Sung-Heun Cho

Diversity and physiological properties of root endophytic actinobacteria in native herbaceous plants of Korea

Endophytic actinobacterial diversity in the native herbaceous plant species of Korea was analyzed using a culture-based approach. Sixty one actinobacterial strains were isolated, and assigned to 15 genera based on 16S rRNA gene analysis. The members of the genus Streptomyces comprised 45.9% of the total isolates, followed by Micromonospora (18.8%), Rhodococcus (6.6%), Microbispora (4.9%), and Micrococcus (4.9%). Other minor constituents included members of Microbacterium, Streptacidiphilus, Arthrobacter, Dietzia, Kitasatospora, Herbiconiux, Mycobacterium, Nocardia, Rathayibacter, and Tsukamurella. Among the isolates, 65.6% exhibited at least one hydrolytic enzyme activity out of four, and 45.9% exhibited antagonistic activity against at least one fungal pathogen out of five, thus demonstrating that endophytic actinobacteria can be an important source of bioactive compounds. Notably, most strains of Streptomyces proved active for both enzymatic and antagonistic activities.

Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov.

The taxonomic positions of five Gram-negative, non-spore-forming and non-motile bacterial strains isolated from the rhizosphere of sand dune plants were examined using a polyphasic approach. The analysis of the 16S rRNA gene sequence indicated that all of the isolates fell into four distinct phylogenetic clusters belonging to the genus Chryseobacterium of the family Flavobacteriaceae. The 16S rRNA gene sequence similarities of isolates to mostly related type strains of Chryseobacterium ranged from 97.5% to 98.5%. All strains contained MK-6 as the predominant menaquinone, and iso-C(15:0), iso-C(17:0) 3-OH and a summed feature of iso-C(15:0) 2-OH and/or C(16:1) omega7c as the dominant fatty acids. Combined phenotypic, genotypic and chemotaxonomic data supported that they represented four novel species in the genus Chryseobacterium, for which the names Chryseobacterium hagamense sp. nov. (type strain RHA2-9(T)=KCTC 22545(T)=NBRC 105253(T)), Chryseobacterium elymi sp. nov. (type strain RHA3-1(T)=KCTC 22547(T)=NBRC 105251(T)), Chryseobacterium lathyri sp. nov. (type strain RBA2-6(T)=KCTC 22544(T)=NBRC 105250(T)), and Chryseobacterium rhizosphaerae sp. nov. (type strain RSB3-1(T)=KCTC 22548(T)=NBRC 105248(T)) are proposed.

Gramella gaetbulicola sp. nov., a member of the family Flavobacteriaceae isolated from foreshore soil

A Gram-reaction-negative, yellow-pigmented, gliding, rod-shaped, aerobic bacterium (RA5-111(T)) was isolated from foreshore soil. The taxonomic status of the novel isolate was determined using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities, strain RA5-111(T) could be assigned to the genus Gramella, with sequence similarities of 97.7, 97.3 and 96.2 % to the type strains of Gramella echinicola, Gramella portivictoriae and Gramella marina, respectively. Chemotaxonomic and phenotypic characteristics also supported the affiliation of strain RA5-111(T) with the genus Gramella. The genomic DNA G+C content was 39.1 mol%. The isolate contained MK-6 as the predominant menaquinone, iso-C(15 : 0), iso-C(17 : 0) 3-OH and a summed feature (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) as major fatty acids, and phosphatidylethanolamine and unknown phospholipids as the polar lipids. DNA-DNA relatedness, phenotypic, genotypic and chemotaxonomic data clearly indicate that the isolate represents a novel species of the genus Gramella, for which the name Gramella gaetbulicola sp. nov. is proposed. The type strain is RA5-111(T) ( = KCTC 23022(T) = JCM 16528(T) = NBRC 106272(T)).

Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake

A non-motile, red-pigmented bacterium, designated strain HMD1010(T), was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010(T) formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C(16 : 1)ω5c (21.9 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c; 17.2 %), iso-C(15 : 0) (14.5 %) and summed feature 4 (anteiso-C(17 : 1) B and/or iso-C(17 : 1) I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010(T) represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010(T) ( = KCTC 22745(T)  = CECT 7546(T)).

Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils

The taxonomic positions of 22 spore-forming, extensively branched actinobacteria isolated from Pinus soils were examined using a polyphasic approach. Analysis of the 16S rRNA gene sequences indicated that all of the isolates fell into three distinctive phylogenetic clusters within the genus Streptacidiphilus of the family Streptomycetaceae, and also that Streptacidiphilus jiangxiensis was the species closest to the three phyloclusters, with 16S rRNA gene sequence similarities ranging from 98.0 to 99.2 %. However, the low DNA-DNA relatedness values between representatives of the three clusters and S. jiangxiensis clearly differentiated them from one another. Representative isolates were also found to have chemotaxonomic features typical of the genus Streptacidiphilus and were distinguishable from all established species of Streptacidiphilus on the basis of a combination of phenotypic properties. It is evident from this study that each of the three phyloclusters should be equated with three novel Streptacidiphilus species, for which the following names are proposed: Streptacidiphilus anmyonensis sp. nov. (type strain AM11(T) =NBRC 103185(T) =KCTC 19278(T)), Streptacidiphilus rugosus sp. nov. (type strain AM16(T) =NBRC 103186(T) =KCTC 19279(T)) and Streptacidiphilus melanogenes sp. nov. (type strain SB-B34(T) =NBRC 103184(T) =KCTC 19280(T)).

