• ALGAE
• /
• v.34 no.1
• /
• pp.57-70
• /
• 2019

DNA metabarcoding is currently used for large-scale taxonomic identification to understand the community composition in various marine ecosystems. However, before being widely used in this emerging field, this experimental and analytic approach still has several technical challenges to overcome, such as polymerase chain reaction (PCR) bias, and lack of well-established metabarcoding markers, a task which is difficult but not impossible to achieve. In this study, we present an adapted PCR-free small-organelles enriched metagenomics (SoEM) method for marine biodiversity assessment. To avoid PCR bias and random artefacts, we extracted target DNA sequences without PCR amplification from marine environmental samples enriched with small organelles including mitochondria and plastids because their genome sequences provide a valuable source of molecular markers for phylogenetic analysis. To experimentally enrich small organelles, we performed subcellular fractionation using modified differential centrifugation for marine environmental DNA samples. To validate our SoEM method, two marine environmental samples from the coastal waters were tested the taxonomic capturing capacity against that of traditional DNA metabarcoding method. Results showed that, regardless of taxonomic levels, at least 3-fold greater numbers of taxa were identified in our SoEM method, compared to those identified by the conventional multi-locus DNA metabarcoding method. The SoEM method is thus effective and accurate for identifying taxonomic diversity and presents a useful alternative approach for evaluating biodiversity in the marine environment.

• Journal of Species Research
• /
• v.10 no.1
• /
• pp.12-22
• /
• 2021

During a comprehensive investigation of indigenous prokaryotic species in Korea, 25 and 10 bacterial strains assigned to the classes Alphaproteobacteria and Betaproteobacteria, respectively, were isolated from diverse environmental habitats, including soil, mud, tidal field, sea water, sand, rusted iron, and leaf. Based on their high 16S rRNA gene sequence similarities (>98.7%) and the formation of robust phylogenetic clades with type species, each strain was assigned to an independent and predefined bacterial species. Since there were no published or official reports regarding these 35 isolates in Korea, they - 25 species of 14 families in the 5 orders of Alphaproteobacteria and 10 species of 3 families in the two orders of Betaproteobacteria - have been reported as unrecorded species in Korea. In addition, Gram reaction, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are also described in the species description sections.

• Journal of Species Research
• /
• v.10 no.3
• /
• pp.191-200
• /
• 2021

To study the biodiversity of bacterial species, here we report indigenous prokaryotic species of Korea. A total of 23 bacterial strains affiliated to the class Alphaproteobacteria were isolated from various environmental sources including seaweeds, seawater, fresh water, wetland/marsh, tidal sediment, plant roots, sewage and soil. Considering higher than 98.8% 16S rRNA gene sequence similarities and formation of a well-defined phylogenetic clade with named species, it was confirmed that each strain belonged to the predefined bacterial species of the class Alphaproteobacteria. There is no official report of these 23 species in Korea; 20 species of 16 genera (Mameliella, Yangia, Paracoccus, Ruegeria, Loktanella, Phaeobacter, Dinoroseobacter, Tropicimonas, Lutimaribacter, Litoreibacter, Sulfitobacter, Roseivivax, Labrenzia, Hyphomonas, Maricaulis, Thalassospira) in the order Rhodobacterales and 3 species of a single genus (Brevundimonas) in the order Caulobacterales. Gram-staining, cell morphology, basic biochemical characteristics, isolation sources, optimum temperature, growth media, and strain IDs are detailed in the species description as well as Table 1.

• Biomedical Science Letters
• /
• v.28 no.2
• /
• pp.83-91
• /
• 2022

This study was performed to investigate the contamination status of microorganisms that cause food poisoning in shellfish distributed in the metropolitan area of South Korea. The analyses were conducted according to the sample type, season, and region. In particular, the genotype of food poisoning viruses that explosively cause collective food poisoning was analyzed. Total 483 each of four types of shellfish (Crassostrea gigas, Mytilus coruscus, Pectea albicans albicans, and Scapharca subcrenata) were collected from four distribution sites located in the metropolitan area. We investigated foodborne pathogen by multiplex PCR and RT/Nested PCR from shellfish. As a result, Vibrio parahaemolyticus and Bacillus cereus were detected in 13 and 21 samples and Norovirus (NoV) GI and GII were detected in 7 and 12 samples, respectively. V. parahaemolyticus and NoV GI and GII showed differences in types of shellfish and seasons, and no correlation was confirmed with regional differences. Also, as a result of genotyping for the detected NoV GI and GII, they were confirmed as NoV GI.7, GI.5 and GII.3, which are causes of collective food poisoning. Therefore, cross-infection with shellfish can cause food poisoning. In particular, attention must be paid to the handling and cooking of shellfish in organizations that implement group feeding, and it is necessary to establish a management system for microorganisms that cause food poisoning in the process of shellfish farming and distribution.

