Jong-Ok Ka

Members of the phylum Acidobacteria are dominant and metabolically active in rhizosphere soil

A culture-independent survey was performed to search for 16S rRNA gene sequences representing dominant and metabolically active bacteria in rhizosphere soil. PCR- and reverse transcription-PCR-derived clone libraries were constructed from DNA and RNA directly extracted from the soil sample. Acidobacteria-related sequences occupied an unusually large proportion (>50%) of both rDNA- and rRNA-derived clone libraries. This study suggested that the bacteria belonging to the phylum Acidobacteria might be numerically dominant as well as metabolically active in the soil sample, implying that the phylum Acidobacteria might be highly involved in the biogeochemical cycles of the rhizosphere soil.

Analyses of bacterial communities in meju, a Korean traditional fermented soybean bricks, by cultivation-based and pyrosequencing methods

Despite the importance of meju as a raw material used to make Korean soy sauce (ganjang) and soybean paste (doenjang), little is known about the bacterial diversity of Korean meju. In this study, the bacterial communities in meju were examined using both culture-dependent and independent methods in order to evaluate the diversity of the bacterial population. Analyses of the 16S rRNA gene sequences of the bacterial strains isolated from meju samples showed that the dominant species were related to members of the genera Bacillus, Enterococcus, and Pediococcus. The community DNAs extracted from nine different meju samples were analyzed by barcoded pyrosequencing method targeting of the V1 to V3 hypervariable regions of the 16S rRNA gene. In total, 132,374 sequences, with an average read length of 468 bp, were assigned to several phyla, with Firmicutes (93.6%) representing the predominant phylum, followed by Proteobacteria (4.5%) and Bacteroidetes (0.8%). Other phyla accounted for less than 1% of the total bacterial sequences. Most of the Firmicutes were Bacillus and lactic acid bacteria, mainly represented by members of the genera Enterococcus, Lactococcus, and Leuconostoc, whose ratio varied among different samples. In conclusion, this study indicated that the bacterial communities in meju were very diverse and a complex microbial consortium containing various microorganisms got involved in meju fermentation than we expected before.

Altererythrobacter namhicola sp. nov. and Altererythrobacter aestuarii sp. nov., isolated from seawater

Two non-motile, orange- or yellow-pigmented bacteria, designated strains KYW48(T) and KYW147(T), were isolated from seawater collected from the South Sea, Republic of Korea. Cells of both strains were Gram-reaction-negative, aerobic and catalase- and oxidase-positive. The major fatty acids of strain KYW48(T) were C(18 : 1)ω7c (35.3 %), summed feature 3 (iso-C(15 : 0) 2-OH and/or C(16 : 1)ω7c) (22.7 %), C(17 : 1)ω6c (19.8 %), C(14 : 0) 2-OH (7.4 %) and C(16 : 0) (5.9 %), and those of strain KYW147(T) were C(18 : 1)ω7c (36.0 %), summed feature 3 (18.3 %), C(16 : 0) (14.7 %), 11-methyl C(18 : 1)ω7c (10.7 %), C(16 : 0) 2-OH (9.1 %) and C(18 : 1)ω9c (8.0 %). The predominant isoprenoid quinone of both strains was ubiquinone 10 (Q-10). The DNA G+C contents of strains KYW48(T) and KYW147(T) were 63.8 and 67.2 mol%, respectively. A phylogenetic tree based on 16S rRNA gene sequences showed that strains KYW48(T) and KYW147(T) were grouped with the members of the family Erythrobacteraceae and formed a distinct clade with the members of the genus Altererythrobacter (<95.7 % sequence similarity). On the basis of the evidence presented in this study, the novel species Altererythrobacter namhicola sp. nov. (type strain KYW48(T)  = KCTC 22736(T)  = JCM 16345(T)) and Altererythrobacter aestuarii sp. nov. (type strain KYW147(T)  = KCTC 22735(T)  = JCM 16339(T)) are proposed.