Myroides marinus sp. nov., a member of the family Flavobacteriaceae, isolated from seawater

A Gram-negative, aerobic, non-motile, yellow-pigmented, rod-shaped bacterium (strain JS-08(T)) isolated from seawater was subjected to a polyphasic taxonomic study. 16S rRNA gene sequence analysis indicated that strain JS-08(T) belongs to the genus Myroides, a member of the phylum Bacteroidetes. Its closest phylogenetic relative was Myroides odoratimimus JCM 7460(T), with which it shared 97.0 % 16S RNA gene sequence similarity. Strain JS-08(T) contained menaquinone-6 (MK-6) as the predominant menaquinone, and the dominant fatty acids were iso-C(15 : 0), iso-C(17 : 0) 3-OH and a summed feature consisting of iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c. The DNA G+C content of strain JS-08(T) was 34.2 mol%. Based on phenotypic, genotypic and phylogenetic evidence, it is suggested that strain JS-08(T) represents a novel species of the genus Myroides, for which the name Myroides marinus sp. nov. is proposed. The type strain is JS-08(T) ( = KCTC 23023(T)  = JCM 16529(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 insulae sp. nov., isolated from soil.

A Gram-stain-positive, motile, endospore-forming, and strictly aerobic rod-shaped bacterium designated DS80T was isolated from an island soil. The strain DS80T grew at temperatures between 15 and 40°C (optimum = 30°C) and at pH values ranging from 5.0 to 9.0 (optimum = 7.0). The phylogenetic analysis based on the comparisons of the 16S rRNA gene sequences showed that the isolate was affiliated to the genus Paenibacillus and was mostly related to Paenibacillus assamensis GPTSA11T (with the sequence similarity of 96.33%) and Paenibacillus urinalis 5402403T(95.48%). The G+C content of the genomic DNA was 44.0 mol% and the major fatty acids were anteiso-C15:0, iso-C15:0, iso-C16:0, and C16:1ω11c. Strain DS80T contained MK-7 as the major menaquinone, and phosphatidylglycerol, phosphatidylethanolamine, and diphosphatidylglycerol as the major polar lipids. The peptidoglycan contained a major amount of meso-diaminopimelic acid. The chemotaxonomic profile of strain DS80T was consistent with that of Paenibacillus. However, the phenotypic properties clearly separated the strain from other species of the genus. Accordingly, a new species, Paenibacillus insulae sp. nov., is proposed (type strain =DS80T =JCM 17278T =KCTC 13833T).

Amycolatopsis acidiphila sp. nov., a moderately acidophilic species isolated from coal mine soil

Little is known on members of the genus Amycolatopsis inhabiting acidic habitats. In this study, a moderately acidophilic Amycolatopsis strain, designated 2-5T, was isolated from coal mine soil, and subjected to a polyphasic taxonomic characterization. Analysis based on 16S rRNA gene sequences indicated that the strain was most closely related to the type strain of Amycolatopsis bartoniae, sharing 99.30 % similarity, while similarity to all other Amycolatopsis species was less than 97 %. The DNA-DNA relatedness between the new isolate and the type strain of A. bartoniae was 56.5±0.7 %. The optimal pH range of the isolate for growth was 5.5-6.0, but growth also occurred at pH 4.5 and 7.5. The isolate tolerated up to 6 % (w/v) NaCl (optimum, 0 %), and the temperature range for growth was 15-40 °C (optimum, 30 °C). The isolate was able to utilize most substrates tested for sole carbon sources, showing its metabolic versatility. The isolate exhibited antimicrobial activity against Serratia marcescens and weak antifungal activity against Fusarium proliferatum. The chemotaxonomic profiles of strain 2-5T included polar lipids containing phosphatidylethanolamine, phsphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol dimannosides, fatty acids containing C17 : 1ω6c and iso-C16 : 0 as the major components, MK-9(H4) as the predominant menaquinone, and meso-diaminopimelic acid and arabinose, galactose, glucose and ribose as the diagnostic diamino acid and sugars in the cell wall. The combined phenotypic, chemotaxonomic and genotypic analyses clearly indicated that the isolate merits recognition as represnting a novel species of Amycolatopsis, for which the name Amycolatopsis acidiphila sp. nov. is proposed. The type strain is 2-5T (=KCTC 39523T=JCM 30562T).