• Title/Summary/Keyword: indigenous prokaryotic species in Republic of Korea

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A report of 36 unrecorded bacterial species belonging to the phyla Actinomycetota, Bacillota, Bacteroidota, Deinococcota, and Pseudomonadota isolated in Republic of Korea

  • Che-Ok Jeon;Wonyong Kim;Jin-Woo Bae;Chi-Nam Seong;Wan-Taek Im;Seung-Bum Kim;Jang-Cheon Cho;Myung Kyum Kim;Chang-Jun Cha;Taegun Seo;Jung-Hoon Yoon
    • Journal of Species Research
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    • v.12 no.4
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    • pp.415-429
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    • 2023
  • As part of a comprehensive investigation of indigenous prokaryotic species in the Republic of Korea, 37 bacterial strains belonging to 36 species were isolated from diverse environmental habitats. These strains were assigned to five phyla, namely Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of definite phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Deinococcota, five species belonging to the phylum Actinomycetota, four species belonging to the phylum Bacillota, nine species belonging to the phylum Bacteroidota, and 17 species belonging to the phylum Pseudomonadota (comprising eight species of the class Alphaproteobacteria, one species of the class Betaproteobacteria, and eight species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 36 species in the Republic of Korea, they have been reported as unrecorded species in the Republic of Korea. Their Gram stain, cell morphology, colony, basic biochemical characteristics, strain ID, and isolation source of each species are described in the species descriptions.

A report of 156 unrecorded bacterial species of Republic of Korea belonging to the phyla Acidobacteriota, Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota isolated in 2022

  • Kiseong Joh;Wonyong Kim;Myung Kyum Kim;Seung-Bum Kim;Chang-Jun Cha;Wan-Taek Im;Taegun Seo;Che-Ok Jeon;Jung-Hoon Yoon
    • Journal of Species Research
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    • v.12 no.4
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    • pp.374-414
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    • 2023
  • As part of a comprehensive investigation of indigenous prokaryotic species in Republic of Korea in 2022, 156 bacterial strains were isolated from diverse environmental habitats. These strains were assigned to six phyla, namely Acidobacteriota, Deinococcota, Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota. Each strain was identified based on 16S rRNA gene sequence similarity (>98.7%) and the formation of robust phylogenetic clades with their closest reported species. Among isolates, there is one species belonging to the phylum Acidobacteriota, one species belonging to the phylum Deinococcota, 28 species belonging to the phylum Actinomycetota, 19 species belonging to the phylum Bacillota, 19 species belonging to the phylum Bacteroidota, and 88 species belonging to the phylum Pseudomonadota (comprising 34 species of the class Alphaproteobacteria, 20 species of the class Betaproteobacteria, and 34 species of the class Gammaproteobacteria). Based on 16S rRNA gene sequence analysis, each strain was assigned to independent and predefined bacterial species. Since there were no published or official reports regarding these 156 isolates in Republic of Korea, they are reported as unrecorded species in Republic of Korea. The Gram stain, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are described in the species descriptions.

A report of 21 unrecorded bacterial species of Korea belonging to the phylum Bacteroidota isolated in 2021

  • Chang-Jun Cha;Che Ok Jeon;Kiseong Joh;Wonyong Kim;Seung Bum Kim;Myung Kyum Kim;Jung-Hoon Yoon
    • Journal of Species Research
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    • v.12 no.spc2
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    • pp.23-32
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    • 2023
  • During screening for indigenous prokaryotic species in Republic of Korea in 2021, a total of 21 bacterial strains assigned to the phylum Bacteroidota were isolated from a variety of environmental habitats including pine cone, seaweed, soil, sea sediment, brackish water and moss. Based on the 16S rRNA gene sequence similarity value of more than 98.7% and formation of a robust phylogenetic clade with the type strain of the closest bacterial species, it was found that the 21 strains belong to independent and recognized bacterial species. There has been no official report that the identified 21 species have been isolated in Republic of Korea up to date. Therefore, 16 species in six genera of two families in the order Flavobacteriales, two species in two genera of two families in the order Cytophagales, one species in one genus of one family in the order Chitinophagales and two species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidota isolated in Republic of Korea. Their Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

