• Korean Journal of Ichthyology
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• v.27 no.4
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• pp.284-292
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• 2015

Monthly variation of species composition and abundance of fish eggs were examined to know the spawning time and location of the fishes inhabiting the coastal region of Jejudo Island. Samplings had been performed at the four locations (Jeju port, Seongsanpo, Seogwipo port and Chagwido) with a bongo net which was towed monthly at the sea surface from August 2006 to July 2007. The fish eggs were identified based on phylogenetic analyses with the DNA sequences generated through PCR-amplification and sequencing of the mitochondrial cytochrome b gene. Among a total of 43 taxa classified during the study period, 34 were identified to species, 4 to families, and the remaining 5 were unidentified. Of them, 23 taxa were occurred at Jeju port, 21 at Seongsanpo, 19 at Seogwipo port and 18 at Chagwido, whereas 15 taxa were found in September 2006, 12 in June 2007, 6 to 8 in August 2006 and January~May 2007, 5 in each October and November 2006, 3 in each December 2006 and July 2007. Among 34 species of fish eggs, Engraulis japonicus and Callanthias japonicus most frequently appeared at 16 times out of 48 observations in total. When those eggs were collected, the surface seawater temperature ranged $14.0{\sim}28.6^{\circ}C$ for E. japonicus and $14.9{\sim}20.5^{\circ}C$ for C. japonicus. The success rates of PCR-amplification and species identification in this study were 68.3% and 79.1%, respectively.

• Korean journal of applied entomology
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• v.56 no.4
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• pp.371-376
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• 2017

In a nationwide survey of the occurrence and density of the migratory locust (Locusta migratoria), high density was continuously observed in the reclaimed areas of Mangun-myeon in Muan-gun, Jeollanam-do, and Sanye-myeon in Haenam-gun, Jeollanam-do, Korea. We have analyzed the nucleotide sequences of NADH dehydrogenase subunit (NAD) 2, NAD4, and NAD5 genes in order to determine the origins of the migratory locusts at two sites. According to the analysis, the migratory locusts in Haenam-gun were closely related with those in Liaoning Province and Heilongjiang Province in the northeast China. In contrast, the migratory locusts in Muan-gun were most similar to those in Japan. Because Korean migratory locusts were not included in the previous global study on the evolution and migration of migratory locusts, we did not know the origin of Korean migratory locusts, earlier. Phylogenetic analyses this study suggested that the migratory locusts from the northeast Chinese population might have migrated and settled in Haenam-gun in Korea. Moreover, another northeast Chinese population might have migrated to Muan-gun in Korea though Sakhalin, Russia and Hokkaido, Japan. However, the possibility that the migratory locusts moved from northeast China might be isolated from each other in Korea, and that the Muan population might migrate to Japan cannot be excluded.

• The Korean Journal of Mycology
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• v.41 no.3
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• pp.142-148
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• 2013

Sorghum (Sorghum bicolor Moench) was traditionally grown on a small scale, however, at present its cultivation is getting momentum in terms of food and animal feed crop throughtout the Korea. Grain mold symptoms of the plant were frequently observed during disease surveys in Korea from 2007 to 2009. The symptoms were highly variable. Severely infected grain was fully covered with mold and partially infected grain may look normal or discolored. Ninety isolates of Fusarium species were obtained from the diseased plants collected from several locations in the country. Among the collected Fusarium isolates, 41 were identified as Fusarium thapsinum, 23 as F. proliferatum, 12 as F. graminearum, 5 as F. incarnatum, and 3 as F. equiseti based on their morphological and cultural characteristics. Elongation factor 1 alpha gene sequences of the isolates were used for phylogenetic analysis. Analyses of the sequences revealed that the isolates were confirmed to be identical with related species of NCBI GenBank. Pathogenicity tests showed that three dominant species, F. thapsinum, F. proliferatum and F. graminearum were strongly virulent to grains of sorghum. This study is the first report of sorghum grain mold caused by Fusarium species in Korea.

• Korean Journal of Microbiology
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• v.33 no.2
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• pp.149-156
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• 1997

We have employed comparative RFL,P(Restriction Fragment Ixngth Pol~iniorphism) analysis and molecular phylogenetic techniques to investigate the diversity of uncultured microorganisms associated with the anaerobic PCP degradation in PCP-adapted enrichment cultures inoculated by samples from anaerobic cewage sludgc(Jangrim, Pusan) and leachate of landfill site(Kimhae). 16s rDNA cloncs were obtairted by PCR amplification of mixed population DNAs extracted directly from the nonactive and active stage ol each PCP-adapted culture. After three rounds of comparative RFLP analyses. two RFLP types. designated as Ala and Hld, were found prevalent and common in both active stage samples. Thc analysis of phylogenctic diversity bawd on the 5'-terminal 180 nt of sequences from whole clones of the Ala and Bld RFLP types showed close similarity among themselves. In case of Bld clones, 7XQ of them shared identical sequences. Thcse resuliq suggest that the clones of both RFLP types wcre originated from highly affiliated microorganisms which are e~iriched as a result of metabolic activity to PCP. The full-length 16s rRNA sequence of each representative clone from both RFLP types was determined. and an Ala clone w i n found to he related to Clo.strrdiurn ulfutzac~(Genk~ank No. Z69203) and a Bld clone to Thermobacteroides proteolyticus(Genbank No. X09335), with sequence similarities of 89%' and 97%. respectively.

