Genetically based susceptibility to herbivory influences the ectomycorrhizal fungal communities of a foundation tree species

First Report of Fungal Endophyte Communities and Non-Defensive Phytochemistry of Biocontrol-Inoculated Whitebark Pine Seedlings in a Restoration Planting

Plant endosymbionts (endophytes) influence host plant health and express genotype-dependent ecological relationships with plant hosts. A fungal species intended to confer host plant resistance to a forest pathogen was used as inoculum to test for effects of inoculation on disease resistance, microbiomes, and phytochemistry of a threatened pine species planted in a restoration setting. Correlations of inoculation presence/absence, phytochemistry, spatial location of seedlings, maternal seed sources, and fungal endophytic communities in the foliage of six-year-old whitebark pine (Pinus albicaulis) seedlings were assessed five years after an experimental inoculation of seedlings with foliar endophytic fungi cultured from whitebark pine trees at Crater Lake National Park, including Paramyrothecium roridum. We hypothesized that P. roridum would modify host microbiomes in a manner that combats white pine blister rust disease. Our assessment of seedlings in the field five years after inoculation allowed us to consider whether inoculation stimulated long-lasting changes in microbiome communities and whether effects varied by seedling genetic family. Tests for effects of endophyte inoculation on disease resistance were inconclusive due to current low levels of rust infection observed at the field site. Foliar fungal endophyte richness and Shannon diversity varied with maternal seed sources. Isotopic stoichiometry and phytochemistry did not vary with seedling spatial proximity, inoculation treatment, or maternal seed family. However, endophyte community composition varied with both seedling spatial proximity and maternal seed sources. Endophytic communities did not vary with the inoculation treatment, and the hypothesized biocontrol was not detected in inoculated seedlings. We draw three conclusions from this work: (1) fungal microbiomes of whitebark pine seedlings across our study site did not vary with host phytochemical signatures of ecophysiological status, (2) the inoculation of P. albicaulis seedlings with a mixture of fungal endophytes did not lead to persistent systemic changes in seedling foliar microbiomes, and (3) in correspondence with other studies, our data suggest that maternal seed source and spatial patterns influence fungal endophyte community composition.

Tree genotypes affect rock lichens and understory plants: examples of trophic-independent interactions

Genetic variation in foundation tree species can strongly influence communities of trophic‐dependent organisms, such as herbivorous insects, pollinators, and mycorrhizal fungi. However, the extent and manner in which this variation results in unexpected interactions that reach trophic‐independent organisms remains poorly understood, even though these interactions are essential to understanding complex ecosystems. In pinyon–juniper woodland at Sunset Crater (Arizona, USA), we studied pinyon (Pinus edulis) that were either resistant or susceptible to stem‐boring moths (Dioryctria albovittella). Moth herbivory alters the architecture of susceptible trees, thereby modifying the microhabitat beneath their crowns. We tested the hypothesis that this interaction between herbivore and tree genotype extends to affect trophic‐independent communities of saxicolous (i.e., growing on rocks) lichens and bryophytes and vascular plants beneath their crowns. Under 30 pairs of moth‐resistant and moth‐susceptible trees, we estimated percent cover of lichens, bryophytes, and vascular plants. We also quantified the cover of leaf litter and rocks as well as light availability. Four major findings emerged. (1) Compared to moth‐resistant trees, which exhibited monopodial architecture, the microhabitat under the shrub‐like susceptible trees was 60% darker and had 21% more litter resulting in 68% less rock exposure. (2) Susceptible trees had 56% and 87% less cover, 42% and 80% less richness, and 38% and 92% less diversity of saxicolous and plant communities, respectively, compared to resistant trees. (3) Both saxicolous and plant species accumulated at a slower rate beneath susceptible trees, suggesting an environment that might inhibit colonization and/or growth. (4) Both saxicolous and plant communities were negatively affected by the habitat provided by susceptible trees. The results suggest that herbivory of moth‐susceptible trees generated litter at high enough rates to reduce rock substrate availability, thereby suppressing the saxicolous communities. However, our results did not provide a causal pathway explaining the suppression of vascular plants. Nonetheless, the cascading effects of genetic variation in pinyon appear to extend beyond trophic‐dependent moths to include trophic‐independent saxicolous and vascular plant communities that are affected by specific tree–herbivore interactions that modify the local environment. We suggest that such genetically based interactions are common in nature and contribute to the evolution of complex communities.

