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Supplementary material 1 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Datafile 1
Supplementary material 2 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Datafile 2
Supplementary material 5 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Table S1 and Figs S1–S4
Supplementary material 4 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Datafile 4
Figure 6 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 6 Taxonomic composition to family level of ECM fungi in gallery forest and woodlands. Abundance measured as fraction of reads (A) and richness measured as fraction of species hypotheses (SH) (B).
Figure 3 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 3 Species accumulation curves for each plot. Curves are based on SHs, by sequencing depth (A) and number of trees sampled (B), presented separately for three gallery forest sites (left panels) and six woodland sites (right panels). Points represent the observed species richness at the actual sequencing depth and trees sampled in A, B respectively. Thin lines represent the accumulation curve calculated by rarefaction (darker) and extrapolation (lighter); shaded regions represent the associated 95% confidence intervals. Dotted lines represent the asymptotic estimate for each site.
Figure 4 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 4 NMDS ordination of fungal communities based on Bray-Curtis dissimilarity of species hypothesis-based community composition, grouped into woodland (W) and gallery forests (GF) samples, for All fungi, axis 1–2 (A) and axis 2–3 (B), and for ECM fungi, axis 1–2 (C) and axis 3–4 (D). Stress value = 0.1902 for all fungi and 0.1723 for ECM fungi. Ellipses represent 95% confidence intervals around the mean of each vegetation type.
Figure 5 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 5 Fungal guild assignment of the soil fungal community in gallery forest and woodlands. Abundance measured as fraction of reads (A) and richness measured as fraction of species hypotheses (SH) (B) Guilds representing less than 2% of both abundance and richness are grouped together in "other".
Figure 2 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 2 NMDS ordination of tree communities based on Bray-Curtis dissimilarities between sites, based on total basal areas of each ECM trees species separately and all non-ECM trees combined. The nine sites were classified into two distinct woodland types, woodlands in red and gallery forests in blue. Site abbreviations: Bissandougou Forest Reserve (BISS-W), Moussaya Forest Reserve (MOUS-W), Kota Waterfall (KOTA-G and KOTA-W), Kouadianikro Forest Reserve (KDNK-W), Kou Forest Reserve (KOUF-G), Niangoloko Forest Reserve (NIAN-W) and Farako Forest Reserve (FA01-W and FA15-W). ECM tree species abbreviations: Afzelia africana (Aa), Ac: Anthonotha crassifolia (Ac), Bg: Berlinia grandiflora (Bg), Id: Isoberlinia doka (Id), I. tomentosa (It), Monotes kerstingii (Mk), Uapacaguineensis (Ug) and Uapaca togoensis (Ut).
Figure 1 from: Meidl P, Furneaux B, Tchan KI, Kluting K, Ryberg M, Guissou M-L, Soro B, Traoré A, Konomou G, Yorou NS, Rosling A (2021) Soil fungal communities of ectomycorrhizal dominated woodlands across West Africa. MycoKeys 81: 45-68. https://doi.org/10.3897/mycokeys.81.66249
Figure 1 Sampling sites of the West African Centre for Tropical Mycology's 2018 National Geographic Explorer Grant expedition. Shapes and colors separate the different woodland types with blue circles for gallery forests and red triangles for woodlands. With site names (abbreviations): Bissandougou (BISS-W), Moussaya (MOUS-W), Kota (KOTA-G and KOTA-W), Kouadianikro (KDNK-W), Kou (KOUF-G), Niangoloko (NIAN-W) and Farako (FA01-W and FA15-W). The dotted line represents the route taken on the sampling trip, beginning on the coast of Benin and concluding in Ivory Coast. Ecoregions are from White (1983), digitized in Olson et al. (2001).
Data from: Host plant phylogeny and abundance predict root-associated fungal community composition and diversity of mutualists and pathogens
• Interactions between plants and their root-associated fungi (RAF) may influence the relative abundance of tree species and determine forest community diversity. Such plant-soil feedbacks in turn depend on the degree to which spatial distance and phylogenetic relatedness of host trees structure pathogen and mutualist communities, but research detailing these aspects of RAF communities is lacking. Here, we characterize plant-RAF associations across a diverse plant community, focusing on the degree to which RAF communities are structured by spatial distance, host phylogenetic relatedness, and host abundance. We compare results for different functional groups, including both putative mutualists and pathogens, an aspect poorly examined hitherto. • We collected roots at regular intervals along ten 50 m by 2 m transects, then used DNA barcoding to identify host plants, and characterize the associated fungal community. Variance partitioning was used to measure the relative contributions of host phylogenetic relatedness and spatial distance to explaining RAF community composition. A weighted linear regression was used to measure the correlation between host abundance and RAF diversity. • Phylogenetic distance among hosts was a better predictor of RAF community composition than spatial distance, but this relationship was stronger for putative pathogens than for mutualists, suggesting that pathogens show stronger host preference than mutualists. Across all functional groups, RAF showed similar levels of spatial structure. Additionally, RAF communities of locally abundant plants were less diverse than RAF communities of rare plants. • Synthesis: We found that RAF communities are structured by the phylogenetic relatedness of hosts and, to a lesser extent, by spatial distance, with pathogens showing stronger host preference than mutualists. Abundant hosts had less diverse RAF communities than rare hosts, which is notable because abundant plants tend to experience weaker negative plant-soil feedback. Going forward, mechanisms underlying the host abundance-RAF diversity relationship warrant further investigation. Additionally, the survey approach presented here could be paired with experiments linking RAF community composition to plant recruitment.