Roseomonas soli sp. nov., isolated from an agricultural soil cultivated with Chinese cabbage (Brassica campestris)

A bacterial strain, designated 5N26(T), was isolated from an agricultural soil cultivated with Chinese cabbage (Brassica campestris). Cells of this strain were Gram-reaction-negative, strictly aerobic, motile, non-spore-forming rods, and catalase- and urease-negative. The major fatty acids of strain 5N26(T) were C16 : 0 (7.5 %), C18 : 1 2-OH (13.4 %) and summed feature 8 (C18:1ω6c and/or C18:1ω7c; 63.2%). The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine and one unidentified aminolipid. The G+C content of the genomic DNA of strain 5N26(T) was 68.3 mol%. 16S rRNA gene sequence analysis showed that strain 5N26(T) was phylogenetically related to Roseomonas lacus TH-G33(T) and Roseomonas terrae DS-48(T) (97.0 % and 96.6 % sequence similarity, respectively). The results of genotypic and phenotypic data showed that strain 5N26(T) could be distinguished from phylogenetically related species, and that this strain represented a novel species within the genus Roseomonas, for which the name Roseomonas soli sp. nov. (type strain 5N26(T) = KACC 16376(T) = NBRC 109097(T)) is proposed.

Inactivation of environmental mycobacteria by free chlorine and UV

The resistance of environmental mycobacteria (EM) against chlorine and ultraviolet (UV) was evaluated for determination of the Ct value and UV dose to inactivate EM. Chlorine disinfection experiments were done on Mycobacterium fortuitum in oxidant demand-free buffered water at the worst condition (pH 8.5, 4 degrees C) and normal condition (pH 7.0, 20 degrees C). The Ct value for 3log inactivation of M. fortuitum was 600 times greater than that of Escherichia coli. UV experiments were performed for various species of Mycobacterium avium, M. fortuitum, Mycobacterium intracellulare, and Mycobacterium lentiflavum. A UV collimated beam device was used for irradiation of four species suspended in phosphate buffered saline with doses of 5, 10, 20, 50, and 100mJ/cm(2). UV sensitivity of mycobacteria was species-specific. More than 3log of M. avium, M. intracellulare, and M. lentiflavum could be inactivated at 20mJ/cm(2), whereas M. fortuitum was so resistant that 3log inactivation required a dose of more than 50mJ/cm(2). Mycobacteria were found 2-10 times more resistant to UV than E. coli for 3log inactivation. There was no significant difference in the inactivation of mycobacteria with either low-pressure or medium-pressure UV irradiation.

Growth promotion of Xanthium italicum by application of rhizobacterial isolates of Bacillus aryabhattai in microcosm soil

This study was conducted using rhizobacteria, which are able to exert beneficial effects upon plant growth in the infertile soil collected from barren lakeside areas. Four strains of plant growth promoting bacteria were isolated from the rhizosphere of a common wild plant, Erigeron canadensis. Isolated strains LS9, LS11, LS12, and LS15 were identified as Bacillus aryabhattai by 16S rDNA sequence analysis. B. aryabhattai LS9, LS11, LS12, and LS15 could solubilize 577.9, 676.8, 623.6, and 581.3 mg/L of 0.5% insoluble calcium phosphate within 2 days of incubation. Production of indole acetic acid, a typical growth promoting phytohormone auxin, by strain LS15 was 471.3 mg/L in 2 days with the addition of auxin precursor L-tryptophan. All the strains also produced other phytohormones such as indole butyric acid, gibberellins, and abscisic acid, and strain LS15 showed the highest production rate of gibberellin (GA3), 119.0 μg/mg protein. Isolated bacteria were used in a microcosm test for growth of wild plant Xanthium italicum, which can be utilized as a pioneer plant in barren lands. Seed germination was facilitated, and the lengths of roots, and shoots and the dry weights of germinated seedlings after 16 days were higher than those of the uninoculated control plants. Root lengths of seedlings of X. italicum increased by 121.1% in LS11-treated samples after 16 days. This plant growth-promoting capability of B. aryabhattai strains may be utilized as an environmentally friendly means of revegetating barren lands, especially sensitive areas such as lakeside lands.

Complete Genome Sequence of the Fenitrothion-Degrading Burkholderia sp. Strain YI23

Burkholderia species are ubiquitous in soil environments. Many Burkholderia species isolated from various environments have the potential to biodegrade man-made chemicals. Burkholderia sp. strain YI23 was isolated from a golf course soil and identified as a fenitrothion-degrading bacterium. In this study, we report the complete genome sequence of Burkholderia sp. strain YI23.

Description of Microvirga aerophila sp. nov. and Microvirga aerilata sp. nov., isolated from air, reclassification of Balneimonas flocculans Takeda et al. 2004 as Microvirga flocculans comb. nov. and emended description of the genus Microvirga.