Genotypic traits and tradeoffs of fast growth in silver birch, a pioneer tree

Fast-growing and slow-growing plant species are suggested to show integrated economics spectrums and the tradeoffs of fast growth are predicted to emerge as susceptibility to herbivory and resource competition. We tested if these predictions also hold for fast-growing and slow-growing genotypes within a silver birch, Betula pendula population. We exposed cloned saplings of 17 genotypes with slow, medium or fast height growth to reduced insect herbivory, using an insecticide, and to increasing resource competition, using naturally varying field plot grass cover. We measured shoot and root growth, ectomycorrhizal (EM) fungal production using ergosterol analysis and soil N transfer to leaves using ¹⁵N-labelled pulse of NH₄⁺. We found that fast-growing genotypes grew on average 78% faster, produced 56% and 16% more leaf mass and ergosterol, and showed 78% higher leaf N uptake than slow-growing genotypes. The insecticide decreased leaf damage by 83% and increased shoot growth, leaf growth and leaf N uptake by 38%, 52% and 76%, without differences between the responses of fast-growing and slow-growing genotypes, whereas root mass decreased with increasing grass cover. Shoot and leaf growth of fast-growing genotypes decreased and EM fungal production of slow-growing genotypes increased with increasing grass cover. Our results suggest that fast growth is genotypically associated with higher allocation to EM fungi, better soil N capture and greater leaf production, and that the tradeoff of fast growth is sensitivity to competition, but not to insect herbivory. EM fungi may have a dual role: to support growth of fast-growing genotypes under low grass competition and to maintain growth of slow-growing genotypes under intensifying competition.

Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community.While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling's terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.

Habitat specialisation controls ectomycorrhizal fungi above the treeline in the European Alps

Alpine habitats are one of the most vulnerable ecosystems to environmental change, however, little information is known about the drivers of plant-fungal interactions in these ecosystems and their resilience to climate change. We investigated the influence of the main drivers of ectomycorrhizal (EM) fungal communities along elevation and environmental gradients in the alpine zone of the European Alps and measured their degree of specialisation using network analysis. We sampled ectomycorrhizas of Dryas octopetala, Bistorta vivipara and Salix herbacea, and soil fungal communities at 28 locations across five countries, from the treeline to the nival zone. We found that: (1) EM fungal community composition, but not richness, changes along elevation, (2) there is no strong evidence of host specialisation, however, EM fungal networks in the alpine zone and within these, EM fungi associated with snowbed communities, are more specialised than in other alpine habitats, (3) plant host population structure does not influence EM fungal communities, and (4) most variability in EM fungal communities is explained by fine-scale changes in edaphic properties, like soil pH and total nitrogen. The higher specialisation and narrower ecological niches of these plant-fungal interactions in snowbed habitats make these habitats particularly vulnerable to environmental change in alpine ecosystems.

Intraspecific Genetic Variation and Species Interactions Contribute to Community Evolution

Evolution has been viewed as occurring primarily through selection among individuals. We present a framework based on multilevel selection for evaluating evolutionary change from individuals to communities, with supporting empirical evidence. Essential to this evaluation is the role that interspecific indirect genetic effects play in shaping community organization, in generating variation among community phenotypes, and in creating community heritability. If communities vary in phenotype, and those phenotypes are heritable and subject to selection at multiple levels, then a community view of evolution must be merged with mainstream evolutionary theory. Rapid environmental change during the Anthropocene will require a better understanding of these evolutionary processes, especially selection acting at the community level, which has the potential to eliminate whole communities while favoring others.

Ectomycorrhizal and Dark Septate Fungal Associations of Pinyon Pine Are Differentially Affected by Experimental Drought and Warming

Changing climates can cause shifts in temperature and precipitation, resulting in warming and drought in some regions. Although each of these factors has been shown to detrimentally affect forest ecosystems worldwide, information on the impacts of the combined effects of warming and drought is lacking. Forest trees rely on mutualistic root-associated fungi that contribute significantly to plant health and protection against climate stresses. We used a six-year, ecosystem-scale temperature and precipitation manipulation experiment targeted to simulate the climate in 2100 in the Southwestern United States to quantify the effects of drought, warming and combined drought and warming on the root colonization (abundance), species composition and diversity of ectomycorrhizal fungi (EMF), and dark septate fungal endophytes in a widespread woodland tree, pinyon pine (Pinus edulis E.). Our results show that pinyon shoot growth after 6 years of these treatments was reduced more by drought than warming. The combined drought and warming treatment reduced the abundance and diversity of EMF more than either treatment alone. Individual ectomycorrhizal fungal taxa, including the drought tolerant Cenococcum geophilum, were present in all treatments but the combined drought and warming treatment. The combined drought and warming treatment also reduced the abundance of dark septate endophytes (DSE), but did not affect their diversity or species composition. The current year shoot growth of the trees correlated positively with ectomycorrhizal fungal diversity, highlighting the importance of diversity in mutualistic relationships to plant growth. Our results suggest that EMF may be more important than DSE to aboveground growth in P. edulis, but also more susceptible to the negative effects of combined climate stressors.

