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Summary Arbuscular mycorrhizal fungi (AMF) are critical to native plant community ecology and influence plant invasions. Research has focused on nutritional benefits of AMF, although evidence shows that they may also confer pathogen resistance. However, most such work has focused on agriculturally relevant plant species. Therefore, whether AMF confer pathogen resistance tonative(wild) plant species, and impact of novel plant–microbial relationships on this benefit, remains understudied.We conducted a series of experiments measuring mycorrhizal‐induced resistance (MIR) to pathogens in native prairie plant species. We tested for pathogenicity across 69 field‐isolated fungi and oomycetes across five plant species. We then conducted experiments assessing growth response to native and non‐native AMF and pathogens in three plant species from native populations and milkweed (Asclepias syriaca) from native and postagricultural populations.We found evidence of MIR in milkweed. Moreover, we identified differential effects of AMF depending on plant species, with milkweed from native populations showing benefits from AMF. Finally, growth response was mediated by local adaptation, with matching AMF–pathogen origin strengthening responses.This work illustrates the importance of locally sourced AMF and plants to native plant ecology and suggests that pathogen resistance may be an important dimension of AMF benefit. 

ABSTRACT Arbuscular mycorrhizal fungi (AMF, phylum Glomeromycota) are essential to plant community diversity and ecosystem functioning. However, increasing human land use represents a major threat to native AMF globally. Characterizing the loss of AMF diversity remains challenging because many taxa are undescribed, resulting in poor documentation of their biogeography and family‐level disturbance sensitivity. We survey sites representing native and human‐altered ecosystems across the American continents—in Alaska, Kansas, and Brazil—to shed light on these gaps. Using a recently developed pipeline for phylogenetic placement of eDNA, we find evidence for three putative novel clades within the Glomeromycota, sister toEntrophosporaceae,Glomeraceae, andArchaeosporaceae, with evidence for geographic structuring. We further find that taxa in theDiversisporaceae,Glomeraceae, andEntrophosporaceaerelatively high families are overrepresented and more diverse in temperate samples. By contrast, the diversity of taxa that cannot be placed into a family is higher in tropical samples, suggesting that tropical sites harbor relatively high undescribed AMF diversity. Moreover, we find evidence thatEntrophosporaceaeis more tolerant, whileGlomeraceaeis more sensitive to disturbance. These results underscore the vast undescribed diversity of AMF while highlighting a way forward to systematically improve our understanding of AMF biogeography and response to human disturbance. 

Abstract Recent work established a backbone reference tree and phylogenetic placement pipeline for identification of arbuscular mycorrhizal fungal (AMF) large subunit (LSU) rDNA environmental sequences. Our previously published pipeline allowed any environmental sequence to be identified as putative AMF or within one of the major families. Despite this contribution, difficulties in implementation of the pipeline remain. Here, we present an updated database and pipeline with (1) an expanded backbone tree to include four newly described genera and (2) several changes to improve ease and consistency of implementation. In particular, packages required for the pipeline are now installed as a single folder (conda environment) and the pipeline has been tested across three university computing clusters. This updated backbone tree and pipeline will enable broadened adoption by the community, advancing our understanding of these ubiquitous and ecologically important fungi. 

Abstract The latitudinal diversity gradient (LDG) dominates global patterns of diversity^1,2, but the factors that underlie the LDG remain elusive. Here we use a unique global dataset³to show that vascular plants on oceanic islands exhibit a weakened LDG and explore potential mechanisms for this effect. Our results show that traditional physical drivers of island biogeography⁴—namely area and isolation—contribute to the difference between island and mainland diversity at a given latitude (that is, the island species deficit), as smaller and more distant islands experience reduced colonization. However, plant species with mutualists are underrepresented on islands, and we find that this plant mutualism filter explains more variation in the island species deficit than abiotic factors. In particular, plant species that require animal pollinators or microbial mutualists such as arbuscular mycorrhizal fungi contribute disproportionately to the island species deficit near the Equator, with contributions decreasing with distance from the Equator. Plant mutualist filters on species richness are particularly strong at low absolute latitudes where mainland richness is highest, weakening the LDG of oceanic islands. These results provide empirical evidence that mutualisms, habitat heterogeneity and dispersal are key to the maintenance of high tropical plant diversity and mediate the biogeographic patterns of plant diversity on Earth. 

Abstract Soil microbes impact plant community structure and diversity through plant–soil feedbacks. However, linking the relative abundance of plant pathogens and mutualists to differential plant recruitment remains challenging. Here, we tested for microbial mediation of pairwise feedback using a reciprocal transplant experiment in a lowland tropical forest in Panama paired with amplicon sequencing of soil and roots. We found evidence that plant species identity alters the microbial community, and these changes in microbial composition alter subsequent growth and survival of conspecific plants. We also found that greater community dissimilarity between species in their arbuscular mycorrhizal and nonpathogenic fungi predicted increased positive feedback. Finally, we identified specific microbial taxa across our target functional groups that differentially accumulated under conspecific settings. Collectively, these findings clarify how soil pathogens and mutualists mediate net feedback effects on plant recruitment, with implications for management and restoration. 

