| 1. |
- Tedersoo, L., et al.
(författare)
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The Global Soil Mycobiome consortium dataset for boosting fungal diversity research
- 2021
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Ingår i: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 111, s. 573-588
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Tidskriftsartikel (refereegranskat)abstract
- Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.
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| 2. |
- Ovaskainen, Otso, et al.
(författare)
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Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA
- 2024
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Ingår i: Scientific Data. - 2052-4463. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.
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| 3. |
- Houdanon, R. D., et al.
(författare)
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Phylogenetic diversity and affiliation of tropical African ectomycorrhizal fungi
- 2023
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Ingår i: Mycosphere. - : MYCOSPHERE PRESS. - 2077-7000 .- 2077-7019. ; 13:1, s. 13-55
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Tidskriftsartikel (refereegranskat)abstract
- Ectomycorrhizal fungi form a mutualistic symbiosis with plant roots, and are key for nutrient cycling in many ecosystems. Here we study the ectomycorrhizal fungal communities in the Oueme Superieur reserve forest in Benin (West Africa). We use phylogenetic methods to test if the species from the study site are closer to other tropical African species than to species from other regions. The Oueme Superieur community was represented by nine Operational Taxonomic Units in Amanitaceae, one in Boletaceae, one in Cantharellaceae, one in Cortinariaceae, two in Inocybaceae, fourteen in Russulaceae and three in Sclerodermataceae. Of these thirty-one Operational Taxonomic Units, twenty had no record in other areas, and unique Operational Taxonomic Units were found in all families except Boletaceae and Sclerodermataceae. The added phylogenetic diversity from these unique Operational Taxonomic Units tended to be higher than expected by chance in all families but Cantharellaceae. The Operational Taxonomic Units are generally fairly distinct and contribute proportionally to the phylogenetic diversity, reflecting that they do not only represent recently diverging species, but also more divergent lineages. Our analyses of the different families show that the communities of Amanitaceae, Inocybaceae, and Russulaceae are more closely related to the general Afrotropic community than expected by chance, at least measured as the nearest taxon distance. The lack of significant patterns in the other families may be due to lack of power, but the wide distribution of many Operational Taxonomic Units suggests that there are not likely to be strong patterns. It is only for Russulaceae that there is a significant pattern in the Oueme Superieur ectomycorrhizal fungal communities at a regional scale, with the Operational Taxonomic Units being less closely related than expected. At a global scale the patterns seem to reflect the overall distribution of the Afrotropic ectomycorrhizal fungal community. The phylogenetic patterns in the Afrotropic communities differ between families, from clustered to no clear pattern to over-dispersed measured as mean average phylogenetic distance. Each family seems to have its own biogeographic history, and there is no clear pattern for the ectomycorrhizal fungal community at large. Despite the lack of comprehensive taxonomic work to identify fungi in a region, it is still possible to draw some conclusions on their diversity using molecular phylogenetic methods. However, limited success in getting good sequence data from specimens, probably due to preservation issues in the field, and the lack of well annotated molecular data from many regions limit the power of these inferences.
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| 4. |
- Badou, Sylvestre A., et al.
(författare)
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Paxilloboletus gen. nov., a new lamellate bolete genus from tropical Africa
- 2022
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Ingår i: Mycological progress. - : Springer Nature. - 1617-416X .- 1861-8952. ; 21:1, s. 243-256
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Tidskriftsartikel (refereegranskat)abstract
- This study presents Paxilloboletus gen. nov., a new lamellate bolete genus represented by two tropical African species, Paxilloboletus africanus sp. nov. and Paxilloboletus latisporus sp. nov. Although the new taxa strongly resemble Paxillus (Paxillaceae), they lack clamp connections and form a separate generic clade within the Boletaceae phylogeny. The new species are lookalikes, morphologically only separable by their spore morphology. Descriptions and illustrations of the new genus and new species are given, as well as comments on ecology, distribution, and morphological differences with other gilled Boletaceae.
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| 5. |
- Furneaux, Brendan R., et al.
(författare)
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Both ectomycorrhizal tree diversity and soil characteristics structure ectomycorrhizal mushroom communities, and production in Sudanian savanna woodlands
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Ectomycorrhiza (ECM) are a symbiosis between plant and fungi where the plant get nutrients and other benefits from the fungi while the fungi get energy rich carbon compounds from the plant.Many ECM fungi form fleshy fruitbodies, including many choice edible mushrooms.Sudanian savanna woodlands are a tropical ecosystem that has a large proportion of ECM trees, but is under severe threat due to human activities.Based on three mushroom seasons of biweekly frutingbody collection we analyze the environmental factors driving the structure of the ECM community, including: composition, diversity, richness and biomass production.As wild edible mushrooms are an important food supplement in the region, we also analyzed the community structure of local choice edibles specifically.Different types of factors have been shown to influence different systems so we consequently take a comprehensive approach to what environmental factors are investigated, including ECM tree community structure, microclimate, and soil characteristics.We find that the spatial variation in ECM fungal community structure within our study area is larger than the variation in ECM fungal community structure of the study area between years.The richness of ECM host trees influenced all aspects of the spatial community structure, with a positive effect on diversity, richness, and biomass production.Microclimate also had an affect on all aspects of the community structure, but the relative importance of soil temperature and soil moisture varied.Soil characteristics were the strongest correlates of species diversity and richness, as well as biomass production, with soil nitrogen levels found to have a negative effect while phosphorus had a positive effect.Soil characteristicss were not found to be important to species composition, but this may be due to lack of statistical power, since the sampling size was lower for these factors than the others.Despite our comprehensive measurements, most of the spatial variation was not explained by any of the included factors.This variation may be due to unmeasured environmental, individual, or population level factors.
