1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Metabolic Diversity of Xylariaceous Fungi Associated with Leaf Litter Decomposition. J Fungi (Basel) 2022; 8:jof8070701. [PMID: 35887457 PMCID: PMC9324366 DOI: 10.3390/jof8070701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/20/2022] [Accepted: 06/28/2022] [Indexed: 11/23/2022] Open
Abstract
Fungi in the family Xylariaceae are primary agents of leaf litter decomposition. However, the diversity of carbon source utilization by xylariaceous fungi and the relative effects on this from environmental and phylogenetic factors are largely unknown. This study assessed the metabolic diversity and redundancy of xylariaceous fungi, associated with leaf litter decomposition, by measuring their in vitro capacity to utilize multiple carbon sources. The work identified the relative influences of geographic and climatic sources, as well as the taxonomic and phylogenetic relatedness, of the fungi. Using Biolog EcoPlateTM, 43 isolates belonging to Nemania, Xylaria, Nodulisporium, Astrocystis, and Hypoxylon, isolated from Castanopsis sieboldii leaf litter at eight sites in Japan, were found to have the capacity to utilize a variety of carbohydrates, amino acids/amines, carboxylic acids, and polymers. The genera of xylariaceous fungi and their origins significantly affected their metabolic diversity and utilization of carbon sources. Variation partitioning demonstrated that dissimilarities in carbon utilization among fungal isolates were mostly attributable to site differences, especially climatic factors: mean annual temperature and precipitation, and maximum snow depth. Moreover, xylariaceous isolates that originated from adjacent sites tended to have similar patterns of carbon source utilization, suggesting metabolic acclimation to local environmental conditions.
Collapse
|
3
|
Hashizume H, Taga S, Sakata MK, Taha MHM, Siddig EE, Minamoto T, Fahal AH, Kaneko S. Detection of multiple mycetoma pathogens using fungal metabarcoding analysis of soil DNA in an endemic area of Sudan. PLoS Negl Trop Dis 2022; 16:e0010274. [PMID: 35275915 PMCID: PMC8942264 DOI: 10.1371/journal.pntd.0010274] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/23/2022] [Accepted: 02/23/2022] [Indexed: 01/14/2023] Open
Abstract
Mycetoma is a tropical disease caused by several fungi and bacteria present in the soil. Fungal mycetoma and eumycetoma are especially challenging to treat; therefore, prevention, early diagnosis, and early treatment are important, but it is also necessary to understand the geographic distribution of these pathogenic fungi. In this study, we used DNA metabarcoding methodology to identify fungal species from soil samples. Soil sampling was implemented at seven villages in an endemic area of Sennar State in Sudan in 2019, and ten sampling sites were selected in each village according to land-use conditions. In total, 70 soil samples were collected from ground surfaces, and DNA in the soil was extracted with a combined method of alkaline DNA extraction and a commercial soil DNA extraction kit. The region for universal primers was selected to be the ribosomal internal transcribed spacer one region for metabarcoding. After the second PCR for DNA library preparation, the amplicon-based DNA analysis was performed using next-generation sequencing with two sets of universal primers. A total of twelve mycetoma-causative fungal species were identified, including the prime agent, Madurella mycetomatis, and additional pathogens, Falciformispora senegalensis and Falciformispora tompkinsii, in 53 soil samples. This study demonstrated that soil DNA metabarcoding can elucidate the presence of multiple mycetoma-causative fungi, which may contribute to accurate diagnosis for patient treatment and geographical mapping. Mycetoma, a chronic subcutaneous and cutaneous disease, designated as a "neglected tropical disease," is prevalent in dry and hot climates. Fungal mycetoma is caused by more than 50 species of soil-dwelling pathogenic fungi, and its diagnosis and treatment can be challenging. The prevention of infection and early diagnosis and treatment are essential, and for this purpose, environmental assessment to understand the fungal habitat is necessary. In this study, we performed DNA metabarcoding analysis using next-generation sequencing (NGS) for mycetoma pathogens from environmental soil samples in Sudan. The results suggest that multiple causative agents of fungal mycetoma are widespread regardless of the environment and can be a source of infection anywhere in an endemic area. Based on the results of this study, we expect that the investigation of fungi in soil using NGS technology may help identify infection routes and create risk maps for the prevention of mycetoma.
