Total Fungal Richness Research Articles

Wild ungulate effects on soil fungal diversity in Mediterranean mixed forests

The effect of wild ungulate density on ecosystems varies according to different factors: climate and physiography conditions, forest type, management history, and herbivore identity. In this study, we evaluated the effect of historically high densities of red deer (Cervus elaphus L.) on the soil fungal communities in Mediterranean ecosystems using 30 paired plots, open on the one hand and exclosure plots on the other one. Plots were established at the end of 2020 in a perimeter-fenced hunting estate of 6600 ha in Toledo, Spain. Three months after plots were established, we analysed fungal communities in 60 soil samples using Illumina 250-bp paired-end sequencing. We estimated changes in total fungal richness and in the richness of trophic groups through Linear Mixed Effects models using fenced/unfenced type and deer habitat use as fixed variables and the location of the plots and the main tree host species as random variables. Fungal composition was analysed using non-metric multidimensional scaling and permutational multivariate ANOVA; edaphic characteristics were incorporated to explain differences. Soil fungal communities were not differentially affected by excluding ungulates for three months. Areas with high deer densities had a richer saprotrophic community and where lowland environments were dominated by the main tree hosts Quercus faginea and Quercus ilex. Arbutus unedo was found in mountain areas where there was less herbivore pressure, a greater richness of ectomycorrhizal and lichenized fungi and soils positively associated to nitrogen, phosphorus, potassium and organic matter levels.

Microplastic fibres affect soil fungal communities depending on drought conditions with consequences for ecosystem functions.

Microplastics affect soil functions depending on drought conditions. However, how their combined effect influences soil fungi and their linkages with ecosystem functions is still unknown. To address this, we used rhizosphere soil from a previous experiment in which we employed microplastic fibres addition and drought in a factorial design, and evaluated their effects on soil fungal communities. Microplastics decreased soil fungal richness under well-watered conditions, likely linked to microplastics leaching toxic substances into the soil, and microplastic effects on root fineness. Under drought, by contrast, microplastics increased pathogen and total fungal richness, likely related to microplastic positive effects on soil properties, such as water holding capacity, porosity or aggregation. Soil fungal richness was the attribute most affected by microplastics and drought. Microplastics altered the relationships between soil fungi and ecosystem functions to the point that many of them flipped from positive to negative or disappeared. The combined effect of microplastics and drought on fungal richness mitigated their individual negative effect (antagonism), suggesting that changes in soil water conditions may alter the action mode of microplastics in soil. Microplastic leaching of harmful substances can be mitigated under drought, while the improvement of soil properties by microplastics may alleviate such drought conditions.

Dynamic response of root-associated fungal community structure to nitrogen and phosphorus additions in a subtropical forest

The impacts of nitrogen (N) and phosphorus (P) additions on root-associated fungi (RAF) of mixed roots in forest soils remain poorly understood. We investigated how RAF communities respond to N and P inputs in a subtropical montane forest using a time-series sampling approach. Our results showed that sampling time had a significant effect on total fungal richness, while the N addition had significant impacts on symbiotrophic rather than saprotrophic fungal richness. RAF community composition was strongly influenced by P addition treatments regardless of sampling time. Furthermore, we found that RAF community structure was mainly affected by soil NO3–-N, C/N and N/P ratios. This influence could be ascribed to the direct control of fungal activities and the indirect effects of fertilization on soil properties. Together, our findings highlight the importance of considering temporal variation in RAF responses to fertilization for a more comprehensive understanding of fungal community dynamics.

Soil fungal communities contribute to the positive diversity–productivity relationship of tree communities under contrasting water availability

