• Microbiology and Biotechnology Letters
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• v.52 no.1
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• pp.1-14
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• 2024

This study focused on isolating and identifying strains from the gut of Epinephelus akaara cultivated in aquaculture facilities on Jeju Island. The aim was to evaluate the potential of utilizing these strains as probiotics for industrial applications. A total of 129 strains were isolated from the gut of E. akaara and screened based on their ability to create a clear zone of 10 mm or more in a preliminary antimicrobial activity test. Twelve strains were selected for further analysis, including bile resistance, acid tolerance at different pH levels, antioxidant activity, antibiotic susceptibility, and biochemical characteristics using the API kit. Through these characteristic experiments, eight strains (G1, G3, G15, G21, B1, B2, B3, B5) were identified as having potential as probiotics. Among these, the B group strains (B1, B2, B3, B5) exhibited significantly higher activity compared to the G group strains (G1, G3, G15, G21). Based on the phylogenetic analysis of the 16S rRNA gene sequences of the selected microorganisms, the strains were named as follows: B1 strain as Lactobacillus paracasei B1, B2 strain as Lactococcus lactis B2, B3 strain as Lactobacillus plantarum B3, B5 strain as Lactococcus lactis subsp. hordniae B5, G1 strain as Bacillus licheniformis G1, G3 strain as Bacillus velezensis G3, G15 strain as Brevibacterium frigoritolerans G15, and G21 strain as Bacillus pumilus G21.

• 한국균학회소식:학술대회논문집
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• 2014.05a
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• pp.27-28
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• 2014

Beauveria bassiana (Cordycipitaceae, Hypocreales, Ascomycota) is an anamorphic fungus having a potential to be used as a biological control agent because it parasitizes a wide range of arthropod hosts including termites, aphids, beetles and many other insects. A number of bioactive secondary metabolites (SMs) have been isolated from B. bassiana and functionally verified. Among them, beauvericin and bassianolide are cyclic depsipeptides with antibiotic and insecticidal effects belonging to the enniatin family. Non-ribosomal peptide synthetases (NRPSs) play a crucial role in the synthesis of these secondary metabolites. NRPSs are modularly organized multienzyme complexes in which each module is responsible for the elongation of proteinogenic and non-protein amino acids, as well as carboxyl and hydroxyacids. A minimum of three domains are necessary for one NRPS elongation module: an adenylation (A) domain for substrate recognition and activation; a tholation (T) domain that tethers the growing peptide chain and the incoming aminoacyl unit; and a condensation (C) domain to catalyze peptide bond formation. Some of the optional domains include epimerization (E), heterocyclization (Cy) and oxidation (Ox) domains, which may modify the enzyme-bound precursors or intermediates. In the present study, we analyzed genomes of B. bassiana and its allied species in Hypocreales to verify the distribution of NRPS-encoding genes involving biosynthesis of beauvericin and bassianolide, and to unveil the evolutionary processes of the gene clusters. Initially, we retrieved completely or partially assembled genomic sequences of fungal species belonging to Hypocreales from public databases. SM biosynthesizing genes were predicted from the selected genomes using antiSMASH program. Adenylation (A) domains were extracted from the predicted NRPS, NRPS-like and NRPS-PKS hybrid genes, and used them to construct a phylogenetic tree. Based on the preliminary results of SM biosynthetic gene prediction in B. bassiana, we analyzed the conserved gene orders of beauvericin and bassianolide biosynthetic gene clusters among the hypocrealean fungi. Reciprocal best blast hit (RBH) approach was performed to identify the regions orthologous to the biosynthetic gene cluster in the selected fungal genomes. A clear recombination pattern was recognized in the inferred A-domain tree in which A-domains in the 1st and 2nd modules of beauvericin and bassianolide synthetases were grouped in CYCLO and EAS clades, respectively, suggesting that two modules of each synthetase have evolved independently. In addition, inferred topologies were congruent with the species phylogeny of Cordycipitaceae, indicating that the gene fusion event have occurred before the species divergence. Beauvericin and bassianolide synthetases turned out to possess identical domain organization as C-A-T-C-A-NM-T-T-C. We also predicted precursors of beauvericin and bassianolide synthetases based on the extracted signature residues in A-domain core motifs. The result showed that the A-domains in the 1st module of both synthetases select D-2-hydroxyisovalerate (D-Hiv), while A-domains in the 2nd modules specifically activate L-phenylalanine (Phe) in beauvericin synthetase and leucine (Leu) in bassianolide synthetase. antiSMASH ver. 2.0 predicted 15 genes in the beauvericin biosynthetic gene cluster of the B. bassiana genome dispersed across a total length of approximately 50kb. The beauvericin biosynthetic gene cluster contains beauvericin synthetase as well as kivr gene encoding NADPH-dependent ketoisovalerate reductase which is necessary to convert 2-ketoisovalarate to D-Hiv and a gene encoding a putative Gal4-like transcriptional regulator. Our syntenic comparison showed that species in Cordycipitaceae have almost conserved beauvericin biosynthetic gene cluster although the gene order and direction were sometimes variable. It is intriguing that there is no region orthologous to beauvericin synthetase gene in Cordyceps militaris genome. It is likely that beauvericin synthetase was present in common ancestor of Cordycipitaceae but selective gene loss has occurred in several species including C. militaris. Putative bassianolide biosynthetic gene cluster consisted of 16 genes including bassianolide synthetase, cytochrome P450 monooxygenase, and putative Gal4-like transcriptional regulator genes. Our synteny analysis found that only B. bassiana possessed a bassianolide synthetase gene among the studied fungi. This result is consistent with the groupings in A-domain tree in which bassianolide synthetase gene found in B. bassiana was not grouped with NRPS genes predicted in other species. We hypothesized that bassianolide biosynthesizing cluster genes in B. bassiana are possibly acquired by horizontal gene transfer (HGT) from distantly related fungi. The present study showed that B. bassiana is the only species capable of producing both beauvericin and bassianolide. This property led to B. bassiana infect multiple hosts and to be a potential biological control agent against agricultural pests.

