Jeotgalibaca ciconiae sp. nov., isolated from the faeces of an Oriental stork.

A novel, Gram-stain-positive, non-spore-forming, facultatively anaerobic bacterium, designated strain H21T32T, was isolated from the faeces of an Oriental stork, Ciconia boyciana. Cells formed cocci grouped in pairs, tetrads or conglomerates, and colonies on solid medium were pale yellow. Strain H21T32T belonged to the genus Jeotgalibaca, family Carnobacteriaceae, order Lactobacillales and class Bacilli. The 16S rRNA gene sequences of the strain showed 97.06-97.34, 96.17-96.31 and 95.93-96.07 % similarity to the type strains of Jeotgalibaca arthritidis, J. porci and J. dankookensis, respectively. The strain grew at 10-37 °C (optimum temperature: 30 °C), with 0-7 % (w/v) NaCl (optimum salinity: 0.5 %) and at pH 7-9 (optimum pH: 8). The main cellular fatty acids were C16 : 1 ω9c, C18 : 1 ω9c and C16 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. Respiratory quinones were not detected. Sugar components of the peptidoglycan were rhamnose, ribose and glucose. Amino acid components of the cell wall were l-alanine, d-glucose, l-lysine, glycine and aspartic acid. The DNA G+C content of the strain was 37.1 mol%. Average nucleotide identity between strain H21T32T and J. arthritidis CECT 9157T was 77.02 %, confirming that strain H21T32T represents a novel species of the genus Jeotgalibaca, for which the name Jeotgalibaca ciconiae sp. nov. is proposed. The type strain is H21T32T (=KCTC 33991T=JCM 33222T).

Tabrizicola piscis sp. nov., isolated from the intestinal tract of a Korean indigenous freshwater fish, Acheilognathus koreensis.

A novel Gram-negative, obligately aerobic, rod-shaped and non-motile bacterium, designated strain K13M18T, was isolated from the intestinal tract of a Korean indigenous fish, oily bitterling (Acheilognathus koreensis). Strain K13M18T formed creamy-pink colonies on a marine agar plate. Results of phylogenetic analysis based on the 16S rRNA gene sequence similarity indicated that strain K13M18T was most closely related to Tabrizicola sediminis DRYC-M-16T, sharing 97.62 % similarity with that strain. Strain K13M18T belonged to the genus Tabrizicola, which formed a cluster with Tabrizicola aquatica RCRI19T, Tabrizicola fusiformis SY72T, Tabrizicola sediminis DRYC-M-16T and Tabrizicola alkalilacus DJCT in a phylogenetic tree based on the 16S rRNA gene sequences. Strain K13M18T grown optimally in 0 % (w/v) NaCl, at pH 7 and 30 °C, in a marine broth medium. The predominant cellular fatty acids were C18 : 1 ω7c and C18 : 1 ω6c. The major respiratory isoprenoid quinone was ubiquinone Q-10. Polar lipids of strain K13M18T contained phosphatidylcholine, phosphatidylglycerol, phosphatidylinositol, diphosphatidylglycerol, six unidentified aminophospholipids, one unidentified aminolipid and an unidentified lipid. Based on genome sequencing, the DNA G+C content of strain K13M18T was 64.08 mol %, with an average nucleotide identity value, calculated by a comparative genomic analysis of strains K13M18T and T. sediminis DRYC-M-16T, of 74.82 %. Based on the phylogenetic, genotypic, and phenotypic information, strain K13M18T is proposed to be a novel species of the genus Tabrizicola. The type strain is K13M18T (=KCTC 62659T=JCM 33230T).

Flammeovirga pectinis sp. nov., isolated from the gut of the Korean scallop, Patinopecten yessoensis.

