• The Plant Pathology Journal
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• v.34 no.1
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• pp.23-34
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• 2018

The Ralstonia solanacearum species complex (RSSC) can be divided into four phylotypes, and includes phenotypically diverse bacterial strains that cause bacterial wilt on various host plants. This study used 93 RSSC isolates responsible for potato bacterial wilt in Korea, and investigated their phylogenetic relatedness based on the analysis of phylotype, biovar, and host range. Of the 93 isolates, twenty-two were identified as biovar 2, eight as biovar 3, and sixty-three as biovar 4. Applied to the phylotype scheme, biovar 3 and 4 isolates belonged to phylotype I, and biovar 2 isolates belonged to phylotype IV. This classification was consistent with phylogenetic trees based on 16S rRNA and egl gene sequences, in which biovar 3 and 4 isolates clustered to phylotype I, and biovar 2 isolates clustered to phylotype IV. Korean biovar 2 isolates were distinct from biovar 3 and 4 isolates pathologically as well as genetically - all biovar 2 isolates were nonpathogenic to peppers. Additionally, in host-determining assays, we found uncommon strains among biovar 2 of phylotype IV, which were the tomato-nonpathogenic strains. Since tomatoes are known to be highly susceptible to RSSC, to the best of our knowledge this is the first report of tomato-nonpathogenic potato strains. These results imply the potential prevalence of greater RSSC diversity in terms of host range than would be predicted based on phylogenetic analysis.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.17 no.2
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• pp.59-75
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• 2012

The species composition of plankton is essential to understand the material and energy cycling within marine ecosystem. It also provides the useful information for understanding the properties of marine environments due to its sensitivity to the physicochemical characteristics and variability of water masses. In this study we adopted metagenomics to evaluate eukaryotic plankton species diversity from coastal waters off Busan. Characteristics of water masses at sampling sites is expected to be very complex due to the mixing of various water masses; Nakdong River runoff, Changjiang diluted water (CDW), South Sea coastal water, and Tsushima warm current. 18S rDNA clone libraries were constructed from surface waters at the three sites off Busan. Clone libraries revealed 94 unique phylotypes from 370 clones; Dinophyceae(42 phylotypes), Ciliophora(15 phylotypes), Bacillariophyta(7 phylotypes), Chlorophyta(2 phylotypes), Haptophyceae(1 phylotype), Metazoa(Arthropoda( 17 phylotypes), Chaetognatha(1 phylotypes), Cnidaria(2 phylotypes), Chordata(1 phylotype)), Rhizaria (Acantharea(2 phylotypes), Polycystinea(1 phylotype)), Telonemida(1 phylotype), Fungi(2 phylotypes). The difference in species diversity at the closely located three sites off Busan may be attributed to the various physicochemical properties of water masses at these sites by the mixture of water masses of various origins. Metagenomic study of species composition may provide useful information for understanding marine ecosystem of coastal waters with various physicochemical properties in the near feature.

• The Plant Pathology Journal
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• v.36 no.5
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• pp.440-449
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• 2020

The purpose of this study was to analyze the genetic and pathogenic characteristics of Ralstonia pseudosolanacearum in roses in Korea, and to examine the similarities and differences between Korean isolates and the first-reported European strains. Between 2017 and 2019, seventeen isolates from rose plants were identified as R. pseudosolanacearum using Ralstonia-specific primers. All 17 isolates were identified as race 1 using race-specific primers, and were confirmed as biovar 3 due to their ability to utilize carbon sources. Multiplex PCR using phylotype discriminating specific primers identified the 17 isolates as phylotype I. Sequevar comparison with reference sequevars using the sequences of the egl, mutS, and fliC genes, and only the egl gene, revealed that the strains evaluated in this study corresponded to sequevar I-33. The pathogenicity in roses differed depending on the rose cultivars. The different methods used for the genetic characterization of R. pseudosolanacearum indicate that the 17 rose bacterial wilt isolates had the same genetic characteristics. The lack of genetic variation in these isolates indicates their recent introduction from other countries (likely European countries). Therefore, appropriate quarantine and control measures should be taken in order to avoid further increases in the pathogenicity and/or secondary host range of R. pseudosolanacearum through genetic mutation.

• Research in Plant Disease
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• v.28 no.1
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• pp.54-56
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• 2022

A peanut plant showing wilt and browned symptom was found in the field of Gochang, Korea, in July 2021. The symptomatic peanut plant was collected from the field and isolation of the pathogen caused the wilt symptom was performed using the collected sample on TZC media. The dominated colony on media was isolated colony on media was isolated and subcultured of purification. The pure cultured bacteria was identified as Ralstonia solanacearum by sequencing of 16S rRNA gene. Multiplex polymerase chain reaction using phylotype-specific primer set identified isolate as phylotype I (R. pseudosolanacearum). Phylogenetic tree was constructed based on 16S rRNA sequence and it was closed with R. pseudosolanacearum. Pathogenicity of the isolates was assessed by soil drenching inoculation on 4-week-old peanut plant. The wilt symptom was successfully reproduced by inoculation of the isolates after 14 days. This is first report of bacterial wilt caused by R. pseudosolanacearum on peanut in Korea.

