The ADnet Bayesian belief network for alder decline: Integrating empirical data and expert knowledge.

The globalization in plant material trading has caused the emergence of invasive pests in many ecosystems, such as the alder pathogen Phytophthora ×alni in European riparian forests. Due to the ecological importance of alder to the functioning of rivers and the increasing incidence of P. ×alni-induced alder decline, effective and accessible decision tools are required to help managers and stakeholders control the disease. This study proposes a Bayesian belief network methodology to integrate diverse information on the factors affecting the survival and infection ability of P. ×alni in riparian habitats to help predict and manage disease incidence. The resulting Alder Decline Network (ADnet) management tool integrates information about alder decline from scientific literature, expert knowledge and empirical data. Expert knowledge was gathered through elicitation techniques that included 19 experts from 12 institutions and 8 countries. An original dataset was created covering 1189 European locations, from which P. ×alni occurrence was modeled based on bioclimatic variables. ADnet uncertainty was evaluated through its sensitivity to changes in states and three scenario analyses. The ADnet tool indicated that mild temperatures and high precipitation are key factors favoring pathogen survival. Flood timing, water velocity, and soil type have the strongest influence on disease incidence. ADnet can support ecosystem management decisions and knowledge transfer to address P. ×alni-induced alder decline at local or regional levels across Europe. Management actions such as avoiding the planting of potentially infected trees or removing man-made structures that increase the flooding period in disease-affected sites could decrease the incidence of alder disease in riparian forests and limit its spread. The coverage of the ADnet tool can be expanded by updating data on the pathogen's occurrence, particularly from its distributional limits. Research on the role of genetic variability in alder susceptibility and pathogen virulence may also help improve future ADnet versions.

Phylogeography, origin and population structure of the self-fertile emerging plant pathogen Phytophthora pseudosyringae.

Phytophthora pseudosyringae is a self-fertile pathogen of woody plants, particularly associated with tree species from the genera Fagus, Notholithocarpus, Nothofagus and Quercus, which is found across Europe and in parts of North America and Chile. It can behave as a soil pathogen infecting roots and the stem collar region, as well as an aerial pathogen infecting leaves, twigs and stem barks, causing particular damage in the United Kingdom and western North America. The population structure, migration and potential outcrossing of a worldwide collection of isolates were investigated using genotyping-by-sequencing. Coalescent-based migration analysis revealed that the North American population originated from Europe. Historical gene flow has occurred between the continents in both directions to some extent, yet contemporary migration is overwhelmingly from Europe to North America. Two broad population clusters dominate the global population of the pathogen, with a subgroup derived from one of the main clusters found only in western North America. Index of association and network analyses indicate an influential level of outcrossing has occurred in this preferentially inbreeding, homothallic oomycete. Outcrossing between the two main population clusters has created distinct subgroups of admixed individuals that are, however, less common than the main population clusters. Differences in life history traits between the two main population clusters should be further investigated together with virulence and host range tests to evaluate the risk each population poses to natural environments worldwide.

Climate acts as an environmental filter to plant pathogens.

Climate shapes the distribution of plant-associated microbes such as mycorrhizal and endophytic fungi. However, the role of climate in plant pathogen community assembly is less understood. Here, we explored the role of climate in the assembly of Phytophthora communities at >250 sites along a latitudinal gradient from Spain to northern Sweden and an altitudinal gradient from the Spanish Pyrenees to lowland areas. Communities were detected by ITS sequencing of river filtrates. Mediation analysis supported the role of climate in the biogeography of Phytophthora and ruled out other environmental factors such as geography or tree diversity. Comparisons of functional and species diversity showed that environmental filtering dominated over competitive exclusion in Europe. Temperature and precipitation acted as environmental filters at different extremes of the gradients. In northern regions, winter temperatures acted as an environmental filter on Phytophthora community assembly, selecting species adapted to survive low minimum temperatures. In southern latitudes, a hot dry climate was the main environmental filter, resulting in communities dominated by drought-tolerant Phytophthora species with thick oospore walls, a high optimum temperature for growth, and a high maximum temperature limit for growth. By taking a community ecology approach, we show that the establishment of Phytophthora plant pathogens in Europe is mainly restricted by cold temperatures.