• Journal of Microbiology and Biotechnology
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• v.17 no.2
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• pp.253-261
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• 2007

Molecular and cultivation techniques were used to characterize the bacterial communities of biobead reactor biofilms in a sewage treatment plant to which an Aerated Up-Flow Biobead process was applied. With this biobead process, the monthly average values of various chemical parameters in the effluent were generally kept under the regulation limits of the effluent quality of the sewage treatment plant during the operation period. Most probable number (MPN) analysis revealed that the population of denitrifying bacteria was abundant in the biobead #1 reactor, denitrifying and nitrifying bacteria coexisted in the biobead #2 reactor, and nitrifying bacteria prevailed over denitrifying bacteria in the biobead #3 reactor. The results of the MPN test suggested that the biobead #2 reactor was a transition zone leading to acclimated nitrifying biofilms in the biobead #3 reactor. Phylogenetic analysis of 16S rDNA sequences cloned from biofilms showed that the biobead #1 reactor, which received a high organic loading rate, had much diverse microorganisms, whereas the biobead #2 and #3 reactors were dominated by the members of Proteobacteria. DGGE analysis with the ammonia monooxygenase (amoA) gene supported the observation from the MPN test that the biofilms of September were fully developed and specialized for nitrification in the biobead reactor #3. All of the DNA sequences of the amoA DGGE bands were very similar to the sequence of the amoA gene of Nitrosomonas species, the presence of which is typical in the biological aerated filters. The results of this study showed that organic and inorganic nutrients were efficiently removed by both denitrifying microbial populations in the anaerobic tank and heterotrophic and nitrifying bacterial biofilms well-formed in the three functional biobead reactors in the Aerated Up-Flow Biobead process.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.254-265
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• 2018

Avian influenza recently damaged the poultry industry, which suffered a huge economic loss reaching billions of U.S. dollars in South Korea. Transmission routes of the pathogens would help plan to control and limit the spread of the devastating biological tragedy. Phylogenetic analyses of pathogen's DNA sequences could sketch transmission trees relating hosts with directed edges. The last decade has seen the methodological development of inferring transmission trees using epidemiological as well as genetic data. Here, I reanalyzed the DNA sequence data that had originated in the highly pathogenic avian influenza H5N8 outbreak of South Korea in 2014. The H5N8 viruses spread geographically contiguously from the origin of the outbreak, Jeonbuk. The Jeonbuk origin viruses were known to spread to four provinces neighboring Jeonbuk. I estimated the transmission tree of the host domestic and migratory wild birds after combining multiple runs of Markov chain Monte Carlo using a Bayesian method for inferring transmission trees. The estimated transmission tree, albeit with a rather large uncertainty in the directed edges, showed that the viruses spread from Jeonbuk through Chungnam to Gyeonggi. Domestic birds of breeder or broiler ducks were estimated to appear to be at the terminal nodes of the transmission tree. This observation confirmed that migratory wild birds played an important role as one of the main infection mediators in the avian influenza H5N8 outbreak of South Korea in 2014.

• Journal of Life Science
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• v.21 no.2
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• pp.235-241
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• 2011

The purpose of this study was to isolate soy curd forming bacterial strains. Soy curd forming bacteria were isolated from Kimchi, a traditional Korean vegetable food that is fermented using lactic acid bacteria. Among 196 bacterial strains, ten isolates (strain No. 2-2-2, 2-15-2, 2-18-1, 2-19-2, 3-4-1, 3-4-2, 3-8-1, 3-8-3, 3-17-1, 4-39-5) formed firm soy curd. The isolated bacterial strains were identified by molecular biological and biochemical analyses. The genomic DNAs extracted from the isolated bacterial strains were used as a template for PCR amplification of 16S rDNA region. By comparing the results of the 16s rDNA sequences with GenBank data, the isolated strains were identified as Leuconostoc mesenteroides group and Lactobacillus sakei group. The phylogenetic position of soy curd forming strains and their related taxa were investigated using neighbor-joining method. L. mesenteroides group was further identified as L. mesenteroides subsp. dextranicum based on biochemical properties. L. sakei group was named Lactobacillus sp., because it showed a variety of biochemical properties.