• Korean Journal of Microbiology
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• v.40 no.3
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• pp.244-247
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• 2004

To investigate the effects of elevated $CO_2$ on the denitrifying bacterial community structure in a wetland soil, dynamics of bacterial community structure was explored in an artificial wetland ecosystem with one of three plant species (T. latifolia, S. lacustris, and 1. effusus) under two levels of $CO_2$(370 ppm or 740 ppm) after 110day incubation. For the analysis of bacterial community structure, functional genes such as nitrite reductase genes (nirS) were PCR-amplified followed by cloning of PCR products and screening by restriction fragment length polymorphism (RFLP). nirS gene fragments were amplified in all analyzed soil samples. Species richness estimated by the number of distinct phylotypes were 83 and 95 in the ambient $CO_2$ treatment and the elevated treatment, respectively. Two phylotypes (type 1 and type 2) were dominant in both of the treatments. Elevated $CO_2$ treatment increased species richness of denitrifying as well as changed a large proportion of denitrifier phylotypes compared to those of the ambient treatment. Overall, the data in this study suggested that the denitrifying communities in the wetland soil are diverse and that the richness of denitrifying bacterial community might be affected by elevated $CO_2$ treatment.

• Korean Journal of Microbiology
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• v.43 no.3
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• pp.232-235
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• 2007

Mesophilic Crenarchaeota have been known to be predominant among ammonia-oxidizing microorganisms in terrestrial and marine environments. In this study, we determined the archaeal phylotypes carrying specific amoA by combining digital PCR and multiplex-nested PCR. Analysis of samples in which amoA and 16S rRNA gene were amplified showed that amoA gene diversity was relatively higher than that of 16S rRNA gene. Nitrifying archaeal group I.1a was dominant over I.1b group of crenarchaota and euryarchaeota. This approach could be applied for interrelating a functional gene to a specific phylotype in natural environments.

• The Plant Pathology Journal
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• v.37 no.6
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• pp.566-579
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• 2021

Ralstonia syzygii subsp. indonesiensis (Rsi, former name: Ralstonia solanacearum phylotype IV) PW1001, a causal agent of potato wilt disease, induces hypersensitive response (HR) on its non-host eggplant (Solanum melongena cv. Senryo-nigou). The disaccharide trehalose is involved in abiotic and biotic stress tolerance in many organisms. We found that trehalose is required for eliciting HR on eggplant by plant pathogen Rsi PW1001. In R. solanacearum, it is known that the OtsA/OtsB pathway is the dominant trehalose synthesis pathway, and otsA and otsB encode trehalose-6-phosphate (T6P) synthase and T6P phosphatase, respectively. We generated otsA and otsB mutant strains and found that these mutant strains reduced the bacterial trehalose concentration and HR induction on eggplant leaves compared to wild-type. Trehalose functions intracellularly in Rsi PW1001 because addition of exogenous trehalose did not affect the HR level and ion leakage. Requirement of trehalose in HR induction is not common in R. solanacearum species complex because mutation of otsA in Ralstonia pseudosolanacearum (former name: Ralstonia solanacearum phylotype I) RS1002 did not affect HR on the leaves of its non-host tobacco and wild eggplant Solanum torvum. Further, we also found that each otsA and otsB mutant had reduced ability to grow in a medium containing NaCl and sucrose, indicating that trehalose also has an important role in osmotic stress tolerance.

• Journal of Microbiology and Biotechnology
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• v.21 no.6
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• pp.567-573
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• 2011

We investigated the phylogenetic diversity of ammoniaoxidizing bacteria (AOB) in Yellow Sea continental shelf sediment by the cloning and sequencing of PCR-amplified amoA and 16S rRNA genes. Phylogenetic analysis of the amoA-related clones revealed that the diversity of AOB was extremely low at the study site. The majority (92.7%) of amoA clones obtained belonged to a single cluster, environmental amoA cluster-3, the taxonomic position of which was previously unknown. Phylogenetic analysis on AOB-specific 16S rRNA gene sequences also demonstrated a very low diversity. All of the cloned 16S rRNA gene sequences comprised a single phylotype that belonged to the members of uncultured Nitrosospira cluster-1, suggesting that AOB belonging to the uncultured Nitrosospira cluster-1 could carry amoA sequences of environmental amoA cluster-3.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.128-134
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• 2000

In the course of flora analysis of soil Archaea, we found very strange 16S rDNA clones, which could possibly constitute a sister clade from known two archael, Crenarchaeota and Euryarchaeota, lineages. Overall signature sequences showed that the clones were closely related to domains Archaea and Eucarya. However, at least nine nucleotides distinguished the novel clones from domains Archaea and Eucarya. Phylogenetic trees drawn by maximum parsimony, neighbor joining and maximum likelihood methods also showed unique phylogenetic position of the clones. A very specific primer set was synthesized to detect the presence of the novel group of organisms in terrestrial environments. A specific DNA fragment was amplified from all of paddy soil DNAs, and this fact suggests that the novel organisms inhabit paddy soils.

• The Sea:JOURNAL OF THE KOREAN SOCIETY OF OCEANOGRAPHY
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• v.17 no.3
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• pp.160-180
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• 2012

We have studied the eukaryotic plankton species diversity to compare the community structure of fresh and brackish waters in the lower reaches of the Nakdong River using metagenomic methods. We constructed 18S rDNA clone libraries of total DNAs extracted from environmental water samples collected at Mulgeum (MG100929, fresh) and Eulsukdo bridge (ES, brackish). Through the steps of colony PCR, PCR-RFLP, sequencing and similarity analysis, we discovered the diverse species composition of eukaryotic plankton. Total 338 clones (170 at MG100929 and 168 at ES) were analyzed, and then we found 74 phylotypes (49 for MG100929 and 25 for ES). From the phylogenetic analysis, we confirmed various eukaryotic plankton of broad range of taxonomic groups, including Stramenopiles, Cryptophyta, Viridiplantae, Alveolata, Rhizaria, Metazoa, and Fungi. We also found several unreported species in Korea and candidates of new taxonomic entities at levels higher than genus. Especially, the cryptic species diversity including unreported phylotypes of Pirsonia (Stramenopiles) and Perkinsea (Alveolata) suggests that the molecular monitoring method can produce new informative biological data in monitoring the changes in the Nakdong River Mouth ecosystem.