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- 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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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.
Journal Articles
- 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
- 295 View
- 1 Download
- 1 Crossref
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- 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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Citations
Citations to this article as recorded by
- Effects of elevated temperatures on soil enzymatic activities and bacterial and fungal community composition and diversity
Precious Mutambara, Kabwe Nkongolo
Ecological Genetics and Genomics.2025; 36: 100382. CrossRef
- Effects of elevated temperatures on soil enzymatic activities and bacterial and fungal community composition and diversity
- 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
- 468 View
- 2 Download
- 7 Web of Science
- 8 Crossref
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Abstract
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- 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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Citations
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Mycobiology.2023; 51(6): 436. CrossRef
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- Diversity of fungi associated with roots of Calanthe orchid species in Korea
- Myung Soo Park , John A. Eimes , Sang Hoon Oh , Hwa Jung Suh , Seung-Yoon Oh , Seobihn Lee , Ki Hyeong Park , Hyuk Joon Kwon , Soo-Young Kim , Young Woon Lim
- J. Microbiol. 2018;56(1):49-55. Published online January 4, 2018
- DOI: https://doi.org/10.1007/s12275-018-7319-9
- 396 View
- 0 Download
- 11 Crossref
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Abstract
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- While symbiotic fungi play a key role in the growth of endangered Calanthe orchid species, the relationship between fungal diversity and Calanthe species remains unclear. Here, we surveyed root associated fungal diversity of six Calanthe orchid species by sequencing the internal transcribed spacer (ITS) region using 454 pyrosequencing. Our results revealed that Paraboeremia and Coprinopsis are dominant fungal genera among Calanthe species. In terms of overall relative abundance, Paraboeremia was the most common fungal genus associated with Calanthe roots, followed by Coprinopsis. Overall fungal diversity showed a significant degree of variation depending on both location and Calanthe species. In terms of number of different fungal genera detected within Calanthe species, C. discolor had the most diverse fungal community, with 10 fungal genera detected. This study will contribute toward a better understanding of those fungi that are required for successful cultivation and conservation of Korean Calanthe species.
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Citations
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Canadian Journal of Plant Science.2025; 105: 1. CrossRef -
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Journal of Fungi.2022; 8(3): 226. CrossRef - Fungal diversity driven by bark features affects phorophyte preference in epiphytic orchids from southern China
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- Preliminary Assessment of Mycobiome at Former Quarry Site That Hosts a Diverse and Abundant Orchid Population
Published 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
- 283 View
- 1 Download
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