• Korean Journal of Plant Taxonomy
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• v.39 no.3
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• pp.135-142
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• 2009

Phylogeny of the family Ophioglossaceae and a phylogenetic position of Mankyua were estimated through analyses of chloroplast rbcL gene sequences and spore morphology. Sequence analysis of the rbcL gene clearly indicated that there are two major lineages in the family Ophioglossaceae: Botrychioid lineage and Ophioglossoid lineage. The Botrichioid lineage is composed of three distinct clades: Botrychium, Helminthostachys and Mankyua, where Helminthostachys and Mankyua were placed as sister groups to the Botrychium. Within the genus Botrychium, subgenera Septridium and Botrychium were monophyletic, while taxa of subgen. Botrypus branched as sister of the two, successively, thus making a non-monophyletic group. Ophioglossum formed the Ophioglossoied lineage, where the subgen. Ophioglossum is monophyletic, while subgen. Cheiroglossa and Ophoderma formed a sister relationship with subgen. Ophioglossum. In terms of external morphology and spores, Mankyua is most similar to Helminthostachys, however, patristic distance in the cladogram and trophophore characteristics of the two genera are distinct. Therefore, Mankyua is a well defined genus within the family in terms of morphology as well as molecular phylogeny which places it in basal position of the Botrychioid lineage on the gene tree.

• Korean Journal of Ichthyology
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• v.33 no.2
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• pp.45-56
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• 2021

A male, presumed to be an intergeneric hybrid between Tanakia lanceolata and Rhodeus pseudosericeus, was collected in the Boryeong Daecheoncheon Stream flowing into the Yellow Sea in the Republic of Korea. Morphological and molecular phylogenetic analyses were performed to discriminate the definite origin of the estimated natural hybrid. As a result of the morphological analysis, the color of the dorsal and anal fin rays edges of the natural hybrid individual, the upper and lower body colors followed the morphological characteristics of T. lanceolata, and that blue longitudinal stripe in the center of the caudal peduncle, the incomplete lateral line, and the barbels absent followed the morphological characteristics of R. pseudosericeus. In addition, as a result of the cytochrome b (cytb) gene analysis of mitochondrial DNA (mtDNA), the natural hybrid showed a nucleotide sequence similarity of 99.82 to 100% with T. lanceolata, and the maternal species was identified as T. lanceolata. As a result of the recombination activating gene 1 (rag1) gene analysis of nuclear DNA (nDNA), the natural hybrid showed double peaks pattern reflecting both the single nucleotide polymorphism sites (38 bp) between T. lanceolata and R. pseudosericeus, and the paternal species was identified as R. pseudosericeus. Therefore, a natural hybrid estimated male of Acheilognathinae analyzed in this study was found to be an intergeneric hybrid between a female T. lanceolata and a male R. pseudosericeus.

• Journal of Microbiology and Biotechnology
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• v.29 no.7
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• pp.1083-1095
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• 2019

Butyrate is known to play a significant role in energy metabolism and regulating genomic activities that influence rumen nutrition utilization and function. Thus, this study investigated the effects of an isolated butyrate-producing bacteria, Clostridium saccharobutylicum, in rumen butyrate production, fermentation parameters and microbial population in Holstein-Friesian cow. An isolated butyrate-producing bacterium from the ruminal fluid of a Holstein-Friesian cow was identified and characterized as Clostridium saccharobutylicum RNAL841125 using 16S rRNA gene sequencing and phylogenetic analyses. The bacterium was evaluated on its effects as supplement on in vitro rumen fermentation and microbial population. Supplementation with $10^6CFU/ml$ Clostridium saccharobutylicum increased (p < 0.05) microbial crude protein, butyrate and total volatile fatty acids concentration but had no significant effect on $NH_3-N$ at 24 h incubation. Butyrate and total VFA concentrations were higher (p < 0.05) in supplementation with $10^6CFU/ml$ Clostridium saccharobutylicum compared with control, with no differences observed for total gas production, $NH_3-N$ and propionate concentration. However, as the inclusion rate (CFU/ml) of C. saccharobutylicum was increased, reduction of rumen fermentation values was observed. Furthermore, butyrate-producing bacteria and Fibrobacter succinogenes population in the rumen increased in response with supplementation of C. saccharobutylicum, while no differences in the population in total bacteria, protozoa and fungi were observed among treatments. Overall, our study suggests that supplementation with $10^6CFU/ml$ C. saccharobutylicum has the potential to improve ruminal fermentation through increased concentrations of butyrate and total volatile fatty acid, and enhanced population of butyrate-producing bacteria and cellulolytic bacteria F. succinogenes.