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| 6. |
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| 7. |
- Furneaux, Brendan R., 1979-
(författare)
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Fungal communities of West African ectomycorrhizal woodlands
- 2020
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Ectomycorrhizal symbiosis is a widespread mutualist relationship between fungi and plants, often trees. It is most well-known in temperate and boreal forests, but also occurs in a variety of tropical ecosystems, including Sudanian savanna woodlands and gallery forests in West Africa. In addition to their important role in nutrient cycling, many ectomycorrhizal fungi also produce edible mushrooms as their fruit-bodies. In this thesis, I explore spatial patterns of above-ground and below-ground diversity in West African ectomycorrhizal communities, as well as the use of wild edible fungi by the local human population. In Papers I and II, I used soil DNA metabarcoding to investigate fungal communities in their vegetative state. Paper I used measurements of the scale of spatial autocorrelation within the fungal community in Sudanian woodlands in Benin as a test to compare different high-throughput DNA sequencing strategies, including short (≈350 bp) amplicon barcoding using the Illumina, Ion Torrent, and PacBio sequencing platforms, as well as long (≈1550 bp) amplicon barcoding using PacBio. There were some differences in species richness and community composition recovered by the two amplicon lengths, attributable to known primer biases for the short amplicons, but these did not lead to different ecological results. Additionally, Paper I introduced new software packages for analysis of long-amplicon metabarcoding data and integrating phylogenetic information into sequence-based taxonomic identification. In Paper II we sampled both Sudanian woodland and gallery forest sites in five countries across West Africa using long-amplicon metabarcoding with PacBio. We found significant differences in fungal community composition between Sudanian woodland and gallery forest sites, but not between different tree species within each vegetation type. Papers III and IV focused above-ground to study the natural production and human use of the mushrooms themselves. In Paper III we exhaustively collected mushrooms from nine Sudanian woodland plots in Benin during three consecutive rainy seasons. We measured the total biomass produced of each morphospecies, as well as environmental variables related to microclimate, host tree availability, and soil chemistry. Mushroom production and diversity were negatively correlated with soil nitrogen levels, and positively correlated with soil phosphorus levels. Although there were no clear differences in the fungal communities associated with the four host trees present in our plots, greater host tree diversity was associated with greater fungal diversity and productivity. Finally, Paper IV combined interviews with local people from four ethnic groups in five villages near the study sites from Paper III about their knowledge and preferences for edible mushrooms with DNA barcoding of specimens. Knowledge and preferences for different mushrooms varied between ethnic groups, but people living in a village where their ethnic group is a minority tended to absorb knowledge about mushrooms from the majority group in the village. Women over age 35 were the most knowledgeable about mushrooms, but the degree of gender difference varied between groups. We compiled a list of the most choice edible mushrooms in the area, which can inform the possibility for commercial trade in wild mushrooms to supplement the income of rural people and encourage sustainable forest management.
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| 8. |
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| 9. |
- Furneaux, Brendan R., et al.
(författare)
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Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities
- 2021
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Ingår i: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 21:6, s. 1833-1849
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Tidskriftsartikel (refereegranskat)abstract
- Fungi form diverse communities and play essential roles in many terrestrial ecosystems, yet there are methodological challenges in taxonomic and phylogenetic placement of fungi from environmental sequences. To address such challenges, we investigated spatiotemporal structure of a fungal community using soil metabarcoding with four different sequencing strategies: short-amplicon sequencing of the ITS2 region (300-400 bp) with Illumina MiSeq, Ion Torrent Ion S5 and PacBio RS II, all from the same PCR library, as well as long-amplicon sequencing of the full ITS and partial LSU regions (1200-1600 bp) with PacBio RS II. Resulting community structure and diversity depended more on statistical method than sequencing technology. The use of long-amplicon sequencing enables construction of a phylogenetic tree from metabarcoding reads, which facilitates taxonomic identification of sequences. However, long reads present issues for denoising algorithms in diverse communities. We present a solution that splits the reads into shorter homologous regions prior to denoising, and then reconstructs the full denoised reads. In the choice between short and long amplicons, we suggest a hybrid approach using short amplicons for sampling breadth and depth, and long amplicons to characterize the local species pool for improved identification and phylogenetic analyses.
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| 10. |
- Gohar, Daniyal, et al.
(författare)
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Global diversity and distribution of mushroom-inhabiting bacteria
- 2022
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Ingår i: Environmental Microbiology Reports. - : John Wiley & Sons. - 1758-2229. ; 14:2, s. 254-264
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Tidskriftsartikel (refereegranskat)abstract
- Mushroom-forming fungi are important sources of food and medicine in many regions of the world, and their development and health are known to depend on various microbes. Recent studies have examined the structure of mushroom-inhabiting bacterial (MIB) communities and their association with local environmental variables, but global-scale diversity and determinants of these communities remain poorly understood. Here we examined the MIB global diversity and community composition in relation to climate, soil and host factors. We found a core global mushroom microbiome, accounting for 30% of sequence reads, while comprising a few bacterial genera such as Halomonas, Serratia, Bacillus, Cutibacterium, Bradyrhizobium and Burkholderia. Our analysis further revealed an important role of host phylogeny in shaping the communities of MIB, whereas the effects of climate and soil factors remained negligible. The results suggest that the communities of MIB and free-living bacteria are structured by contrasting community assembly processes and that fungal-bacterial interactions are an important determinant of MIB community structure.
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