A report of 17 unrecorded bacterial species of Korea belonging to the phylum Bacteroidetes

  • Cho, Jang-Cheon;Seong, Chi Nam;Joh, Kiseong;Cha, Chang-Jun;Bae, Jin-Woo;Yi, Hana;Lee, Soon Dong;Kim, Myung Kyum;Yoon, Jung-Hoon
    • Journal of Species Research
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    • v.7 no.3
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    • pp.231-239
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    • 2018
  • While screening indigenous prokaryotic species in Republic of Korea in 2017, a total of 17 bacterial strains assigned to the phylum Bacteroidetes were isolated from a variety of environmental habitats including water of fountain, tidal flat, plant root, soil, the gut of Russian grayling butterfly, ginseng field, seawater, lagoon and seashore sand. From the 16S rRNA gene sequence similarity of more than 98.7% and the formation of a robust phylogenetic clade with the closest species, it was found that the 17 strains belong to independent and recognized bacterial species. There has been no official report that the identified 17 species have been previously isolated in the Republic of Korea. Thus, 15 species in 10 genera of one family in the order Flavobacteriales, one species in one genus of one family in the order Cytophagales, and one species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidetes found in the Republic of Korea. Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

A report on 38 unrecorded bacterial species in Korea in the class Gammaproteobacteria

  • Weerawongwiwat, Veeraya;Kim, Myung Kyum;Joh, Kiseong;Kim, Seung-Bum;Seong, Chi-Nam;Yi, Hana;Yoon, Jung-Hoon;Kim, Wonyong
    • Journal of Species Research
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    • v.10 no.3
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    • pp.201-216
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    • 2021
  • During an investigation of indigenous prokaryotic species in the Republic of Korea, a total of 38 bacterial strains belonging to the class Gammaproteobacteria were isolated from diverse environments. Samples were collected from soil, seawater, sand, sedimentary soil, rabbit feces, rat intestines, marine wetland, and tidal flats. The strains were identified to the species level using the high 16S rRNA gene sequences and showed high similarity (>98.7%) with the closest bacterial species and formed a robust clade in the neighbor-joining phylogenetic tree; it was determined that each strain belonged to independent, predefined bacteria species within the class Gammaproteobacteria. The 38 strains of Gammaproteobacteria analyzed in this study have not been reported in the Republic of Korea. Therefore, this study describes 20 genera of 13 families in 8 orders: Aeromonadales, Alteromonadales, Cellvibrionales, Enterobacterales, Lysobacterales, Oceanospirillales, Pseudomonadales, and Vibrionales. For each species, we describe Gram reaction, strain ID, isolation source, colony and cell morphology, cultural, physiological, and basic biochemical characteristics.

A report of 31 unrecorded bacterial species isolated from freshwater

  • Hyangmi Kim;Sanghwa Park;Kyung June Yim;Ja Young Cho;Eui-Jin Kim
    • Korean Journal of Environmental Biology
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    • v.40 no.4
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    • pp.442-454
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    • 2022
  • A total of 31 bacterial strains were isolated from the Geum River basin in the Republic of Korea during our investigation of indigenous prokaryotic species. The isolated bacterial strains had high 16S rRNA gene sequence similarity (>98.7%) with those of validly published bacterial species, which have not been reported in Republic of Korea. The 31 bacterial strains were phylogenetically diverse and assigned to 4 phyla, 8 classes, 18 orders, 21 families, and 27 genera. At the genus level, the unreported species were affiliated with Kineococcus, Pedococcus, Rhodoluna, Salinibacterium, Rhodoluna, Arthrobacter, Williamsia, Nakamurella, Nocardioides of the class Actinobacteria, Patulibacter of the class Thermoleophilia, Pontibacter, Hymenobacter of the class Cytophagia, Flavobacterium of the class Flavobacteriia, Geomicrobium of the class Bacilli, Brevundimonas, Gellertiella, Rhizobium, Paracoccus, Taonella, Sphingomonas of the class Alphaproteobacteria, Burkholderia, Polaromonas, Hydrogenophaga, Chitinilyticum, Azospira, Zoogloea of the class Betaproteobacteria, and Pseudomonas of the class Gammaproteobacteria. The unreported bacterial species were further characterized by examining their morphological, cultural, physiological, and biochemical properties. The detailed descriptions of the 31 bacterial strains were provided.