Oomycete Soil Diversity Associated with Betula and Alnus in Forests and Urban Settings in the Nordic-Baltic Region.

This study aimed to determine the differences and drivers of oomycete diversity and community composition in alder- and birch-dominated park and natural forest soils of the Fennoscandian and Baltic countries of Estonia, Finland, Lithuania, Norway, and Sweden. For this, we sequenced libraries of PCR products generated from the DNA of 111 soil samples collected across a climate gradient using oomycete-specific primers on a PacBio high-throughput sequencing platform. We found that oomycete communities are most affected by temperature seasonality, annual mean temperature, and mean temperature of the warmest quarter. Differences in composition were partly explained by the higher diversity of Saprolegniales in Sweden and Norway, as both total oomycete and Saprolegniales richness decreased significantly at higher longitudes, potentially indicating the preference of this group of oomycetes for a more temperate maritime climate. None of the evaluated climatic variables significantly affected the richness of Pythiales or Peronosporales. Interestingly, the relative abundance and richness of Pythiales was higher at urban sites compared to forest sites, whereas the opposite was true for Saprolegniales. Additionally, this is the first report of Phytophthora gallica and P. plurivora in Estonia. Our results indicate that the composition of oomycetes in soils is strongly influenced by climatic factors, and, therefore, changes in climate conditions associated with global warming may have the potential to significantly alter the distribution range of these microbes, which comprise many important pathogens of plants.

Hot Water Treatment Causes Lasting Alteration to the Grapevine (Vitis vinifera L.) Mycobiome and Reduces Pathogenic Species Causing Grapevine Trunk Diseases.

The effective management of grapevine trunk diseases (GTDs) is an ongoing challenge. Hot water treatment (HWT) is an environmentally friendly and economically viable option; however, the short-term effects of HWT on grapevine (Vitis vinifera L.) health and production are not fully understood. The aim of this study was to compare the effects of HWT on plant growth and fungal community structure in nursery stock until plants were completely established in the field. We assessed eleven graft and three rootstock varieties from four local nurseries in a region of Catalonia (NE Spain) where GTDs are a serious threat. After treatment, the plants were left to grow under field conditions for two growing seasons. Metabarcoding of the ITS region was used to study the mycobiomes of plant graft unions and root collars. We also assessed the influence of plant physiological indicators in community composition. Hot water treatment caused lasting changes in GTD communities in both the root collar and graft union that were not always characterized as a reduction of GTD-related fungi. However, HWT reduced the relative abundance of some serious GTD-associated pathogens such as Cadophora luteo-olivacea in graft tissues, and Phaeomoniella chlamydospora and Neofusicoccum parvum in the root collar. Treatment had the greatest influence on the total and GTD-related fungal communities of Chardonnay and Xarel·lo, respectively. Total community variation was driven by treatment and nursery in rootstocks, whereas HWT most significantly affected the GTD community composition in R-110 rootstock. In conclusion, changes in fungal abundance were species-specific and mostly dependent on the plant tissue type; however, HWT did reduce plant biomass accumulation in the short-term.

Interaction of drought- and pathogen-induced mortality in Norway spruce and Scots pine.

Pathogenic diseases frequently occur in drought-stressed trees. However, their contribution to the process of drought-induced mortality is poorly understood. We combined drought and stem inoculation treatments to study the physiological processes leading to drought-induced mortality in Norway spruce (Picea abies) and Scots pine (Pinus sylvestris) saplings infected with Heterobasidion annosum s.s. We analysed the saplings' water status, gas exchange, nonstructural carbohydrates (NSCs) and defence responses, and how they related to mortality. Saplings were followed for two growing seasons, including an artificially induced 3-month dormancy period. The combined drought and pathogen treatment significantly increased spruce mortality; however, no interaction between these stressors was observed in pine, although individually each stressor caused mortality. Our results suggest that pathogen infection decreased carbon reserves in spruce, reducing the capacity of saplings to cope with drought, resulting in increased mortality rates. Defoliation, relative water content and the starch concentration of needles were predictors of mortality in both species under drought and pathogen infection. Infection and drought stress create conflicting needs for carbon to compartmentalize the pathogen and to avoid turgor loss, respectively. Heterobasidion annosum reduces the functional sapwood area and shifts NSC allocation patterns, reducing the capacity of trees to cope with drought.