Abstract Island biogeography has classically focused on abiotic drivers of species distributions. However, recent work has highlighted the importance of mutualistic biotic interactions in structuring island floras. The limited occurrence of specialist pollinators and mycorrhizal fungi have been found to restrict plant colonization on oceanic islands. Another important mutualistic association occurs between nearly 15,000 plant species and nitrogen-fixing (N-fixing) bacteria. Here, we look for evidence that N-fixing bacteria limit establishment of plants that associate with them. Globally, we find that plants associating with N-fixing bacteria are disproportionately underrepresented on islands, with a 22% decline. Further, the probability of N-fixing plants occurring on islands decreases with island isolation and, where present, the proportion of N-fixing plant species decreases with distance for large, but not small islands. These findings suggest that N-fixing bacteria serve as a filter to plant establishment on islands, altering global plant biogeography, with implications for ecosystem development and introduction risks. 

ABSTRACT Conspecific density dependence (CDD) in plant populations is widespread, most likely caused by local‐scale biotic interactions, and has potentially important implications for biodiversity, community composition, and ecosystem processes. However, progress in this important area of ecology has been hindered by differing viewpoints on CDD across subfields in ecology, lack of synthesis across CDD‐related frameworks, and misunderstandings about how empirical measurements of local CDD fit within the context of broader ecological theories on community assembly and diversity maintenance. Here, we propose a conceptual synthesis of local‐scale CDD and its causes, including species‐specific antagonistic and mutualistic interactions. First, we compare and clarify different uses of CDD and related concepts across subfields within ecology. We suggest the use of local stabilizing/destabilizing CDD to refer to the scenario where local conspecific density effects are more negative/positive than heterospecific effects. Second, we discuss different mechanisms for local stabilizing and destabilizing CDD, how those mechanisms are interrelated, and how they cut across several fields of study within ecology. Third, we place local stabilizing/destabilizing CDD within the context of broader ecological theories and discuss implications and challenges related to scaling up the effects of local CDD on populations, communities, and metacommunities. The ultimate goal of this synthesis is to provide a conceptual roadmap for researchers studying local CDD and its implications for population and community dynamics. 

Abstract Arbuscular mycorrhizal fungi (AMF; Glomeromycota) are difficult to culture; therefore, establishing a robust amplicon-based approach to taxa identification is imperative to describe AMF diversity. Further, due to low and biased sampling of AMF taxa, molecular databases do not represent the breadth of AMF diversity, making database matching approaches suboptimal. Therefore, a full description of AMF diversity requires a tool to determine sequence-based placement in the Glomeromycota clade. Nonetheless, commonly used gene regions, including the SSU and ITS, do not enable reliable phylogenetic placement. Here, we present an improved database and pipeline for the phylogenetic determination of AMF using amplicons from the large subunit (LSU) rRNA gene. We improve our database and backbone tree by including additional outgroup sequences. We also improve an existing bioinformatics pipeline by aligning forward and reverse reads separately, using a universal alignment for all tree building, and implementing a BLAST screening prior to tree building to remove non-homologous sequences. Finally, we present a script to extract AMF belonging to 11 major families as well as an amplicon sequencing variant (ASV) version of our pipeline. We test the utility of the pipeline by testing the placement of known AMF, known non-AMF, and Acaulospora sp. spore sequences. This work represents the most comprehensive database and pipeline for phylogenetic placement of AMF LSU amplicon sequences within the Glomeromycota clade. 

Abstract Soil-borne pathogens structure plant communities, shaping their diversity, and through these effects may mediate plant responses to climate change and disturbance. Little is known, however, about the environmental determinants of plant pathogen communities. Therefore, we explored the impact of climate gradients and anthropogenic disturbance on root-associated pathogens in grasslands. We examined the community structure of two pathogenic groups—fungal pathogens and oomycetes—in undisturbed and anthropogenically disturbed grasslands across a natural precipitation and temperature gradient in the Midwestern USA. In undisturbed grasslands, precipitation and temperature gradients were important predictors of pathogen community richness and composition. Oomycete richness increased with precipitation, while fungal pathogen richness depended on an interaction of precipitation and temperature, with precipitation increasing richness most with higher temperatures. Disturbance altered plant pathogen composition and precipitation and temperature had a reduced effect on pathogen richness and composition in disturbed grasslands. Because pathogens can mediate plant community diversity and structure, the sensitivity of pathogens to disturbance and climate suggests that degradation of the pathogen community may mediate loss, or limit restoration of, native plant diversity in disturbed grasslands, and may modify plant community response to climate change.