A novel Gram-stain-negative, aerobic, rod-shaped, reddish-orange-coloured, gliding bacterial strain, designated L12M1T, was isolated from the gut of the Korean scallop, Patinopecten yessoensis. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain L12M1T formed a monophyletic clade with the strains in the genus Flammeovirga and showed highest 16S rRNA gene sequence similarity to Flammeovirga kamogawensis YS10T (98.66 %). The major cellular fatty acids of strain L12M1T were iso-C15 : 0 and C20 : 4ω6,9,12,15c. The predominant isoprenoid quinone was MK-7. The major polyamines were spermidine, cadaverine and the minor polyamine was putrescine. The DNA G+C content was 32.1 mol%. The phylogenetic, phenotypic, biochemical, chemotaxonomic and genotypic results indicated that strain L12M1T represents a novel species of the genus Flammeovirga, for which the name Flammeovirga pectinis sp. nov. is proposed. The type strain is L12M1T (=KCTC 62750T=JCM 33169T).

Undibacterium piscinae sp. nov., isolated from Korean shiner intestine.

A novel Gram-stain-negative, non-spore-forming, obligate aerobic, motile, rod-shaped, and flagellated bacterium, designated S11R28T, was isolated from the intestinal tract of a Korean shiner, Coreoleuciscus splendidus. Based on 16S rRNA gene sequences, strain S11R28T was identified as member of the genus Undibacterium in class Betaproteobacteria, and was closely related to Undibacterium parvum DSM 23061T (98.49 %). The isolate grew at 4-25 °C, pH 6-9, with 0 % (w/v) NaCl, and grew optimally at 20 °C, pH 8, in the absence of NaCl. The main cellular fatty acids were C16 : 0 and summed features 3 (C16 : 1ω7c and/or C16 : 1ω6c). The strain possessed diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as predominant polar lipids, and ubiquinone Q-8 as a respiratory quinone. The polyamine profile composed of 2-hydroxyputrescine, spermidine, putrescine, and benzoic acid. A genomic DNA G+C content was 51.4 mol%. The average nucleotide identity between strains S11R28T and U. parvum DSM 23061T was 78.66 %. Thus, Undibacterium piscinae can be considered a novel species within the genus Undibacterium with the type strain S11R28T (=KCTC 62668T=JCM 33224T).

Cupriavidus sp. strain Ni-2 resistant to high concentration of nickel and its genes responsible for the tolerance by genome comparison.

The widespread use of metals influenced many researchers to examine the relationship between heavy metal toxicity and bacterial resistance. In this study, we have inoculated heavy metal-contaminated soil from Janghang region of South Korea in the nickel-containing media (20 mM Ni2+) for the enrichment. Among dozens of the colonies acquired from the several transfers and serial dilutions with the same concentrations of Ni, the strain Ni-2 was chosen for further studies. The isolates were identified for their phylogenetic affiliations using 16S rRNA gene analysis. The strain Ni-2 was close to Cupriavidus metallidurans and was found to be resistant to antibiotics of vancomycin, erythromycin, chloramphenicol, ampicillin, gentamicin, streptomycin, and kanamycin by disk diffusion method. Of the isolated strains, Ni-2 was sequenced for the whole genome, since the Ni-resistance seemed to be better than the other strains. From the genome sequence we have found that there was a total of 89 metal-resistance-related genes including 11 Ni-resistance genes, 41 heavy metal (As, Cd, Zn, Hg, Cu, and Co)-resistance genes, 22 cation-efflux genes, 4 metal pumping ATPase genes, and 11 metal transporter genes.

Iodobacter ciconiae sp. nov., a bacterium isolated from feces of oriental stork, Ciconia boyciana.

A novel Gram-stain-negative, facultatively anaerobic, non-motile, non-violet-pigmented, rod-shaped bacterium, designated strain H11R3T, was isolated from the feces of Oriental stork, Ciconia boyciana, collected from Seoul Grand Park Zoo, Republic of Korea. Phylogenetic analysis of the 16S rRNA gene sequence revealed that H11R3T formed a monophyletic clade with Iodobacter fluviatilisDSM 3764T, Iodobacter arcticusDSM 100243T, and Iodobacter limnosediminisDSM 103822T, with sequence similarities of 98.8, 98.6 and 98.4 %, respectively. H11R3T grew optimally at 15 °C, pH 8, with 0.5 % (w/v) NaCl. The predominant isoprenoid quinone was ubiquinone-8 (Q-8), and polar lipids included phosphatidylethanolamine, three unidentified lipids, four unidentified phospholipids, and two unidentified aminophospholipids. The major fatty acids were summed feature 3 and C16 : 0, and the DNA G+C content of the genome is 48.0 mol%. The average nucleotide identity (ANI) value between strains H11R3T and I. fluviatilis NCTC 11159T (=DSM 3764T) is 83.7 %. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characteristics, strain H11R3T represents a novel species of the genus Iodobacter for which the name Iodobacterciconiae sp. nov. is proposed. The type strain is H11R3T (=KCTC 62666T=JCM 33283T).

