• Korean Journal of Ecology and Environment
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• v.55 no.4
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• pp.352-359
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• 2022

Recently, with the development of genetic technology, interest in environmental DNA (eDNA) to study biodiversity according to molecular biological approaches is increasing. Environmental DNA has many advantages over traditional research methods for biological communities distributed in the environment but highly depends on the established base sequence database. This study conducted a comprehensive analysis of the habitat status and classification at the genus level, which is mainly used in eDNA (12S rRNA, 16S rRNA, 18S rRNA, COI, and CYTB), focusing on Korean registration taxon groups (phytoplankton, zooplankton, macroinvertebrates, and fish). As a result, phytoplankton and zooplankton showed the highest taxa proportion in 18S rRNA, and macroinvertebrates observed the highest ratio in the nucleotide sequence database in COI. In fish, all genes except 18S rRNA showed a high taxon ratio. Based on the Korean registration taxon group, the gene construction of the top 20 genera according to bio density observed that most of the phytoplankton were registered in 18S rRNA, and the most significant number of COI nucleotide sequences were established in macroinvertebrates. In addition, it was confirmed that there is a nucleotide sequence for the top 20 genera in 12S rRNA, 16S rRNA, and CYTB in fish. These results provided comprehensive information on the genes suitable for eDNA research for each taxon group.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• The Plant Pathology Journal
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• v.17 no.4
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• pp.189-193
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• 2001

The relationships between the phytoplasmas infecting Zizyphus jujuba and Paulownia coreana were investigated by PCR-RELP. The 16S rRNA genes of the phytoplasmas were analyzed and compared with each other after PCR amplification. The amplified bands 1.4 kb in size were analyzed by both restriction digestion and sequencing after cloning into a plasmid vector. In some cases, two different kinds of inserts were observed in the isolates that originated from a single plant. However, many of them appeared to be the amplification products of chloroplastic 16S rRNA gene of host plants. The phytoplasma gene could be differentiated from the chloroplastic gene by restriction digestion of the plasmids carrying the amplification products. Only the recombinant plasmids carrying phytoplasma 16S rRNA gene produced a 1.4 kb band when digested with the enzyme BanII. Of the 52 recombinant plasmids analyzed, 42 appeared to contain inserts that originated from the chloroplastic 16S rRNA gene of the host plants. No variation was detected among 16S rRNA gene of nine phytoplasma isolates infecting Z. jujuba. However, the phytoplasmas infecting Z. jujuba were different from that infecting P. coreana.

• Journal of Species Research
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• v.11 no.4
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• pp.321-329
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• 2022

Four species of cyanobacteria that are unrecorded in Korea were isolated from freshwater and brackish water. These four species are Laspinema thermale of Laspinemaceae, Planktothricoides raciborskii and Planktothrix spiroides of Microcoleaceae, and Cephalothrix lacustris of Phormidiaceae, all belonging to the order Oscillatoriales. Laspinema thermale is morphologically characterized as apical cells that are longer than other cells. In this strain, the similarity of the 16S rRNA gene sequence with the previously reported L. thermale strains were 99.30-99.50%. Planktothricoides raciborskii, which is characterized by bluntly conical morphology of apical cells, showed 98.80-99.50% of similarity of the 16S rRNA gene sequence to the previously reported P. raciborskii strains. Planktothrix spiroides are characterized by floating due to gas vacuoles. In this strain, the similarity of the 16S rRNA gene sequence with the previously reported P. spiroides strains were 99.80-99.90%. Cephalothrix lacustris, characterized by having calyptra in apical cells, showed 99.80-99.90% similarity of the 16S rRNA gene sequence to previously reported C. lacustris strains. Also, these species were clustered in the same clade in phylogenetic analysis using 16S rRNA gene sequences with each corresponding species.

• Journal of Life Science
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• v.22 no.2
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• pp.167-176
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• 2012

Three protease-producing halophilic bacteria were isolated from fermenting anchovy. Isolated FAM 10, FAM 114, and FAM 115 were found to grow optimally at salt concentrations of 2-4%, 10%, and 6%, respectively, and could grow in salinity of up to 18-22%. The salinity conditions for optimum protease production were 6% in FAM 10 and 10% in FAM 114 and FAM 115. The protease activity of FAM 10 was gradually inhibited by the addition of NaCl up to 10%, and was not evident at 14%, whereas FAM 114 and FAM 115 displayed protease activity at 14% NaCl and could not be measured at 18%. These results demonstrated that the three isolated strains belong to protease-producing, moderately halophilic bacteria. Strain FAM 10, FAM 114, and FAM 115 were identified as Salinivibrio sp., Halobacillus sp., and Halobacillus sp. respectively, based on comparative analyses of the 16S rRNA gene and the 16S-23S intergenic space sequence (IGS), biochemical testing, and Gram staining. Salinivibrio sp. FAM 10 had two 16S rDNAs containing different sequences at position 191 and four IGSs that harbored no tRNA gene and tRNA genes for isoleucine, alanine, glutamate, lysine, and/or valine. Halobacillus sp. FAM 114 and FAM 115 had completely identical 16S rRNA gene sequences and showed 99% identity to the sequences of various Halobacillus strains. The three IGSs found in the genome of both strains displayed 99% sequence identity with Halobacillus aidingensis and Halobacillus sp. JM-Hb, and had $IGS^0$ with no tRNA gene and $IGS^{IA}$ with tRNA genes for isoleucine and alanine.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.156-159
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• 2006

A base substitution was introduced at the position 789 in Escherichia coli 16S rRNA, which was previously identified as an invariant residue for ribosome function and the ability of the mutant ribosomes to translate chloramphenicol acetyltransfernse mRNA was measured by determining the degree of resistance to chloramphenicol of cells expressing these mutant ribosomes. As expected, mutant ribosomes containing a base sub-stitution at the position 789 showed significantly reduced protein-synthesis ability and to identify a functional role played by this residue in protein synthesis, we developed an efficient genetic method to select second-site revertants in 16S rRNA that restore protein-synthesis function to these mutant ribosomes.

