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Seo CW, Kim SH, Lim YW, Park MS. Re-Identification on Korean Penicillium Sequences in GenBank Collected by Software GenMine. MYCOBIOLOGY 2022; 50:231-237. [PMID: 36158042 PMCID: PMC9467555 DOI: 10.1080/12298093.2022.2116816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/16/2022] [Accepted: 08/21/2022] [Indexed: 06/16/2023]
Abstract
Penicillium species have been actively studied in various fields, and many new and unrecorded species continue to be reported in Korea. Moreover, unidentified and misidentified Korean Penicillium species still exist in GenBank. Therefore, it is necessary to revise the Korean Penicillium inventory based on accurate identification. We collected Korean Penicillium nucleotide sequence records from GenBank using the newly developed software, GenMine, and re-identified Korean Penicillium based on the maximum likelihood trees. A total of 1681 Korean Penicillium GenBank nucleotide sequence records were collected from GenBank. In these records, 1208 strains with four major genes (Internal Transcribed Spacer rDNA region, β-tubulin, Calmodulin and RNA polymerase II) were selected for Penicillium re-identification. Among 1208 strains, 927 were identified, 82 were identified as other genera, the rest remained undetermined due to low phylogenetic resolution. Identified strains consisted of 206 Penicillium species, including 156 recorded species and 50 new species candidates. However, 37 species recorded in the national list of species in Korea were not found in GenBank. Further studies on the presence or absence of these species are required through literature investigation, additional sampling, and sequencing. Our study can be the basis for updating the Korean Penicillium inventory.
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Affiliation(s)
- Chang Wan Seo
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Sung Hyun Kim
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Young Woon Lim
- School of Biological Sciences, and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Myung Soo Park
- Department of Crops and Forestry, Korea National University of Agriculture and Fisheries, Jeonju, South Korea
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Park MS, Lee JW, Kim SH, Park JH, You YH, Lim YW. Penicillium from Rhizosphere Soil in Terrestrial and Coastal Environments in South Korea. MYCOBIOLOGY 2020; 48:431-442. [PMID: 33312010 PMCID: PMC7717687 DOI: 10.1080/12298093.2020.1823611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/18/2020] [Accepted: 09/09/2020] [Indexed: 05/20/2023]
Abstract
Penicillium, the most common genus plays an important ecological role in various terrestrial and marine environments. However, only a few species have been reported from rhizosphere soil. As part of a project to excavate Korean indigenous fungi, we investigated rhizosphere soil of six plants in the forest (terrestrial habitat) and sand dunes (coastal habitat) and focused on discovering Penicillium species. A total of 64 strains were isolated and identified as 26 Penicillium species in nine sections based on morphological characteristics and the sequence analysis of β-tubulin and calmodulin. Although this is a small-scale study in a limited rhizosphere soil, eight unrecorded species and four potential new species have been identified. In addition, most Penicillium species from rhizosphere soil were unique to each plant. Penicillium halotolerans, P. scabrosum, P. samsonianum, P. jejuense, and P. janczewskii were commonly isolated from rhizosphere soil. Eight Penicillium species, P. aurantioviolaceum, P. bissettii, P. cairnsense, P. halotolerans, P. kananaskense, P. ortum, P. radiatolobatum, and P. verhagenii were recorded for the first time in Korea. Here, we provide the detailed morphological description of these unrecorded species.
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Affiliation(s)
- Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Jun Won Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Sung Hyun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Ji-Hyun Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Young-Hyun You
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
- CONTACT Young Woon Lim
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Park MS, Oh SY, Fong JJ, Houbraken J, Lim YW. The diversity and ecological roles of Penicillium in intertidal zones. Sci Rep 2019; 9:13540. [PMID: 31537866 PMCID: PMC6753150 DOI: 10.1038/s41598-019-49966-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/03/2019] [Indexed: 12/30/2022] Open
Abstract
Members of the genus Penicillium are commonly isolated from various terrestrial and marine environments, and play an important ecological role as a decomposer. To gain insight into the ecological role of Penicillium in intertidal zones, we investigated the Penicillium diversity and community structure using a culture-dependent technique and a culture independent metagenomic approach using ITS (ITS-NGS) and partial β-tubulin (BenA-NGS) as targets. The obtained isolates were tested for halotolerance, enzyme activity, and polycyclic aromatic hydrocarbons (PAHs) degradation. A total of 96 Penicillium species were identified from the investigated intertidal zones. Although the BenA-NGS method was efficient for detecting Penicillium, some species were only detected using conventional isolation and/or the ITS-NGS method. The Penicillium community displayed a significant degree of variation relative to season (summer and winter) and seaside (western and southern coast). Many Penicillium species isolated in this study exhibited cellulase and protease activity, and/or degradation of PAHs. These findings support the important role of Penicillium in the intertidal zone for nutrient recycling and pollutant degradation.
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Affiliation(s)
- Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | - Seung-Yoon Oh
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea
| | | | - Jos Houbraken
- Westerdijk Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, Netherlands
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 08826, South Korea.