Heritable genetic variation but no local adaptation in a pine-ectomycorrhizal interaction

Local adaptation of plants to mycorrhizal fungi helps determine the outcome of mycorrhizal interactions. However, there is comparatively little work exploring the potential for evolution in interactions with ectomycorrhizal fungi, and fewer studies have explored the heritability of mycorrhizal responsiveness, which is required for local adaptation to occur. We set up a reciprocal inoculation experiment using seedlings and soil from four populations of Scots pine (Pinus sylvestris) from Scotland, measuring seedling response to mycorrhizal inoculation after 4 months. We estimated heritability for the response traits and tested for genotype × environment interactions. While we found that ectomycorrhizal responsiveness was highly heritable, we found no evidence that pine populations were locally adapted to fungal communities. Instead, we found a complex suite of interactions between pine population and soil inoculum. Our results suggest that, while Scots pine has the potential to evolve in response to mycorrhizal fungi, evolution in Scotland has not resulted in local adaptation. Long generation times and potential for rapid shifts in fungal communities in response to environmental change may preclude the opportunity for such adaptation in this species, and selection for other factors such as resistance to fungal pathogens may explain the pattern of interactions found.

Long-Term Studies Reveal Differential Responses to Climate Change for Trees Under Soil- or Herbivore-Related Stress

Worldwide, trees are confronting increased temperature and aridity, exacerbating susceptibility to herbivory. Long-term studies comparing patterns of plant performance through drought can help identify variation among and within populations in vulnerability to climate change and herbivory. We use long-term monitoring data to examine our overarching hypothesis that the negative impacts of poor soil and herbivore susceptibility would be compounded by severe drought. We studied pinyon pine, Pinus edulis, a widespread southwestern tree species that has suffered extensive climate-change related mortality. We analyzed data on mortality, growth, male reproduction, and herbivory collected for 14-32 years in three areas with distinct soil-types. We used standardized precipitation-evapotranspiration index (SPEI) as a climate proxy that summarizes the impacts of drought due to precipitation and temperature variation on semi-arid forests. Several key findings emerged: (1) Plant performance measurements did not support our hypothesis that trees growing in stressful, coarse-textured soils would suffer more than trees growing in finer-textured soils. Stem growth at the area with coarse, young cinder soils (area one) responded only weakly to drought, while stem growth on more developed soils with sedimentary (area two) and volcanic (area three) substrates, was strongly negatively affected by drought. Male reproduction declined less with drought at area one and more at areas two and three. Overall mortality was 30% on coarse cinder soils (area one) and averaged 55% on finer soil types (areas two and three). (2) Although moth herbivore susceptible trees were hypothesized to suffer more with drought than moth resistant trees, the opposite occurred. Annual stem growth was negatively affected by drought for moth resistant trees, but much less strongly for moth susceptible trees. (3) In contrast to our hypothesis, moths declined with drought. Overall, chronically water-stressed and herbivore-susceptible trees had smaller declines in performance relative to less-stressed trees during drought years. These long-term findings support the idea that stressed trees might be more resistant to drought since they may have adapted or acclimated to resist drought-related mortality.

Common garden experiments disentangle plant genetic and environmental contributions to ectomycorrhizal fungal community structure

The interactions among climate change, plant genetic variation and fungal mutualists are poorly understood, but probably important to plant survival under drought. We examined these interactions by studying the ectomycorrhizal fungal (EMF) communities of pinyon pine seedlings (Pinus edulis) planted in a wildland ecosystem experiencing two decades of climate change-related drought. We established a common garden containing P. edulis seedlings of known maternal lineages (drought tolerant, DT; drought intolerant, DI), manipulated soil moisture and measured EMF community structure and seedling growth. Three findings emerged: EMF community composition differed at the phylum level between DT and DI seedlings, and diversity was two-fold greater in DT than in DI seedlings. EMF communities of DT seedlings did not shift with water treatment and were dominated by an ascomycete, Geopora sp. By contrast, DI seedlings shifted to basidiomycete dominance with increased moisture, demonstrating a lineage by environment interaction. DT seedlings grew larger than DI seedlings in high (28%) and low (50%) watering treatments. These results show that inherited plant traits strongly influence microbial communities, interacting with drought to affect seedling performance. These interactions and their potential feedback effects may influence the success of trees, such as P. edulis, in future climates.