• The Plant Pathology Journal
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• v.16 no.2
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• pp.98-104
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• 2000

For the taxonomic evaluaition, 15 strains of the genus Pectobacterium and Erwinia were analyzed for 16S-23S rDNA intergenic spacer regions (ISRs). These species contained two types of ISRs, large and small ISRs. Large ISRs were on the range of 474-569 bp size, and coding transfer $\textrm{RNA}^{11e}$($\textrm{tRNA}^{11e}$) and $\textrm{tRNA}^{Ala}$. Small ISRs were 354-459 bp in length and coding $\textrm{tRNA}^{Glu}$. The sequence variations of two ISRs among species and strains were very high as compared with 16S rRNA gene sequences. By phylogenetic trees on the basis of two ISRs, Pectobacterium ere differentiated into P. carotovorum-P. cactiaidum group and P. chrysanthemi group. However, the taxonomic position of E. cypripedii and E. rhapontici, which were not clear on taxonomic delineation between Pectobacterium and Erwinia, were not clearly resolved on the basis of ISRs.

• Microbiology and Biotechnology Letters
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• v.39 no.1
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• pp.93-96
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• 2011

It has been shown that a nucleotide substitution at position 770 in Escherichia coli 16S rRNA, which is implicated in forming the evolutionary conserved B2c intersubunit bridge, has a detrimental effect on ribosome function. In order to isolate second-site revertants that complement ribosomes containing C770G, we performed a random mutagenesis of the 16S rRNA gene and selected clones that could produce more CAT protein translated by specialized ribosome. One of the clones contained two nucleotide substitutions at positions 569 and 904 (C569G and U904C) and these mutations partially complemented the loss of protein-synthesis ability caused by C770G. Further studies using the isolated revertant will provide information about which part of 16S rRNA is interacting with C770 and the consequence of the structure formed by these interactions in the process of protein synthesis.

• The Plant Pathology Journal
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• v.16 no.5
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• pp.252-256
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• 2000

The 16S-23S rRNA intergenic spacer regions (ISRs) were sequenced and analyzed to design specific primer for identification of Pectobacterium chrysanthemi. Two types ISRs, large and small ISRs, were identified from three strains (ATCC 11663, KACC 10163 and KACC 10165) of P. chrysanthemi and Pectobacterium carotovorum subsp. carotovorum ATCC 15713.Large ISRs contained transfer RNA-Ile(tRNA$^{Ile}$)and tRNA$^{Ala}$, and small ISRs contained tRNA$^{Glu}$. Size of the small ISRs of P. chrysanthemi ranged on 354-356 bp, while it was 451 bp in small ISR of P. carotovorum subsp. carotovorum ATCC 15713. From hypervariable region of small ISRs, species-specific primer for P. chrysanthemi with 20 bp length (CHPG) was designed from hypervariable region of small ISRs, which was used as forward promer to detect P. chrysanthemi strains with R23-1R produced PCR product of about 260bp size (CHSF) only from P. chrysanthemi strains, not from other Pectobacterium spp. and Erwinia spp. Direct PCR from bacterial cell without extracting DNA successfully amplified a specific fragment, CHSF, from P. chrysanthemi ATCC 11663. The limit of PCR detection was 1${\pm}10^2$ cfu/ml.

• The Plant Pathology Journal
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• v.28 no.3
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• pp.295-298
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• 2012

Genetic diversity among Pseudomonas syringae pv. morsprunorum isolates from Prunus mume in Korea and Japan was investigated by comparative sequence analysis of the 16S rRNA gene. The strains included 24 field isolates recovered from P. mume in Korea along with seven Japanese strains. Two strains isolated from P. salicina in Japan, one strain from P. avium in the United Kingdom, and the pathotype strain were also used for comparison with their 16S rRNA gene sequences. Nearly complete 16S rRNA gene sequences were sequenced in all 35 strains, and three sequence types, designated types I, II and III, were identified. Eleven strains consisting of five Korean isolates, five Japanese strains, and one strain from the United Kingdom belonged to type I, whereas the pathotype strain and another 19 Korean isolates belonged to type III. Another four Japanese strains belonged to type II. Type I showed 98.9% sequence homology with type III. Type I and II had only two heterogeneous bases. The 16S rRNA sequence types were correlated with the races of P. syringae pv. morsprunorum. Type I and II strains belonged to race 1, whereas type III isolates were included in race 2. Sequence analyses of the 16S rRNA gene from P. syringae pv. morsprunorum were useful in identifying the races and can further be used for epidemiological surveillance of this pathogen.