Rainfall homogenizes while fruiting increases diversity of spore deposition in Mediterranean conditions

Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada

In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015-2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.

A case study on the application of spore sampling for the monitoring of macrofungi

Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.

Microstrobilinia castrans, a new genus and species of the Sclerotiniaceae parasitizing pollen cones of Picea spp

The fungal pathogens of spruce are well known in Europe and elsewhere. Therefore, it was surprising to discover a new fungal species and genus in Central Europe that attacks the pollen cones of three spruce species. The new ascomycete forms apothecia on stromatized pollen cones of Norway spruce (Picea abies) and Serbian spruce (Picea omorika) in mountain areas and on West Himalayan spruce (Picea smithiana) planted in urban lowland regions of Switzerland, Germany, and Italy. It was also detected in France, based on metabarcode sequences deposited in the GlobalFungi database. Its sudden appearance and the different origins of the host trees in Europe and Asia leave the origin of the fungus unclear. The new fungus might be a neomycete for Europe. A phylogenetic analysis using SSU, LSU, ITS, RPB2, and TEF1 sequences classified the fungus as a member of Sclerotiniaceae (Helotiales, Leotiomycetes). However, it differs morphologically from the other genera of this family in having an ascus without apical apparatus containing four mainly citriform spores with 16 nuclei each. Furthermore, it is the only known cup fungus that parasitizes pollen cones of conifers by stromatizing their tissue and infecting pollen grains. The fungus does not seem to cause major damage to the spruce populations, as only a few pollen cones per tree are affected. All this leads us to describe the newly discovered fungus as the new species and new genus Microstrobilinia castrans, the fungus that castrates pollen cones of spruce.

Farm-scale differentiation of active microbial colonizers

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce

The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.

Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding

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.

Vegetation type determines spore deposition within a forest-agricultural mosaic landscape

Predicting fungal community assembly is partly limited by our understanding of the factors driving the composition of deposited spores. We studied the relative contribution of vegetation, geographical distance, seasonality and weather to fungal spore deposition across three vegetation types. Active and passive spore traps were established in agricultural fields, deciduous forests and coniferous forests across a geographic gradient of ∼600 km. Active traps captured the spore community suspended in air, reflecting the potential deposition, whereas passive traps reflected realized deposition. Fungal species were identified by metabarcoding of the ITS2 region. The composition of spore communities captured by passive traps differed more between vegetation types than across regions separated by >100 km, indicating that vegetation type was the strongest driver of composition of deposited spores. By contrast, vegetation contributed less to potential deposition, which followed a seasonal pattern. Within the same site, the spore communities captured by active traps differed from those captured by passive traps. Realized deposition tended to be dominated by spores of species related to vegetation. Temperature was negatively correlated with the fungal species richness of both potential and realized deposition. Our results indicate that vegetation may be able to maintain similar fungal communities across distances, and likely be the driving factor of fungal spore deposition at landscape level.