Genetic-Based Susceptibility of a Foundation Tree to Herbivory Interacts With Climate to Influence Arthropod Community Composition, Diversity, and Resilience

Understanding how genetic-based traits of plants interact with climate to affect associated communities will help improve predictions of climate change impacts on biodiversity. However, few community-level studies have addressed such interactions. Pinyon pine (Pinus edulis) in the southwestern U.S. shows genetic-based resistance and susceptibility to pinyon needle scale (Matsucoccus acalyptus). We sought to determine if susceptibility to scale herbivory influenced the diversity and composition of the extended community of 250+ arthropod species, and if this influence would be consistent across consecutive years, an extreme drought year followed by a moderate drought year. Because scale insects alter the architecture of susceptible trees, it is difficult to separate the direct influences of susceptibility on arthropod communities from the indirect influences of scale-altered tree architecture. To separate these influences, scales were experimentally excluded from susceptible trees for 15 years creating susceptible trees with the architecture of resistant trees, hereafter referred to as scale-excluded trees. Five patterns emerged. (1) In both years, arthropod abundance was 3-4X lower on susceptible trees compared to resistant and scale-excluded trees. (2) Species accumulation curves show that alpha and gamma diversity were 2-3X lower on susceptible trees compared to resistant and scale-excluded trees. (3) Reaction norms of arthropod richness and abundance on individual tree genotypes across years showed genotypic variation in the community response to changes in climate. (4) The genetic-based influence of susceptibility on arthropod community composition is climate dependent. During extreme drought, community composition on scale-excluded trees resembled susceptible trees indicating composition was strongly influenced by tree genetics independent of tree architecture. However, under moderate drought, community composition on scale-excluded trees resembled resistant trees indicating traits associated with tree architecture became more important. (5) One year after extreme drought, the arthropod community rebounded sharply. However, there was a much greater rebound in richness and abundance on resistant compared to susceptible trees suggesting that reduced resiliency in the arthropod community is associated with susceptibility. These results argue that individual genetic-based plant-herbivore interactions can directly and indirectly impact community-level diversity, which is modulated by climate. Understanding such interactions is important for assessing the impacts of climate change on biodiversity.

The community and ecosystem consequences of intraspecific diversity: a meta-analysis

Understanding the relationships between biodiversity and ecosystem functioning has major implications. Biodiversity-ecosystem functioning relationships are generally investigated at the interspecific level, although intraspecific diversity (i.e. within-species diversity) is increasingly perceived as an important ecological facet of biodiversity. Here, we provide a quantitative and integrative synthesis testing, across diverse plant and animal species, whether intraspecific diversity is a major driver of community dynamics and ecosystem functioning. We specifically tested (i) whether the number of genotypes/phenotypes (i.e. intraspecific richness) or the specific identity of genotypes/phenotypes (i.e. intraspecific variation) in populations modulate the structure of communities and the functioning of ecosystems, (ii) whether the ecological effects of intraspecific richness and variation are strong in magnitude, and (iii) whether these effects vary among taxonomic groups and ecological responses. We found a non-linear relationship between intraspecific richness and community and ecosystem dynamics that follows a saturating curve shape, as observed for biodiversity-function relationships measured at the interspecific level. Importantly, intraspecific richness modulated ecological dynamics with a magnitude that was equal to that previously reported for interspecific richness. Our results further confirm, based on a database containing more than 50 species, that intraspecific variation also has substantial effects on ecological dynamics. We demonstrated that the effects of intraspecific variation are twice as high as expected by chance, and that they might have been underestimated previously. Finally, we found that the ecological effects of intraspecific variation are not homogeneous and are actually stronger when intraspecific variation is manipulated in primary producers than in consumer species, and when they are measured at the ecosystem rather than at the community level. Overall, we demonstrated that the two facets of intraspecific diversity (richness and variation) can both strongly affect community and ecosystem dynamics, which reveals the pivotal role of within-species biodiversity for understanding ecological dynamics.