Abstract Plant diversity has often been linked to increased productivity; however, this apparent diversity–productivity relationship may rely on intertrophic interactions such as those between plants and soil microbes. Soil fungi can create complementarity between plant species via altered plant resource partitioning, facilitation via fungal networks or biotic feedbacks, thereby promoting plant diversity–productivity relationships. Furthermore, these relationships are likely to be context dependent in response to resource availability. We used a biodiversity–ecosystem function experiment with trees exposed to high and low water availability treatments to determine the contribution of soil fungal communities to the diversity–productivity relationship in tree communities. We used amplicon sequencing of soil fungi to assess fungal richness, community composition and richness of functional guilds. We then applied structural equation modelling to determine relationships between tree diversity, fungal communities and tree productivity and the role of water availability in these relationships. Tree species richness and functional diversity both increased above‐ground tree productivity and influenced soil fungal community composition. Fungal community composition had a direct impact on tree productivity and enhanced net diversity effects on productivity. Therefore, fungal communities mediated a positive, indirect effect of tree richness on productivity. While total fungal richness was not associated with tree diversity, pathogen richness decreased and mycorrhizal richness increased with tree richness. Pathogen and mycorrhizal richness had either no impact or a weak negative effect on productivity. Tree species traits strongly affected fungal communities and these changes promoted productivity. Finally, water availability greatly influenced fungal communities but did not interact with tree diversity to affect productivity; indicating possible resilience of tree communities to altered precipitation regimes and associated changes in fungal communities. Synthesis: Our study highlights the crucial role that fungal communities play in shaping the relationship between tree diversity, traits and productivity, and resilience to altered water availability.

Prescribed burning in spring or autumn did not affect the soil fungal community in Mediterranean Pinus nigra natural forests

In the context of global change, wildfires are not only a threat but are also increasing in their severity in forest ecosystems worldwide, affecting and modifying vegetation, wildlife, and fungal dynamics. Mediterranean ecosystems are frequently affected by fire and prescribed burning is being increasingly used as a tool to reduce the risk and severity of wildfires. Although some of the effects of prescribed burning have been studied, the best moment to perform a prescribed burn to reduce the impact of fire on fungal communities has not been fully investigated. In this study, we analysed the effect of prescribed burning in two different seasons (spring and autumn) on soil fungi associated with naturalPinusnigraforests. Four years after prescribed burning was applied, our analyses showed that the total fungal richness and the composition of fungal communities in spring-burned, autumn-burned, and unburned control plots did not differ significantly. However, analyses of specific phyla and functional trophic groups did reveal some significant differences between spring- or autumn-burned plots and unburned control plots. Valuable edible fungi, which were not affected by the prescribed burning, were also found in the study area. Thus, our results suggest that prescribed burning is not only an interesting tool that could be used to reduce the risk of wildfire but also is compatible with the conservation of fungal communities, and could even promote specific valuable edible species, generating complementary incomes for the rural population. Although further studies are needed, our analyses suggest that the season (spring or autumn) in which prescribed burning is performed does not affect fungal conservation and, therefore, does not need to be one of the factors taken into consideration when selecting the most appropriate time to perform a prescribed burning.

Aboveground and Belowground Plant Traits Explain Latitudinal Patterns in Topsoil Fungal Communities From Tropical to Cold Temperate Forests.

Soil fungi predominate the forest topsoil microbial biomass and participate in biogeochemical cycling as decomposers, symbionts, and pathogens. They are intimately associated with plants but their interactions with aboveground and belowground plant traits are unclear. Here, we evaluated soil fungal communities and their relationships with leaf and root traits in nine forest ecosystems ranging from tropical to cold temperate along a 3,700-km transect in eastern China. Basidiomycota was the most abundant phylum, followed by Ascomycota, Zygomycota, Glomeromycota, and Chytridiomycota. There was no latitudinal trend in total, saprotrophic, and pathotrophic fungal richness. However, ectomycorrhizal fungal abundance and richness increased with latitude significantly and reached maxima in temperate forests. Saprotrophic and pathotrophic fungi were most abundant in tropical and subtropical forests and their abundance decreased with latitude. Spatial and climatic factors, soil properties, and plant traits collectively explained 45% of the variance in soil fungal richness. Specific root length and root biomass had the greatest direct effects on total fungal richness. Specific root length was the key determinant of saprotrophic and pathotrophic fungal richness while root phosphorus content was the main biotic factor determining ectomycorrhizal fungal richness. In contrast, spatial and climatic features, soil properties, total leaf nitrogen and phosphorus, specific root length, and root biomass collectively explained >60% of the variance in fungal community composition. Soil fungal richness and composition are strongly controlled by both aboveground and belowground plant traits. The findings of this study provide new evidence that plant traits predict soil fungal diversity distribution at the continental scale.