• Horticultural Science & Technology
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• v.34 no.2
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• pp.305-313
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• 2016

Brassica juncea (2n = 4x = 36, AABB genome, 1,068 Mb) is a U's triangle species and an amphidiploid derivative of B. rapa and B. nigra. Fifteen varieties were used to study the ITS (internal transcribed spacer) regions of ribosomal DNA and MITEs (miniature inverted-repeat transposable elements) with a view of developing specific molecular markers. ITSs and MITEs are an excellent resource for developing DNA markers for genomics and evolutionary studies because most of them are stably inherited and present in high copy numbers. The ITS (ITS1 and ITS2) sequence was compared with the consensus sequence of B. rapa and B. nigra. Variation in ITS1 created two separate groups among 15 varieties, with 10 varieties in one group and 5 in the other. Phylogenetic analysis revealed two major clusters for those 10 and 5 varieties. Among the 160 different MITE primers used to evaluate the selected 15 varieties of B. juncea, 70 were related to the Stowaway, 79 to the Tourist, 6 to the hAT, and 5 to the Mutator super-families of MITEs. Of 160 markers examined, 32 were found to be polymorphic when fifteen different varieties of B. juncea were evaluated. The variety 'Blackgat' was different from the other mustard varieties with respect to both phenotype and genotype. The diversity of 47 additional accessions could be verified using eight selected molecular markers derived from MITE family sequences. The polymorphic markers identified in this study can be used for varietal classification, variety protection, and other breeding purposes.

• Korean Journal of Microbiology
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• v.49 no.1
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• pp.58-63
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• 2013

A taxonomic study was carried out to assess the phylogenetic characteristics of isolate JJM57 from marine red algae Laurencia sp. collected from intertidal zone in Jeju Island, South Korea. Comparative analysis of 16S rRNA gene sequence shows that this isolate belongs to the genus Oceanisphaera. It shows 98.02% and 97.7% sequence similarity with Oceanisphera litoralis DSM $15406^T$ and Oceanisphera donghaensis KCTC $12522^T$, respectively. Strain JJM57 is a Gram-negative, aerobic, moderately halophilic bacterium able to grow in different NaCl concentration ranges from 0.5 to 8.0% and at varying temperatures from 4 to $37^{\circ}C$. Sharing some of the physiological and biochemical properties with O. litoralis and O. donghaensis, JJM57 strain differs in the utilization of ethanol, proline, and alanine. The G+C contents of the strain JJM57 is 61.94 mol% and it is rich in $C_{16:1}$ ${\omega}7c$ and/or iso-$C_{15:0}$ 2-OH, $C_{16:0}$, and $C_{18:1}$ ${\omega}7c$ fatty acids. The DNA-DNA relatedness data separates the strain JJM57 from other species such as O. litoralis and O. donghaensis. On the basis of these polyphasic evidences, present study proposed that strain JJM57 (=KCTC 22371 =AM983543 =CCUG 60764) represents a novel bacterial species of Oceanisphaera.

