Geographically structured host specificity is caused by the range expansions and host shifts of a symbiotic fungus

Death caps (Amanita phalloides) frequently establish from sexual spores, but individuals can grow large and live for more than a decade in invaded forests

Global change is reshaping Earth's biodiversity, but the changing distributions of nonpathogenic fungi remain largely undocumented, as do mechanisms enabling invasions. The ectomycorrhizal Amanita phalloides is native to Europe and invasive in North America. Using population genetics and genomics, we sought to describe the life history traits of this successfully invading symbiotic fungus. To test whether death caps spread underground using hyphae, or aboveground using sexual spores, we mapped and genotyped mushrooms from European and US sites. Larger genetic individuals (genets) would suggest spread mediated by vegetative growth, while many small genets would suggest dispersal mediated by spores. To test whether genets are ephemeral or persistent, we also sampled from populations over time. At nearly every site and across all time points, mushrooms resolve into small genets. Individuals frequently establish from sexual spores. But at one Californian site, a single individual measuring nearly 10 m across dominated. At two Californian sites, the same genetic individuals were discovered in 2004, 2014, and 2015, suggesting single individuals (both large and small) can reproduce repeatedly over relatively long timescales. A flexible life history strategy combining both mycelial growth and spore dispersal appears to underpin the invasion of this deadly perennial ectomycorrhizal fungus.

Plant Species' Capacity for Range Shifts at the Habitat and Geographic Scales: A Trade-Off-Based Framework

Climate change is causing rapid shifts in the abiotic and biotic environmental conditions experienced by plant populations, but we lack generalizable frameworks for predicting the consequences for species. These changes may cause individuals to become poorly matched to their environments, potentially inducing shifts in the distributions of populations and altering species' habitat and geographic ranges. We present a trade-off-based framework for understanding and predicting whether plant species may undergo range shifts, based on ecological strategies defined by functional trait variation. We define a species' capacity for undergoing range shifts as the product of its colonization ability and the ability to express a phenotype well-suited to the environment across life stages (phenotype-environment matching), which are both strongly influenced by a species' ecological strategy and unavoidable trade-offs in function. While numerous strategies may be successful in an environment, severe phenotype-environment mismatches result in habitat filtering: propagules reach a site but cannot establish there. Operating within individuals and populations, these processes will affect species' habitat ranges at small scales, and aggregated across populations, will determine whether species track climatic changes and undergo geographic range shifts. This trade-off-based framework can provide a conceptual basis for species distribution models that are generalizable across plant species, aiding in the prediction of shifts in plant species' ranges in response to climate change.

Persistence of ecologically similar fungi in a restricted floral niche

Fungi in the genera Knoxdaviesia and Sporothrix dominate fungal communities within Protea flowerheads and seed cones (infructescences). Despite apparently similar ecologies, they show strong host recurrence and often occupy the same individual infructescence. Differences in host chemistry explain their host consistency, but the factors that allow co-occupancy of multiple species within individual infructescences are unknown. Sporothrix splendens and K. proteae often grow on different senescent tissue types within infructescences of their P. repens host, indicating that substrate-related differences aid their co-occupancy. Sporothrix phasma and K. capensis grow on the same tissues of P. neriifolia suggesting neutral competitive abilities. Here we test the hypothesis that differences in host-tissues dictate competitive abilities of these fungi and explain their co-occupancy of this spatially restricted niche. Media were prepared from infructescence bases, bracts, seeds, or pollen presenters of P. neriifolia and P. repens. As expected, K. capensis was unable to grow on seeds whilst S. phasma could. As hypothesised, K. capensis and S. phasma had equal competitive abilities on pollen presenters, appearing to explain their co-occupancy of this resource. Growth of K. proteae was significantly enhanced on pollen presenters while that of S. splendens was the same as the control. Knoxdavesia proteae grew significantly faster than S. splendens on all tissue types. Despite this, S. splendens was a superior competitor on all tissue types. For K. proteae to co-occupy infructescences with S. splendens for extended periods, it likely needs to colonize pollen presenters before the arrival of S. splendens.