Rhizocompartments and environmental factors affect microbial composition and variation in native plants.

Molecular analysis based on large-scale sequencing of the plant microbiota has revealed complex relationships between plants and microbial communities, and environmental factors such as soil type can influence these relationships. However, most studies on root-associated microbial communities have focused on model plants such as Arabidopsis, rice or crops. Herein, we examined the microbiota of rhizocompartments of two native plants, Sedum takesimense Nakai and Campanula takesimana Nakai, using archaeal and bacterial 16S rRNA gene amplicon profiling, and assessed relationships between environmental factors and microbial community composition. We identified 390 bacterial genera, including known plant-associated genera such as Pseudomonas, Flavobacterium, Bradyrhizobium and Rhizobium, and uncharacterized clades such as DA101 that might be important in root-associated microbial communities in bulk soil. Unexpectedly, Nitrososphaera clade members were abundant, indicating functional association with roots. Soil texture/type has a greater impact on microbial community composition in rhizocompartments than chemical factors. Our results provide fundamental knowledge on microbial diversity, community and correlations with environmental factors, and expand our understanding of the microbiota in rhizocompartments of native plants.

Arthrobacter dokdonellae sp. nov., isolated from a plant of the genus Campanula.

A Gram-stain-positive, oxidase- and catalase-positive motile, aerobic, and rod-shaped bacterial strain, designated as DCT-5T, was isolated from a native plant belonging to the genus Campanula at Dokdo island, Republic of Korea. Growth of the strain DCT-5T was observed at 15-37°C (optimum 30°C) on R2A broth, pH 6.0-8.0 (optimum 7.0), and 0-5% (w/v) NaCl concentration (optimum 0%). The 16S rRNA gene sequence analysis revealed that strain DCT-5T was most closely related to Arthrobacter silviterrae KIS14-16T, Arthrobacter livingstonensis LI2T, Arthrobacter stackebrandtii CCM 2783T, Arthrobacter cryoconiti Cr6-08T, Arthrobacter ramosus CCM 1646T, and Arthrobacter psychrochitiniphilus GP3T with pairwise sequence similarities of 98.76%, 97.47%, 97.25%, 97.11%, 97.11%, and 97.00%, respectively. The DNA G+C content of strain DCT-5T was 64.7 mol%, and its DNA-DNA relatedness values with A. silviterrae KIS14-16T, A. livingstonensis LI2T, A. stackebrandtii CCM 2783T, A. psychrochitiniphilus GP3T, A. ramosus CCM 1646T, and A. cryoconiti Cr6-08T were 32.57 ± 2.02%, 28.75 ± 0.88%, 31.93 ± 1.15%, 34.73 ± 1.86%, 29.12 ± 1.56%, and 27.23 ± 0.88%, respectively. The major quinone was MK-9(H2) and major fatty acids were anteiso-C15:0, anteiso-C17:0, iso-C15:0, and iso-C16:0. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), unidentified glycolipid (GL), two unidentified aminophospholipids (APLs), and three unidentified lipids (Ls). The peptidoglycan type was A3α. On the basis of phenotypic, phylogenetic, genotypic, and chemotaxonomic characteristics, strain DCT-5T represents a novel species of the genus Arthrobacter, for which the name Arthrobacter dokdonellae sp. nov. is proposed. The type strain is DCT-5T (= KCTC 49189T = LMG 31284T).

Paraburkholderia dokdonella sp. nov., isolated from a plant from the genus Campanula.

