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Phylogeny of Desmodesmus (Scenedesmaceae, Chlorophyceae) in Korea based on multigene data analysis (다유전자 분석을 통한 한국산 녹조류 Desmodesmus속의 계통)

  • Yeong Chae Yoo;Nam-Ju Lee;Ga Yeong Jeon;Ok-Min Lee;Eun Chan Yang
    • Korean Journal of Environmental Biology
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    • v.41 no.4
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    • pp.345-363
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    • 2023
  • The genus Desmodesmus (Chodat) S.S. An, T. Friedl & E. Hegewald is ubiquitous in freshwater ecosystems, such as rivers, ponds, and wetlands. The actual species diversity and distribution of the genus is unknown because of morphological plasticity affected by habitats. Currently, 38 Desmodesmus species have been reported in Korea most of which transferred from the genus Scenedesmus recently, however, no phylogenetic relationships have been studied yet. Despite the challenges in analyzing relationships among Desmodesmus species through the morphology, ecology, and original description, this study focused on examining species-level relationships using the FBCC culture strains isolated from Korea. A total of 299 sequences (66 of 18S rRNA, 47 of atpB, 67 of petA, 52 of rbcL, and 67 of tufA) were newly determined and used for phylogenetic analysis. Four plastid genes tend to have higher variation than 18S rRNA in the variable sites and P-distance. From the combined phylogeny, the Desmodesmus included six clades such as Clade-1: D. pseudoserratus and D. serratus, Clade-2: D. communis, D. dispar, D. maximus, D. pannonicus, unidentified Desmodesmus sp., Clade-3: D. bicaudatus and D. intermedius, Clade-4: D. microspina, D. multivariablis, D. pleiomorphus, D. subspicatus, Clade-5: D. abundans, D. kissii, and D. spinosus, and Clade-6: D. armatus, D. armatus var. longispina, D. opoliensis, unidentified Desmodesmus spp. The new sequence data from FBCC strains will be used to identify species and study the molecular ecology of scenedesmacean green algae in freshwater ecosystems. The phylogenetic information from this study will expand our understanding of Desmodesmus species diversity in Korea.

Isolation and characterization of new Methanosarcina mazei strains KOR-3, -4, -5, and -6 from an anaerobic digester using pig slurry

  • Battumur, Urantulkhuur;Yoon, Youngman;Bae, Gui Sek;Kim, Chang-Hyun
    • Asian-Australasian Journal of Animal Sciences
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    • v.30 no.8
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    • pp.1198-1205
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    • 2017
  • Objective: An experiment was conducted to isolate and identify new methanogens in Korea from an anaerobic digester that uses pig slurry. Methods: An anaerobic digestate sample was collected from an anaerobic digester using pig slurry. Pre-reduced media were used for the growth and isolation of methanogens. Growth temperature range, pH range, NaCl concentration range, substrate utilization, and antibiotic tolerance were investigated to determine the physiological characteristics of isolated methanogens. The isolates were also examined microscopically for their morphology and Gram-stained. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification purpose. Results: Four strains, designated KOR-3, -4, -5, and -6, were isolated and were non-motile, irregular coccoid, and 0.5 to $1.5{\mu}m$ in diameter. Moreover, the cell walls of isolated strains were Gram-negative. KOR-3 and KOR-4 strains used acetate for methane production but did not use $H_2+CO_2$, formate, or methanol as a growth substrate KOR-5 and KOR-6 strains utilized acetate, methanol, and trimethylamine for methanogenesis but did not use $H_2+CO_2$ or formate as a growth substrate. The optimum temperature and pH for growth of four strains were $39^{\circ}C$ and 6.8 to 7.2, respectively. The optimum concentration of NaCl for growth of KOR-3, KOR-5, and KOR-6 were 1.0% (w/v). The optimum NaCl concentration for KOR-4 was 0.5% (w/v). All of the strains tolerated ampicillin, penicillin G, kanamycin, streptomycin, and tetracycline; however, chloramphenicol inhibited cell growth. Phylogenetic analysis of 16S rRNA and mcrA genes demonstrated that strains KOR-3, -4, -5, and -6 are related to Methanosarcina mazei (M. mazei, 99% sequence similarity). Conclusion: On the basis of physiological and phylogenetic characteristics, strains KOR-3, -4, -5, and -6 are proposed to be new strains within the genus Methanosarcina, named M. mazei KOR-3, -4, -5, and -6.

