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Park KH, Oh SY, Cho Y, Seo CW, Kim JS, Yoo S, Lim J, Kim CS, Lim YW. Mycorrhizal Fungal Diversity Associated with Six Understudied Ectomycorrhizal Trees in the Republic of Korea. J Microbiol 2023; 61:729-739. [PMID: 37665554 DOI: 10.1007/s12275-023-00073-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/10/2023] [Accepted: 08/13/2023] [Indexed: 09/05/2023]
Abstract
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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Affiliation(s)
- Ki Hyeong Park
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, 51140, Republic of Korea
| | - Yoonhee Cho
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Chang Wan Seo
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ji Seon Kim
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Shinnam Yoo
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jisun Lim
- RetiMark Co. Ltd, Seoul, 04387, Republic of Korea
| | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, 11186, Republic of Korea
| | - Young Woon Lim
- School of Biological Sciences, Institute of Microbiology, Seoul National University, Seoul, 08826, Republic of Korea.
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Oh SY, Park KH, Baldrian P, Fong JJ, Kwon HJ, Kim SY, Lim YW. Fungal diversity living in the root and sporophore of the endemic Korean fern Mankyua chejuense. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Park KH, Oh SY, Yoo S, Fong JJ, Kim CS, Jo JW, Lim YW. Influence of Season and Soil Properties on Fungal Communities of Neighboring Climax Forests ( Carpinus cordata and Fraxinus rhynchophylla). Front Microbiol 2020; 11:572706. [PMID: 33193174 PMCID: PMC7655983 DOI: 10.3389/fmicb.2020.572706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/30/2020] [Indexed: 11/13/2022] Open
Abstract
Trees in forest ecosystems constantly interact with the soil fungal community, and this interaction plays a key role in nutrient cycling. The diversity of soil fungal communities is affected by both environmental factors and host tree species. We investigated the influence of both of these factors by examining the total fungal communities in the rhizospheric soil of climax tree species that have similar ecological roles (Carpinus cordata, an ectomycorrhizal [ECM] tree, and Fraxinus rhynchophylla, an arbuscular mycorrhizal [AM] tree) in temperate forests with continental climates of Mt. Jeombong, South Korea. Fungal communities were assessed by Illumina-MiSeq sequencing the internal transcribed spacer (ITS) region of environmental DNA, and comparing their environmental factors (season and soil properties). We found that soil fungi of the two forest types differed in terms of community structure and ecological guild composition. The total fungal community composition changed significantly with seasons and soil properties in the F. rhynchophylla forest, but not in the C. cordata forest. However, potassium and carbon were significantly correlated with fungal diversity in both forests, and a positive correlation was found only between symbiotrophs of C. cordata and the carbon to nitrogen (C/N) ratio. Thus, the effects of environmental factors on soil fungal communities depended on the host trees, but some factors were common in both forests. Our results indicate that individual tree species should be considered when anticipating how the fungal communities will respond to environmental change.
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Affiliation(s)
- Ki Hyeong Park
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | - Seung-Yoon Oh
- Department of Biology and Chemistry, Changwon National University, Changwon, South Korea
| | - Shinnam Yoo
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
| | | | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Jong Won Jo
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Young Woon Lim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, South Korea
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Montero-Vargas M, Escudero-Leyva E, Díaz-Valerio S, Chaverri P. Step-by-Step Pipeline for the Ecological Analysis of Endophytic Fungi using ITS nrDNA Data. ACTA ACUST UNITED AC 2020; 56:e96. [PMID: 31910332 DOI: 10.1002/cpmc.96] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The nuclear ribosomal DNA internal transcribed spacer (ITS) is accepted as the genetic marker or barcode of choice for the identification of fungal samples. Here, we present a protocol to analyze fungal ITS data, from quality preprocessing of raw sequences to identification of operational taxonomic units (OTUs), taxonomic classification, and assignment of functional traits. The pipeline relies on well-established and manually curated data collections, namely the UNITE database and the FUNGuild script. As an example, real ITS data from culturable endophytic fungi were analyzed, providing detailed descriptions for every step, parameter, and downstream analysis, and finishing with a phylogenetic analysis of the sequences and assigned ecological roles. This article constitutes a comprehensive guide for researchers that have little familiarity with bioinformatic analysis of essential steps required in further ecological studies of fungal communities. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Raw sequencing data processing Support Protocol: Building a BLAST database Basic Protocol 2: Obtaining information from databases Basic Protocol 3: Phylogenetic analysis.
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Affiliation(s)
- Maripaz Montero-Vargas
- Colaboratorio Nacional de Computación Avanzada (CNCA), CeNAT-CONARE, San José, Costa Rica
| | - Efraín Escudero-Leyva
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.,Centro Nacional de Innovaciones Biotecnológicas (CENIBiot), CeNAT-CONARE, San José, Costa Rica
| | - Stefani Díaz-Valerio
- Colaboratorio Nacional de Computación Avanzada (CNCA), CeNAT-CONARE, San José, Costa Rica
| | - Priscila Chaverri
- Escuela de Biología and Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica.,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland
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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: 18] [Impact Index Per Article: 3.6] [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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