The novel Gram-stain-negative, rod-shaped, aerobic bacterial strain DCR-13T was isolated from a native plant belonging to the genus Campanula on Dokdo, an island in the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence indicated that this strain is closely related to Paraburkholderia peleae PP52-1T (98.43% 16S rRNA gene sequence similarity), Paraburkholderia oxyphila NBRC 105797T (98.42%), Paraburkholderia sacchari IPT 101T (98.28%), Paraburkholderia mimosarum NBRC 106338T (97.80%), Paraburkholderia denitrificans KIS30-44T (97.46%), and Paraburkholderia paradise WAT (97.45%). This analysis of the 16S rRNA gene sequence also suggested that DCR-13T and the six closely related strains formed a clade within the genus Paraburkholderia, but that DCR-13T was clearly separated from the established species. DCR-13T had ubiquinone 8 as its predominant respiratory quinone, and its genomic DNA G + C content was 63.9 mol%. The isolated strain grew at a pH of 6.0-8.0 (with an optimal pH of 6.5), 0-4% w/v NaCl (with an optimal level of 0%), and a temperature of 18-42°C (with an optimal temperature of 30°C). The predominant fatty acids were C16:0, summed feature 8 (C18:1ω7c/C18:1ω6c), C17:0 cyclo, C19:0 cyclo ω8c, summed feature 3 (C16:1ω6c/C16:1ω7c) and summed feature 2 (C12:0 aldehyde), and the major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. On the basis of polyphasic evidence, it is proposed that strain DCR-13T (= KCTC 62811T = LMG 30889T) represents the type strain of a novel species, Paraburkholderia dokdonella sp. nov.

Paenibacillus seodonensis sp. nov., isolated from a plant of the genus Campanula.

Strain DCT-19T, representing a Gram-stain-positive, rodshaped, aerobic bacterium, was isolated from a native plant belonging to the genus Campanula on Dokdo, the Republic of Korea. Comparative analysis of the 16S rRNA gene sequence showed that this strain was closely related to Paenibacillus amylolyticus NRRL NRS-290T (98.6%, 16S rRNA gene sequence similarity), Paenibacillus tundrae A10bT (98.1%), and Paenibacillus xylanexedens NRRL B-51090T (97.6%). DNADNA hybridization indicated that this strain had relatively low levels of DNA-DNA relatedness with P. amylolyticus NRRL NRS-290T (30.0%), P. xylanexedens NRRL B-51090T (29.0%), and P. tundrae A10bT (24.5%). Additionally, the genomic DNA G + C content of DCT-19T was 44.8%. The isolated strain grew at pH 6.0-8.0 (optimum, pH 7.0), 0-4% (w/v) NaCl (optimum, 0%), and a temperature of 15-45°C (optimum 25-30°C). The sole respiratory quinone in the strain was menaquinone-7, and the predominant fatty acids were C15:0 anteiso, C16:0 iso, and C16:0. In addition, the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. Based on its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain DCT-19T is proposed as a novel species in the genus Paenibacillus, for which the name Paenibacillus seodonensis sp. nov. is proposed (=KCTC 43009T =LMG 30888T). The type strain of Paenibacillus seodonensis is DCT-19T.

Brevibacterium hankyongi sp. nov., isolated from compost.

A Gram-positive, strictly aerobic, non-motile, milky-white to creamy coloured and rod-shaped bacterium, designated BS05T, was isolated from compost. Phylogenetic analysis based on 16S rRNA gene sequence comparison revealed that the strain formed a distinct lineage within the genus Brevibacterium and was most closely related to Brevibacterium avium NCFB 3055T (96.3 %), Brevibacterium oceani BBH7T (96.2 %) and Brevibacterium epidermidis NBRC 14811T (96.1 %). The DNA G+C content was 62.3 mol%. The predominant quinone was MK-8(H2). The major fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 0. The cell-wall peptidoglycan of strain BS05T contained meso-diaminopimelic acid. The major polar lipid was phosphatidylglycerol. Moreover, the low sequence similarity of the 16S rRNA gene sequencing, physiological, biochemical and chemotaxonomic analyses allowed the phenotypic and genotypic differentiation of strain BS05T from the recognized species of the genus Brevibacterium. Therefore, strain BS05T represents a novel species of the genus Brevibacterium, for which the name Brevibacteriumhankyongi sp. nov. is proposed, with the type strain BS05T (=KACC 18875T=LMG 29562T).

Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil.

Strain 17bor-2T, a gamma-resistant, pink-to-red-coloured, aerobic, catalase-positive, oxidase-negative and Gram-stain-negative bacterium, was isolated from gamma ray-irradiated soil. The isolate grew aerobically at 18-37 °C (optimum, 28-30 °C), pH 6.0-8.0 (pH 6.5-7.5) and in the presence of 0-1 % (w/v) NaCl (0 % NaCl). Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 17bor-2T belonged to the genus Deinococcus with a highest sequence similarity of 96.4 % to Deinococcus alpinitundrae ME-04-04-52T. The major fatty acids of the strain were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and cyclo C17 : 0. The only respiratory quinone was MK-8. The major polar lipids of the strain were phosphoglycolipid, aminophospholipid and an unknown glycolipid. The DNA G+C content of strain 17bor-2T was 62.8 mol%. On the basis of its phenotypic, genotypic and chemotaxonomic characteristics, strain 17bor-2T should be classified as a novel species in the genus Deinococcus, for which the name Deinococcusirradiatisoli sp. nov. is proposed. The type strain is 17bor-2T (=KCTC 33907T=NBRC 113037T).

Roseomonas radiodurans sp. nov., a gamma-radiation-resistant bacterium isolated from gamma ray-irradiated soil.

A bacterial strain, designated 17Sr1-1T, was isolated from gamma ray-irradiated soil. Cells of this strain were Gram-stain-negative, strictly aerobic, motile and non-spore-forming rods. Growth occurred at 18-42 ˚C and pH 6.0-8.0, but no growth occurred at 2 % NaCl concentration. The major fatty acids of strain 17Sr1-1T were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), iso-C17 : 1ω5c and C16 : 0. The polar lipid profile contained diphosphatidylglycerol, glycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and four unidentified lipids. The G+C content of the genomic DNA of 17Sr1-1T was 71.9 mol%. The 16S rRNA gene sequence analysis showed that strain 17Sr1-1T was phylogenetically related to Roseomonas pecuniae N75T and Roseomonas rosea 173-96T (96.6 and 96.3 % sequence similarity, respectively). The genotypic and phenotypic data showed that strain 17Sr1-1T could be distinguished from its phylogenetically related species, and that this strain represented a novel species within the genus Roseomonas, for which the name Roseomonas radiodurans sp. nov. (type strain 17Sr1-1T=KCTC 52899T=NBRC 112872T) is proposed as the first reported gamma ray-resistant Roseomonas species.

Paenibacillus albilobatus sp. nov., isolated from acidic soil on Jeju Island.

A rod-shaped, white color colony with lobate architectures, strain h2T was isolated from a moderately acidic soil on Jeju Island, Republic of Korea. Comparative analysis of the 16S rRNA gene sequence showed that the strain h2T is closely related to Paenibacillus relictisesami DSM 25385T (97.4%, 16S rRNA gene sequence similarity), Paenibacillus azoreducens KACC 11244T (97.2%), and Paenibacillus cookii LMG 18419T (97.0%). DNA-DNA hybridization indicated that the strain h2T has relatively low levels of DNA-DNA relatedness with respect to P. relictisesami DSM 25385T (10.2%) and P. azoreducens KACC 11244T (13.7%). Additionally, the genomic DNA G + C content of h2T is 51.5 mol%. The isolated strain grew at pH 4.0-9.0 (optimum, pH 6.0-7.0) and 0-5% (w/v) NaCl (optimum, 0%) and a temperature of 15-45°C (optimum 35°C). The quinones in the strain are MK-6 and MK-7, and the predominant fatty acid is C15:0 anteiso (32.1%) followed by C17:0 anteiso (26.5%), and C16:0 iso (21.0%). Based on its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain h2T is proposed as a novel species in the genus Paenibacillus, for which the name Paenibacillus albilobatus sp. nov. is proposed (= KCCM 43269T = JCM 32395T = LMG 30408T). The type strain of Paenibacillus albilobatus is h2T.

