDDH and >95-96 % ANI). The only respiratory quinone in both strains was menaquinone 6. The polar lipid profile of strain ADR-1T comprised phosphatidylethanolamine, four unidentified aminolipids and three unidentified lipids, while strain SC2-2T contained phosphatidylethanolamine, two unidentified aminolipids, one unidentified aminophospholipid and five unidentified polar lipids. The major fatty acids (>10 %) of strain ADR-1T were iso-C15 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl), iso-C17 : 0 3-OH and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), and those of strain SC2-2T were iso-C15 : 0 and anteiso-C15 : 0. On the basis of the results of phenotypic and phylogenetic analyses, strains ADR-1T and SC2-2T represent two distinct novel species in the genus Chryseobacterium, for which the names Chryseobacterium oryzae sp. nov. (type strain ADR-1T=KACC 19311T=NBRC 113104T) and Chryseobacterium suipulveris sp. nov. (type strain SC2-2T=KACC 19313T=NBRC 113106T) are proposed.

Ferruginibacter albus sp. nov., isolated from a mountain soil, and Mucilaginibacter robiniae sp. nov., isolated from a black locust flower, Robinia pseudoacacia.

Two bacterial strains, designated KIS38-8T and F39-2T, were isolated from a mountain soil sample and a black locust flower (Robinia pseudoacacia) in Republic of Korea, respectively. The phylogenetic tree based on 16S rRNA gene sequences showed that strain KIS38-8T was classified into the genus Ferruginibacter with the highest sequence similarity to Ferruginibacter lapsinanis HU1-HG42T (96.6 %), and strain F39-2T was grouped into the genus Mucilaginibacter with the highest sequence similarity to Mucilaginibacter daejeonensis Jip 10T (97.6 %). Orthologous average nucleotide identity and digital DNA-DNA hybridization values between strain KIS38-8T and closely related Ferruginibacter strains were less than 72 and 19 %, respectively, while those values between strain F39-2T and closely related Mucilaginibacter strains were less than 73 and 21 %, respectively. The DNA G+C contents of strain KIS38-8T and F39-2T were 36.4 and 41.4 mol%, respectively. On the basis of the phenotypic and genotypic evidence, strains KIS38-8T and F39-2T are considered to represent novel species of the genus Ferruginibacter and Mucilaginibacter, respectively, for which the names Ferruginibacter albus sp. nov. (type strain KIS38-8T=KACC 17328T=NBRC 113101T) and Mucilaginibacter robiniae sp. nov. (type strain F39-2T=KACC 19733T=JCM 33062T) have been proposed.

Duganella dendranthematis sp. nov. and Massilia forsythiae sp. nov., isolated from flowers.

Two aerobic, Gram-stain-negative, motile, mesophilic, rod-shaped and catalase-positive bacterial strains designated AF9R3T and GN2-R2T were isolated from flowers collected in the Republic of Korea. Strain AF9R3T grew at 4-33 °C, pH 4.0-9.0 and with 0-1 % NaCl (w/v), and strain GN2-R2T grew at 10-33 °C, pH 4.0-9.0 and with 0-1 % NaCl (w/v). Phylogenetic analysis on the basis of 16S rRNA gene sequences indicated that strains AF9R3T and GN2-R2T belonged to the genera Duganella and Massilia, respectively, showing high sequence similarity to Duganella levis CY42WT (99.4 %) and Massilia putida 6 NM-7T (98.0 %), respectively. Both strains contained summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids, and ubiquinone Q-8 as the predominant quinone. Strain AF9R3T had diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and strain GN2-R2T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the major polar lipids. Orthologous average nucleotide identity and digital DNA-DNA hybridization values of strain AF9R3T to its closest relative D. levis CY42WT were 92.6 and 56.5 %, and those of strain GN2-R2T to its closest relative M. putida 6 NM-7T were 81.4 and 24.8 %. Based on genotypic and phenotypic data, strains AF9R3T and GN2-R2T are considered to represent novel species of the genus Duganella and Massilia, respectively, for which the names Duganella dendranthematis sp. nov. (type strain AF9R3T=KACC 21258T=NBRC 114510T) and Massilia forsythiae sp. nov. (type strain GN2-R2T=KACC 21261T=NBRC 114511T) have been proposed.