• Research in Plant Disease
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• v.29 no.4
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• pp.433-439
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• 2023

Bacterial leaf blight in carrot is one of the most important diseases in the worldwide. In the past decade, its introduction into Korea is causing great concern due to the potential damage to carrot crops domestically. This bacterial disease is caused by Xanthomonas hortorum pv. carotae (Xhc). This study aimed to isolate and identify bacterial strains from the soil of carrot farms in Jeju Island. The bacterial isolates showing characteristics similar with those of Xhc were selected when cultured on artificial media. Through DNA sequencing and analysis based on NCBI data, some of the selected bacterial strains were identified as Xhc. Furthermore, the bacterial strains caused the typical symptom of bacterial leaf blight after inoculation on carrot leaves. The results of this study showed the potential establishment of Xhc in the soil of Jeju Island and it may be valuable data for establish a strategy preventing the domestic spread of carrot bacterial leaf blight in the future.

• Journal of Microbiology
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• v.42 no.1
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• pp.9-13
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• 2004

Culture-independent approaches, based on 16S rDNA sequences, are extensively used in modern microbial ecology. Sequencing of the clone library generated from environmental DNA has advantages over fingerprint-based methods, such as denaturing gradient gel electrophoresis, as it provides precise identification and quantification of the phylotypes present in samples. However, to date, no method exists for comparing multiple bacterial community structures using clone library sequences. In this study, an automated method to achieve this has been developed, by applying pair wise alignment, hierarchical clustering and principle component analysis. The method has been demonstrated to be successful in comparing samples from various environments. The program, named CommCluster, was written in JAVA, and is now freely available, at http://chunlab.snu.ac.kr/commcluster/.

• BMB Reports
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• v.35 no.3
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• pp.348-351
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• 2002

AquI DNA methyltransferase, M.AquI, catalyses the transfer of a methyl group from S-adenosyl-L-methionine to the C5 position of the outermost deoxycytidine base in the DNA sequence 5'CYCGRG3'. M.AquI is encoded by two overlapping ORFs (termed $\alpha$ and $\beta$) instead of the single ORF that is customary for Class II methyltransferase genes. The structural organization of the M.AquI protein sequence is quite similar to that of other bacterial C5-DNA methyltransferases. Ten conserved motifs are also present in the correct order, but only on two polypeptides. We separately subcloned the genes that encode the $\alpha$ and $\beta$ subunits of M.AquI into expression vectors. The overexpressed His-fusion $\alpha$ and $\beta$ subunits of the enzyme were purified to homogeneity in a single step by Nickel-chelate affinity chromatography. The purified recombinant proteins were assayed for biological activity by an in vitro DNA tritium transfer assay. The $\alpha$ and $\beta$ subunits of M.AquI alone have no DNA methyltransferase activity, but when both subunits are included in the assay, an active enzyme that catalyses the transfer of the methyl group from S-adenosyl-L-methionine to DNA is reconstituted. We also showed that the $\beta$ subunit alone contains all of the information that is required to generate recognition of specific DNA duplexes in the absence of the $\alpha$ subunit.

• The Korean Journal of Zoology
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• v.33 no.3
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• pp.365-372
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• 1990

For the effort to produce transgenic amphibians, a plasmid DNA sequence (cytoplasmic actin promoter-linked bacterial $\beta$-galactosidase gene) was microinjected into fertilized Xenopus eggs. It appeared that the injection of 20 nl solution containing 1-2 ng of DNA was not toxic, but over 4 ng was toxic to embryonic development. The translational product of $\beta$-gal gene ($\beta$-galactosidase) had enzyme activity in all three germ layers of the embryo. Expression of the injected $\beta$-gal genes was first detected at mid-gastrula stage, and the activity persisted up to stage 43 (feeding tadpole) with decreased level of retention. However, the level of the expression was various among the injected individuals as well as each experiment. That is, $\beta$-galactosidase activities did not appear in all cells, instead a localized distribution pattern. Although other possibilities could not be omitted, this mosaic distribution of gene expression seemed to arise from unequal partition of the injected DNA into each blastomere during early cleavage.

• Biomedical Science Letters
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• v.10 no.2
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• pp.75-84
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• 2004

Massive identification of differentially expressed patterns has been used as a tool to detect genes that are involved in disease related process. We employed circular single stranded sense molecules as probe DNA for a DNA chip. The circular single stranded DNAs derived from 1,152 unigene cDNA clones were purified in a high throughput mode from the culture supernatant of bacterial transformants containing recombinant phagemids and arrayed onto silanized slide glasses. The DNA chip was examined for its utility in detection of differential expression profile by using cDNA hybridization. Hybridization of the single stranded probe DNA were performed with Cy3- or Cy5-labeled target cDNA preparations at $60^\circ$C. Dot scanning performed with the hybridized slide showed 29 up-regulated and 6 down-regulated genes in a cancerous liver tissue when compared to those of adjacent noncancerous liver tissue. These results indicate that the circular single stranded sense molecules can be employed as probe DNA of arrays in order to obtain a precious panel of differentially expressed genes.