Using aggregated field collection data and the novel r package fungarium to investigate fungal fire association

Understanding which fungi exhibit certain ecological traits, such as habitat, host, or substrate associations, and knowing how these traits change across space and time can provide invaluable insight into the roles fungi play in their respective ecosystems. Archived sporocarp data, such as the collection and observation records accessible through the Mycology Collections Portal (MyCoPortal), are well suited for trait investigations, since these records circumvent the need for field work, are geographically and temporally diverse, and often have detailed and trait-relevant environmental metadata. However, there are inefficiencies and inadequacies in the MyCoPortal online interface that affect data set generation and trait searching, and many of the available records have outdated or misspelled taxon names as well as misspelled location names. Thus, we created the r package fungarium, which enables the efficient download of complete MyCoPortal data sets from within the R environment, enhances the identification of trait-relevant records, confirms or updates taxon names while also accounting for spelling errors, and fixes misspelled location names. Utilizing this package and MyCoPortal data, we demonstrated methods for analyzing taxonomic, geographic, and temporal patterns in ecological traits, using fire association as an example. We found that fire association, which was quantified via fire-associated enrichment factors (fire-associated records/total records), differed substantially between taxa, and these differences were qualitatively supported by existing literature, as hypothesized. Sampling bias within the MyCoPortal data and limitations of the burned acreage data set used (i.e., Monitoring Trends in Burn Severity) were identified as confounding factors in our geographic and temporal analyses, as evidenced by the unexpected lack of correlation between fire association and burned acreage on county and year bases. However, both confounding factors likely depend on the trait analyzed and external data set used. Overall, the fungarium package and associated methods presented here effectively enable the use of archived sporocarp data for future ecological trait studies.

Interplay between differential competition and actions of spore-vectors explain host exclusivity of saprobic fungi in Protea flowers

Protea flowers host saprobic Knoxdaviesia and Sporothrix fungi that are dispersed by pollinating insects and birds. Different Protea species contain sympatric populations of different fungal species. For example, P. repens host S. splendens and K. proteae, while P. neriifolia host K. capensis and S. phasma. Even though all fungi can grow vigorously on alternative hosts and they share the same spore vector species, they rarely colonise alternative hosts. We investigated the role of fungal differential competitive abilities on their usual and alternative hosts to explain their host exclusivity. In a de Wit replacement series experiment, S. splendens outcompeted and later overgrew all other fungi on media prepared from its usual and alternative hosts. Host exclusivity of S. splendens on P. repens may therefore be maintained by restricted movement of spore vectors rather than weaker competitive abilities on alternative hosts. On their preferred hosts, S. splendens and S. phasma rapidly overgrew Knoxdavesia species with which they do not usually share a host, explaining host exclusivity of the Knoxdavesia species. Knoxdaviesia proteae likely only persist on P. repens with sympatric S. splendens if it colonizes flowers earlier, in a different area, or completes its life cycle before being overgrown. On their usual P. neriifolia host, K. capensis and S. phasma had neutralistic interactions and S. phasma could not overgrow K. capensis, explaining their co-existence. Host exclusivity of saprobic Protea-associated Knoxdaviesia and Sporothrix may therefore be maintained by both the activities of spore vectors and differential competitive abilities on different hosts, but the influence of other competing microbes and micro-niche differentiation cannot be excluded.