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.

Variation in Fungal Community in Grapevine (Vitis vinifera) Nursery Stock Depends on Nursery, Variety and Rootstock.

Grapevine trunk diseases (GTDs) are caused by cryptic complexes of fungal pathogens and have become a growing problem for new grapevine (Vitis vinifera) plantations. We studied the role of the nursery, variety, and rootstock in the composition of the fungal communities in root collars and graft unions of planting material in Catalonia (NE Spain). We compared necrosis and fungal communities in graft unions and root collars at harvest, and then after three months of cold storage. We evaluated combinations of eleven red and five white varieties with four common rootstocks coming from six nurseries. Fungal communities were characterized by isolation and metabarcoding of the ITS2 region. Our data suggests that nursery followed by rootstock and variety had significant effects on necrosis and fungal community structure in graft and root tissues. Within the plant, we found large differences in terms fungal community distribution between graft and root tissues. Graft unions housed a significantly higher relative abundance of GTD-related Operational Taxonomic Units (OTUs) than root collars. More severe necrosis was correlated with a lower relative abundance of GTD-related OTUs based on isolation and metabarcoding analyses. Our results suggest that nurseries and therefore their plant production practices play a major role in determining the fungal and GTD-related fungal community in grapevine plants sold for planting. GTD variation across rootstocks and varieties could be explored as a venue for minimizing pathogen load in young plantations.

Halophytophthora fluviatilis Pathogenicity and Distribution along a Mediterranean-Subalpine Gradient.

Halophytophthora species have been traditionally regarded as brackish water oomycetes; however, recent reports in inland freshwater call for a better understanding of their ecology and possible pathogenicity. We studied the distribution of Halophytophthora fluviatilis in 117 forest streams by metabarcoding river filtrates taken in spring and autumn and by direct isolation from floating leaves. Pathogenicity on six Fagaceae species and Alnus glutinosa was assessed by stem inoculations. The distribution of H. fluviatilis was correlated with high mean annual temperatures (>93.5% of reports in Ta > 12.2 °C) and low precipitation records. H. fluviatilis was therefore widely distributed in forest streams in a warm-dry climate, but it was mostly absent in subalpine streams. H. fluviatilis was primarily detected in autumn with few findings in spring (28.4% vs. 2.7% of streams). H. fluviatilis was able to cause small lesions on some tree species such as Quercus pubescens, Q. suber and A. glutinosa. Our findings suggest that H. fluviatilis may be adapted to warm and dry conditions, and that it does not pose a significant threat to the most common Mediterranean broadleaved trees.

Insect defoliation is linked to a decrease in soil ectomycorrhizal biomass and shifts in needle endophytic communities.

Insect outbreaks of increasing frequency and severity in forests are predicted due to climate change. Insect herbivory is known to promote physiological changes in forest trees. However, little is known about whether these plant phenotypic adjustments have cascading effects on tree microbial symbionts such as fungi in roots and foliage. We studied the impact of defoliation by the pine processionary moth in two infested Pinus nigra forests through a multilevel sampling of defoliated and non-defoliated trees. We measured tree growth, nutritional status and carbon allocation to chemical defenses. Simultaneously, we analysed the putative impact of defoliation on the needle endophytes and on the soil fungal communities. Higher concentrations of chemical defenses were found in defoliated trees, likely as a response to defoliation; however, no differences in non-structural carbohydrate reserves were found. In parallel to the reductions in tree growth and changes in chemical defenses, we observed shifts in the composition of needle endophytic and soil fungal communities in defoliated trees. Defoliated trees consistently corresponded with a lower biomass of ectomycorrhizal fungi in both sites, and a higher alpha diversity and greater relative abundance of belowground saprotrophs and pathogens. However, ectomycorrhizal alpha diversity was similar between non-defoliated and defoliated trees. Specific needle endophytes in old needles were strongly associated with non-defoliated trees. The potential role of these endophytic fungi in pine resistance should be further investigated. Our study suggests that lower biomass of ectomycorrhizal fungi in defoliated trees might slow down tree recovery since fungal shifts might affect tree-mycorrhizal feedbacks and can potentially influence carbon and nitrogen cycling in forest soils.

