Flavobacterium edaphi sp. nov., isolated from soil from Jeju Island, Korea.

An aerobic, Gram-stain-negative, bright yellow-pigmented, oxidase and catalase-positive, non-motile, non-spore forming, rod-shaped strain designated DMN11T was isolated from the soil of crossroads of Jeju Island in South Korea. Colonies were circular, bright yellow-pigmented and smooth with regular edges and measured approximately 1-2 mm in diameter. Flexirubin-type pigments were absent. Phylogenetic tree analysis based on the 16SrRNA gene sequence revealed that the strain DMN11T formed a lineage within the family Flavobacteriaceae of the phylum Bacteroidetes, and it was the most closely related to Flavobacterium suzhouense XIN-1T and Flavobacterium hauense BX12T (98.6% and 98.2% similarity, respectively). The major isoprenoid quinone was MK-6. The major fatty acids were summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c), iso-C15:0 and iso-C15:0 3OH. The polar lipid profile of the strain DMN11T showed the presence of phosphatidylethanolamine (PE) as major lipid. The DNA G+C content was 35.3 mol%, as determined by the thermal denaturation method. The mean levels of DNA-DNA relatedness of the strain DMN11T with F. suzhouense XIN-1T and F. hauense BX12T were 20.5% and 29.2%, respectively. Thus, the data accumulated in this study support the suggestion that the strain DMN11T is considered to represent a novel species of the genus Flavobacterieum, for which the name Flavobacterium edaphi sp. nov. is proposed. The type strain is DMN11T (= KCTC 62114T = JCM 32372T).

Edaphocola aurantiacus gen. nov., sp. nov., a new member of the family Chitinophagaceae isolated from wetland soil in South Korea.

A short rod-shaped, yellow-orange pigmented, strictly aerobic bacterium, designated as strain H2T, was isolated from the wetland soil of Halla Mountain, Jeju-island, South Korea. Growth was observed at temperatures of 10-30 °C (optimum at 25-30 °C), pH of 6-8 (optimum at pH 7), and salt concentrations of 0-1% (w/v) NaCl (optimum at 0%). The strain H2T was found to be a catalase and oxidase-positive, non-motile, Gram-negative bacterium. On the basis of 16S rRNA gene sequence similarity and phylogenetic analysis, strain H2T was found to be related to the members of the Chitinophagaceae family, being closely related to Taibaiella chishuiensis AY17T (94.3% sequence similarity). The major polar lipids are phosphatidylethanolamine and glycolipid. Strain H2T contained MK-7 as the only menaquinone as well as iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major fatty acids (> 15%). The DNA G+C content of strain H2T was determined to be 48.3 mol%. Based on the phylogenetic, phenotypic characteristics and chemotaxonomic analysis data, strain H2T (= KCTC 62115T = JCM 32353T) should be classified as representative of a novel species of a novel genus within the family Chitinophagaceae, for which the name Edaphocola aurantiacus gen. nov., sp. nov., is proposed.

Tellurirhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea.

Strain U15T, rod-shaped, catalase and oxidase positive, non-motile, hot pink pigmented, Gram-negative bacterium, was isolated from soil of Udo port, Udo Island, South Korea. Growth was observed at 10-48 °C, pH 6-11, and 0% (w/v) NaCl. Optimum growth conditions are 30-40 °C, pH 7-10, and 0% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA sequences showed that strain U15T forms a distinct clade with type strains of the family Cytophagaceae, with similarities below 89%. The major polar lipids are phosphatidylethanolamine and phosphatidylserine. Strain U15T was found to contain MK-7 as the only menaquinone, and iso-C15:0, C16:1ω5c, iso-C17:0 3-OH and summed feature 3 (comprising C16:1ω7c and/or C16:1ω6c) as the major fatty acids (> 10%). The DNA G + C content of strain U15T was determined to be 54.3 mol%. Based on the phylogenetic, phenotypic characteristics and chemotaxonomic analysis data, strain U15T (= KCTC 62116T = JCM 32361T) should be classified as representing a novel species of a novel genus within the family Cytophagaceae for which the name Tellurirhabdus rosea gen. nov., sp. nov., is proposed.

Paenibacillus mobilis sp. nov., a Gram-stain-negative bacterium isolated from soil.