A pulse of summer precipitation after the dry season triggers changes in ectomycorrhizal formation, diversity, and community composition in a Mediterranean forest in California, USA

Rapid responses of microbial biomass and community composition following a precipitation event have been reported for soil bacteria and fungi, but measurements characterizing ectomycorrhizal fungi remain limited. The response of ectomycorrhizal fungi after a precipitation event is crucial to understanding biogeochemical cycles and plant nutrition. Here, we examined changes in ectomycorrhizal formation, diversity, and community composition at the end of a summer drought and following precipitation events in a conifer-oak mixed forest under a semiarid, Mediterranean-type climate in CA, USA. To study the effects of different amounts of precipitation, a water addition treatment was also undertaken. Ectomycorrhizal fungal diversity and community composition changed within 6 days following precipitation, with increased simultaneous mortality and re-growth. Ectomycorrhizal diversity increased and community composition changed both in the natural rainfall (less than 10 mm) and water addition (50 mm) treatments, but larger decreases in ectomycorrhizal diversity were observed from 9 to 16 days after precipitation in the water addition treatment. The changes were primarily a shift in richness and abundance of Basidiomycota species, indicating higher drought sensitivity of Basidiomycota species compared with Ascomycota species. Our results indicate that ectomycorrhizal formation, diversity, and community composition rapidly respond to both precipitation events and to the amount of precipitation. These changes affect ecosystem functions, such as nutrient cycling, decomposition, and plant nutrient uptake, in semiarid regions.

Genetically determined fungal pathogen tolerance and soil variation influence ectomycorrhizal traits of loblolly pine

Selection on genetically correlated traits within species can create indirect effects on one trait by selection on another. The consequences of these trait correlations are of interest because they may influence how suites of traits within species evolve under differing selection pressures, both natural and artificial. By utilizing genetic families of loblolly pine either tolerant (t) or susceptible (s) to two different suites of pathogenic fungi responsible for causing either pine decline or fusiform rust disease, we investigated trait variation and trait correlations within loblolly pine (Pinus taeda L.) by determining how ectomycorrhizal (EM) colonization relates to pathogen susceptibility. We detected interactions between susceptibility to pathogenic fungi and soil inoculation source on loblolly pine compatibility with the EM fungi Thelephora, and on relative growth rate of loblolly pine. Additionally, we detected spatial variation in the loblolly pine-EM fungi interaction, and found that variation in colonization rates by some members of the EM community is not dictated by genetic variation in the host plant but rather soil inoculation source alone. The work presented here illustrates the potential for indirect selection on compatibility with symbiotic EM fungi as a result of selection for resistance to fungal pathogens. Additionally, we present evidence that the host plant does not have a single "mycorrhizal trait" governing interactions with all EM fungi, but rather that it can interact with different fungal taxa independently. Synthesis. An understanding of the genetic architecture of essential traits in focal species is crucial if we are to anticipate and manage the results of natural and artificial selection. As demonstrated here, an essential but often overlooked symbiosis (that between plants and mycorrhizal fungi) may be indirectly influenced by directed selection on the host plant.

Host Genotype and Nitrogen Form Shape the Root Microbiome of Pinus radiata

A central challenge in community ecology is understanding the role that phenotypic variation among genotypes plays in structuring host-associated communities. While recent studies have investigated the relationship between plant genotype and the composition of soil microbial communities, the effect of genotype-by-environment interactions on the plant microbiome remains unclear. In this study, we assessed the influence of tree genetics (G), nitrogen (N) form and genotype-by-environment interaction (G x N) on the composition of the root microbiome. Rhizosphere communities (bacteria and fungi) and root-associated fungi (including ectomycorrhizal and saprotrophic guilds) were characterised in two genotypes of Pinus radiata with contrasting physiological responses to exogenous organic or inorganic N supply. Genotype-specific responses to N form influenced the composition of the root microbiome. Specifically, (1) diversity and composition of rhizosphere bacterial and root-associated fungal communities differed between genotypes that had distinct responses to N form, (2) shifts in the relative abundance of individual taxa were driven by the main effects of N form or host genotype and (3) the root microbiome of the P. radiata genotype with the most divergent growth responses to organic and inorganic N was most sensitive to differences in N form. Our results show that intraspecific variation in tree response to N form has significant consequences for the root microbiome of P. radiata, demonstrating the importance of genotype-by-environment interactions in shaping host-associated communities.