Two bacterial strains, 5420S-12(T) and 5420S-16(T), isolated from air samples, were characterized using a polyphasic approach. 16S rRNA gene sequence analysis showed that strain 5420S-12(T) was related phylogenetically to Microvirga subterranea FaiI4(T) (97.4 % sequence similarity) and Microvirga guangxiensis 25B(T) (97.1 %) and that strain 5420S-16(T) was closely related to Balneimonas flocculans TFB(T) (98.0 %) and Microvirga guangxiensis 25B(T) (97.2 %). The G+C content of the genomic DNA was 62.2 mol% for strain 5420S-12(T) and 61.5 mol% for strain 5420S-16(T). The major fatty acid was C(18 : 1)ω7c. The results of DNA-DNA hybridization and the phenotypic data showed that strains 5420S-12(T) and 5420S-16(T) could be distinguished from phylogenetically related species and represent two novel species within the genus Microvirga, for which the names Microvirga aerophila sp. nov. (type strain 5420S-12(T) =KACC 12743(T) =NBRC 106136(T)) and Microvirga aerilata sp. nov. (type strain 5420S-16(T) =KACC 12744(T) =NBRC 106137(T)) are proposed. Furthermore, the reclassification of Balneimonas flocculans as Microvirga flocculans comb. nov. (type strain TFB(T) =JCM 11936(T) =KCTC 12101(T) =IAM 15034(T) =ATCC BAA-817(T)) is proposed and an emended description of the genus Microvirga is provided.

Diversity of bacterial community in freshwater of Woopo wetland

Diversity of bacterial community in water layer of Woopo wetland was investigated. Cultivable bacterial strains were isolated by the standard dilution plating technique and culture-independent 16S rRNA gene clones were obtained directly from DNA extracts of a water sample. Amplified rDNA restriction analysis (ARDRA) was applied onto both of the isolates and 16S rRNA gene clones. Rarefaction curves, coverage rate and diversity indices of ARDRA patterns were calculated. Representative isolates and clones of all the single isolate/clone phylotype were partially sequenced and analyzed phylogenetically. Sixty-four and 125 phylotypes were obtained from 203 bacterial isolates and 235 culture-independent 16S rRNA gene clones, respectively. Bacterial isolates were composed of 4 phyla, of which Firmicutes (49.8%) and Actinobacteria (32.0%) were predominant. Isolates were affiliated with 58 species. Culture-independent 16S rRNA gene clones were composed of 8 phyla, of which Proteobacteria (62.2%), Actinobacteria (15.5%), and Bacteroidetes (13.7%) were predominant. Diversity of 16S rRNA gene clones originated from cultivation-independent DNA extracts was higher than that of isolated bacteria.

Effects of phosphate addition on biofilm bacterial communities and water quality in annular reactors equipped with stainless steel and ductile cast iron pipes.

The impact of orthophosphate addition on biofilm formation and water quality was studied in corrosion-resistant stainless steel (STS) pipe and corrosion-susceptible ductile cast iron (DCI) pipe using cultivation and culture-independent approaches. Sample coupons of DCI pipe and STS pipe were installed in annular reactors, which were operated for 9 months under hydraulic conditions similar to a domestic plumbing system. Addition of 5 mg/L of phosphate to the plumbing systems, under low residual chlorine conditions, promoted a more significant growth of biofilm and led to a greater rate reduction of disinfection by-products in DCI pipe than in STS pipe. While the level of THMs (trihalomethanes) increased under conditions of low biofilm concentration, the levels of HAAs (halo acetic acids) and CH (chloral hydrate) decreased in all cases in proportion to the amount of biofilm. It was also observed that chloroform, the main species of THM, was not readily decomposed biologically and decomposition was not proportional to the biofilm concentration; however, it was easily biodegraded after the addition of phosphate. Analysis of the 16S rDNA sequences of 102 biofilm isolates revealed that Proteobacteria (50%) was the most frequently detected phylum, followed by Firmicutes (10%) and Actinobacteria (2%), with 37% of the bacteria unclassified. Bradyrhizobium was the dominant genus on corroded DCI pipe, while Sphingomonas was predominant on non-corroded STS pipe. Methylobacterium and Afipia were detected only in the reactor without added phosphate. PCR-DGGE analysis showed that the diversity of species in biofilm tended to increase when phosphate was added regardless of the pipe material, indicating that phosphate addition upset the biological stability in the plumbing systems.