Patterns of Genetic Diversification in the Invasive Hybrid Plant Pathogen Phytophthora × alni and Its Parental Species P. uniformis.

In pathogenic fungi and oomycetes, interspecific hybridization may lead to the formation of new species having a greater impact on natural ecosystems than the parental species. From the early 1990s, a severe alder (Alnus spp.) decline due to an unknown Phytophthora species was observed in several European countries. Genetic analyses revealed that the disease was caused by the triploid hybrid P. × alni, which originated in Europe from the hybridization of P. uniformis and P. × multiformis. Here, we investigated the population structure of P. × alni (158 isolates) and P. uniformis (85 isolates) in several European countries using microsatellite markers. Our analyses confirmed the genetic structure previously observed in other European populations, with P. uniformis populations consisting of at most two multilocus genotypes (MLGs) and P. × alni populations dominated by MLG Pxa-1. The genetic structure of P. × alni populations in the Czech Republic, Hungary and Sweden seemed to reflect the physical isolation of river systems. Most rare P. × alni MLGs showed a loss of heterozygosity (LOH) at one or a few microsatellite loci compared with other MLGs. This LOH may allow a stabilization within the P. × alni genome or a rapid adaptation to stress situations. Alternatively, alleles may be lost because of random genetic drift in small, isolated populations, with no effect on fitness of P. × alni. Additional studies would be necessary to confirm these patterns of population diversification and to better understand the factors driving it.

Functional Ecology of Forest Disease.

Global change is pressing forest pathologists to solve increasingly complex problems. We argue that understanding interactive effects between forest pathogens and global warming, globalization, and land-use changes may benefit from a functional ecology mindset. Traits can be more informative about ecological functions than species inventories and may deliver a more mechanistic description of forest disease. Myriad microbes with pathogenic potential interact with forest ecosystems at different organizational levels. Elucidation of functional traits may enable the microbial complexity to be reduced into manageable categories with predictive power. In this review, we propose guidelines that allow the research community to develop a functional forest pathology approach. We suggest new angles by which functional questions can be used to resolve burning issues on tree disease. Building up functional databases for pathogenicity is key to implementing these approaches.

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.

The invasive forest pathogen Hymenoscyphus fraxineus boosts mortality and triggers niche replacement of European ash (Fraxinus excelsior).

Determining the impacts of invasive pathogens on tree mortality and growth is a difficult task, in particular in the case of species occurring naturally at low frequencies in mixed stands. In this study, we quantify such effects by comparing national forest inventory data collected before and after pathogen invasion. In Norway, Fraxinus excelsior is a minor species representing less than 1% of the trees in the forests and being attacked by the invasive pathogen Hymenoscyphus fraxineus since 2006. By studying deviations between inventories, we estimated a 74% higher-than-expected average ash mortality and a 13% slower-than-expected growth of the surviving ash trees, indicating a lack of compensation by the remaining ash. We could confidently assign mortality and growth losses to ash dieback as no mortality or growth shifts were observed for co-occurring tree species in the same plots. The mortality comparisons also show regional patterns with higher mortality in areas with the longest disease history in Norway. Considering that ash is currently mostly growing in mixed forests and that no signs of compensation were observed by the surviving ash trees, a significant habitat loss and niche replacement could be anticipated in the mid-term.

Genetic Variation Explains Changes in Susceptibility in a Naïve Host Against an Invasive Forest Pathogen: The Case of Alder and the Phytophthora alni Complex.

Predicting whether naïve tree populations have the potential to adapt to exotic pathogens is necessary owing to the increasing rate of invasions. Adaptation may occur as a result of natural selection when heritable variation in terms of susceptibility exists in the naïve population. We searched for signs of selection on black alder (Alnus glutinosa) stands growing on riverbanks invaded by two pathogens differing in aggressiveness, namely, Phytophthora uniformis (PU) and Phytophthora × alni (PA). We compared the survival and heritability measures from 72 families originating from six invaded and uninvaded (naïve) sites by performing in vitro inoculations. The results from the inoculations were used to assess the relative contribution of host genetic variation on natural selection. We found putative signs of natural selection on alder exerted by PU but not by PA. For PU, we found a higher survival in families originating from invaded sites compared with uninvaded sites. The narrow sense heritability of susceptibility to PU of uninvaded populations was significantly higher than to PA. Simulated data supported the role of heritable genetic variation on natural selection and discarded a high aggressiveness of PA decreasing the transmission rate as an alternative hypothesis for a slow natural selection. Our findings expand on previous attempts of using heritability as a predictor for the likelihood of natural adaptation of naïve tree populations to invasive pathogens. Measures of genetic variation can be useful for risk assessment purposes or when managing Phytophthora invasions.