Data from: Encroachment of shrubs into subalpine grasslands in the Pyrenees modifies the structure of soil fungal communities and soil properties.
The encroachment of shrubs into grasslands is common in terrestrial ecosystems dominated by grass. Land abandonment and favourable climatic trends in recent decades have favoured the expansion of shrubs into subalpine grasslands in many mountainous regions across Europe. The advance of the succession from grassland to shrubland is expected to have a major impact on ecosystem functioning. We used DNA metabarcoding to assess whether the structure of soil fungal communities varied along the succession from subalpine grassland to shrubland in the Pyrenees, and investigated whether shrub encroachment was associated with changes in soil properties. The expansion of shrubs increased the soil C:N ratio and/or reduced the N, P, or K contents. Plant-driven changes in soil properties were strongly associated with the compositional turnover of fungi, including arbuscular mycorrhizal, ectomycorrhizal, ericoid, root endophytic, saprotrophic, lichenised, and pathogenic fungi. Total richness and the richness of most functional groups were correlated with soil P, N, and the C:N or N:P ratios. We show that the interplay between abiotic factors (changes in soil properties) and biotic factors (occurrence and identity of shrubs) played a key role in the structure and uniqueness of soil fungal communities along the succession.
Data from: Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils
A central aim of current microbial ecology research is to investigate the mechanisms shaping the assembly of soil microbial communities. Despite the importance of bacterial and fungal mediation of carbon cycling in forest ecosystems, knowledge concerning their distribution patterns and underlying mechanisms remains insufficient. Here, soils were sampled from six bamboo forests across the main planting area of Moso bamboo in southern China. The bacterial and fungal diversities were assessed by sequencing 16S rRNA and ITS gene amplicons, respectively, with an Illumina MiSeq. Based on structural equation modeling, dispersal limitation had strongest impact on bacterial beta diversity, while the mean annual precipitation had a smaller impact by directly or indirectly mediating the soil organic carbon density. However, only the mean annual temperature and precipitation played direct roles in fungal beta diversity. Moreover, the co-occurrence network analyses revealed a possibly much higher network connectivity in the fungal network than in the bacteria. With less dispersal limitation, stronger environmental selection, and a potentially more connected network, the fungal community had more important roles in the soil carbon metabolisms in bamboo forests. Fungal beta diversity and the clustering coefficient explained approximately 14.4% and 6.1% of the variation in the carbon metabolic profiles among sites, respectively, but that of bacteria only explained approximately 1.7% and 1.8%, respectively. This study explored soil microbial spatial patterns along with the underlying mechanisms of dispersal limitation, selection, and connectivity of ecological networks, thus providing novel insights into the study of the distinct functional traits of different microbial taxa.
Data from: Large-scale fungal diversity assessment in the Andean Yungas forests reveals strong community turnover among forest types along an altitudinal gradient
The Yungas, a system of tropical and subtropical montane forests on the eastern slopes of the Andes, are extremely diverse and severely threatened by anthropogenic pressure and climate change. Previous mycological works focused on macrofungi (e.g., agarics, polypores) and mycorrhizae in Alnus acuminata forests, while fungal diversity in other parts of the Yungas has remained mostly unexplored. We carried out Ion Torrent sequencing of ITS2 rDNA from soil samples taken at 24 sites along the entire latitudinal extent of the Yungas in Argentina. The sampled sites represent the three altitudinal forest types: the piedmont (400–700 masl), montane (700–1500 masl), and montane cloud (1500–3000 masl) forests. The deep sequence data presented here (i.e. 4 108 126 quality-filtered sequences) indicate that fungal community composition correlates most strongly with elevation, with many fungi showing preference for a certain altitudinal forest type. For example, ectomycorrhizal and root endophytic fungi were most diverse in the montane cloud forests, particularly at sites dominated by Alnus acuminata, while the diversity values of various saprobic groups were highest at lower elevations. Despite the strong altitudinal community turnover, fungal diversity was comparable across the different zonal forest types. Besides elevation, soil pH, N, P, and organic matter contents correlated with fungal community structure as well, although most of these variables were co-correlated with elevation. Our data provide an unprecedented insight into the high diversity and spatial distribution of fungi in the Yungas forests.