• Proceedings of the Microbiological Society of Korea Conference
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• 2002.10a
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• pp.100-105
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• 2002

The diversity of epiphytic bacterial communities on deciduous oak tree (Quercus dentate Thunb.) leaves was examined both in the natural forest area with a clean air and in the industrial estate to assess effects of acidic deposition to the phyllosphere using 16S rDNA sequence data. In addition, acid-tolerant epiphytic bacterial communities were compared. A total of 78 epiphytic and 444 acid-tolerant clones were obtained from clone libraries, resulting in 20 and 17 phylotypes by analysis of restriction fragment length polymorphism (RFLP) for PCR-amplified 16S rDNA products. A low bacterial diversity in both areas was found. As tree leaves grow older, bacterial diversities were slightly increased in the level of subphylum. The community structure of epiphytic bacteria in both areas in April consisted of only two subphyla, $\beta-and\;\gamma-Proteobacteria$. In August two additional subphyla in both areas were found, but the composition was a little different, Acidobacteria and Cytophaga-Flexibacter-Bacteroids (CFB) group in the industrial estate and a -Proteobacteria and CFB group in the natural area, respectively. Acidobacteria could be an indicator of epiphytic bacteria for acidic deposition on plant leaves, whereas a -Proteobacteria be one of epiphytic bacteria that naturally survive on leaves that are not affected by acidic deposition. The acid-tolerant bacterial communities in April were composed of two subphyla, $\gamma-Proteobacteria$ and Low G+C gram-positive bacteria in both areas, and in August a-Proteobacteria was added to the community just in the natural forest area. The direct influence of acidic deposition on the acid-tolerant bacterial phylogenetic composition could not be detected in higher taxonomic levels such as subphylum, but at narrower or finer levels it could be observed by a detection of Xanthomonadales group of $\gamma-Proteobacteria$ just in the industrial estate.

• The Plant Pathology Journal
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• v.37 no.6
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• pp.521-532
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• 2021

Knowledge and better understanding of functions of the microbial community are pivotal for crop management. This study was conducted to study bacterial structures including Acidovorax species community structures and diversity from the watermelon cultivated soils in different regions of South Korea. In this study, soil samples were collected from watermelon cultivation areas from various places of South Korea and microbiome analysis was performed to analyze bacterial communities including Acidovorax species community. Next generation sequencing (NGS) was performed by extracting genomic DNA from 92 soil samples from 8 different provinces using a fast genomic DNA extraction kit. NGS data analysis results revealed that, total, 39,367 operational taxonomic unit (OTU), were obtained. NGS data results revealed that, most dominant phylum in all the soil samples was Proteobacteria (37.3%). In addition, most abundant genus was Acidobacterium (1.8%) in all the samples. In order to analyze species diversity among the collected soil samples, OTUs, community diversity, and Shannon index were measured. Shannon (9.297) and inverse Simpson (0.996) were found to have the highest diversity scores in the greenhouse soil sample of Gyeonggi-do province (GG4). Results from NGS sequencing suggest that, most of the soil samples consists of similar trend of bacterial community and diversity. Environmental factors play a key role in shaping the bacterial community and diversity. In order to address this statement, further correlation analysis between soil physical and chemical parameters with dominant bacterial community will be carried out to observe their interactions.

• Journal of Microbiology and Biotechnology
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• v.16 no.12
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• pp.1882-1889
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• 2006

A 16S rDNA clone library was generated to investigate the bacterial diversity in intertidal sediment from the coast of the Yellow Sea, P. R. China. A total of 102 clones were sequenced and grouped into 73 OTUs using a phylogenetic approach. The sequenced clones fell into 11 bacterial lineages: Proteobacteria, Bacteroidetes, Planctomycetes, Chloroflexi, Acidobacteria, Actinobacteria, Firmicutes, Spirochaetes, and candidate divisions of BRCl, OP3, and OP1l. Based on a phylogenetic analysis of these bacteria, together with the ten most closely related sequences deposited in the GenBank, it was concluded that intertidal bacteria are most likely derived from marine bacteria with a remarkable diversity, and some are particularly abundant in intertidal sediment.

• Journal of Microbiology and Biotechnology
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• v.13 no.1
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• pp.15-21
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• 2003

Two microbial communities of activated sludge in the same municipal wastewater, but treated with different systems, were studied and compared using molecular microbiological approaches. The bacterial 16S rDNA sequences from 124 clones were analyzed, however, the majority of them were not closely related to any known species, and found to belong to 8 different phylogenetic groups and 3 different unidentified groups. The relative frequencies of each group were similar between the two microbial communities. Fingerprinting using terminal restriction fragment length polymorphism (T-RFLP) showed that the putative Nitrospira-related populations were more diverse and quantitatively higher in the KNR process system than in the other system using a conventional activated sludge process. The relationship between the bacterial community composition and the higher removal efficiency of nitrogen and phosphorus in the KNR process is discussed.

• Journal of Microbiology
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• v.45 no.1
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• pp.1-5
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• 2007

The bacterial compositions between the dental unit water system and human saliva were characterized and compared by direct sequence analysis of 16S rDNA clone libraries. Based on the species richness estimation, bacterial diversity in the dental unit water system (DUW) was more diverse than that of the human saliva (HS). The Chaol estimates of species richness in HS and DUW samples were 12.0 and 72.4, respectively. The total numbers of OTUs observed in the combined libraries accounted for 83% (HS) and 59% (DUW) of the Chaol diversity estimate as defined at the 80% similarity threshold. Based on the sequence analysis, the phylum Proteobacteria was the major group in both clone libraries at phylum level. DUW clone library contained 80.0% Proteobacteria, 8.0% Bacteroides, 4.0% Nitrospira, 4.0% Firmicutes, 2.0% Planctomycetes and 2.0% Acidobacteria. On the other hand, human saliva (HS) clone library contained 55.5% Proteobacteria, 36.1% Firmicutes and 8.4% Bacteroides. The majority of bacteria identified belonged to phylum Proteobacteria in both samples. In dental unit water system (DUW), Alphaproteobacteria was detected as the major group. There was no evidence of the bacterial contamination due to a dental treatment. Most sequences were related to microorganisms derived from biofilm in oligotrophic environments.