KSHV vPK inhibits Wnt signaling via preventing interactions between ß-catenin and TCF4.

Viral factors interact with host cellular proteins, leading to dysregulation of signaling pathways. The Wnt pathway is known to participate in embryonic development and oncogenesis under dysregulation conditions. A downstream factor of the Wnt signaling pathway, ß-catenin, activates T-cell factor (TCF)-dependent transcription, which contributes to cell proliferation and tumorigenesis. In this study, we demonstrated that viral protein kinase (vPK) encoded by Kaposi's sarcoma-associated herpesvirus inhibits the Wnt signaling pathway without affecting nuclear localization and expression of ß-catenin. Coimmunoprecipitation and chromatin immunoprecipitation assays revealed that vPK interacts with ß-catenin, reducing the binding affinity on TCF binding regions as well as interactions of ß-catenin with TCF4. Overexpression of vPK led to reduced mRNA expression of cyclin D1, a well-known transcriptional product of Wnt signaling, suggesting that vPK effectively regulates the host signaling pathway through direct interactions with cellular proteins.

Adhaeribacter swui sp. nov., isolated from wet mud.

Strain 17mud1-7T, a pink, aerobic, catalase-positive, oxidase-positive and Gram-reaction-negative bacterium, was isolated from wet mud. The isolate grew aerobically at 18-37 °C (optimum 28 °C), at pH 6.0-8.0 (optimum pH 7.0) and in the presence of 0-1 % (w/v) NaCl (optimum 0 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 17mud1-7T belonged to the genus Adhaeribacter with highest sequence similarity of 96.4 % to Adhaeribacter aerophilus 6424S-25T. The strain showed the typical chemotaxonomic characteristics of the genus Adhaeribacter, with the presence of menaquinone MK-7 as the respiratory quinone, and summed feature 4 (composed of iso-C17 : 1 I/anteiso-C17 : 1 B), iso-C15 : 0 and C16 : 1ω5c as the major fatty acids are. The polar lipid profile contained two aminophosphoglycolipids, two glycolipids and three unidentified lipids. The DNA G+C content of strain 17mud1-7T was 45.9 mol%. Strain 17mud1-7T should thus be classified as representing a novel species in the genus Adhaeribacter, for which the name Adhaeribacter swui sp. nov. is proposed. The type strain is 17mud1-7T (=KCTC 52873T=NBRC 112824T).

Physiological and genomic insights into the lifestyle of arsenite-oxidizing Herminiimonas arsenitoxidans.

Arsenic, a representative toxic metalloid, is responsible for serious global health problems. Most organisms possess arsenic resistance strategies to mitigate this toxicity. Here, we reported a microorganism, strain AS8, from heavy metal/metalloid-contaminated soil that is able to oxidize arsenite, and investigated its physiological and genomic traits. Its cells were rod-shaped and Gram-negative, and formed small beige-pigmented colonies. 16S rRNA-based phylogenetic analysis indicated that the strain belongs to the genus Herminiimonas and is closely related to Herminiimonas glaciei UMB49T (98.7% of 16S rRNA gene sequence similarity), Herminiimonas arsenicoxydans ULPAs1T (98.4%), and Herminiimonas saxobsidens NS11T (98.4%). Under chemolithoheterotrophic conditions, the strain utilized some organic acids and amino acids as carbon and/or nitrogen sources but not electron sources. Further, the strain grew as a sulfur oxidizer in a complex medium (trypticase soy agar). Unexpectedly, most carbohydrates failed to support its growth as sole carbon sources. Genome sequencing supported these observations, and very few ABC transporters capable of oligo/monosaccharide uptake were identified in the AS8 genome. The genome harbored genes required for the colonization, flagella biosynthesis, urea degradation, and heavy metal and antibiotic resistance. Based on these polyphasic and genomic analyses, we propose that the strain AS8 be named Herminiimonas arsenitoxidans.

Distribution, Characterization, and Diversity of the Endophytic Fungal Communities on Korean Seacoasts Showing Contrasting Geographic Conditions.