Collapse
Affiliation(s)
- Hiroki Hashizume
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Suguru Taga
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Masayuki K. Sakata
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | | | | | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, Kobe, Japan
| | | | - Satoshi Kaneko
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
- Department of Ecoepidemiology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
- * E-mail:
| |
Collapse
|
4
|
Zhang B, Xue K, Zhou S, Wang K, Liu W, Xu C, Cui L, Li L, Ran Q, Wang Z, Hu R, Hao Y, Cui X, Wang Y. Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas. eLife 2022; 11:70164. [PMID: 35073255 PMCID: PMC8828049 DOI: 10.7554/elife.70164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biotas on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4000 km in both alpine and temperate biotas. Prokaryotic similarities increased over geographic distance after tipping points of 1760–1920 km, generating a significant U-shape pattern. Such pattern was likely due to decreased disparities in environmental heterogeneity over geographic distance when across biotas, supported by three lines of evidences: (1) prokaryotic similarities still decreased with the environmental distance, (2) environmental selection dominated prokaryotic assembly, and (3) short-term environmental heterogeneity followed the U-shape pattern spatially, especially attributed to dissolved nutrients. In sum, these results demonstrate that environmental selection overwhelmed the geographic ‘distance’ effect when across biotas, overturning the previously well-accepted geographic pattern for microbes on a large scale.
Collapse
Affiliation(s)
- Biao Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Shutong Zhou
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Kui Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Wenjing Liu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Cong Xu
- Aerospace Information Research Institute, University of Chinese Academy of Sciences
| | - Lizhen Cui
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Linfeng Li
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Qinwei Ran
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Zongsong Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Ronghai Hu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Xiaoyong Cui
- Key Laboratory of Adaptation and Evolution of Plateau Biota, University of Chinese Academy of Sciences
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences
| |
Collapse
|
5
|
Elevation Matters More than Season in Shaping the Heterogeneity of Soil and Root Associated Ectomycorrhizal Fungal Community. Microbiol Spectr 2022; 10:e0195021. [PMID: 35019700 PMCID: PMC8754124 DOI: 10.1128/spectrum.01950-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Ectomycorrhizal (EcM) fungi play important roles in forest ecosystems, and their richness and composition can change along with elevation and season changes. However, no study has estimated the relative importance of altitudinal and seasonal heterogeneity in predicting the distribution of EcM fungal communities by simultaneously considering different sample types (root versus soil). In this study, we collected root and soil samples along a > 1,500-m elevation gradient during wet and dry seasons from Baima Snow Mountain, located in “the Mountains of Southwest China,” one of the 34 biodiversity hot spots, and we analyzed them using next-generation sequencing. Regardless of the sample type, similar EcM fungal richness pattern with increasing elevation (decline in the forest zone, and an increase at the alpine meadow zone) and strong community turnovers among different elevational zones and between two seasons were detected, and changes of EcM fungal community similarity on 400-m altitude gradient were equivalent to the community turnover between dry and wet seasons. Elevation and edaphic factors were shown to have the largest effects on EcM fungal community. The heterogeneity of richness and community composition was stronger among different elevational zones than across different seasons, mainly because the elevation variations in the EcM fungal community were shaped by the combined effects of different environmental factors, while seasonal changes were mainly controlled by temperature and fast-changing soil nutrients. IMPORTANCE Altitude and season represent two important environmental gradients that shape the structure of biome, including the heterogeneity of EcM fungi. Previous studies have separately considered the influences of altitude and season on EcM fungal communities, but the relative importance of altitude and season is still unknown. The present study revealed that elevation influences the heterogeneity of EcM fungal community more than season; this may be because the variability of environmental factors is higher across different elevations than that across seasons.