A report of nine unrecorded bacterial species in the phylum Bacteroidetes collected from freshwater environments in Korea

  • Park, Sanghwa;Beak, Kiwoon;Han, Ji-Hye;Nam, Yoon-Jong;Lee, Mi-Hwa
    • Journal of Species Research
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    • v.7 no.3
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    • pp.187-192
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    • 2018
  • During a comprehensive study of indigenous prokaryotic species in South Korea, nine bacterial species in the phylum Bacteroidetes were isolated from freshwater environmental samples that were collected from three major rivers in the Republic of Korea. High 16S rRNA gene sequence similarity (${\geq}98.7%$) and robust phylogenetic clades with the closely related species suggest that each strain was correctly assigned to an independent and predefined bacterial species. There were no previous reports of these nine species in Korea. Within the phylum Bacteroidetes, four species were assigned to the genus Flavobacterium, order Flavobacteriales, and five species to three genera of two families in the order Cytophagales. Gram reaction, colony and cell morphology, basic biochemical characteristics, isolation source, and strain IDs are described in the species description section.

Unrecorded bacterial species belonging to the phylum Actinobacteria originated from Republic of Korea

  • Kim, Mi-Sun;Lee, Ji-Hee;Kim, Seung-Bum;Cho, Jang-Cheon;Lee, Soon Dong;Joh, Ki-seong;Cha, Chang-Jun;Im, Wan-Taek;Bae, Jin-Woo;Jahng, Kwangyeop;Yi, Hana;Seong, Chi-Nam
    • Journal of Species Research
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    • v.6 no.1
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    • pp.25-41
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    • 2017
  • As a subset study for the collection of Korean indigenous prokaryotic species, 62 bacterial strains belonging to the phylum Actinobacteria were isolated from various sources. Each strain showed higher 16S rRNA gene sequence similarity (>98.75%) and formed a robust phylogenetic clade with closest species of the phylum Actinobacteria which were defined with valid names, already. There is no official description on these 62 actinobacterial species in Korea. Consequently, unrecorded 62 species of 25 genera in the 14 families belonging to the order Actinomycetales of the phylum Actinobacteria were found in Korea. Morphological properties, basic biochemical characteristics, isolation source and strain IDs are described in the species descriptions.

Review of the Korean Indigenous Species Investigation Project (2006-2020) by the National Institute of Biological Resources under the Ministry of Environment, Republic of Korea (한반도 자생생물 조사·발굴 연구사업 고찰(2006~2020))