Prolonged impacts of past agriculture and ungulate overabundance on soil fungal communities in restored forests

AbstractSoil fungi can help improve ecosystem restoration, yet our understanding of how they reassemble in degraded land is limited. Here, using DNA metabarcoding, we studied the fungal community structure in reforested sites following agricultural abandonment and ungulate overabundance. Two treatments, namely “reforestation using different numbers of tree species” and “deer exclusion,” have been applied for multiple decades in the study sites. We found that local fungal richness (alpha diversity) and total fungal richness (gamma diversity) were 1.9–2.9 and 1.3–1.9 times greater, respectively, in reforested stands than in natural forests. These results were regardless of the number of tree species planted in the reforested stands. Conversely, reforested stands had a spatially homogenized community structure with relatively lower degrees of compositional dissimilarity among sites within each stand (beta diversity). These findings were attributable to lower environmental heterogeneity, stronger dispersal limitation, and a comparatively shorter time since the onset of community assembly in reforested stands. Deer exclosures had no detectable effect on fungal community structure. Overall, the agricultural legacy in fungal community structure appears to have persisted for decades, even under proactive restoration of aboveground vegetation. Direct human intervention belowground may therefore be necessary for the recovery of soil biota once altered.

Mulching has negative impact on fungal and plant diversity in Slovak oligotrophic grasslands

Mulching (cutting of vegetation without removal of clippings) is used as a low-cost method for maintaining remote or abandoned grasslands in Slovakia. The likely consequence of mulching is seasonal nutrient enrichment resulting from decomposition of plant litter by saprotrophic organisms. The potential changes in biodiversity of the ecosystem caused by long-term application of mulching are to date only very poorly understood. In order to examine the impact of mulching on soil mycobiota, we compared six different grassland management regimes applied over nine years on a sub-montane oligotrophic Nardus pasture in the Central Slovakia. The diversity of soil fungi was assessed using DNA metabarcoding of the ITS2 regions of the nrRNA locus performed by Illumina MiSeq.We focused on a particular group of macrofungi which is characteristic of traditionally managed and undisturbed European grasslands, and which are often the dominant soil fungi in these habitats. These are collectively known as CHEGD fungi (the acronym of the constituent taxa: Clavariaceae, Hygrophoraceae, Entolomataceae, Geoglossaceae and Dermoloma). We compared the relative abundance and diversity of CHEGD fungi with the total fungal and plant diversity. CHEGD fungi were dominant across all management treatments. Although there were no statistical effects of treatments on total fungal richness and diversity, CHEGD fungi and vascular plants diversity and richness were lower on plots where mulching or no management were imposed, suggesting that such management regimes would have a negative impact on grassland fungi. However, no single treatment covered the total CHEGD diversity of the study, indicating that the localized use of mulching in addition to traditional managements can enhance overall diversity of grasslands in the area. Our results also suggest that the impact of mulching depends on the season when the grassland is mulched and it might be reduced by combination with other management treatments. The high relative abundance and sensitivity of CHEDG fungi in oligotrophic grasslands to management treatments makes them excellent indicators of grassland natural quality and is consistent with the ecological importance of this fungal group.

Primer and Database Choice Affect Fungal Functional but Not Biological Diversity Findings in a National Soil Survey

The internal transcribed spacer (ITS) region is the accepted DNA barcode of fungi. Its use has led to a step-change in the assessment and characterisation of fungal communities from environmental samples by precluding the need to isolate, culture, and identify individuals. However, certain functionally important groups, such as the arbuscular mycorrhizas (Glomeromycetes), are better characterised by alternative markers such as the 18S rRNA region. Previous use of an ITS primer set in a nationwide metabarcoding soil biodiversity survey revealed that fungal richness declined along a gradient of productivity and management intensity. Here, we wanted to discern whether this trend was also present in data generated from universal 18S primers. Furthermore, we wanted to extend this comparison to include measures of functional diversity and establish trends with soil types and soil organic matter (SOM) content. Over the 413 individual sites examined (arable, grassland, woodland, moorland, heathland), we found congruent trends of total fungal richness and β-diversity across land uses, SOM class and soil type with both ITS and 18S primer sets. A total of 24 fungal classes were shared between datasets, in addition to 15 unique to ITS1 and 12 unique to 18S. However, using FUNGUILD, divergent trends of functional group richness became apparent, especially for symbiotrophic fungi, likely driven by an increased detection rate of Glomeromycetes in the 18S dataset. The disparate trends were also apparent when richness and β-diversity were compared to soil properties. Additionally, we found SOM class to be a more meaningful variable than soil type biodiversity analyses because organic matter was calculated for each sample whereas soil type was assigned from a national soil map. We advocate that a combination of fungal primers should be used in large-scale soil biodiversity surveys to capture important groups that can be underrepresented by universal barcodes. Utilising such an approach can prevent the oversight of ubiquitous but poorly described species as well as critically important functional groups.