Collapse
|
6
|
Matsuoka S, Sugiyama Y, Shimono Y, Ushio M, Doi H. Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding. Environ Microbiol 2021; 23:4797-4806. [PMID: 34258854 DOI: 10.1111/1462-2920.15669] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over 2 years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a 'trap' for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.
Collapse
Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Yoshito Shimono
- Graduate School of Bioresources, Mie University, Tsu, Japan.,Osaka Museum of Nature History, Osaka, Japan
| | - Masayuki Ushio
- Hakubi Center, Kyoto University, Kyoto, Japan.,Center for Ecological Research, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, Kobe, Japan
| |
Collapse
|
7
|
Nakadai R. Degrees of compositional shift in tree communities vary along a gradient of temperature change rates over one decade: Application of an individual-based temporal beta-diversity concept. Ecol Evol 2020; 10:13613-13623. [PMID: 33391667 PMCID: PMC7771126 DOI: 10.1002/ece3.6579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/24/2022] Open
Abstract
Temporal patterns in communities have gained widespread attention recently, to the extent that temporal changes in community composition are now termed "temporal beta-diversity." Previous studies of beta-diversity have made use of two classes of dissimilarity indices: incidence-based (e.g., Sørensen and Jaccard dissimilarity) and abundance-based (e.g., Bray-Curtis and Ružička dissimilarity). However, in the context of temporal beta-diversity, the persistence of identical individuals and turnover among other individuals within the same species over time have not been considered, despite the fact that both will affect compositional changes in communities. To address this issue, I propose new index concepts for beta-diversity and the relative speed of compositional shifts in relation to individual turnover based on individual identity information. Individual-based beta-diversity indices are novel dissimilarity indices that consider individual identity information to quantitatively evaluate temporal change in individual turnover and community composition. I applied these new indices to individually tracked tree monitoring data in deciduous and evergreen broad-leaved forests across the Japanese archipelago with the objective of quantifying the effect of climate change trends (i.e., rates of change in both annual mean temperature and annual precipitation) on individual turnover and compositional shifts at each site. A new index explored the relative contributions of mortality and recruitment processes to temporal changes in community composition. Clear patterns emerged showing that an increase in the temperature change rate facilitated the relative contribution of mortality components. The relative speed of compositional shift increased with increasing temperature change rates in deciduous forests but decreased with increasing warming rates in evergreen forests. These new concepts provide a way to identify novel and high-resolution temporal patterns in communities.
Collapse
Affiliation(s)
- Ryosuke Nakadai
- Department of Environmental and Biological Sciences, Faculty of Science and ForestryUniversity of Eastern FinlandJoensuuFinland
- Department of Ecosystem Studies, Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| |
Collapse
|
8
|
Osono T, Matsuoka S, Hirose D. Diversity and Geographic Distribution of Ligninolytic Fungi Associated With Castanopsis sieboldii Leaf Litter in Japan. Front Microbiol 2020; 11:595427. [PMID: 33329481 PMCID: PMC7732466 DOI: 10.3389/fmicb.2020.595427] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022] Open
Abstract
The diversity and geographic pattern of ligninolytic fungi were investigated within the distribution range of an evergreen tree, Castanopsis sieboldii (Fagaceae), in Japan. Fungal isolates obtained from 18 sites in subtropical and temperate regions in Japan were classified into 50 operational taxonomic units in Ascomycota and Basidiomycota according to the base sequence of the rDNA internal transcribed spacer region. Ordination by nonmetric multidimensional scaling showed the separation of fungal compositions between the study sites which was significantly related to the latitude, longitude, and mean annual temperature (MAT) of the study sites. We applied variation partitioning to separate the magnitude of the climatic, spatial, and leaf property factors and found the roles of MAT and spatial factors in structuring fungal assemblages, suggesting the importance of both niche processes and such non-niche processes as priority effect and dispersal limitation. The bleached area on leaf litter was greater at sites with higher MAT and precipitation located at lower latitudes and at sites where some major ligninolytic fungi occurred at greater relative frequencies, indicating that not only the climatic conditions but also the biogeographic patterns of distribution of ligninolytic fungi influence the decomposition of lignin in leaf litter.