Invasive forest pathogens in Europe: Cross-country variation in public awareness but consistency in policy acceptability.

Political action can reduce introductions of diseases caused by invasive forest pathogens (IPs) and public support is important for effective prevention. The public's awareness of IP problems and the acceptability of policies aiming to combat these pathogens were surveyed in nine European countries (N = 3469). Although awareness of specific diseases (e.g., ash dieback) varied, problem awareness and policy acceptability were similar across countries. The public was positive towards policies for informational measures and stricter standards for plant production, but less positive towards restricting public access to protected areas. Multilevel models, including individual and country level variables, revealed that media exposure was positively associated with awareness of IP problems, and strengthened the link between problem awareness and policy acceptability. Results suggest that learning about IPs through the media and recognizing the associated problems increase policy acceptability. Overall, the study elaborates on the anthropogenic dimension of diseases caused by IPs.

Drought and Phytophthora Are Associated With the Decline of Oak Species in Southern Italy.

Forest decline induced by climate change is a global phenomenon that affects many tree species, mainly in drought-prone areas as the Mediterranean region. In southern Italy, several oak species have shown decline symptoms and elevated mortality since the 2000s due to drought stress. However, it remains to be answered whether decline occurred alone or whether a pathogen was also involved. To this aim, we compared two coexisting oak species in a forest located in southern Italy which are assumed to be less (Quercus cerris) and more tolerant to drought (Quercus pubescens). We sampled fifteen couples of neighboring declining (D) and non-declining (ND) trees of both species. Wood cores were taken from all trees to perform dendrochronological analyses to detect the decline onset and link it to potential climatic drivers. Carbon isotope ratios (d13C) were analyzed in wood of the two vigor classes to compare their water-use efficiency. Phytophthora presence was also assessed in soil samples from ten D-ND couples of trees per species. The oak species most affected by drought-induced decline in terms of leaf shedding and mortality was Q. cerris, i.e., the least tolerant to drought. In both species, the D trees showed a reduced growth rate compared with ND trees from 2000 onward when drought and warming intensified. Q. pubescens showed higher growth sensitivity to precipitation, temperature and drought than Q. cerris. This sensitivity to climate was magnified in D trees whose growth decreased in response to warm and dry conditions during the prior winter and the late summer. The Q. pubescens D trees were more efficient in their water use than ND trees before the growth divergence between D and ND trees amplified. In the studied area, Phytophthora quercina was isolated from 40% of the sampled trees, and tended to be more frequent amongst ND than amongst D trees. Our data suggests that droughts and warm summer conditions triggered oak decline. The high prevalence of P. quercina in the studied area warrants further study as a potential predisposing factor.

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits.

Diversity of microbial organisms is linked to global climatic gradients. The genus Phytophthora includes both aquatic and terrestrial plant pathogenic species that display a large variation of functional traits. The extent to which the physical environment (water or soil) modulates the interaction of microorganisms with climate is unknown. Here, we explored the main environmental drivers of diversity and functional trait composition of Phytophthora communities. Communities were obtained by a novel metabarcoding setup based on PacBio sequencing of river filtrates in 96 river sites along a geographical gradient. Species were classified as terrestrial or aquatic based on their phylogenetic clade. Overall, terrestrial and aquatic species showed contrasting patterns of diversity. For terrestrial species, precipitation was a stronger driver than temperature, and diversity and functional diversity decreased with decreasing temperature and precipitation. In cold and dry areas, the dominant species formed resistant structures and had a low optimum temperature. By contrast, for aquatic species, temperature and water chemistry were the strongest drivers, and diversity increased with decreasing temperature and precipitation. Within the same area, environmental filtering affected terrestrial species more strongly than aquatic species (20% versus 3% of the studied communities, respectively). Our results highlight the importance of functional traits and the physical environment in which microorganisms develop their life cycle when predicting their distribution under changing climatic conditions. Temperature and rainfall may be buffered differently by water and soil, and thus pose contrasting constrains to microbial assemblies.

