Yochan Joung

Nocardioides endophyticus sp. nov. and Nocardioides conyzicola sp. nov., isolated from herbaceous plant roots

Two Gram-stain-positive, non-motile, non-spore-forming, rod-shaped actinobacterial strains were isolated from the surface-sterilized roots of mugwort (Artemisia princeps) and horse-weed (Conyza canadensis), and subjected to taxonomic characterization. 16S rRNA gene sequence analysis indicated that the isolates, designated MWE 3-5(T) and HWE 2-02(T), should be placed in the genus Nocardioides of the family Nocardioidaceae. The strains were closely related to Nocardioides hankookensis DS-30(T), which exhibited 16S rRNA gene sequence similarity values of 97.99 and 99.09u200a% with strains MWE 3-5(T) and HWE 2-02(T), respectively. The genome relatedness of N. hankookensis DS-30(T) with strain MWE 3-5(T) was 35.8u200a%, and that with strain HWE 2-02(T) was 36.4u200a%, whereas that between the two isolates was 43.2u200a%. Strains MWE 3-5(T) and HWE 2-02(T) possessed MK-8(H4) as the major isoprenoid quinone, and ll-diaminopimelic acid in the cell-wall peptidoglycan. The main fatty acids were iso-C16u200a:u200a0, iso-C17u200a:u200a0 and C18u200a:u200a1ω9c for strain MWE 3-5(T) and iso-C16u200a:u200a0, 10-methyl C18u200a:u200a0 and C18u200a:u200a1ω9c for strain HWE 2-02(T). Based on phenotypic, genotypic and phylogenetic studies, the following two novel species are proposed: Nocardioides endophyticus sp. nov. (type strain, MWE 3-5(T)u200a=u200aKCTC 29122(T)u200a=u200aJCM 18532(T)) and Nocardioides conyzicola sp. nov. (type strain, HWE 2-02(T)u200a=u200aKCTC 29121(T)u200a=u200aJCM 18531(T)).

Bacterial diversity in the indoor air of pharmaceutical environment.

To monitor bacterial diversity of ISO Class 8 pharmaceutical clean room environment using conventional culture‐based methods and pyrosequencing analysis.

Paenibacillus oenotherae sp. nov. and Paenibacillus hemerocallicola sp. nov., isolated from the roots of herbaceous plants.

Two Gram-staining-positive, aerobic, endospore-forming, motile bacteria, strains DT7-4T and DLE-12T, were isolated from roots of evening primrose (Oenothera biennis) and day lily (Hemerocallis fulva), respectively, and subjected to taxonomic characterization. Analysis of 16S rRNA gene sequences indicated that the two strains fell into two distinct phylogenetic clusters belonging to the genus Paenibacillus. Strain DT7-4T was most closely related to Paenibacillus phyllosphaerae PALXIL04T and Paenibacillus taihuensis THMBG22T, with 96.3% 16S rRNA gene sequence similarity to each, and strain DLE-12T was most closely related to Paenibacillus ginsengarvi Gsoil 139T and Paenibacillus hodogayensis SGT, with 96.6 and 93.3% sequence similarity, respectively. Both isolates contained anteiso-C15u2009:u20090 as the dominant fatty acid, meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and MK-7 as the respiratory menaquinone. The cellular polar lipids were composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and unidentified polar lipids. The DNA G+C contents of strains DT7-4T and DLE-12T were 50.1u2009±u20090.7 and 55.2u2009±u20090.5u200amol%, respectively. The chemotaxonomic properties of both isolates were typical of members of the genus Paenibacillus. However, our biochemical and phylogenetic analyses distinguished each isolate from related species. Based on our polyphasic taxonomic analysis, strains DT7-4T and DLE-12T should be recognized as representatives of novel species of Paenibacillus, for which the names Paenibacillus oenotherae sp. nov. (type strain DT7-4Tu2009=u2009KCTC 33186Tu2009=u2009JCM 19573T) and Paenibacillus hemerocallicola sp. nov. (type strain DLE-12Tu2009=u2009KCTC 33185Tu2009=u2009JCM 19572T) are proposed.