A novel Gram-stain-negative bacterium, designated strain S8T, was isolated from a soil sample obtained in Gyeonggi Province, Republic of Korea. Cells of strain S8T were endospore-forming, motile by means of peritrichous flagella, and rod-shaped. S8T colonies were round, convex, wavy and white. Strain S8T grew optimally at 37 °C, pH 6-8, and up to 2.0 % (w/v) NaCl. Based on 16S rRNA gene sequence similarity, strain S8T was affiliated with the genus Paenibacillus in the family Paenibacillaceae and was most closely related to Paenibacillus yonginensis DCY84T and Paenibacillus physcomitrellae XBT (98.8 and 97.1 % sequence similarity). The DNA G+C content of the novel strain was 53.1±0.3 mol%. Strain S8T contained diphosphatidylglycerol, phosphatidylglycerol, two phospholipids, four aminophospholipids, an aminolipid and three unidentified lipids. The major fatty acid was anteiso-branched C15 : 0. The quinone was menaquinone MK-7. The peptidoglycan of strain S8T contained meso-diaminopimelic acid. The DNA-DNA hybridization values of strain S8T with P. yonginensis KCTC 33428T and P. physcomitrellae DSM 29851T were 44 % and 32 %, respectively. Data from the DNA-DNA hybridization, biochemical, phylogenetic and physiological analyses indicate that strain S8T (=KCTC 33848T=JCM 31672T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus mobilis sp. nov. is proposed.

Edaphorhabdus rosea gen. nov., sp. nov., a new member of the family Cytophagaceae isolated from soil in South Korea.

A Gram-stain negative, aerobic, oxidase and catalase positive, non-flagellated, pink coloured bacterium with gliding motility, designated as strain UDD1T was isolated from soil. The bacterium lacked flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain UDD1T formed a lineage within the family Cytophagaceae of the phylum Bacteroidetes, and forms a distinct clade with type strains of the closely related genus Pontibacter with similarities of 91.36-93.62%. Strain UDD1T contained MK-7 as the predominant menaquinone and summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B) and iso-C15:0 as the major fatty acids. The major polar lipids were phosphatidylethanolamine and an unidentified glycolipid. The DNA G+C content of strain UDD1T was 49 mol%. On the basis of phenotypic, genotypic and phylogenetic analyses, the strain UDD1T represents a novel species of a new genus in the family Cytophagaceae, for which the name Edaphorhabdus rosea gen. nov., sp. nov., is proposed. The type strain of Edaphorhabdus rosea is UDD1T (= KCTC 62117T = JCM 32366T). The Digital Protologue Database Taxon number for strain UDD1T is GA00058.

Hydrogenophaga soli sp. nov., isolated from rice field soil.

A novel Gram-stain-negative bacterial strain, designated strain S10T, was isolated from soil collected in a rice field in Goyang, South Korea. Cells of strain S10T were strictly aerobic, motile and rod-shaped. Colonies were round, convex, smooth and white. The strain grew optimally at 37 °C, pH 7.0 and 0 % (w/v) NaCl. Phylogenetic analysis of the 16S rRNA gene sequence of strain S10T revealed that the bacterium belongs to the family Comamonadaceae and is related to members of the genus Hydrogenophaga, with Hydrogenophaga caeni EMB71T being its closest relative (97.9 % sequence similarity). The DNA G+C content of strain S10T was 68.2 mol%. Strain S10T contained phosphatidylethanolamine and diphosphatidylglycerol as the major polar lipids. The major fatty acids were C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The predominant respiratory quinone was ubiquinone Q-8. DNA-DNA hybridization values of strain S10T with Hydrogenophaga caeni KCTC 12613T, Hydrogenophaga atypica DSM 15342T and Hydrogenophaga defluvii DSM 15341T were 16.1±4.8, 49.0±3.2 and 21.9±8.8 %, respectively. Based on phylogenetic distinctiveness, DNA-DNA hybridization and specific physiological and biochemical characteristics, strain S10T (=KCTC 52520T=JCM 31711T) is classified as a novel species of the genus Hydrogenophaga, for which the name Hydrogenophagasoli sp. nov. is proposed.

Rufibacter soli sp. nov., a Bacterium Isolated from Soil.