Identification of Daphne Mottle Virus Isolated from Daphne odora, a New Member of the Genus Potyvirus (서향에서 분리한 신종 포티바이러스(Daphne Mottle Virus)의 동정)

  • Park, Chung Youl;Park, Jungan;Lee, Boo-Ja;Bak, Sangmin;Lee, Hong-Kyu;Kim, Jeong-Sun;Yoon, Youngnam;Suh, Sang Jae;Lee, Su-Heon
    • Research in Plant Disease
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    • v.22 no.1
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    • pp.59-63
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    • 2016
  • A new poty-like virus was isolated from plants of winter daphne (Daphne odora) that showed virus-like symptoms on leaves, from four regions of Korea during 2014. Filamentous-shaped particles were observed by transmission electron microscopy of preparations extracted from symptomatic leaves and examined by the direct negative stain method. RT-PCR assay showed that three samples were positive for both Cucumber mosaic virus and potyvirus, and only one sample was positive for potyvirus only. A BLAST comparison to partial sequences from helper-component proteinase, cylindrical inclusion and coat protein genes detected the highest nucleotide identity of 76%, 72%, and 72% with Daphne mosaic virus, respectively, levels below the potyvirus species discrimination threshold. The new potyvirus was isolated using indicator plants (Chenopodium amaranticolor), in which local lesions were produced. In this study, we identified a novel potyvirus from winter daphne, which we have named Daphne mottle virus (DapMoV).

A checklist of endemic plants on the Korean Peninsula (한반도 특산식물 목록)

  • Chung, Gyu Young;Chang, Kae Sun;Chung, Jae-Min;Choi, Hyeok Jae;Paik, Weon-Ki;Hyun, Jin-Oh
    • Korean Journal of Plant Taxonomy
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    • v.47 no.3
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    • pp.264-288
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    • 2017
  • In order to organize a new checklist for endemic vascular plants of the Korean Peninsula, 358 taxa of the Korea Forest Service and 375 taxa of the National Institute of Biological Resources were reviewed. In addition, the names of previously published endemic plants above the rank of variety were checked up to 2016. From the two lists, a total of 444 taxa were identified. Among them, 289 taxa were common on the two lists, but 69 and 86 taxa were listed only by the Korea Forest Service and by the National Institute of Biological Resources, respectively. Taxonomic documents including journal papers and dissertations were examined with regard to the 444 taxa. In some cases, opinions of Korean experts in this field were also reflected. From the results, 312 taxa in total were recognized as plants endemic to the Korean Peninsula, while 132 taxa could not be included on the endemic list. On the other hand, 48 taxa, none of which existed on the two lists, were newly listed. In conclusion, the new checklist of vascular plants endemic to Korea was confirmed, with a total of 360 taxa consisting of 64 families, 172 genera, 297 species, 4 subspecies, 51 varieties and 8 hybrids. The new common name Halla-seol-aeng-cho is given to Primula farinosa L. subsp. modesta (Bisset & S. Moore) Pax var. hannasanensis (T. Yamaz.) T. Yamaz. Sillaphyton Pimenov (Deok-u-gi-reum-na-mul-sok) is newly identified as a genus endemic to Korea. However, Pentactina Nakai could not be included on the list of Korean vascular endemic genera.

Synopsis of the Suborder Tetraodontoidei (Pisces ; Tetraodontiformes) from Korea (한국진(韓國塵) 참복아목(亞目) 어류(魚類))

  • Kim, Ik-Soo;Lee, Wan-Ok
    • Korean Journal of Ichthyology
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    • v.2 no.1
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    • pp.1-27
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    • 1990
  • Twenty four species belonging to 10 genera and 4 families in the suborder Tetraodontoidei in Korea were reviewed and provisional keys to species, genera and families are provided. Among them available specimens of seventeen species in this taxa collected during 1986 to 1990 from Korean waters were examined and recorded on the morphometric characters, their body color and collection sites. And two species are reported for the first time to Korea with their descriptions and figures : Lagocephallus gloveri Abe et Tabeta, 1983 and L. wheeleri Abe,Tabeta et Kitahama, 1984. Taki/ugu chiηensis Abe, previously recorded from Pusan, Korea as paratype locality but not included in the list of Chyung, 1977, is listed in the present paper with the new korean name, "Chambok". Many of this taxa are also distributed throughout the waters of China and Japan. But it is found that the distribution of three species of genus Takifugu are restricted only to the west coast of Korea as well as to the adjacent waters of China in the Yellow Sea ; T. obscurus, T. flavidus and T. basilevskianus. Taxonomy and distribution of this taxa were discussed with references to the information obtained so far.

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Soil Nematode Fauna in Dokdo Island of Korea (독도의 토양 선충상)

  • Kim, Dong-Geun;Park, Byung-Yong;Ryu, Young-Hyun
    • Research in Plant Disease
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    • v.18 no.4
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    • pp.381-386
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    • 2012
  • Nematode fauna in Dokdo island was investigated for two years between 2008 and 2009. Population density and biomass were $239,500m^2$ (26,000-836,000) and $103.9mg/m^2$ (3.0-388.6), respectively. Total of 31 species of nematodes were identified : Acrobeloides is the most important genus with prominence value (PV) of 117.8, followed by Rhabditidae (PV = 81.9), Prismatolaimus (PV = 39.0), and Aphelenchoides (PV = 31.4). Among feeding group, bacteriovorus nematode composed 77% of density and 62% of biomass followed by plant-parasitic and fungivorus nematodes. A species of Pratylenchus having distinctive tail terminus is under study as a new species. Biological indices, Shannon and Wiener index (2.46), Simpson's diversity index (0.86), Species evenness (0.73), Species richness (1.30) indicate that nematode fauna in Dokdo island is diverse and unique. This study may give a general idea of nematode fauna at the Dokdo island.