  • Bae, Yeon Jae;Cho, Kijong;Min, Gi-Sik;Kim, Byung-Jik;Hyun, Jin-Oh;Lee, Jin Hwan;Lee, Hyang Burm;Yoon, Jung-Hoon;Hwang, Jeong Mi;Yum, Jin Hwa
    • Korean Journal of Environmental Biology
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    • v.39 no.1
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    • pp.119-135
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    • 2021
  • Korea has stepped up efforts to investigate and catalog its flora and fauna to conserve the biodiversity of the Korean Peninsula and secure biological resources since the ratification of the Convention on Biological Diversity (CBD) in 1992 and the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits (ABS) in 2010. Thus, after its establishment in 2007, the National Institute of Biological Resources (NIBR) of the Ministry of Environment of Korea initiated a project called the Korean Indigenous Species Investigation Project to investigate indigenous species on the Korean Peninsula. For 15 years since its beginning in 2006, this project has been carried out in five phases, Phase 1 from 2006-2008, Phase 2 from 2009-2011, Phase 3 from 2012-2014, Phase 4 from 2015-2017, and Phase 5 from 2018-2020. Before this project, in 2006, the number of indigenous species surveyed was 29,916. The figure was cumulatively aggregated at the end of each phase as 33,253 species for Phase 1 (2008), 38,011 species for Phase 2 (2011), 42,756 species for Phase 3 (2014), 49,027 species for Phase 4 (2017), and 54,428 species for Phase 5(2020). The number of indigenous species surveyed grew rapidly, showing an approximately 1.8-fold increase as the project progressed. These statistics showed an annual average of 2,320 newly recorded species during the project period. Among the recorded species, a total of 5,242 new species were reported in scientific publications, a great scientific achievement. During this project period, newly recorded species on the Korean Peninsula were identified using the recent taxonomic classifications as follows: 4,440 insect species (including 988 new species), 4,333 invertebrate species except for insects (including 1,492 new species), 98 vertebrate species (fish) (including nine new species), 309 plant species (including 176 vascular plant species, 133 bryophyte species, and 39 new species), 1,916 algae species (including 178 new species), 1,716 fungi and lichen species(including 309 new species), and 4,812 prokaryotic species (including 2,226 new species). The number of collected biological specimens in each phase was aggregated as follows: 247,226 for Phase 1 (2008), 207,827 for Phase 2 (2011), 287,133 for Phase 3 (2014), 244,920 for Phase 4(2017), and 144,333 for Phase 5(2020). A total of 1,131,439 specimens were obtained with an annual average of 75,429. More specifically, 281,054 insect specimens, 194,667 invertebrate specimens (except for insects), 40,100 fish specimens, 378,251 plant specimens, 140,490 algae specimens, 61,695 fungi specimens, and 35,182 prokaryotic specimens were collected. The cumulative number of researchers, which were nearly all professional taxonomists and graduate students majoring in taxonomy across the country, involved in this project was around 5,000, with an annual average of 395. The number of researchers/assistant researchers or mainly graduate students participating in Phase 1 was 597/268; 522/191 in Phase 2; 939/292 in Phase 3; 575/852 in Phase 4; and 601/1,097 in Phase 5. During this project period, 3,488 papers were published in major scientific journals. Of these, 2,320 papers were published in domestic journals and 1,168 papers were published in Science Citation Index(SCI) journals. During the project period, a total of 83.3 billion won (annual average of 5.5 billion won) or approximately US $75 million (annual average of US $5 million) was invested in investigating indigenous species and collecting specimens. This project was a large-scale research study led by the Korean government. It is considered to be a successful example of Korea's compressed development as it attracted almost all of the taxonomists in Korea and made remarkable achievements with a massive budget in a short time. The results from this project led to the National List of Species of Korea, where all species were organized by taxonomic classification. Information regarding the National List of Species of Korea is available to experts, students, and the general public (https://species.nibr.go.kr/index.do). The information, including descriptions, DNA sequences, habitats, distributions, ecological aspects, images, and multimedia, has been digitized, making contributions to scientific advancement in research fields such as phylogenetics and evolution. The species information also serves as a basis for projects aimed at species distribution and biological monitoring such as climate-sensitive biological indicator species. Moreover, the species information helps bio-industries search for useful biological resources. The most meaningful achievement of this project can be in providing support for nurturing young taxonomists like graduate students. This project has continued for the past 15 years and is still ongoing. Efforts to address issues, including species misidentification and invalid synonyms, still have to be made to enhance taxonomic research. Research needs to be conducted to investigate another 50,000 species out of the estimated 100,000 indigenous species on the Korean Peninsula.