Share the wealth: Trees with greater ectomycorrhizal species overlap share more carbon

The mutualistic symbiosis between forest trees and ectomycorrhizal fungi (EMF) is among the most ubiquitous and successful interactions in terrestrial ecosystems. Specific species of EMF are known to colonize specific tree species, benefitting from their carbon source, and in turn, improving their access to soil water and nutrients. EMF also form extensive mycelial networks that can link multiple root-tips of different trees. Yet the number of tree species connected by such mycelial networks, and the traffic of material across them, are just now under study. Recently we reported substantial belowground carbon transfer between Picea, Pinus, Larix and Fagus trees in a mature forest. Here, we analyze the EMF community of these same individual trees and identify the most likely taxa responsible for the observed carbon transfer. Among the nearly 1,200 EMF root-tips examined, 50%-70% belong to operational taxonomic units (OTUs) that were associated with three or four tree host species, and 90% of all OTUs were associated with at least two tree species. Sporocarp 13 C signals indicated that carbon originating from labelled Picea trees was transferred among trees through EMF networks. Interestingly, phylogenetically more closely related tree species exhibited more similar EMF communities and exchanged more carbon. Our results show that belowground carbon transfer is well orchestrated by the evolution of EMFs and tree symbiosis.

Fungarium specimens: a largely untapped source in global change biology and beyond

For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow.This article is part of the theme issue 'Biological collections for understanding biodiversity in the Anthropocene'.

Comparative Methods for Molecular Determination of Host-Specificity Factors in Plant-Pathogenic Fungi

Many plant-pathogenic fungi are highly host-specific. In most cases, host-specific interactions evolved at the time of speciation of the respective host plants. However, host jumps have occurred quite frequently, and still today the greatest threat for the emergence of new fungal diseases is the acquisition of infection capability of a new host by an existing plant pathogen. Understanding the mechanisms underlying host-switching events requires knowledge of the factors determining host-specificity. In this review, we highlight molecular methods that use a comparative approach for the identification of host-specificity factors. These cover a wide range of experimental set-ups, such as characterization of the pathosystem, genotyping of host-specific strains, comparative genomics, transcriptomics and proteomics, as well as gene prediction and functional gene validation. The methods are described and evaluated in view of their success in the identification of host-specificity factors and the understanding of their functional mechanisms. In addition, potential methods for the future identification of host-specificity factors are discussed.

Environment and host identity structure communities of green algal symbionts in lichens

An understanding of how biotic interactions shape species' distributions is central to predicting host-symbiont responses under climate change. Switches to locally adapted algae have been proposed to be an adaptive strategy of lichen-forming fungi to cope with environmental change. However, it is unclear how lichen photobionts respond to environmental gradients, and whether they play a role in determining the fungal host's upper and lower elevational limits. Deep-coverage Illumina DNA metabarcoding was used to track changes in the community composition of Trebouxia algae associated with two phylogenetically closely related, but ecologically divergent fungal hosts along a steep altitudinal gradient in the Mediterranean region. We detected the presence of multiple Trebouxia species in the majority of thalli. Both altitude and host genetic identity were strong predictors of photobiont community assembly in these two species. The predominantly clonally dispersing fungus showed stronger altitudinal structuring of photobiont communities than the sexually reproducing host. Elevation ranges of the host were not limited by the lack of compatible photobionts. Our study sheds light on the processes guiding the formation and distribution of specific fungal-algal combinations in the lichen symbiosis. The effect of environmental filtering acting on both symbiotic partners appears to shape the distribution of lichens.

Diversity and Structure of Fungal Communities in Neotropical Rainforest Soils: The Effect of Host Recurrence

The patterns of the distribution of fungal species and their potential interactions with trees remain understudied in Neotropical rainforests, which harbor more than 16,000 tree species, mostly dominated by endomycorrhizal trees. Our hypothesis was that tree species shape the non-mycorrhizal fungal assemblages in soil and litter and that the diversity of fungal communities in these two compartments is partly dependent on the coverage of trees in the Neotropical rainforest. In French Guiana, a long-term plantation and a natural forest were selected to test this hypothesis. Fungal ITS1 regions were sequenced from soil and litter samples from within the vicinity of tree species. A broad range of fungal taxa was found, with 42 orders and 14 classes. Significant spatial heterogeneity in the fungal communities was found without strong variation in the species richness and evenness among the tree plots. However, tree species shaped the fungal assemblages in the soil and litter, explaining up to 18 % of the variation among the communities in the natural forest. These results demonstrate that vegetation cover has an important effect on the structure of fungal assemblages inhabiting the soil and litter in Amazonian forests, illustrating the relative impact of deterministic processes on fungal community structures in these highly diverse ecosystems.