Coarse woody debris and wood-colonizing fungi differences between a reserve stand and a managed forest in the Taborz region of Poland

The aim of this research was to evaluate the amount of woody debris (m3/ha) on the forest floor and the associated wood-colonizing fungi. The study was performed in the Taborz region, known for its Scots pine provenance experiments, against the background of a recently launched Polish legislation to protect the biodiversity on the forest floor in managed (harvested) stands. We investigated a managed stand (136-years-old) and the reserve stand ‘Sosna Taborska’ (261-years-old). In the reserve stand, the mean volume of woody debris was six times higher than in the managed forests, i.e. 65 versus 11 m3/ha. In addition, in the reserve stand, the number of fungi taxa colonizing the dead wood was larger than in the managed stands, with a higher number of fruitbodies. Total fungal richness was higher in the reserve than in the managed stand, i.e. 28 versus 12 species. The dominant taxa at both sites were Fomitopsis pinicola and Fomes fomentarius, although some taxa were only found in the reserve (e.g., Stereum hirsutum). The volume of woody debris as well as the diversity of fungi in the managed stand were lower than in the reserve, albeit greater than in other Scots pine stands in Poland. These results testify to the gains in biodiversity yielded by the management conservation management approach at the reserve stand.

Long-term warming alters richness and composition of taxonomic and functional groups of arctic fungi.

Fungi, including symbionts, pathogens and decomposers, play crucial roles in community dynamics and nutrient cycling in terrestrial ecosystems. Despite their ecological importance, the response of most arctic fungi to climate warming is unknown, so are their potential roles in driving the observed and predicted changes in tundra communities. We carried out deep DNA sequencing of soil samples to study the long-term effects of experimental warming on fungal communities in dry heath and moist tussock tundra in Arctic Alaska. The data presented here indicate that fungal community composition responds strongly to warming in the moist tundra, but not in the dry tundra. While total fungal richness was not significantly affected by warming, there were clear correlations among operational taxonomic unit richness of various ecological and taxonomic groups and long-term warming. Richness of ectomycorrhizal, ericoid mycorrhizal and lichenized fungi generally decreased with warming, while richness of saprotrophic, plant and animal pathogenic, and root endophytic fungi tended to increase in the warmed plots. More importantly, various taxa within these functional guilds followed opposing trends that highlight the importance of species-specific responses to warming. We recommend that species-level ecological differences be taken into account in climate change and nutrient cycling studies that involve arctic fungi.

The contribution of DNA metabarcoding to fungal conservation: diversity assessment, habitat partitioning and mapping red-listed fungi in protected coastal Salix repens communities in the Netherlands.

Western European coastal sand dunes are highly important for nature conservation. Communities of the creeping willow (Salix repens) represent one of the most characteristic and diverse vegetation types in the dunes. We report here the results of the first kingdom-wide fungal diversity assessment in S. repens coastal dune vegetation. We carried out massively parallel pyrosequencing of ITS rDNA from soil samples taken at ten sites in an extended area of joined nature reserves located along the North Sea coast of the Netherlands, representing habitats with varying soil pH and moisture levels. Fungal communities in Salix repens beds are highly diverse and we detected 1211 non-singleton fungal 97% sequence similarity OTUs after analyzing 688,434 ITS2 rDNA sequences. Our comparison along a north-south transect indicated strong correlation between soil pH and fungal community composition. The total fungal richness and the number OTUs of most fungal taxonomic groups negatively correlated with higher soil pH, with some exceptions. With regard to ecological groups, dark-septate endophytic fungi were more diverse in acidic soils, ectomycorrhizal fungi were represented by more OTUs in calcareous sites, while detected arbuscular mycorrhizal genera fungi showed opposing trends regarding pH. Furthermore, we detected numerous red listed species in our samples often from previously unknown locations, indicating that some of the fungal species currently considered rare may be more abundant in Dutch S. repens communities than previously thought.