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ABSTRACT Wind is the primary dispersal mechanism of most fungal spores but is rarely considered in studies of fungal communities, limiting inference of assembly mechanisms and forecasting responses to climate change. We compiled wind‐connectivity models—‘windscapes’—to model potential dispersal of fungal spores at the continental scale and linked them with a molecular dataset of North American soil fungi. Our analyses demonstrate that prevailing windflow patterns exhibit a significantly stronger signal on fungal community structure than do geographic distances amongst sites. Notably, the signature of wind was detectable for mushrooms and fungi producing primarily wind‐dispersed spores. Contrastingly, fungi primarily reliant on animal dispersal exhibited a strong signature of geographic distance but not wind‐connectivity. Additionally, we show that directionally ‘downwind’ sites are more diverse than comparatively ‘upwind’ sites. Altogether, our findings suggest that future wind patterns will shape the adaptation potential of fungal communities dispersing into suitable climatic niches. 

Monitoring the “health” of an ecological community is a critical component of conservation planning. We propose that aggregating intraspecific genetic variation across all species of an ecological community (Community Genetic Distribution; CGD) provides a new way to measure biodiversity that is unifying across taxa, economically scalable, and geographically transferable. Such community-scale data provides information about past dynamics that can unveil processes structuring contemporary biodiversity, and can identify communities that are resilient to perturbation. Using the CGD, high-throughput biodiversity genetic inventories (e.g. metabarcoding/eDNA) can be leveraged to identify the genetic signatures of pristine and disturbed systems. We show examples of the CGD from empirical systems, how it responds through space and time to human disturbance, and how it successfully recovers restoration and succession gradients from metabarcoding datasets with the goal of obtaining insight on community genetic health and developing indicator metrics which can identify communities that are resilient to perturbation. We outline ways in which the CGD complements and extends information in the suite of currently described essential biodiversity variables, and how it can contribute to the targets of the Kunming-Montreal Global Biodiversity Framework. 

Climate change will likely shift plant and microbial distributions, creating geographic mismatches between plant hosts and essential microbial symbionts (e.g., ectomycorrhizal fungi, EMF). The loss of historical interactions, or the gain of novel associations, can have important consequences for biodiversity, ecosystem processes, and plant migration potential, yet few analyses exist that measure where mycorrhizal symbioses could be lost or gained across landscapes. Here, we examine climate change impacts on tree-EMF codistributions at the continent scale. We built species distribution models for 400 EMF species and 50 tree species, integrating fungal sequencing data from North American forest ecosystems with tree species occurrence records and long-term forest inventory data. Our results show the following: 1) tree and EMF climate suitability to shift toward higher latitudes; 2) climate shifts increase the size of shared tree-EMF habitat overall, but 35% of tree-EMF pairs are at risk of declining habitat overlap; 3) climate mismatches between trees and EMF are projected to be greater at northern vs. southern boundaries; and 4) tree migration lag is correlated with lower richness of climatically suitable EMF partners. This work represents a concentrated effort to quantify the spatial extent and location of tree-EMF climate envelope mismatches. Our findings also support a biotic mechanism partially explaining the failure of northward tree species migrations with climate change: reduced diversity of co-occurring and climate-compatible EMF symbionts at higher latitudes. We highlight the conservation implications for identifying areas where tree and EMF responses to climate change may be highly divergent. 

ABSTRACT The Importance of the Regional Species PoolThe regional species pool—the set of species capable of entering a local community—is a foundational concept for understanding ecological processes that occur between local and extensive (biogeographic) spatial scales. However, the lack of precise definitions for the regional species pool, coupled with limited research into the dynamics of regional biodiversity, has impeded the development of a comprehensive framework to explain the mechanisms shaping these pools. Processes Governing Regional Species PoolsAlthough ecological processes at local and extensive scales are relatively well understood, the mechanisms shaping regional biota remain less clear. Regional species pools are likely shaped by a unique set of processes that often overlap minimally with those operating at local or extensive scales. Despite their significance, our understanding of the specific mechanisms driving the dynamics of regional species pools remains incomplete. The Need for a Theory of Regional Species PoolsWe argue that it is essential to prioritise the study of the regional species pool for two reasons. First, the regional species pool bridges spatial and temporal scales from ecological dynamics in landscapes to the long‐term processes shaping the biotas of entire biogeographic provinces. As such, understanding the dynamics of species pools addresses fundamental questions about the origin, maintenance, and dynamics of biodiversity. Second, effective biodiversity conservation in the Anthropocene hinges on understanding the processes that operate at regional scales. 