Occurrence of Chiroteuthis picteti (Teuthoidea: Chiroteuthidae) from Korea (Chiroteuthis picteti (Teuthoidea: Chiroteuthidae)의 국내출현)

  • Kang, Hyunjung;Choi, Jung Hwa;Choi, Kwang Ho;Lee, Dongwoo;Kim, Yeonghye
    • The Korean Journal of Malacology
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    • v.29 no.4
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    • pp.381-384
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    • 2013
  • One specimen (13.4 cm ML) of Chiroteuthis picteti belonging to the family Chiroteuthidae, firstly collected from Songjeong, Southeast coastal water of Korea on May 18, 2013. It was identified as C. picteti based on the following combination of morphological character: mantle slenderly cylindrical; fin oval shape, both lobes having no anterior free lobe, FL 58.2% of ML; arms long with a formula IV > III > II > I. We propose a new Korean name, "Kin-pal-o-jing-eo-gua", "Kin-pal-o-jing-eo-sok", and "Kin-pal-o-jing-eo" for the family, genus and species, respectively.

New Record of the Two Carangid Fishes (Perciformes, Carangidae) from Korea (한국산 전갱이과 어류 2 미기록종)

  • Kim, Yong-Uk;Kim, Young-Seop;Ahn, Geon;Kim, Jin-Koo
    • Korean Journal of Ichthyology
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    • v.11 no.1
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    • pp.17-22
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    • 1999
  • Two specimens of Decapterus macrosoma Bleeker and Carangoides orthogrammus (Jordan et Gilbert) were collected separately from the south-eastern sea of Cheju island and Cheju fish market in September, 1998. We named "Gin-ga-ra-ji" for D. macrosoma and "No-rang-jeom-muni-yu-jeon-gaeng-i" for C. orthogrammus since they are first recorded in the Korean waters. D. macrosoma shows some differences like the extent of scales on its dorsal head, the number of scutes, the shape of lateral line, and the length of pectoral fin in comparison of those of same genus. C. orthogrammus is characterized in having high body depth, scutes located on the straight lateral line, a few number of the yellow spot on the side of body, elongated rayon the front end of 2nd dorsal and anal fin, and the area of no scales in the base of breast.

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Taxonomic Review of the Family Trachipteridae (Lampridiformes) from Korea (한국산 투라치과(Lampridiformes: Trachipteridae) 어류의 분류학적 재검토)

  • Ji, Hwan sung;Yoon, Sang Chul;Kim, Jin Koo
    • Korean Journal of Ichthyology
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    • v.21 no.4
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    • pp.273-282
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    • 2009
  • The taxonomic review of the family Trachipteridae was carried out based on the Trachipterus ishikawae (7 specimens), Zu cristatus (4 specimens), Desmodema polystictum (2 specimens) collected from the East Sea, South Sea and adjacent waters of Jeju Island of Korea from June 2006 to August 2008. Among them, D. polystictum was revealed as an unrecorded species from Korea, being characterized by the following characters: the ventral edge smooth; body color silvery white with a lot of large dark rounded spot. We proposed the new Korean name of the genus Desmodema as "Jeom-tu-ra-chi-sog", D. polystictum as "Jeom-tu-ra-chi". Z. cristatus has a elongated first six dorsal fin and pelvic fin rays. T. ishikawae has a row of sharp tubercles along the ventral edge, and straightly elongated body form. In meristic characters, the number of dorsal fin rays were 178~195 in T. ishikawae, 137~148 in Z. cristatus and 125~130 in D. polystictum, the number of vertebrae were well distinguished among three species; T. ishikawae (80~83), D. polystictum (72~74) and Z. cristatus (65~68).

First Record of the Oilfish, Ruvettus pretiosus (Perciformes: Gempylidae) from Korea (한국산 갈치꼬치과 어류 1미기록종, Ruvettus pretiosus)

  • Kim, Byeong Yeob;Song, Choon Bok
    • Korean Journal of Ichthyology
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    • v.29 no.3
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    • pp.224-228
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    • 2017
  • Two specimens of Ruvettus pretiosus (227.0 and 238.3 mm in standard length), belonging to the family Gempylidae, was firstly collected by using a gill net from the eastern coastal waters of Jejudo Island, Korea in November 2013. This species is characterized by having the following morphological traits: XV, 17~19+2 dorsal fin rays; II, 15~16+2 anal fin rays; belly keeled between pelvic fin and anus; body covered with cycloid scales, interspaced with rows of sharp bony tubercles. R. pretiosus can be easily distinguished from three Korean Snake mackerels (Thyrsitoides marleyi, Rexea prometheoides and Gempylus serpens) by having belly keeled between pelvic fin and anus, and cycloid scales covered the body and interspaced with rows of sharp bony tubercles. Based on morphological and molecular approaches, the specimens were identified as R. pretiosus. We propose new Korean names, "Gi-reum-chi-sok" and "Gi-reum-chi" for the genus and species, respectively.