Loss of functional diversity and network modularity in introduced plant-fungal symbioses

The introduction of alien plants into a new range can result in the loss of co-evolved symbiotic organisms, such as mycorrhizal fungi, that are essential for normal plant physiological functions. Prior studies of mycorrhizal associations in alien plants have tended to focus on individual plant species on a case-by-case basis. This approach limits broad scale understanding of functional shifts and changes in interaction network structure that may occur following introduction. Here we use two extensive datasets of plant-fungal interactions derived from fungal sporocarp observations and recorded plant hosts in two island archipelago nations: New Zealand (NZ) and the United Kingdom (UK). We found that the NZ dataset shows a lower functional diversity of fungal hyphal foraging strategies in mycorrhiza of alien as compared with native trees. Across species this resulted in fungal foraging strategies associated with alien trees being much more variable in functional composition compared with native trees, which had a strikingly similar functional composition. The UK data showed no functional difference in fungal associates of alien and native plant genera. Notwithstanding this, both the NZ and UK data showed a substantial difference in interaction network structure of alien trees compared with native trees. In both cases, fungal associates of native trees showed strong modularity, while fungal associates of alien trees generally integrated into a single large module. The results suggest a lower functional diversity (in one dataset) and a simplification of network structure (in both) as a result of introduction, potentially driven by either limited symbiont co-introductions or disruption of habitat as a driver of specificity due to nursery conditions, planting, or plant edaphic-niche expansion. Recognizing these shifts in function and network structure has important implications for plant invasions and facilitation of secondary invasions via shared mutualist populations.

Ectomycorrhizal communities of ponderosa pine and lodgepole pine in the south-central Oregon pumice zone

Forest ecosystems of the Pacific Northwest of the USA are changing as a result of climate change. Specifically, rise of global temperatures, decline of winter precipitation, earlier loss of snowpack, and increased summer drought are altering the range of Pinus contorta. Simultaneously, flux in environmental conditions within the historic P. contorta range may facilitate the encroachment of P. ponderosa into P. contorta territory. Furthermore, successful pine species migration may be constrained by the distribution or co-migration of ectomycorrhizal fungi (EMF). Knowledge of the linkages among soil fungal diversity, community structure, and environmental factors is critical to understanding the organization and stability of pine ecosystems. The objectives of this study were to establish a foundational knowledge of the EMF communities of P. ponderosa and P. contorta in the Deschutes National Forest, OR, USA, and to examine soil characteristics associated with community composition. We examined EMF root tips of P. ponderosa and P. contorta in soil cores and conducted soil chemistry analysis for P. ponderosa cores. Results indicate that Cenococcum geophilum, Rhizopogon salebrosus, and Inocybe flocculosa were dominant in both P. contorta and P. ponderosa soil cores. Rhizopogon spp. were ubiquitous in P. ponderosa cores. There was no significant difference in the species composition of EMF communities of P. ponderosa and P. contorta. Ordination analysis of P. ponderosa soils suggested that soil pH, plant-available phosphorus (Bray), total phosphorus (P), carbon (C), mineralizable nitrogen (N), ammonium (NH4), and nitrate (NO3) are driving EMF community composition in P. ponderosa stands. We found a significant linear relationship between EMF species richness and mineralizable N. In conclusion, P. ponderosa and P. contorta, within the Deschutes National Forest, share the same dominant EMF species, which implies that P. ponderosa may be able to successfully establish within the historic P. contorta range and dominant EMF assemblages may be conserved.

