• Korean Journal of Microbiology
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• v.47 no.1
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• pp.66-73
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• 2011

Bacterial density distributions of gut microbes in the digestive organs of Harmonia axyridis collected from three different sources (JK, CK, and CJ) were $6.0{\times}10^4$ CFU/gut under aerobic culture condition and $8.0{\times}10^6$ CFU/gut under anaerobic culture condition. Seven colony types were observed under aerobic condition and three types of similarity were detected under anaerobic condition. In total, 116 strains, including 34 strains under aerobic condition, were isolated from the digestive organs of H. axyridis. Based on the analysis of the 16S rRNA gene sequence, aerobic gut microbes were assigned to the Proteobacteria, Actinobacteria, Firmicutes, and Deinococcus-Thermus. A large number of isolates belonged to the genus Bacillus and Staphylococcus of the Firmicutes commonly found in H. axyridis from different sites. Anaerobic gut microbes were found to be similar according to colony morphological, phylogenetic analysis using ARDRA. Eighty-two anaerobic gut microbes were clustered into 17 different ARDRA types according to HaeIII. Representative anaerobic gut microbes in each ARDRA group were divided into five species of ${\gamma}$-Proteobacteria based on 16S rRNA gene sequence analysis; Hafnia alvei, Enterobacter ludwigii, Enterobacter kobei, Pseudomonas oryzihabitans and Pseudomonas koreensis. Phylogenetic analysis indicated that about 70% of the isolates belonged to ${\gamma}$-Proteobacteria, suggesting predominance of gut microbes.

• KSBB Journal
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• v.19 no.1
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• pp.72-77
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• 2004

The aim of this study was to isolate and identify the spoilage bacteria in the low salt cucumber brine. The PCR amplicons comprising a portion of the 16S rRNA gene of the isolated colonies were directly sequenced and the untrimmed whole sequencing results of the unknown strains were aligned with the type strains using BLAST of NCBI. Then Sequence Aligner and Sequence Match of RDP confirmed the outcome. The identified isolates were eight species and belong to three genuses: Clostridium, Lactobacillus, and Bacillus. The RFLP pattern of the 16S rRNA gene of isolates verified the identified species. From now on the complex spoiling process of law salt fermented cucumber could be analyzed using the isolated species individually or with certain combinations.

• Journal of Korean society of Dental Hygiene
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• v.18 no.5
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• pp.843-852
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• 2018

Objectives: The study aimed to isolate the abundant bacteria in dental caries in children and to investigate the bacterial species involved in addition to those that have been previously reported. Methods: The specimens were collected from the supragingival plaques of each dental caries area, pit and fissure caries, deep dentinal caries, smooth surface caries, and dental caries, and from healthy subjects in the control group. Bacteria were cultured from these specimens, DNA was extracted from the isolated bacteria, and the 16S rRNA gene sequences were analyzed and identified. Results: Based on the results of the 16S rRNA gene sequence analysis for the 90 strains of dominant bacteria from the 45 specimens, 5, 7, 8, 7, and 13 species were identified from the supragingival plaques from healthy teeth, pit and fissure caries, deep dentinal caries, smooth surface caries, and dental caries, respectively. In healthy teeth, Actinomyces naeslundii dominated. Corynebacterium durum, Ralstonia pickettii, and Streptococcus intermedius showed equal distribution. The dominant bacterial species in dental caries, S. sanguinis, showed the greatest difference in prevalence in pit and fissure caries. In deep dentinal caries, S. mutans and Lactobacillus rhamnosus were dominant; in smooth surface caries, S. mutans and S. sanguinis were dominant; and in the supragingival plaques of dental caries, S. sanguinis and S. mutans were dominant. Conclusions: The bacterial species isolated from dental caries encompassed four phyla, eight genera, and 22 species. In addition, the SS1-2 strain, belonging to the genus Neisseria, was identified as a new species from among the isolated strains.