• Horticultural Science & Technology
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• v.30 no.2
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• pp.178-184
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• 2012

This study was carried out to decide ITS (internal transcribed spacer) sequence of some Korean native $Aster$ species and to resolve their relationship among Korean native $Aster$, including $Kalimeris$, $Gymnaster$, $Heteropappus$ genus separated from $Aster$ in a previously study based on the pappus length. We registered 11 ITS sequences of $Aster$ species including $A.$ $glehni$ to GenBank and those sequences were used for the cluster analysis with $Kalimeris$ species. The size of ITS1 was varied from 248 to 256 bp, while ITS2 was varied from 220 to 222 bp. The G + C content of the ITS region ranged from 49.4 to 53.5%. Pairwise comparison results showed that the substitution rate of ITS1 and ITS2 region was 9% and 10%, respectively. $Kalimeris$ sensu strict substitution rate was lower than that of $Aster$ sensu strict species. The strict consensus parsimonious cluster analysis showed $A.$ $tripolium$ is the first branching from the clade and the next is $A.$ $scaber$. The $Kalimeris$ species except for the $A.$ $hispidus$ were grouped into the same clade with high bootstrap value (91%) within $Aster$. $Gymnaster$ and $Heteropappus$ that has been classified by morphological characters were also grouped into broad sense $Aster$ clade. These results implied these three genera could be merged together into $Aster$ based on the ITS sequences.

• Journal of Korean Society of Environmental Engineers
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• v.31 no.1
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• pp.51-57
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• 2009

Biofouling in seawater reverse osmosis (SWRO) desalination process causes many problems such as flux decline, biodegradation of membrane, increased cleaning time, and increased energy consumption and operational cost. Therefore biofouling is considered as the most critical problem in system operation. To control biofouling in early stage, detection of the most problematic bacteria causing biofouling is required. In this study, six model bacteria were chosen; Bacillus sp., Flavobacterium sp., Mycobacterium sp., Pseudomonas aeruginosa, Pseudomonas fluorescens, and Rhodobacter sp. based on report in the literature and phylogenetic analysis of seawater intake and fouled RO membrane. The adhesion to RO membrane, the high pressure resistance, and the hydrophobicity of the six model bacteria were examined to find out their fouling potential. Rhodobacter sp. and Mycobacterium sp. were found to attach very well to RO membrane surface compared to others used in this study. The test of hydrophobicity revealed that the bacteria which have high hydrophobicity or similar contact angle with RO membrane ($63^{\circ}$ of contact angle) easily attached to RO membrane surface. P. aeruginosa which is highly hydrophilic ($23.07^{\circ}$ of contact angle) showed the least adhesion characteristic among six model bacteria. After applying a pressure of 800 psi to the sample, Rhodobacter sp. was found to show the highest reduction rate; with 59-73% of the cells removed from the membrane under pressure. P. fluorescens on the other hand analyzed as the most pressure resistant bacteria among six model bacteria. The difference between reduction rates using direct counting and plate counting indicates that the viability of each model bacteria was affected significantly from the high pressure. Most cells subjected to high pressure were unable to form colonies even thought they maintained their structural integrity.

• Research in Plant Disease
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• v.30 no.1
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• pp.26-33
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• 2024

In 2023, symptoms like damping-off disease were observed in 74 paprika growing in greenhouses in Cheorwon-gun, Gangwon-do, Korea. In this study, we tried to find the cause of the damping-off disease outbreak. We collected symptomatic seedlings and observed the typical crescent-shaped conidia of Fusarium oxysporum by microscope. To confirm the presence of F. oxysporum in the samples, polymerase chain reaction was performed using primers specific for F. oxysporum; the resulting sequence showed 99.11% identity with F. oxysporum. To confirm the pathogenicity of the F. oxysporum (CW) isolated from the samples, healthy paprika plants were inoculated with F. oxysporum CW and damping-off symptoms were observed 2 weeks later. To investigate whether the damping-off disease outbreak in Cheorwon-gun was caused by F. oxysporum-contaminated seeds, 100 paprika seeds were disinfected and placed in Murashige and Skoog medium. Typical pink F. oxysporum hyphae were found only in control non-disinfected seeds. An 18S rRNA-based and a TEF genebased phylogenetic analysis showed that the F. oxysporum CW isolate was not grouped with a F. oxysporum isolate reported from Cheorwon-gun in 2019. This study is the first report that an outbreak of damping-off disease in paprika in Cheorwon-gun, Gangwon-do, Korea, was caused by contamination of F. oxysporum seeds.