Diplodia Tip Blight on Its Way to the North: Drivers of Disease Emergence in Northern Europe.

Disease emergence in northern and boreal forests has been mostly due to tree-pathogen encounters lacking a co-evolutionary past. However, outbreaks involving novel interactions of the host or the pathogen with the environment have been less well documented. Following an increase of records in Northern Europe, the first large outbreak of Diplodia sapinea on Pinus sylvestris was discovered in Sweden in 2016. By reconstructing the development of the epidemic, we found that the attacks started approx. 10 years back from several isolated trees in the stand and ended up affecting almost 90% of the trees in 2016. Limited damage was observed in other plantations in the surroundings of the affected stand, pointing to a new introduced pathogen as the cause of the outbreak. Nevertheless, no genetic differences based on SSR markers were found between isolates of the outbreak area and other Swedish isolates predating the outbreak or from other populations in Europe and Asia Minor. On a temporal scale, we saw that warm May and June temperatures were associated with higher damage and low tree growth, while cold and rainy conditions seemed to favor growth and deter disease. At a spatial scale, we saw that spread occurred predominantly in the SW aspect-area of the stand. Within that area and based on tree-ring and isotope (δ13C) analyses, we saw that disease occurred on trees that over the years had shown a lower water-use efficiency (WUE). Spore traps showed that highly infected trees were those producing the largest amount of inoculum. D. sapinea impaired latewood growth and reduced C reserves in needles and branches. D. sapinea attacks can cause serious economic damage by killing new shoots, disrupting the crown, and affecting the quality of stems. Our results show that D. sapinea has no limitations in becoming a serious pathogen in Northern Europe. Management should focus on reducing inoculum, especially since climate change may bring more favorable conditions for this pathogen. Seedlings for planting should be carefully inspected as D. sapinea may be present in a latent stage in asymptomatic tissues.

Mushroom Emergence Detected by Combining Spore Trapping with Molecular Techniques.

Obtaining reliable and representative mushroom production data requires time-consuming sampling schemes. In this paper, we assessed a simple methodology to detect mushroom emergence by trapping the fungal spores of the fruiting body community in plots where mushroom production was determined weekly. We compared the performance of filter paper traps with that of funnel traps and combined these spore trapping methods with species-specific quantitative real-time PCR and Illumina MiSeq to determine the spore abundance. Significantly more MiSeq proportional reads were generated for both ectomycorrhizal and saprotrophic fungal species using filter traps than were obtained using funnel traps. The spores of 37 fungal species that produced fruiting bodies in the study plots were identified. Spore community composition changed considerably over time due to the emergence of ephemeral fruiting bodies and rapid spore deposition (lasting from 1 to 2 weeks), which occurred in the absence of rainfall events. For many species, the emergence of epigeous fruiting bodies was followed by a peak in the relative abundance of their airborne spores. There were significant positive relationships between fruiting body yields and spore abundance in time for five of seven fungal species. There was no relationship between fruiting body yields and their spore abundance at plot level, indicating that some of the spores captured in each plot were arriving from the surrounding areas. Differences in fungal detection capacity by spore trapping may indicate different dispersal ability between fungal species. Further research can help to identify the spore rain patterns for most common fungal species.IMPORTANCE Mushroom monitoring represents a serious challenge in economic and logistical terms because sampling approaches demand extensive field work at both the spatial and temporal scales. In addition, the identification of fungal taxa depends on the expertise of experienced fungal taxonomists. Similarly, the study of fungal dispersal has been constrained by technological limitations, especially because the morphological identification of spores is a challenging and time-consuming task. Here, we demonstrate that spores from ectomycorrhizal and saprotrophic fungal species can be identified using simple spore traps together with either MiSeq fungus-specific amplicon sequencing or species-specific quantitative real-time PCR. In addition, the proposed methodology can be used to characterize the airborne fungal community and to detect mushroom emergence in forest ecosystems.