Abstract AimEfforts to predict the responses of soil fungal communities to climate change are hindered by limited information on how fungal niches are distributed across environmental hyperspace. We predict the climate sensitivity of North American soil fungal assemblage composition by modelling the ecological niches of several thousand fungal species. LocationOne hundred and thirteen sites in the United States and Canada spanning all biomes except tropical rain forest. Major Taxa StudiedFungi. Time Period2011–2018. MethodsWe combine internal transcribed spacer (ITS) sequences from two continental‐scale sampling networks in North America and cluster them into operational taxonomic units (OTUs) at 97% similarity. Using climate and soil data, we fit ecological niche models (ENMs) based on logistic ridge regression for all OTUs present in at least 10 sites (n = 8597). To describe the compositional turnover of soil fungal assemblages over climatic gradients, we introduce a novel niche‐based metric of climate sensitivity, the Sørensen climate sensitivity index. Finally, we map climate sensitivity across North America. ResultsENMs have a mean out‐of‐sample predictive accuracy of 73.8%, with temperature variables being strong predictors of fungal distributions. Soil fungal climate niches clump together across environmental space, which suggests common physiological limits and predicts abrupt changes in composition with respect to changes in climate. Soil fungi in North American climates are more likely to be limited by cold and dry conditions than by warm and wet conditions, and ectomycorrhizal fungi generally tolerate colder temperatures than saprotrophic fungi. Sørensen climate sensitivity exhibits a multimodal distribution across environmental space, with a peak in climates corresponding to boreal forests. Main ConclusionsThe boreal forest occupies an especially precarious region of environmental space for the composition of soil fungal assemblages in North America, as even small degrees of warming could trigger large compositional changes characterized mainly by an influx of warm‐adapted species. 

Aim Ectomycorrhizal fungi (ECMF) are partners in a globally distributed tree symbiosis implicated in most major ecosystem functions. However, resilience of ECMF to future climates is uncertain. We forecast these changes over the extent of North American Pinaceae forests. Location About 68 sites from North American Pinaceae forests ranging from Florida to Ontario in the east and southern California to Alaska in the west. Taxon Ectomycorrhizal fungi (Asco‐ and Basidiomycetes). Methods We characterized ECMF communities at each site using molecular methods and modelled climatic drivers of diversity and community composition with general additive, generalized dissimilarity models and Threshold Indicator Taxa ANalysis (TITAN). Next, we projected our models across the extent of North American Pinaceae forests and forecast ECMF responses to climate changes in these forests over the next 50 years. Results We predict median declines in ECMF species richness as high as 26% in Pinaceae forests throughout a climate zone comprising more than 3.5 million square kilometres of North America (an area twice that of Alaska state). Mitigation of greenhouse gas emissions can reduce these declines, but not prevent them. The existence of multiple diversity optima along climate gradients suggest regionally divergent trajectories for North American ECMF, which is corroborated by corresponding ECMF community thresholds identified in TITAN models. Warming of forests along the boreal–temperate ecotone results in projected ECMF species loss and declines in the relative abundance of long‐distance foraging ECMF species, whereas warming of eastern temperate forests has the opposite effect. Main Conclusions Our results reveal potentially unavoidable ECMF species‐losses over the next 50 years, which is likely to have profound (if yet unclear) effects on ECMF‐associated biogeochemical cycles. 

Abstract Soil microbial communities play critical roles in various ecosystem processes, but studies at a large spatial and temporal scale have been challenging due to the difficulty in finding the relevant samples in available data sets as well as the lack of standardization in sample collection and processing. The National Ecological Observatory Network (NEON) has been collecting soil microbial community data multiple times per year for 47 terrestrial sites in 20 eco‐climatic domains, producing one of the most extensive standardized sampling efforts for soil microbial biodiversity to date. Here, we introduce the neonMicrobe R package—a suite of downloading, preprocessing, data set assembly, and sensitivity analysis tools for NEON’s newly published 16S and ITS amplicon sequencing data products which characterize soil bacterial and fungal communities, respectively. neonMicrobe is designed to make these data more accessible to ecologists without assuming prior experience with bioinformatic pipelines. We describe quality control steps used to remove quality‐flagged samples, report on sensitivity analyses used to determine appropriate quality filtering parameters for the DADA2 workflow, and demonstrate the immediate usability of the output data by conducting standard analyses of soil microbial diversity. The sequence abundance tables produced byneonMicrobecan be linked to NEON’s other data products (e.g., soil physical and chemical properties, plant community composition) and soil subsamples archived in the NEON Biorepository. We provide recommendations for incorporatingneonMicrobeinto reproducible scientific workflows, discuss technical considerations for large‐scale amplicon sequence analysis, and outline future directions for NEON‐enabled microbial ecology. In particular, we believe that NEON marker gene sequence data will allow researchers to answer outstanding questions about the spatial and temporal dynamics of soil microbial communities while explicitly accounting for scale dependence. We expect that the data produced by NEON and theneonMicrobeR package will act as a valuable ecological baseline to inform and contextualize future experimental and modeling endeavors.