Commercial Sphagnum peat moss is a vector for exotic ectomycorrhizal mushrooms

Sphagnum peat moss is one of the most commonly used substrates for forest plant and houseplant production. It is extracted from peat bogs in the circumboreal region and exported worldwide. Commercial peat moss is pasteurized, and is therefore believed to be free of viable ectomycorrhizal propagules. We used a bioassay with Pinus montezumae to demonstrate that commercial peat moss carries viable ectomycorrhizal spores, able to form mycorrhizae. Ectomycorrhizal fungi on seedling root-tips were sequenced for phylogenetic analyses using the ITS rDNA barcode region. We found three species: Suillus brevipes, Sphaerosporella brunnea, and Thelephora terrestris. S. brevipes and T. terrestris were found as viable inoculum transported in the peat moss, while S. brunnea was a greenhouse contaminant. S. brevipes and T. terrestris have biological characteristics (such as heat resistant and long living spores) that facilitate their survival to the extraction, transport, and storage processes of peat moss. This allows them to colonize nursery seedlings and to become potential invasive species in plantation areas. S. brevipes and T. terrestris are two of the most introduced fungi by anthropic activities; it has been argued that the vehicle for the introductions are their pine symbionts. This is the first time it has been demonstrated that peat moss is an important vehicle for the introduction of these fungi; a fact potentially related to the pattern of introduction of these ectomycorrhizal species from the northern hemisphere to elsewhere in the world.

The mid-domain effect in ectomycorrhizal fungi: range overlap along an elevation gradient on Mount Fuji, Japan

Mid-domain effect (MDE) models predict that the random placement of species' ranges within a bounded geographical area leads to increased range overlap and species richness in the center of the bounded area. These models are frequently applied to study species-richness patterns of macroorganisms, but the MDE in relation to microorganisms is poorly understood. In this study, we examined the characteristics of the MDE in richness patterns of ectomycorrhizal (EM) fungi, an ecologically important group of soil symbionts. We conducted intensive soil sampling to investigate overlap among species ranges and the applicability of the MDE to EM fungi in four temperate forest stands along an elevation gradient on Mount Fuji, Japan. Molecular analyses using direct sequencing revealed 302 EM fungal species. Of 73 EM fungal species found in multiple stands, 72 inhabited a continuous range along the elevation gradient. The maximum overlap in species range and the highest species richness occurred at elevations in the middle of the gradient. The observed richness pattern also fit within the 95% confidence interval of the mid-domain null model, supporting the role of the MDE in EM fungal richness. Deviation in observed richness from the mean of the mid-domain null estimation was negatively correlated with some environmental factors, including precipitation and soil C/N, indicating that unexplained richness patterns could be driven by these environmental factors. Our results clearly support the existence of microbial species' ranges along environmental gradients and the potential applicability of the MDE to better understand microbial diversity patterns.

Ectomycorrhizal fungi of exotic pine plantations in relation to native host trees in Iran: evidence of host range expansion by local symbionts to distantly related host taxa

Introduction of exotic plants change soil microbial communities which may have detrimental ecological consequences for ecosystems. In this study, we examined the community structure and species richness of ectomycorrhizal (EcM) fungi associated with exotic pine plantations in relation to adjacent native ectomycorrhizal trees in Iran to elucidate the symbiont exchange between distantly related hosts, i.e. Fagales (Fagaceae and Betulaceae) and Pinaceae. The combination of morphological and molecular identification approaches revealed that 84.6 % of species with more than one occurrence (at least once on pines) were shared with native trees and only 5.9 % were found exclusively on pine root tips. The community diversity of ectomycorrhizal fungi in the pine plantations adjacent to native EcM trees was comparable to their adjacent native trees, but the isolated plantations hosted relatively a species-poor community. Specific mycobionts of conifers were dominant in the isolated plantation while rarely found in the plantations adjacent to native EcM trees. These data demonstrate the importance of habitat isolation and dispersal limitation of EcM fungi in their potential of host range expansion. The great number of shared and possibly compatible symbiotic species between exotic Pinaceae and local Fagales (Fagaceae and Betulaceae) may reflect their evolutionary adaptations and/or ancestral compatibility with one another.