• Journal of Life Science
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• v.26 no.11
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• pp.1237-1244
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• 2016

A comprehensive analysis of the genetic diversity and relationship of the cold-water fishery walleye pollock (Theragra chalcogramma), the most abundant economically important fishery resource in the East sea of Korea, has not been carried out, despite its importance in Korea. The present study assessed the genetic diversity and relationship between five walleye pollock populations (Korean population, Russian population, USA population, and Japanese populations) of T. chalcogramma using eight microsatellite DNA (msDNA) markers to provide the scientific data for the preservation and management of the Pollock fishery resource. The results of the analysis of 186 individuals of the Pollock revealed a range of 7.13-10.63 numbers of alleles (mean number of alleles=9.05). The means of observed heterozygosity ($H_O$), expected heterozygosity ($H_E$) were 0.732 and 0.698, respectively. The results of genetic distance, Pairwise $F_{ST}$, UPGMA (UPGMA: un-weighted pair-group method with an arithmetical average) (the phylogenetic tree), PCA (PCA: Principal Coordinate analysis) analysis pointed to significant differences between the Korean population, Russian population, USA population, and Japanese populations, although small (p<0.05). These results shed light on the genetic diversity and relationships of T. chalcogramma and can be utilized for research on the evaluation and conservation of Korean T. chalcogramma as genetic resources.

• Korean Journal of Poultry Science
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• v.35 no.4
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• pp.361-366
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• 2009

The purpose of this study was to assess the genetic variation and establish the relationship amongst breeds and strains using 7 chicken specific microsatellite markers. A total of 317 DNA samples from four Korean native chicken (KNC) strains (KR: Korean Native Red chicken strain, KY: Korean Native Yellow chicken strain, KL: Korean Native Black chicken strain, KO: Ogol chicken strain) and three introduced endemic chicken breeds (LE: Leghorn chicken breed, RI: Rhode Island Red chicken breed, CO: Cornish chicken breed). The size of microsatellite markers was decided using GeneMapper Software (v.4.0) after being analyzed using an ABI 3130 Genetic Analyzer. Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The lowest distance (0.074) was observed between the KY and KL breeds and the highest distance (0.779) between the KL and LE breeds. The KNC strains (KR, KY, KL) have comparatively near genetic distance each other. On the other side, each individual was not ramified to different groups and were spread evenly in phylogenetic dendrogram about all the KNC of each strain populations. But the endemic breed populations (LE, RI, CO) were ramified to different groups. The microsatellite polymorphism data were shown to be useful for assessing the genetic relationship between Korean native strains and other foreign breeds.

• Korean journal of applied entomology
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• v.50 no.2
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• pp.157-165
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• 2011

Enterobacteria were isolated in the gut of the predacious multicolored Asian ladybird beetle, Harmonia axyridis, and their effects to the development of H. axyridis were examined. Populations of H. axyridis in this experiment were collected from Kimjae at Cheonbuk province (JK population), Geumsan at Chungnam province (CK population) and laboratory population at Laboratory of Insect Physiology in Chungnam National University, Daejeon. Thirty-four enterobacteria isolates were purified and isolated from the digestive tract of H. axyridis, and a total of 4 strains were classified into group by analysis of 16S rRNA gene sequences. About 70% of total isolates were phylogenetic groups of Bacillus genus and Staphylococcus genus, and they were commonly separated from the digestive tract of H. axyridis. After investigating their susceptibility against antibiotics with 18 representative enterobacteria isolates, ofloxacin and penicillin were selected for examination in this study of their ability to inhibit the growth of all of isolates. In order to remove the enterobacteria from the aphids, ofloxacin and penicillin were given to the green peach aphid, Myzus persicae, and the turnip aphid, Lipaphis erysimi. These aphids were provided to H. axyridis as prey. The weight of pupa, developmental periods of each larval instar, the number of eggs and their hatching ratio of H. axyridis with treatment aphids were lower compared with non-treatment aphids. Staphylococcus saprophyticus is a representative enterobacteria and commonly isolated from the digestive tract of H. axyridis. In the absence of S. saprophyticus, the developmental periods of each larval instar increased; however, the weights of pupa, the number of eggs, and their hatching ratio decreased.