Sphingomonas aeria sp. nov. from indoor air of a pharmaceutical environment

A proteobacterial strain designated R1-3T was isolated from indoor air of a pharmaceutical environment. Cells were Gram-stain-negative, oxidase- and catalase-positive, aerobic, motile and rod-shaped. Strain R1-3T grew optimally at pH 7, 30xa0°C and in 0–2xa0% NaCl on R2A agar. The 16S rRNA gene sequence analysis indicated that strain R1-3T belongs to the genus Sphingomonas, and is closely related to Sphingomonas paucimobilis ATCC 29837T (98.4xa0% sequence similarity). However, the DNA–DNA relatedness between the two strains was 43xa0±xa05xa0% (reciprocalxa0=xa037xa0±xa03xa0%), which was well below the suggested level for species distinction. Sphingomonas yabuuchiae GTC868T (97.7xa0% 16S rRNA gene sequence similarity) and Sphingomonas pseudosanguinis G1-2T (97.6xa0%) were also found as distantly related taxa. Strain R1-3T was sensitive to most of the tested antibiotics except for erythromycin and streptomycin. The major fatty acid was a summed feature consisting of C18:1 ω7c and/or C18:1 ω6c, and minor proportions of C14:0 2-OH, C16:0 and a summed feature consisting of C16:1 ω7c and/or C16:1 ω6c were also present. The DNA Gxa0+xa0C content was 67.2xa0±xa01.0xa0mol%. The major polyamines were sym-homospermidine and spermidine. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, and minor amounts of a sphingoglycolipid, a phospholipid, an aminoglycolipid and an unidentified lipid were also present. The phenotypic, phylogenetic and chemotaxonomic data not only supported the affiliation of strain R1-3T to the genus Sphingomonas, but also distinguished R1-3T from related species. On the basis of physiological, chemotaxonomic and phylogenetic evidences, strain R1-3T clearly merits recognition as a novel species of Sphingomonas, for which the name Sphingomonas aeria sp. nov. is proposed. The type strain is R1-3T (=xa0KCTC 42061Txa0=xa0JCM 19859T).

Conyzicola lurida gen. nov., sp. nov., isolated from the root of Conyza canadensis

A novel Gram-stain-positive, non-spore-forming, pale yellow, irregular rod-shaped bacterium designated strain HWE2-01(T) was isolated from the surface-sterilized root of horseweed (Conyza canadensis). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HWE2-01(T) belongs to the family Microbacteriaceae and showed sequence similarity levels of 97.1-97.7% with species of the genus Salinibacterium, 95.9-97.6% with species of the genus Leifsonia and 97.1% with Homoserinimonas aerilata. The highest sequence similarity (97.7%) was with Salinibacterium xinjiangense 0543(T). The genomic DNA G+C content of the novel strain was 68.1 mol%. The predominant cellular fatty acid of strain HWE2-01(T) was anteiso-C15u200a:u200a0, major menaquinones were MK-10, MK-9 and MK-11, and diagnostic polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The peptidoglycan of the novel strain contained 2,4-diaminobutyric acid, alanine, glycine and glutamic acid. The cell-wall sugars of strain HWE2-01(T) were galactose, mannose and rhamnose. The murein was of the acetyl type. Based on the results of the phenotypic and phylogenetic analysis, strain HWE2-01(T) differed in some respects from other members of the family Microbacteriaceae. Therefore, strain HWE2-01(T) is proposed to represent a novel species of a new genus in the family Microbacteriaceae with the name Conyzicola lurida gen. nov., sp. nov. (type strainu200a=u200aHWE2-01(T)u200a=u200aKCTC 29231(T)u200a=u200aJCM 19257(T)).