A gram-negative bacterium, designated FJY1(T), was isolated from a soil sample obtained from a university campus in South Korea. Examination showed that FJY1(T) was red-pigmented, aerobic, motile, and composed of nonspore-forming rods. This strain grew in a temperature range of 15-37 °C and a pH range of 7-9. Based on 16S rRNA gene sequence similarity, strain FJY1(T) was most closely related to Rufibacter roseus H359(T) and Rufibacter tibetensis 1351(T), with sequence similarities of 95.98 and 95.46 %, respectively. Its major cellular fatty acids were iso-C15:0 (18.16 %) and summed feature 4 (C17:1 iso I and C17:1 anteiso B; 15.17 %). The DNA G+C content of FJY1(T) was 49.7 mol%; its predominant quinone was MK-7; and its major polar lipid was phosphatidylethanolamine. Phylogenetic analysis and analysis of its physiological and biochemical characteristics indicated that this isolate constituted a novel species, for which we propose the name Rufibacter soli sp. nov., with the type strain FJY1(T) (=KCTC 42815(T) = JCM 31024(T)).

Alterations in Acetylation of Histone H4 Lysine 8 and Trimethylation of Lysine 20 Associated with Lytic Gene Promoters during Kaposi's Sarcoma-Associated Herpesvirus Reactivation.

Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with formation of Kaposi's sarcoma, multicentric Castleman's disease, and primary effusion lymphoma. Replication and transcription activator (RTA) genes are expressed upon reactivation of KSHV, which displays a biphasic life cycle consisting of latent and lytic replication phases. RTA protein expression results in KSHV genome amplification and successive viral lytic gene expression. Transcriptional activity of viral lytic genes is regulated through epigenetic modifications. In Raji cells latently infected with Epstein-Barr virus, various modifications, such as acetylation and methylation, have been identified at specific lysine residues in histone H4 during viral reactivation, supporting the theory that expression of specific lytic genes is controlled by histone modification processes. Data obtained from chromatin immunoprecipitation and quantitative real-time PCR analyses revealed alterations in the H4K8ac and H4K20me3 levels at lytic gene promoters during reactivation. Our results indicate that H4K20me3 is associated with the maintenance of latency, while H4K8ac contributes to KSHV reactivation in infected TREx BCBL-1 RTA cells.

Alterations in the airborne bacterial community during Asian dust events occurring between February and March 2015 in South Korea.

During Asian dust events, a relatively high concentration of particulate matter is transported by wind from arid and semi-arid regions, such as the Gobi and Taklamakan deserts, to nearby countries, including China, Korea, and Japan. The dust particles contain various microorganisms, which can affect human health as well as the environmental microbe population. In the current study, we investigated the characteristics of the airborne bacterial community during Asian dust events between February and March 2015 in South Korea. Bacterial diversity indexes such as operational taxonomic units, Chao1 and Inverse Simpson index were increased, along with total 16S rRNA gene copy number during Asian dust events. The bacterial community structure during Asian dust events was clearly distinguishable from that during non-Asian dust days. The genera Bacillus and Modestobacter were increased 3.9- and 2.7-fold, respectively, while Escherichia-Shigella was decreased by 89.8%. A non-metric multidimensional scaling plot with metadata analysis revealed association of particulate matter concentration, but not temperature, humidity or wind speed, with bacterial community structure, suggesting that the newly transported dust particles contain various microorganisms that influence the airborne bacterial environment.

Paenibacillus swuensis sp. nov., a bacterium isolated from soil.

Strain DY6(T), a Gram-positive endospore-forming motile rod-shaped bacterium, was isolated from soil in South Korea and characterized to determine its taxonomic position. Phylogenetic analyses based on the 16S rRNA gene sequence of strain DY6(T) revealed that strain DY6(T) belongs to the genus Paenibacillus in the family Paenibacillaceae in the class Bacilli. The highest degree of sequence similarities of strain DY6(T) were found with Paenibacillus gansuensis B518(T) (97.9%), P. chitinolyticus IFO 15660(T) (95.3%), P. chinjuensis WN9T (94.7%), and P. rigui WPCB173(T) (94.7%). Chemotaxonomic data revealed that the predominant fatty acids were anteiso-C(15:0) (38.7%) and C(16:0) (18.0%). A complex polar lipid profile consisted of major amounts of diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The predominant respiratory quinone was MK-7. Based on these phylogenetic, chemotaxonomic, and phenotypic data, strain DY6(T) (=KCTC 33026(T) =JCM 18491(T)) should be classified as a type strain of a novel species, for which the name Paenibacillus swuensis sp. nov. is proposed.