This study analyzed the distribution of endophytic fungi in 3 coastal environments with different climatic, geographical, and geological characteristics: the volcanic islands of Dokdo, the East Sea, and the West Sea of Korea. The isolated fungal endophytes were characterized and analyzed with respect to the characteristics of their host environments. For this purpose, we selected common native coastal halophyte communities from three regions. Molecular identification of the fungal endophytes showed clear differences among the sampling sites and halophyte host species. Isolates were also characterized by growth at specific salinities or pH gradients, with reference to previous geographical, geological, and climate studies. Unlike the East Sea or West Sea isolates, some Dokdo Islands isolates showed endurable traits with growth in high salinity, and many showed growth under extremely alkaline conditions. A smaller proportion of West Sea coast isolates tolerate compared to the East Sea or Dokdo Islands isolates. These results suggest that these unique fungal biota developed through a close interaction between the host halophyte and their environment, even within the same halophyte species. Therefore, this study proposes the application of specific fungal resources for restoring sand dunes and salt-damaged agricultural lands and industrialization of halophytic plants.

Evolutionary, computational, and biochemical studies of the salicylaldehyde dehydrogenases in the naphthalene degradation pathway.

Salicylaldehyde (SAL) dehydrogenase (SALD) is responsible for the oxidation of SAL to salicylate using nicotinamide adenine dinucleotide (NAD+) as a cofactor in the naphthalene degradation pathway. We report the use of a protein sequence similarity network to make functional inferences about SALDs. Network and phylogenetic analyses indicated that SALDs and the homologues are present in bacteria and fungi. The key residues in SALDs were analyzed by evolutionary methods and a molecular simulation analysis. The results showed that the catalytic residue is most highly conserved, followed by the residues binding NAD+ and then the residues binding SAL. A molecular simulation analysis demonstrated the binding energies of the amino acids to NAD+ and/or SAL and showed that a conformational change is induced by binding. A SALD from Alteromonas naphthalenivorans (SALDan) that undergoes trimeric oligomerization was characterized enzymatically. The results showed that SALDan could catalyze the oxidation of a variety of aromatic aldehydes. Site-directed mutagenesis of selected residues binding NAD+ and/or SAL affected the enzyme's catalytic efficiency, but did not eliminate catalysis. Finally, the relationships among the evolution, catalytic mechanism, and functions of SALD are discussed. Taken together, this study provides an expanded understanding of the evolution, functions, and catalytic mechanism of SALD.

Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil.

Two gamma- and UVC-resistant bacterial strains, designated JSH3-1T and 9-2-2, were isolated from garden soil in South Korea. Cells were Gram-stain-positive, aerobic, non-motile and spherical. A polyphasic approach was used to study the taxonomic properties of strains JSH3-1T and 9-2-2. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences of strains JSH3-1T and 9-2-2 indicated highest similarity with Deinococcus radiomollis PO-04-20-132T (94.7 and 94.9 %, respectively); levels of sequence similarity with the type strains of other Deinococcus species were less than 94.0 %. Strains JSH3-1T and 9-2-2 shared relatively high 16S rRNA gene sequence similarity (98.7 %) and had a high DNA reassociation value of 81±0.5 %. Meanwhile, they showed low levels of DNA reassociation (<25 %) with other closely related species of the genus Deinococcus. The two strains showed chemotaxonomic features typical of the genus Deinococcus, with the presence of menaquinone 8 as the respiratory quinone. The predominant fatty acids were iso-C17 : 0, iso-C13 : 0 and anteiso-C13 : 0. The polar lipids comprised phosphoglycolipid, aminophospholipid, glycolipid and unknown aminolipids. The DNA G+C contents of strains JSH3-1T and 9-2-2 were 62.0 and 61.9 mol%, respectively. On the basis of their phenotypic and genotypic characteristics, and phylogenetic distinction, strains JSH3-1T (=KCTC 33790T=JCM 31311T) and 9-2-2 (=KCTC 33789=JCM 31310) should be classified within a novel species of the genus Deinococcus, for which the name Deinococcus ruber sp. nov. is proposed.