Data from: Effects of two grass species on the composition of soil fungal communities
Many studies have shown effects of plants species on fungal communities, but these are often confounded with soil effects. Thus, the specific role of plant species in structuring rhizospheric and soil fungal communities is poorly described. Our study used microcosms in which plants were grown under artificial conditions to bridge this gap. Two perennial grasses dominating subalpine grasslands, Festuca paniculata and Dactylis glomerata, were grown at two levels of fertilization on standard soil. Fungal communities were determined by 454 pyrosequencing of the internal transcribed spacer 1 region. Among the fungal communities characterized by the primers used, original communities were associated to each plant species and also diverged between rhizosphere and bulk soils within each plant species, though there were no significant fertilization effects. Differences regarded global composition of the fungal communities and abundant molecular operational taxonomic units (MOTUs). Both plant species and location effects were reflected more in the abundance than in the composition of MOTUs. The observed differences in fungal communities coincide with differing strategies of plant root growth, with D. glomerata having greater root mass, length, and area than F. paniculata. Our study, by dissociating soil effects from plant effects, demonstrated that plant species exert a key control on soil fungi. We suggest that such effects may be linked to inter-specific differences in root traits and their consequences on nitrogen uptake.
Data from: Abrupt changes in the composition and function of fungal communities along an environmental gradient in the High Arctic
Fungi play a key role in soil-plant interactions, nutrient cycling, and carbon flow and are essential for the functioning of arctic terrestrial ecosystems. Some studies have shown that the composition of fungal communities is highly sensitive to variations in environmental conditions, but little is known about how the conditions control the role of fungal communities (i.e. their ecosystem function). We used DNA metabarcoding to compare taxonomic and functional composition of fungal communities along a gradient of environmental severity in Northeast Greenland. We analysed soil samples from fell fields, heaths, and snowbeds, three habitats with very contrasting abiotic conditions. We also assessed within-habitat differences by comparing three widespread microhabitats (patches with high cover of Dryas, Salix, or bare soil). The data suggest that, along the sampled mesotopographic gradient, the greatest differences in both fungal richness and community composition are observed among habitats, while the effect of microhabitat is weaker, although still significant. Furthermore, we found that richness and community composition of fungi are shaped primarily by abiotic factors and to a lesser, though still significant extent, by floristic composition. Along this mesotopographic gradient, environmental severity is strongly correlated with richness in all fungal functional groups: positively in saprotrophic, pathogenic, and lichenised fungi, and negatively in ectomycorrhizal and root-endophytic fungi. Our results suggest complex interactions amongst functional groups, possibly due to nutrient limitation or competitive exclusion, with potential implications on soil carbon stocks. These findings are important in light of the environmental changes predicted for the Arctic.
Effects of transformation of inefficient Camellia oleifera plantation on soil quality and fungal community(supplementary)
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Figure 4 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 4 Heatmap using Pearson's correlation coefficient between the OTUs generated from the ITS2 and LSU D1-D2 metabarcodes and the analysed beetle species and forest types. Rectangles indicate the strength of association between an OTU and beetle/forest (strongly negative, grey, to strongly positive, red). Fungal OTUs (on the horizontal axis) were classified to genus or species level where possible; they are shown in random order and cannot be linked taxonomically between both markers.
Supplementary material 1 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure S1. Length distribution of the ITS (grey) and LSU (orange) OTUs
Figure 7 from: Ceballos-Escalera A, Richards J, Arias MB, Inward DJG, Vogler AP (2022) Metabarcoding of insect-associated fungal communities: a comparison of internal transcribed spacer (ITS) and large-subunit (LSU) rRNA markers. MycoKeys 88: 1-33. https://doi.org/10.3897/mycokeys.88.77106
Figure 7 Closed reference clustering of OTUs and phylogenetic trees at different thresholds A results from the closed reference clustering of OTUs at each clustering threshold against composite LSU/ITS2 reference sequences. LSU matches in green, ITS2 matches in blue, linked matches (for which both an ITS2 and LSUOTU were matched to a reference sequence of the same species) in yellow. Underlined taxa indicate new matches at each clustering threshold B phylogenetic tree of LSUOTUs under increasingly stringent clustering thresholds, with arrows marking newly added taxa as threshold values are increased.
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