• Korean Journal of Organic Agriculture
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• v.23 no.4
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• pp.847-858
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• 2015

Bacillus amyloliquefaciens GR4-5 was isolated from the rhizosphere soil of Korean ginseng and displayed broad-spectrum suppression of ginseng root rot pathogens. The survivability of B. amyloliquefaciens GR4-5 in soil was investigated under three different conditions; indoor, outdoor - of which soil was put in 14 mL tube after treatment - and field environments. Soil samples were collected over a four-week period from three experimental designs, and assessed for 16S rRNA gene copy number by quantitative polymerase chain reaction (qPCR). In outdoor condition, the 16S rRNA gene copy number of Bacillus spp. was 8.35 log copies g $soil^{-1}$ immediately after the GR4-5 treatment. Two weeks later, the 16S rRNA gene copy number of Bacillus spp. (6.70 log copies g $soil^{-1}$) was similar to that of the control (6.38 log copies g $soil^{-1}$). In indoor condition, the 16S rRNA gene copy number of Bacillus spp. maintained in a certain level for a longer period than those in outdoor and field. The 16S rRNA gene copy number of Bacillus spp. in field experiment was reduced faster than that of outdoor condition. Our results show that B. amyloliquefaciens GR4-5 can survive in bulk soil for 1 week, indicating its potential use as a biocontrol agent following 7 day application intervals. This study presents that outdoor microcosm system design could be a useful method to assess easily the survivability of beneficial microorganisms.

• Korean Journal of Microbiology
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• v.46 no.4
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• pp.352-358
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• 2010

Bacterial community composition in activated sludge wastewater treatment bioreactors were analyzed using 16S rRNA gene-based pyrosequencing for the four different wastewater treatment processes. Sequences within the orders Rhodocyclales, Burkholderiales, Sphingobacteriales, Myxococcales, Xanthomonadales, Acidobacteria group 4, Anaerolineales, Methylococcales, Nitrospirales, and Planctomycetales constituted 54-68% of total sequences retrieved in the activated sludge samples, which demonstrated that a few taxa constituted majority of the activated sludge bacterial community. The relative ratio of the order members was different for each treatment process, which was assumed to be affected by different operational and environmental conditions of each treatment process. In addition, activated sludge had very diverse bacterial species (Chao1 richness estimate: 1,374-2,902 operational taxonomic units), and the diversity was mainly originated from rare species. Particularly, the bacterial diversity was higher in membrane bioreactor than conventional treatment processes, and the long solids retention time of the operational strategy of the membrane bioreactor appeared to be appropriate for sustaining diverse slow growing bacteria. This study investigating bacterial communities in different activated sludge processes using a high-throughput pyrosequencing technology would be helpful for understanding microbial ecology in activated sludge and for improving wastewater treatment in the future.

• Korean Journal of Microbiology
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• v.53 no.4
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• pp.316-319
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• 2017

The antibiotic resistant genes (ARG) and mobile genetic elements (MGE) were investigated with the effluent of waste-water treatment plant (WWTP), and river waters of upstream and downstream in order to elucidate the effect of effluent on antibiotic resistance in a natural river. Total numbers of 134~183 of ARG and MGE were detected and the abundance of ARG and MGE was 0.063~0.422 copies per one of 16S rRNA gene in three water samples. Effluent sample contained the highest amount of the total number and abundance of ARG and MGE whereas total viable cells were observed in the lowest amount among the three samples. This indicated that the genes were originated from cells died during the wastewater treatment process. In addition, the co-relationship of abundance between ARG and MGE suggested that acquired resistance was a prevalent mechanism among the antibiotic-resistant bacteria existing in WWTP.

• Korean Journal of Microbiology
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• v.34 no.4
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• pp.194-199
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• 1998

Bacterial diversity was determined by amplification and sequencing of 16S rDNA at Tancheon and Jungrang in Han river. Twenty-seven clones constructed were divided 7 groups using RFLP. Fifteen clones were classified 4 groups in Tancheon and the group (HT-1 clone) including many clones was affiliated a high similarity with Aerobacter cryaerophilus (the class Proteobacteria including members of the delta subdivisions). The other two groups (HT-6 and HT-9 clone) including several clones were classified with the class Cytophagales in Tancheon. Twelve clones were classified 3 groups in Jungrang and the group (HJ-1 clone) including many clones was affiliated a high similarity with Sphingomonas sp. (the class Proteobacteria including members of the alpha subdivisions). As a whole results, the class Proteobacteria (alpha, beta and delta subdivision), the order Cytophagales, and the order Actinomycetales were detected.