Collapse
Affiliation(s)
- Takashi Osono
- Faculty of Science and Engineering, Doshisha University, Kyoto, Japan
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Dai Hirose
- School of Pharmacy, Nihon University, Funabashi, Japan
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Větrovský T, Morais D, Kohout P, Lepinay C, Algora C, Awokunle Hollá S, Bahnmann BD, Bílohnědá K, Brabcová V, D'Alò F, Human ZR, Jomura M, Kolařík M, Kvasničková J, Lladó S, López-Mondéjar R, Martinović T, Mašínová T, Meszárošová L, Michalčíková L, Michalová T, Mundra S, Navrátilová D, Odriozola I, Piché-Choquette S, Štursová M, Švec K, Tláskal V, Urbanová M, Vlk L, Voříšková J, Žifčáková L, Baldrian P. GlobalFungi, a global database of fungal occurrences from high-throughput-sequencing metabarcoding studies. Sci Data 2020; 7:228. [PMID: 32661237 PMCID: PMC7359306 DOI: 10.1038/s41597-020-0567-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/05/2020] [Indexed: 02/08/2023] Open
Abstract
Fungi are key players in vital ecosystem services, spanning carbon cycling, decomposition, symbiotic associations with cultivated and wild plants and pathogenicity. The high importance of fungi in ecosystem processes contrasts with the incompleteness of our understanding of the patterns of fungal biogeography and the environmental factors that drive those patterns. To reduce this gap of knowledge, we collected and validated data published on the composition of soil fungal communities in terrestrial environments including soil and plant-associated habitats and made them publicly accessible through a user interface at https://globalfungi.com . The GlobalFungi database contains over 600 million observations of fungal sequences across > 17 000 samples with geographical locations and additional metadata contained in 178 original studies with millions of unique nucleotide sequences (sequence variants) of the fungal internal transcribed spacers (ITS) 1 and 2 representing fungal species and genera. The study represents the most comprehensive atlas of global fungal distribution, and it is framed in such a way that third-party data addition is possible.
Collapse
Affiliation(s)
- Tomáš Větrovský
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Daniel Morais
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Kohout
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Clémentine Lepinay
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Camelia Algora
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sandra Awokunle Hollá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Barbara Doreen Bahnmann
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Květa Bílohnědá
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vendula Brabcová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Federica D'Alò
- Laboratory of Systematic Botany and Mycology, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Zander Rainier Human
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Mayuko Jomura
- Department of Forest Science and Resources, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa, Japan
| | - Miroslav Kolařík
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Kvasničková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Salvador Lladó
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Rubén López-Mondéjar
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tijana Martinović
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Mašínová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Meszárošová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lenka Michalčíková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Tereza Michalová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sunil Mundra
- Department of Biology, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Section for Genetics and Evolutionary Biology, University of Oslo, Blindernveien 31, 0316, Oslo, Norway
| | - Diana Navrátilová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Iñaki Odriozola
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Sarah Piché-Choquette
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Martina Štursová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Karel Švec
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Vojtěch Tláskal
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Michaela Urbanová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lukáš Vlk
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Jana Voříšková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Lucia Žifčáková
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic
| | - Petr Baldrian
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Praha 4, Czech Republic.
