Journal of Microbiology

Research article

Temporal changes in culturable fungal community composition with their plastic degradation capacities in the marine plastisphere through mesocosm experiments: Sumin Jo, Ji Seon Kim, Wonjun Lee, Chang Wan Seo, Young Woon Lim; J. Microbiol. 2026;64(8):e2605011. Published online August 31, 2026; DOI: https://doi.org/10.71150/jm.2605011

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Abstract PDF Supplementary Material: Plastic waste in marine environments provides novel habitats for diverse organisms, forming distinct microbial ecosystems known as the ‘plastisphere’. Although bacteria of the plastisphere have been widely studied, the role of fungi in plastisphere formation and plastic degradation remains largely unexplored. Thus, we investigated temporal changes in culturable fungal community composition on three common plastic types—high-density polyethylene, low-density polyethylene, and polypropylene—across the early (seven days) and mature (30 days) plastisphere developmental stages through a marine mesocosm experiment. In total, 436 fungal strains were isolated and identified as belonging to 179 taxa, with Penicillium, Cladosporium, Trichoderma, Aspergillus, and Fusarium as the dominant genera. Temporal shifts in the species richness of the dominant genera were observed: Cladosporium showed higher species richness at the early stage, whereas that of Trichoderma increased at the mature stage. Plastic degradation assays revealed that 54.6% of the strains exhibited measurable degradation capacity, with patterns varying by plastic type rather than fungal developmental stage. Scanning electron microscope observations revealed surface damage patterns including cracks, pitting, and erosion on the plastic surfaces. These findings provide novel insights into the composition and functional heterogeneity of culturable fungal communities in the marine plastisphere and suggest that plastisphere fungi play diverse ecological roles beyond direct plastic degradation.

Article

Effects of sequencing platforms on the profiling of root mycorrhizal communities in Pinus densiflora: Ki Hyeong Park, Seung-Yoon Oh, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Chang Wan Seo, Chang Sun Kim, Young Woon Lim; J. Microbiol. 2026;64(1):e2509008. Published online January 31, 2026; DOI: https://doi.org/10.71150/jm.2509008

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Abstract PDF Supplementary Material: Next-generation sequencing (NGS) has become a powerful and efficient tool for surveying mycorrhizal mycobiome diversity, surpassing classical methods in accuracy and throughput. Long-read NGS techniques are increasingly applied under the assumption that they provide better taxonomic resolution, yet their use often lacks a balanced evaluation against the established strengths and limitations of widely used short-read NGS technologies. This study compares Illumina MiSeq and PacBio Sequel platforms in analyzing the mycorrhizal mycobiome of Pinus densiflora roots, focusing on how sequencing platforms and database choice influence taxonomic resolution and diversity patterns. Both platforms detected mycorrhizal taxa with similar taxonomic resolution, recovering nearly all taxa previously reported from pine roots. Most mycorrhizal taxa were shared between datasets, although several taxa were detected exclusively by one platform. In terms of diversity, the short-read dataset showed higher diversity due to greater sequencing depth, whereas the long-read dataset offered improved identification of rare or closely related taxa owing to longer sequence information. Moreover, supplementing reference databases with locally derived sequences enhanced taxonomic resolution and the detection of native taxa in both approaches, with a stronger effect for the long-read dataset. Overall, our results emphasize that short- and long-read sequencing each have distinct advantages for mycorrhizal community analysis, and that the use of curated local reference databases is essential to maximize taxonomic resolution and improve the detection of regionally unique taxa.

Article

FunVIP: Fungal Validation and Identification Pipeline based on phylogenetic analysis: Chang Wan Seo, Shinnam Yoo, Yoonhee Cho, Ji Seon Kim, Martin Steinegger, Young Woon Lim; J. Microbiol. 2025;63(4):e2411017. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2411017

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Abstract PDF Supplementary Material

The increase of sequence data in public nucleotide databases has made DNA sequence-based identification an indispensable tool for fungal identification. However, the large proportion of mislabeled sequence data in public databases leads to frequent misidentifications. Inaccurate identification is causing severe problems, especially for industrial and clinical fungi, and edible mushrooms. Existing species identification pipelines require separate validation of a dataset obtained from public databases containing mislabeled taxonomic identifications. To address this issue, we developed FunVIP, a fully automated phylogeny-based fungal validation and identification pipeline (https://github.com/Changwanseo/FunVIP). FunVIP employs phylogeny-based identification with validation, where the result is achievable only with a query, database, and a single command. FunVIP command comprises nine steps within a workflow: input management, sequence-set organization, alignment, trimming, concatenation, model selection, tree inference, tree interpretation, and report generation. Users may acquire identification results, phylogenetic tree evidence, and reports of conflicts and issues detected in multiple checkpoints during the analysis. The conflicting sample validation performance of FunVIP was demonstrated by re-iterating the manual revision of a fungal genus with a database with mislabeled sequences, Fuscoporia. We also compared the identification performance of FunVIP with BLAST and q2-feature-classifier with two mass double-revised fungal datasets, Sanghuangporus and Aspergillus section Terrei. Therefore, with its automatic validation ability and high identification performance, FunVIP proves to be a highly promising tool for achieving easy and accurate fungal identification.