Flavobacterium fluminis sp. nov. to accommodate an aerobic, halotolerant and gliding flavobacterium isolated from freshwater

A Gram-stain-negative, aerobic, oxidase-positive, catalase-positive and rod-shaped bacterium designated strain 3R17T was isolated from freshwater. Strain 3R17T produced bright-yellow, circular, convex and smooth colonies on R2A agar, tryptic soy agar, potato dextrose agar, nutrient agar and brain-heart infusion agar media. The strain was motile by gliding. The strain grew at 4-30u2009°C (optimum, 25u2009°C), at pH 6-9 (optimum, pH 7) and in the presence of up to 3u200a% NaCl (optimum, 0u200a%) on R2A agar. The 16S rRNA gene sequence analysis indicated that 3R17T represents a member of the genus Flavobacterium and is most closely related to Flavobacterium resistens BD-b365T, with a sequence similarity of 97.78u200a%, but the strain formed a distinct phylogenetic lineage of its own. Fatty acid analysis indicated that a summed feature comprising C16u200a:u200a1ω7c and/or C16u200a:u200a1ω6c, iso-C15u200a:u200a0, iso-C15u200a:u200a1G, anteiso-C15u200a:u200a0, C16u200a:u200a0, iso-C17u200a:u200a0 3-OH and iso-C15u200a:u200a0 3-OH were the major components (>5u200a%). Strain 3R17T contained phosphatidylethanolamine (PE) and several unidentified aminolipids as main polar lipids, and MK-6 as the predominant isoprenoid quinone. Flexirubin pigments were not produced. The DNA G+C content was 35.4u2009mol%. The combination of physiological and chemotaxonomic properties distinguished 3R17T from related species of the genus Flavobacterium. On the basis of polyphasic taxonomy, 3R17T evidently represents a novel species within the genus Flavobacterium, for which the name Flavobacterium fluminis sp. nov. is proposed. The type strain is 3R17T (=KCTC 42062T=JCM 30338T).

Fluviicoccus keumensis gen. nov., sp. nov., isolated from freshwater.

A Gram-stain-negative, non-spore-forming and coccus-shaped bacterial strain, designated 4DR5T, was isolated from freshwater and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-40u2009°C (optimum 30u2009°C), at pHu20096-9 (optimum pHu20097) and in the presence of 0-0.4u2009% (w/v) NaCl (optimum 0u2009%) on R2A agar. On the basis of 16S rRNA gene sequence similarity, strain 4DR5T was assigned to the family Moraxellaceae of the class Gammaproteobacteria, and its closest related taxa were species of the genera Perlucidibaca (93.67u2009% sequence similarity), Agitococcus (93.07u2009%), Paraperlucidibaca (92.31-92.38u2009%), Alkanindiges (91.79u2009%) and Acinetobacter (90.24-91.23u2009%). The predominant isoprenoid quinone detected in strain 4DR5T was Q-10. The major cellular fatty acids were a summed feature consisting of C16u2009:u20091ω7c and/or C16u2009:u20091ω6c, one consisting of C18u2009:u20091ω7c and/or C18u2009:u20091ω6c, and C16u2009:u20090. The major polar lipid was phosphatidylethanolamine. The genomic DNA G+C content of the strain was 61.2u200amol%. The phylogenetic, chemotaxonomic and biochemical data not only supported the affiliation of strain 4DR5T to the family Moraxellaceae, but also separated it from other established genera within the family. Therefore, the novel isolate evidently represents a novel species of a new genus of Moraxellaceae, for which the name Fluviicoccus keumensis gen. nov., sp. nov. is proposed. Theu2002type strain of Fluviicoccus keumensis is 4DR5T (u2009=u2009KCTC 32475Tu2009=u2009JCM 19370T).

Taibaiella soli sp. nov., isolated from pine forest soil.