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Lee S, Park MS, Lee H, Kim JJ, Eimes JA, Lim YW. Fungal Diversity and Enzyme Activity Associated with the Macroalgae, Agarum clathratum. MYCOBIOLOGY 2019; 47:50-58. [PMID: 31001450 PMCID: PMC6452909 DOI: 10.1080/12298093.2019.1580464] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/12/2018] [Accepted: 01/18/2019] [Indexed: 06/09/2023]
Abstract
Agarum clathratum, a brown macroalgae species, has recently become a serious environmental problem on the coasts of Korea. In an effort to solve this problem, fungal diversity associated with decaying A. clathratum was investigated and related β-glucosidase and endoglucanase activities were described. A total of 233 fungal strains were isolated from A. clathratum at 15 sites and identified 89 species based on morphology and a multigene analysis using the internal transcribed spacer region (ITS) and protein-coding genes including actin (act), β-tubulin (benA), calmodulin (CaM), and translation elongation factor (tef1). Acremonium, Corollospora, and Penicillium were the dominant genera, and Acremonium fuci and Corollospora gracilis were the dominant species. Fifty-one species exhibited cellulase activity, with A. fuci, Alfaria terrestris, Hypoxylon perforatum, P. madriti, and Pleosporales sp. Five showing the highest enzyme activities. Further enzyme quantification confirmed that these species had higher cellulase activity than P. crysogenum, a fungal species described in previous studies. This study lays the groundwork for bioremediation using fungi to remove decaying seaweed from populated areas and provides important background for potential industrial applications of environmentally friendly processes.
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Affiliation(s)
- Seobihn Lee
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Hanbyul Lee
- Division of Environmental Science & Ecological Engineering, College of Life Sciences & Biotechnology, Korea University, Seoul, Republic of Korea
| | - Jae-Jin Kim
- Division of Environmental Science & Ecological Engineering, College of Life Sciences & Biotechnology, Korea University, Seoul, Republic of Korea
| | - John A. Eimes
- University College, Sungkyunkwan University, Suwon, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
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Pangging M, Nguyen TTT, Lee HB. New Records of Four Species Belonging to Eurotiales from Soil and Freshwater in Korea. MYCOBIOLOGY 2019; 47:154-164. [PMID: 31448135 PMCID: PMC6691828 DOI: 10.1080/12298093.2018.1554777] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/24/2018] [Accepted: 11/27/2018] [Indexed: 05/05/2023]
Abstract
Four strains of Penicillium and Talaromyces species are described and illustrated in an inventory of fungal species belonging to Eurotiales. The strains, CNUFC-DDS17-1, CNUFC-DDS27-1, CNUFC-PTM72-1, and CNUFC-YJW3-31, were isolated from soil and freshwater samples from South Korea. Based on their morphological characteristics and sequence analyses by the combined β-tubulin and calmodulin gene, the CNUFC-DDS17-1, CNUFC-DDS27-1, CNUFC-PTM72-1, and CNUFC-YJW3-31 isolates were identified as Penicillium pasqualense, Penicillium sanguifluum, Talaromyces apiculatus, and Talaromyces liani, respectively. The designated strains were found to represent a previously undescribed species of Korean fungal biota. In this study, detailed morphological descriptions and phylogenetic relationships of these species are provided.
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Affiliation(s)
- Monmi Pangging
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Thuong T. T. Nguyen
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
| | - Hyang Burm Lee
- Division of Food Technology, Biotechnology and Agrochemistry, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Korea
- CONTACT Hyang Burm Lee
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Park MS, Chung D, Baek K, Lim YW. Three Unrecorded Species Belonging to Penicillium Section Sclerotiora from Marine Environments in Korea. MYCOBIOLOGY 2019; 47:165-172. [PMID: 31448136 PMCID: PMC6691904 DOI: 10.1080/12298093.2019.1601330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/18/2019] [Accepted: 03/18/2019] [Indexed: 05/05/2023]
Abstract
Species that belong to Penicillium section Sclerotiora are commonly found in various terrestrial environments, but only a few have been reported in marine environments. Because the number of Penicillium species reported in marine environments is increasing, we investigated the diversity of Penicillium section Sclerotiora in marine environments in Korea. Based on sequence analyses of β-tubulin and calmodulin loci, 21 strains of section Sclerotiora were identified as P. bilaiae, P. daejeonium, P. exsudans, P. herquei, P. cf. guanacastense, P. mallochii, P. maximae, and P. viticola. Three of them were confirmed as new to Korea: P. exsudans, P. mallochii, and P. maximae. Here, we have provided detailed morphological descriptions of these unrecorded species.
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Affiliation(s)
- Myung Soo Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
| | - Dawoon Chung
- National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Kyunghwa Baek
- National Marine Biodiversity Institute of Korea, Seocheon-gun, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, Republic of Korea
- CONTACT Young Woon Lim School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul 08826, Republic of Korea
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