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Hidden diversity of crust-like Sebacinaceae (Sebacinales, Agaricomycetes) in Asia
Hannah Suh, Chang Wan Seo, Ki Hyeong Park, Shinnam Yoo, Dohye Kim, Yoonhee Cho, Young Woon Lim
IMA Fungus.2026;[Epub] CrossRef
The contribution of environmental DNA to exploring hypogeous fungal diversity and vulnerability
Chang Wan Seo, Shinnam Yoo, Hannah Suh, Dohye Kim, Hyun Lee, Young Woon Lim
BMC Microbiology.2026;[Epub] CrossRef
Development of molecular assays to detect the G143A point mutation responsible for group 11 fungicide insensitivity in Colletotrichum lentis
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Journal of Plant Pathology.2026; 108(2): 1255. CrossRef
Cryptoporus densiflorus , sp. nov. (Polyporaceae), from East Asia and a reassessment of species distributions in Cryptoporus
Jiyun Choi, Abel Severin Lupala, Ji Seon Kim, Yu-Cheng Dai, Young Woon Lim
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Temporal changes in culturable fungal community composition with their plastic degradation capacities in the marine plastisphere through mesocosm experiments
Sumin Jo, Ji Seon Kim, Wonjun Lee, Chang Wan Seo, Young Woon Lim
Journal of Microbiology.2026; 64(8): e2605011. CrossRef
Exploring Macrofungal Biodiversity and Distribution on Kyodong Island, Republic of Korea
Hannah Suh, Abel Severin Lupala, Hae Jin Cho, Sumin Jo, Jiyun Choi, Young Woon Lim
Mycobiology.2025; 53(4): 466. CrossRef
Expanding the Inventory of Seven Unrecorded Marine Penicillium with Morphological Descriptions and Phenotypic Variability
Wonjun Lee, Ji Seon Kim, Sumin Jo, Young Woon Lim
Mycobiology.2025; 53(5): 648. CrossRef
Exploring Fungal Diversity in Marine Plastic (PET) Wastes and Seafoam in Udo Island, South Korea, with Reports of Two New Species ( Leptospora conidiifera and Neodevriesia oceanoplastica )
Wonjun Lee, Sumin Jo, Soo Hyun Maeng, Ji Seon Kim, Myung Kyum Kim, Young Woon Lim
Mycobiology.2025; 53(6): 770. CrossRef
Potential of Trichoderma asperellum against root-rot caused by Fusarium equiseti in tomato plants
Louis Antoniel Joseph, Manoucheca Jean, Frantzdy Luc, Kerley-Vivaldi Jean, Bento Gil Uane, Marisa Aida Diogo Matsinhe, Meque Samuel Tivane, Inocêncio Oliveira Mulaveia
Research, Society and Development.2025; 14(12): e62141250223. CrossRef

Article

Fungal diversity from Fildes Peninsula (Antarctica) and their antibiosis bioactivity against two plant pathogens: Ji Seon Kim, Enzo Romero, Yoonhee Cho, Ramón Ahumada-Rudolph, Christian Núñez, Jonhatan Gómez-Espinoza, Ernesto Moya-Elizondo, Sigisfredo Garnica, Young Woon Lim, Jaime R. Cabrera-Pardo; J. Microbiol. 2025;63(5):e2411029. Published online April 14, 2025; DOI: https://doi.org/10.71150/jm.2411029

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Abstract PDF Supplementary Material

Antarctic fungi can effectively adapt to extreme environments, which leads to the production of unique bioactive compounds. Studies on the discovery of fungi in the diverse environments of Antarctica and their potential applications are increasing, yet remain limited. In this study, fungi were isolated from various substrates on the Fildes Peninsula in Antarctica and screened for their antibiosis activity against two significant plant pathogenic fungi, Botrytis cinerea and Fusarium culmorum. Phylogenetic analysis using multiple genetic markers revealed that the isolated Antarctic fungal strains are diverse, some of which are novel, emphasizing the underexplored biodiversity of Antarctic fungi. These findings suggest that these fungi have potential for the development of new antifungal agents that can be applied in agriculture to manage fungal plant pathogens. Furthermore, the antibiosis activities of the isolated Antarctic fungi were evaluated using a dual-culture assay. The results indicated that several strains from the genera Cyathicula, Penicillium, and Pseudeurotium significantly inhibited pathogen growth, with Penicillium pancosmium showing the highest inhibitory activity against Botrytis cinerea. Similarly, Aspergillus and Tolypocladium strains exhibited strong antagonistic effects against Fusarium culmorum. This study enhances our understanding of Antarctic fungal diversity and highlights its potential for biotechnological applications.