| |
Collapse
|
11
|
Sugiyama Y, Matsuoka S, Osono T. Two-years of investigation revealed the inconsistency of seasonal dynamics of an ectomycorrhizal fungal community in Japanese cool-temperate forest across years. FEMS Microbiol Ecol 2020; 96:5857164. [DOI: 10.1093/femsec/fiaa118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/11/2020] [Indexed: 11/13/2022] Open
Abstract
ABSTRACT
Ectomycorrhizal (ECM) fungal communities show temporal dynamics. Such dynamics have been mainly assessed with 1 year of investigations and have been related to the seasonal changes in environment. Recent study in sub-tropical region has revealed that stochastic temporal-based process can affect ECM fungal community, making the community of the same season different between years. The different community structures across years have also been observed in the Arctic region with a grass host. Nevertheless, in temperate zones, the effect of temporal-based processes and the consistency of seasonal dynamics have never been investigated. We conducted a 2-year root sampling in a cool temperate Fagus crenata forest to test whether the temporal variation of ECM fungal community composition could be explained by season. The explanation powers of temporal distance and environmental factors for the temporal dynamics of ECM fungal community were simultaneously evaluated. The variation in community structure was significantly explained by year but not by season, indicating that seasonal community structure differed between years. This difference in the community structure across years was partly explained by temporal factors. Our study implies that the temporal dynamics of ECM fungal communities in temperate forests are affected by temporal-based factors and can vary across years.
Collapse
Affiliation(s)
- Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606–8501, Japan
| | - Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takashi Osono
- Department of Environmental Systems Science, Faculty of Science and Engineering, Doshisha University, Tatara Miyakodani 1-3, Kyotanabe, Kyoto, 610-0394, Japan
| |
Collapse
|
12
|
Matsuoka S, Iwasaki T, Sugiyama Y, Kawaguchi E, Doi H, Osono T. Biogeographic Patterns of Ectomycorrhizal Fungal Communities Associated With Castanopsis sieboldii Across the Japanese Archipelago. Front Microbiol 2019; 10:2656. [PMID: 31798567 PMCID: PMC6868053 DOI: 10.3389/fmicb.2019.02656] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/31/2019] [Indexed: 11/13/2022] Open
Abstract
Biogeographic patterns in ectomycorrhizal (ECM) fungal communities and their drivers have been elucidated, including effects of host tree species and abiotic (climatic and edaphic) conditions. At these geographic scales, genotypic diversity and composition of single host tree species change with spatial and environmental gradients, reflecting their historical dispersal events. However, whether the host genotypes can be associated with the biogeographic patterns of ECM communities remains unclear. We investigated the biogeographic pattern of ECM fungal community associated with the single host species Castanopsis sieboldii (Fagaceae), whose genotypic diversity and composition across the Japanese archipelago has already been evaluated. ECM communities were investigated in 12 mature Castanopsis-dominated forests covering almost the entire distribution range of C. sieboldii, and we quantified the effect of host genotypes on the biogeographic pattern of ECM fungal communities. Richness and community composition of ECM fungi changed with latitude and longitude; these biogeographic changes of ECM community were significantly correlated with host genotypic variables. Quantitative analyses showed a higher relative explanatory power of climatic and spatial variables than that of host genotypic variables for the biogeographic patterns in the ECM community. Our results suggest historical events of host dispersal can affect the biogeographic patterns of the ECM fungal community, while their explanation power was lower than that for climatic filtering and/or fungal dispersal.
