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The environmental resistome has been recognized as the origin and reservoir of antibiotic resistance genes and considered to be dynamic and ever expanding. In this study, a targeted gene sequencing approach revealed that the polymorphic diversity of the aminoglycoside-inactivating enzyme AAC(6')-Ib was ecological niche-specific. AAC(6')-Ib-cr, previously known as a clinical variant, was prevalent in various soils and the intestines of chickens and humans, suggesting that this variant might not have arisen from adaptive mutations in the clinic but instead originated from the environment. Furthermore, ecologically dominant polymorphic variants of AAC(6')-Ib were characterized and found to display different substrate specificities for quinolones and aminoglycosides, conferring the altered resistance spectra. Interestingly, a novel variant with the D179Y substitution showed an extended resistance spectrum to the recently developed fluoroquinolone gemifloxacin. Our results suggest that soil and animal microbiomes could be major reservoirs of antibiotic resistance; polymorphic diversity expands the antibiotic resistome in the environment, resulting in the potential emergence of novel resistance.

A Gram-staining-positive, motile, facultatively anaerobic, endospore-forming and rod-shaped bacterium, designated strain CJ32 T , was isolated from ginseng soil at Geumsan in Korea. The isolate grew optimally at 30 6C, 2 % (w/v) NaCl and pH 7.0. Colonies of strain CJ32 T were beige and circular with an entire margin on LB agar plates. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CJ32 T was associated with the genus Bacillus and was most closely related to Bacillus graminis YC6957 T (97.3 % similarity) and Bacillus lentus IAM 12466 T (97.1 %). DNA-DNA hybridization with closely related strains was below 31.3 %. The major respiratory isoprenoid quinone was MK-7. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The polar lipid profile of strain CJ32 T consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified lipids, including phospholipids, aminolipids and aminophospholipids. The predominant fatty acids of strain CJ32 T were iso-C 15 : 0 and anteiso-C 15 : 0 . The G+C content of the genomic DNA was 35.1 mol%. Based on phenotypic, genotypic and phylogenetic data, strain CJ32 T should be classified within a novel species of the genus Bacillus, for which the name Bacillus panacisoli sp. nov. is proposed. The type strain is strain CJ32 T (5KACC 17503 T 5JCM 19226 T ).

Fusarium graminearum species complex (FGSC) causes Fusarium head blight in small grain cereals. To date, four species (F. graminearum, F. asiaticum, F. boothii, and F. meridionale ) belonging to FGSC frequently occur in Korean cereals. In addition, we first reported the occurrence of additional species (F. vorosii ) within FGSC, which was isolated from barley, corn, and rice in Korea. Phylogenetic analysis of the Fusarium isolates of this group using combined multi-gene sequences confirmed species identification. Moreover, the macroconidia produced by these isolates were morphologically similar to those of the F. vorosii holotype. Chemical analysis indicated that the F. vorosii isolates produced various trichothecenes such as nivalenol and deoxynivalenol with their acetyl derivatives along with zearalenone. Pathogenicity tests demonstrated that all of the F. vorosii isolates examined were pathogenic on barley, corn, and rice with variation in aggressiveness. This study is the first report of F. vorosii in Korean cereals, their pathogenicity towards barley and corn, and their ability to produce trichothecenes and zearalenone.

A novel bacterial strain, designated CJ29 T , was isolated from ginseng soil of Anseong in South Korea. Cells of strain CJ29 T were Gram-stain-negative, facultatively anaerobic, rod-shaped and non-motile. Strain CJ29 T grew optimally at 28-30 6C and pH 7.0. Based on 16S rRNA gene sequence analysis, strain CJ29 T was shown to belong to the genus Lysobacter within the class Gammaproteobacteria and was related most closely to Lysobacter soli DCY21 T (98.5 % similarity) and Lysobacter niastensis GH41-7 T (98.2 %). DNA-DNA relatedness between strain CJ29 T and its closest relatives was below 55.6 %. The predominant cellular fatty acids of strain CJ29 T were iso-C 15 : 0 , iso-C 16 : 0 and iso-C 17 : 1 v9c. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The major isoprenoid quinone was ubiquinone 8 (Q-8). The G+C content of the genomic DNA was 65.6 mol%. Phenotypic, genotypic and phylogenetic characteristics strongly supported the differentiation of strain CJ29 T from related species of the genus Lysobacter. On the basis of data from this polyphasic taxonomic study, strain CJ29 T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panacisoli sp. nov. is proposed. The type strain is CJ29 T (5KACC 17502 T 5JCM 19212 T ).The genus Lysobacter was first proposed by Christensen & Cook (1978), and classified within the family Xanthomonadaceae belonging to the class Gammaproteobacteria. At the time of writing, the genus Lysobacter comprises 26 species with validly published names (http://www.bacterio.cict.fr/). Species of the genus Lysobacter are commonly found in diverse geographical and environmental habitats, especially in agricultural soil (Liu et al., 2011;Srinivasan et al., 2010;Ten et al., 2009). Members of the genus are generally characterized as Gram-negative, aerobic, non-fruiting and gliding bacteria with a high DNA G+C content typically ranging from 61.7 to 70.1 mol% (Christensen & Cook, 1978;Weon et al., 2006). Species of the genus Lysobacter contain ubiquinone 8 (Q-8) as the major respiratory quinone and show a predominance of iso-branched fatty acids (Fukuda et al., 2013;Luo et al., 2012;Saddler & Bradbury, 2005; Wei et al., 2012). Some members of the genus have potential for development of biocontrol agents based on their ability to lyse a variety of micro-organisms such as Gram-negative and Gram-positive bacteria, filamentous fungi, yeasts, green algae and nematodes (Ahmed et al., 2003;Folman et al., 2004;Kilic-Ekici & Yuen, 2003;Ryazanova et al., 2005). Strain CJ29 T was isolated on R2A agar (BBL) from a soil sample taken from a ginseng field of Anseong in South Korea. The isolate was subsequently cultivated on R2A agar at 30 u C for 3 days and stored as a stock culture in R2A broth (MBCell) supplemented with 30 % (v/v) glycerol. In this study, we describe the morphological, biochemical and phylogenetic characteristics of strain CJ29 T , employing the most closely related type strains, Lysobacter soli KCTC ...