• Journal of Species Research
• /
• v.11 no.4
• /
• pp.310-320
• /
• 2022

As a subset study to discover indigenous prokaryotic species in Korea, we isolated 20 bacterial strains and assigned them to the phyla Actinobacteria, Bacteroidota, Firmicutes, and Proteobacteria. From the high 16S rRNA gene sequence similarity (≥98.7%) and formation of a robust phylogenetic clades, we determined that each strain belonged to independent, predefined bacterial species. There are no official reports of these 20 species in Korea; therefore, 7 strains of the Actinobacteria, 2 strain of the Bacteroidota, 3 strains of the Firmicutes, and 8 strains of the Firmicutes are described in Korea for the first time. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• Korean Journal of Plant Taxonomy
• /
• v.52 no.2
• /
• pp.114-117
• /
• 2022

Lindera angustifolia is mainly distributed in the temperate climate zone of China but shows an extraordinary distribution, disjunctively isolated on the western coastal islands of Korea. We therefore present the complete chloroplast genome of Korean L. angustifolia. The complete plastome was 152,836 bp in length, with an overall GC content of 39.2%. A large single copy (93,726 bp) and a small single copy (18,946 bp) of the genome were separated by a pair of inverted repeats (20,082 bp). The genome consists of 125 genes, including 81 protein-coding, eight ribosomal RNA, and 36 transfer RNA genes. While five RNA editing genes (psbL, rpl2, ndhB×2, and ndhD) were identified in L. angustifolia from China, the "ndhD" gene was not recognized as an RNA editing site in the corresponding Korean individual. A phylogenetic analysis revealed that Korean L. angustifolia is most closely related to the Chinese L. angustifolia with strong bootstrap support, forming a sister group of L. glauca.

• Journal of Species Research
• /
• v.10 no.4
• /
• pp.321-335
• /
• 2021

In 2020, a total of 12 bacterial strains were isolated from soil after a comprehensive investigation of indigenous prokaryotic species in Korea. It was determined that each strain belonged to independent and predefined bacterial species, with high 16S rRNA gene sequence similarity (>98.7%) and formation of a robust phylogenetic clade with the closest species. This study identified four families in the phylum Actinobacteria, two families in the phylum Proteobacteria, one family in the phylum Bacteroidetes one family in the phylum Firmicutes; and four species in the family Nocardiaceae, two species in the family Nocardioidaceae, one species in the family Cellulomonadaceae, one species in the family Hymenobacter, one species in the family Methylobacteriaceae, one species in the family Microbacteriaceae, one species in the family Bacillaceae and one species in the family Sphingomonadaceae. There is no official report of these 12 species in Korea, so they are described as unreported bacterial species in Korea in this study. Gram reaction, basic biochemical characteristics, colony, and cell morphology are included in the species description section.

• Mycobiology
• /
• v.50 no.4
• /
• pp.213-218
• /
• 2022

The genus Mitrula (Mitrulaceae, Helotiales), as also known as swamp beacons, inhabits submerged, decaying vegetation in standing or decaying needles, twigs, leaves, and shallow water. They play an important role in carbon cycling in some freshwater ecosystems. In the herbarium of the Korea National Arboretum (KH), seven Mitrula specimens were collected during mushroom forays in the period from 2019 to 2021. The Korean collections were found to be macromorphologically closely related to M. paludosa and M. elegans, but micro-morphologically they could be distinguished by characteristics of slightly narrower asci and aseptate ascospores. Our molecular phylogenetic analyses of the internal transcribed spacer (ITS) and 28S rDNA regions also revealed that our specimens were related to M. paludosa and M. elegans, but formed a distinct clade. Based on these results, we reported our specimens as new to science and discussed the phylogeny and diversity of Mitrula species.

• Korean Journal of Environmental Biology
• /
• v.40 no.4
• /
• pp.405-412
• /
• 2022

Suncheon Bay Ecological Park, possessing abundant fisheries and biological diversity, was registered as a Ramsar wetland in Korea. Approximately 300 bacterial strains were isolated from the Suncheon Bay in a comprehensive study of indigenous prokaryotic species conducted during 2019-2020 in South Korea. A total of 12 bacterial strains were identified using 16S rRNA gene sequencing, demonstrating >98.7% sequence similarity with validly published species. These species were determined to be unrecorded bacterial species in Korea. A total of six strains were isolated from brackish water and Phragmites communis Trin (reed) species. These unrecorded species were phylogenetically diverse and belonged to three classes, six orders, and ten genera. Regarding the genus and class levels, the previously unrecorded species belonged to Jiella, Martelella, Rhizobium, Paracoccus, Rhodovulum, and Altererythrobacter of the class Alphaproteobacteria; Mycolicibacterium, Demequina, and Microbacterium of the class Actinobacteria; Confluentibacter of the class Flavobacteria. The twelve species were further characterized by gram staining, colony and cell morphology, biochemical properties, and phylogenetic position.

• Animal Systematics, Evolution and Diversity
• /
• v.39 no.3
• /
• pp.99-113
• /
• 2023

The nudibranch is one of the most colorful gastropod species found in oceans worldwide. Unlike many other gastropod groups, the nudibranch loses an external shell in the adult stage, but instead develops various chemical defense systems. More than 2,500 nudibranch species have been reported worldwide, and 73 species are currently recorded in Korean waters. In this study, we present morphological descriptions, DNA barcode information of mtDNA cox1 sequence, and taxonomic review for five nudibranch species: Apata pricei (MacFarland, 1966), Doto rosacea Baba, 1949, Janolus toyamensis Baba and Abe, 1970, Polycera abei (Baba, 1960), and Trinchesia sibogae (Bergh, 1905). Of these, we also provide in-depth discussion of taxonomic issue of A. pricei that was previously subdivided into two subspecies, A. pricei pricei and A. pricei komandorica. Our morphological examination and molecular analyses of the mtDNA cox1 sequences indicate that these two subspecies are not taxonomically warranted. The phylogenetic information for the other nudibranch species from mtDNA cox1 sequence analysis is also included, providing a molecular basis for species identification and inferring their local phylogenies within each of the species groups discussed herein.