Collapse
Affiliation(s)
- Shunsuke Matsuoka
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Takaya Iwasaki
- Department of Biological Sciences, Faculty of Science, Kanagawa University, Hiratsuka, Japan
| | - Yoriko Sugiyama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eri Kawaguchi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Hideyuki Doi
- Graduate School of Simulation Studies, University of Hyogo, Kobe, Japan
| | - Takashi Osono
- Department of Environmental Systems Science, Faculty of Science and Engineering, Doshisha University, Kyoto, Japan
| |
Collapse
|
13
|
Matsuoka S, Sugiyama Y, Sato H, Katano I, Harada K, Doi H. Spatial structure of fungal DNA assemblages revealed with eDNA metabarcoding in a forest river network in western Japan. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.36335] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Growing evidence has revealed high diversity and spatial heterogeneity of fungal communities in local habitats of terrestrial ecosystems. Recently, the analysis of environmental DNA has been undertaken to study the biodiversity of organisms, such as animals and plants, in both aquatic and terrestrial habitats. In the present study, we investigated fungal DNA assemblages and their spatial structure using environmental DNA metabarcoding targeting the internal transcribed spacer 1 (ITS1) region of the rRNA gene cluster in habitats across different branches of rivers in forest landscapes. A total of 1,956 operational taxonomic units (OTUs) were detected. Of these, 770 were assigned as Ascomycota, 177 as Basidiomycota, and 38 as Chytridiomycota. The river water was found to contain functionally diverse OTUs of both aquatic and terrestrial fungi, such as plant decomposers and mycorrhizal fungi. These fungal DNA assemblages were more similar within, rather than between, river branches. In addition, the assemblages were more similar between spatially closer branches. This spatial structuring was significantly associated with geographic distances but not with vegetation of the catchment area and the elevation at the sampling points. Our results imply that information on the terrestrial and aquatic fungal compositions of watersheds, and therefore their spatial structure, can be obtained by investigating the fungal DNA assemblages in river water.
Collapse
|
14
|
Matsuoka S, Suzuki Y, Hobara S, Osono T. Fungal succession and decomposition of composted aquatic plants applied to soil. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
15
|
D'Souza ML, Hebert PDN. Stable baselines of temporal turnover underlie high beta diversity in tropical arthropod communities. Mol Ecol 2018; 27:2447-2460. [DOI: 10.1111/mec.14693] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 01/24/2023]
Affiliation(s)
- Michelle L. D'Souza
- Centre for Biodiversity Genomics; University of Guelph; Guelph ON Canada
- Department of Integrative Biology; College of Biological Science; University of Guelph; Guelph ON Canada
| | - Paul D. N. Hebert
- Centre for Biodiversity Genomics; University of Guelph; Guelph ON Canada
- Department of Integrative Biology; College of Biological Science; University of Guelph; Guelph ON Canada
| |
Collapse
|
16
|
Tian J, Zhu D, Wang J, Wu B, Hussain M, Liu X. Environmental factors driving fungal distribution in freshwater lake sediments across the Headwater Region of the Yellow River, China. Sci Rep 2018; 8:3768. [PMID: 29491438 PMCID: PMC5830880 DOI: 10.1038/s41598-018-21995-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/14/2018] [Indexed: 11/29/2022] Open
Abstract
Dispersal limitation and environmental filtering are two primary processes involved in shaping microbial community structure. The pristine environmental and geographical relatively isolation of small lakes distributed in the Headwater Region of Yellow River (HRYR) offer a unique opportunity to test the relative roles of these two processes on fungal communities. Here, we investigated the fungal community in sediment samples from 10 lakes located in the HRYR using high-throughput sequencing. The results showed that the fungal community was dominated by Sordariomycetes, Leotiomycetes, Dothideomycetes, Pezizomycetes and Agaricomycetes. The results revealed that altitude, mean annual temperature, C/N ration, dissolve organic carbon and total nitrogen were the best predictors for shaping fungal community structure in these lakes. Significant spatial and environmental distance decay relationships in the fungal community were detected. The partial Mantel test indicated that the fungal community structure was significantly correlated with environmental distance but not with geographic distance. Overall, environmental filtering plays a more important role than dispersal limitation in fungal community structure at a local scale in such an pristine and isolated region.
Collapse
Affiliation(s)
- Jianqing Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dan Zhu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- Zoige Peatland and Global Change Research Station, Chinese Academy of Sciences, Hongyuan, 624400, China
| | - Jinzhi Wang
- Beijing Key Laboratory of Wetland Services and Restoration, Institute of Wetland Research, Chinese Academy of Forestry, Beijing, 100091, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Muzammil Hussain
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xingzhong Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
17
|
|