A Gram-stain-negative, motile by gliding, non-spore-forming and oval-shaped bacterial strain designated T1-10T was isolated from pine forest soil, and its taxonomic position was investigated using a polyphasic approach. Growth occurred at 10-37u2009°C (optimum, 30u2009°C), at pH 6-7 and in the presence of 0-1u2009% (w/v) (optimum, 0u2009%) NaCl. Flexirubin-type pigments were produced. On the basis of 16S rRNA gene sequence similarity, strain T1-10T was assigned to the genus Taibaiella of the phylum Bacteroidetes, and the most closely related species was Taibaiella koreensis THG-DT86T with 97.11u2009% sequence similarity, but the strain formed an independent lineage in the phylogenetic tree. The genomic DNA G+C content of strain T1-10T was 42.5 mol%. The main cellular fatty acids were iso-C15u2009:u20091 G, iso-C15u2009:u20090 and iso-C17u2009:u20090 3-OH. The only isoprenoid quinone detected in the strain was MK-7, and the major polyamine was homospermidine. The major polar lipids were phosphatidylethanolamine and unidentified aminophospholipids. Strain T1-10T could be distinguished from related species by physiological and biochemical properties. Phenotypic and phylogenetic data supported that strain T1-10T represents a novel species of the genus Taibaiella, for which the name Taibaiella soli sp. nov. is proposed (type strain T1-10T=KCTC 42277T=JCM 31014T).

Antibiotic resistance among aquatic bacteria in natural freshwater environments of Korea

The taxonomic diversity and antibiotic resistance among freshwater bacterial communities in the major water bodies of Korea was examined using 437 penicillin-resistant, and 110 tetracycline-resistant bacterial isolates. Based on 16S rRNA gene sequence analysis, most isolates were assigned to Proteobacteria, which was then followed by Bacteroidetes. Strains of Aeromonas were found as the most abundant penicillin-resistant populations, whereas those affiliated to diverse species including enteric groups were found as the most abundant tetracycline-resistant populations. Most strains exhibited multiple antibiotic resistance, and all tested strains were resistant to penicillin and hygromycin. High levels of resistance were observed for antibiotics acting on cell wall synthesis, whereas low levels were for those acting on DNA replication or transcription in general. It is apparent from this study that penicillin resistance is widespread among environmental bacteria, although the antibiotic has been generally non-detectable in the environment. It is also likely from the taxonomic composition of the resistant communities that various sources including terrestrial animals and humans may contribute to antibiotic resistance in the freshwater environment.

Filimonas endophytica sp. nov., isolated from surface-sterilized root of Cosmos bipinnatus.

A Gram-stain-negative, yellow, motile by gliding, filamentous bacterium, designated SR 2-06T, was isolated from surface-sterilized root of garden cosmos. 16S rRNA gene sequence analysis indicated that SR 2-06T was related most closely to Filimonas lacunae YT21T of the family Chitinophagaceae at a sequence similarity of 96.90u2009%, while levels of similarity to other related taxa were less than 93.08u2009%. Strain SR 2-06T exhibited similar features to F. lacunae in that it contained MK-7 as the major respiratory quinone, and iso-C15u2009:u20091 G, iso-C15u2009:u20090 and a summed feature consisting of C16u2009:u20091ω6c and/or C16u2009:u20091ω7c as the major fatty acids. However, strain SR 2-06T was distinguished from F. lacunae using a combination of physiological and biochemical properties. The cellular polar lipids were phosphatidylethanolamine, unknown aminophospholipids, unknown aminolipids, an unknown phospholipid and unidentified polar lipids. The DNA G+C content was 46.0u200amol%. The phenotypic and phylogenetic evidence clearly indicates that strain SR 2-06T represents a novel species of the genus Filimonas, for which the name Filimonas endophytica sp. nov. is proposed. The type strain is SR 2-06T (u2009=u2009KCTC 42060Tu2009=u2009JCM 19844T).