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Article

Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea: Ki Hyeong Park , Seung-Yoon Oh , Yoonhee Cho , Chang Wan Seo , Ji Seon Kim , Shinnam Yoo , Jisun Lim , Chang Sun Kim , Young Woon Lim; J. Microbiol. 2023;61(8):729-739. Published online September 4, 2023; DOI: https://doi.org/10.1007/s12275-023-00073-1

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Abstract PDF

Mycorrhizal fungi are key components of forest ecosystems and play essential roles in host health. The host specificity of mycorrhizal fungi is variable and the mycorrhizal fungi composition for the dominant tree species is largely known but remains unknown for the less common tree species. In this study, we collected soil samples from the roots of six understudied ectomycorrhizal tree species from a preserved natural park in the Republic of Korea over four seasons to investigate the host specificity of mycorrhizal fungi in multiple tree species, considering the abiotic factors. We evaluated the mycorrhizal fungal composition in each tree species using a metabarcoding approach. Our results revealed that each host tree species harbored unique mycorrhizal communities, despite close localization. Most mycorrhizal taxa belonged to ectomycorrhizal fungi, but a small proportion of ericoid mycorrhizal fungi and arbuscular mycorrhizal fungi were also detected. While common mycorrhizal fungi were shared between the plant species at the genus or higher taxonomic level, we found high host specificity at the species/OTU (operational taxonomic unit) level. Moreover, the effects of the seasons and soil properties on the mycorrhizal communities differed by tree species. Our results indicate that mycorrhizal fungi feature host-specificity at lower taxonomic levels.

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Article

Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyung Park , Shin Nam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(2):189-197. Published online February 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00017-9

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Abstract PDF

Indoor fungi obtain carbon sources from natural sources and even recalcitrant biodegradable materials, such as plastics and synthetic dye. Their vigorous activity may have negative consequences, such as structural damage to building materials or the destruction of precious cultural materials. The animal specimen room of the Seoul National University stocked 36,000 animal resources that had been well-maintained for over 80 years. Due to abandonment without the management of temperature and humidity during the rainy summer season, many stuffed animal specimens had been heavily colonized by fungi. To investigate the fungal species responsible for the destruction of the historical specimens, we isolated fungi from the stuffed animal specimens and identified them at the species level based on morphology and molecular analysis of the β-tubulin (BenA) gene. A total of 365 strains were isolated and identified as 26 species in Aspergillus (10 spp.), Penicillium (14 spp.), and Talaromyces (2 spp.). Penicillium brocae and Aspergillus sydowii were isolated from most sections of the animal specimens and have damaged the feathers and beaks of valuable specimens. Our findings indicate that within a week of mismanagement, it takes only a few fungal species to wipe out the decades of history of animal diversity. The important lesson here is to prevent this catastrophe from occurring again through a continued interest, not to put all previous efforts to waste.

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Article

Diversity and Dynamics of Marine Arenicolous Fungi in Three Seasides of the Korean Peninsula: Jun Won Lee , Chang Wan Seo , Wonjun Lee , Ji Seon Kim , Ki Hyeong Park , Yoonhee Cho , Young Woon Lim; J. Microbiol. 2023;61(1):63-82. Published online January 30, 2023; DOI: https://doi.org/10.1007/s12275-023-00011-1

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Abstract PDF

Various arenicolous fungal species have been detected from the beach sand in the coastal area. However, little has been revealed regarding their distribution and dynamics. To investigate the overall diversity of marine arenicolous fungi (MAFs) in Korea and whether the composition of MAFs is affected by ocean currents, we isolated and analyzed the fungal community from the western, southern, and eastern seasides of the Korean Peninsula. In total, 603 strains were isolated and identified as 259 species based on appropriate molecular markers for each genus (ITS, BenA, CaM, tef1, and act). The composition of MAFs showed differences among the seasides. Our results indicate that many MAFs inhabit the beach sand on the Korean Peninsula, and the composition of MAFs is also affected by ocean currents flowing along each coast.

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Erratum

Erratum to: Fungal Catastrophe of a Specimen Room: Just One Week is Enough to Eradicate Traces of Thousands of Animals: Ji Seon Kim , Yoonhee Cho , Chang Wan Seo , Ki Hyeong Park , Shinnam Yoo , Jun Won Lee , Sung Hyun Kim , Wonjun Lee , Young Woon Lim; J. Microbiol. 2023;61(6):653-653.; DOI: https://doi.org/10.1007/s12275-023-00060-6

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Abstract PDF: Correction to: Journal of Microbiology (2023) 61:189–197 https://doi.org/10.1007/s12275-023-00017-9 In this article two author names are given erroneaously: Written incorrectly: Ki Hyung Park · Shin Nam Yoo It should be read: Ki Hyeong Park · Shinnam Yoo

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