• Korean journal of applied entomology
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• v.39 no.1
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• pp.5-12
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• 2000

The sweetpotato whiteflies, Bemisia tabaci(Gennadius), were found recently in Korea on Glycine max, Euphorbia pulcherrima, and Rosa hybrida. The biotype identity of Bemisia tabaci in Korea was determined by several DNA markers including the random amplified polymorphic DNAs, and restriction fragments length polymorphism of mitochondrial 12S and 16S rRNA genes. The electromorph profiles of DNA fragments from the rose(Jincheon) and poinsettia(Seoul) populations in Korea are both identical to those of B biotypes distributed in Australia, Israel, and Japan. The populations of B. tabaci collected on Glycine max, Ipomea batatas, and Perilla frutescens in different localities retained the same DNA markes with the population from Lonicera japonica and shikoku of Japan. These populations are non-B biotype and considered as an indigenous type in the Far Eastern Asia Region including Korea and Japan, Morphological Characteristics of B. Tabaci were also observed by the scanning electron microscope and described with the comparison to the other important whitefly pest, Trialeurodes vaporariorum (Westwood).

• Korean Journal of Microbiology
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• v.49 no.4
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• pp.328-335
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• 2013

As a result of conducting a cultural experiment of tomato using chicken feather protein hydrolysate (CPH) which was mass produced by keratin protein degrading bacterium Chryseobacterium sp. FBF-7 (KACC 91463P), we found that the stem and the root of tomato showed significant improvement in growth. For the purpose of phylogenic interpretation, a comparison was drawn between the effect of CPH, a treated CPH and untreated, on the changes of bacterial populations by 454 pyrosequencing based on 16S rRNA gene sequences. Tomato rhizosphere soil untreated with CPH (NCPH) showed 6.54 Shannon index from 3,281 sequence reads, and the rhizosphere soil treated with CPH (TCPH) showed 6.33 Shannon index from 2,167 sequence reads, displaying that it does not affect the diversity. Bacterial populations were composed of 19 phyla in the rhizosphere soil, and the phylum Proteobacteria occupied 40% of total bacterial populations. Bradyrhizobium, Agromonas, Nitrobacter, and Afipia (BANA group) which belong to Bradyrhizobiaceae were abundant and commonly detected in both the treated and untreated soils, suggesting the dominance of bacterial group in rhizosphere soil. The results obtained showed that CPH treatment does not affect the indigenous bacterial populations present in the rhizosphere soil.

• Ocean and Polar Research
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• v.32 no.3
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• pp.309-319
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• 2010

To assess community structure and diversity of archaea, a clone sequencing analysis based on an archaeal 16S rRNA gene was conducted at three sediment depths of the continental slope and Ulleung Basin in the East Sea. A total of 311 and 342 clones were sequenced at the slope and basin sites, respectively. Marine Group I, which is known as the ammonia oxidizers, appeared to predominate in the surface sediment of both sites (97.3% at slope, 88.5% at basin). In the anoxic subsurface sediment of the slope and basin, the predominant archaeal group differed noticeably. Marine Benthic Group B dominated in the subsurface sediment of the slope. Marine Benthic Group D and Miscellaneous Crenarchaeotal Group were the second largest archaeal group at 8-9 cm and 18-19 cm depth, respectively. Marine Benthic Group C of Crenarchaeota occupied the highest proportion by accounting for more than 60% of total clones in the subsurface sediments of the basin site. While archaeal groups that use metal oxide as an electron acceptor were relatively more abundant at the basin sites with manganese (Mn) oxide-enriched surface sediment, archaeal groups related to the sulfur cycle were more abundant in the sulfidogenic sediments of the slope. Overall results indicate that archaeal communities in the Ulleung Basin show clear spatial variation with depth and sites according to geochemical properties the sediment. Archaeal communities also seem to play a significant role in the biogeochemical carbon (C), nitrogen (N), sulfur (S), and metal cycles at each site.