Tree genetics defines fungal partner communities that may confer drought tolerance

Plant genetic variation and soil microorganisms are individually known to influence plant responses to climate change, but the interactive effects of these two factors are largely unknown. Using long-term observational studies in the field and common garden and greenhouse experiments of a foundation tree species (Pinus edulis) and its mutualistic ectomycorrhizal fungal (EMF) associates, we show that EMF community composition is under strong plant genetic control. Seedlings acquire the EMF community of their seed source trees (drought tolerant vs. drought intolerant), even when exposed to inoculum from the alternate tree type. Drought-tolerant trees had 25% higher growth and a third the mortality of drought-intolerant trees over the course of 10 y of drought in the wild, traits that were also observed in their seedlings in a common garden. Inoculation experiments show that EMF communities are critical to drought tolerance. Drought-tolerant and drought-intolerant seedlings grew similarly when provided sterile EMF inoculum, but drought-tolerant seedlings grew 25% larger than drought-intolerant seedlings under dry conditions when each seedling type developed its distinct EMF community. This demonstration that particular combinations of plant genotype and mutualistic EMF communities improve the survival and growth of trees with drought is especially important, given the vulnerability of forests around the world to the warming and drying conditions predicted for the future.

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Ectomycorrhizal (EM) fungi are ubiquitous in temperate and boreal forests, comprising over 20,000 species forming root symbiotic associations with Pinaceae and woody angiosperms. As much as 100 different EM fungal species can coexist and interact with the same tree species, forming complex multispecies networks in soils. The degree of host specificity and structural properties of these interaction networks (e.g., nestedness and modularity) may influence plant and fungal community assembly and species coexistence, yet their structure has been little studied in northern coniferous forests, where trees depend on EM fungi for nutrient acquisition. We used high-throughput sequencing to characterize the composition and diversity of bulk soil and root-associated fungal communities in four co-occurring Pinaceae in a relic foredune plain located at Îles de la Madeleine, Québec, Canada. We found high EM fungal richness across the four hosts, with a total of 200 EM operational taxonomic units (OTUs), mainly belonging to the Agaricomycetes. Network analysis revealed an antinested pattern in both bulk soil and roots EM fungal communities. However, there was no detectable modularity (i.e., subgroups of interacting species) in the interaction networks, indicating a low level of specificity in these EM associations. In addition, there were no differences in EM fungal OTU richness or community structure among the four tree species. Limited shared resources and competitive exclusion typically restrict the number of taxa coexisting within the same niche. As such, our finding of high EM fungal richness and low host specificity highlights the need for further studies to determine the mechanisms enabling such a large number of EM fungal species to coexist locally on the same hosts.

Lack of host specificity leads to independent assortment of dipterocarps and ectomycorrhizal fungi across a soil fertility gradient

Plants interact with a diversity of microorganisms, and there is often concordance in their community structures. Because most community-level studies are observational, it is unclear if such concordance arises because of host specificity, in which microorganisms or plants limit each other's occurrence. Using a reciprocal transplant experiment, we tested the hypothesis that host specificity between trees and ectomycorrhizal fungi determines patterns of tree and fungal soil specialisation. Seedlings of 13 dipterocarp species with contrasting soil specialisations were seeded into plots crossing soil type and canopy openness. Ectomycorrhizal colonists were identified by DNA sequencing. After 2.5 years, we found no evidence of host specificity. Rather, soil environment was the primary determinant of ectomycorrhizal diversity and composition on seedlings. Despite their close symbiosis, our results show that ectomycorrhizal fungi and tree communities in this Bornean rain forest assemble independently of host-specific interactions, raising questions about how mutualism shapes the realised niche.

Species Introductions and Their Cascading Impacts on Biotic Interactions in desert riparian ecosystems

Desert riparian ecosystems of North America are hotspots of biodiversity that support many sensitive species, and are in a region experiencing some of the highest rates of climatic alteration in North America. Fremont cottonwood, Populus fremontii, is a foundation tree species of this critical habitat, but it is threatened by global warming and regional drying, and by a non-native tree/shrub, Tamarix spp., all of which can disrupt the mutualism between P. fremontii and its beneficial mycorrhizal fungal communities. Specialist herbivorous leaf beetles (Diorhabda spp.) introduced for biocontrol of Tamarix are altering the relationship between this shrub and its environment. Repeated episodic feeding on Tamarix foliage by Diorhabda results in varying rates of dieback and mortality, depending on genetic variation in allocation of resources, growing conditions, and phenological synchrony between herbivore and host plant. In this article, we review the complex interaction between climatic change and species introductions and their combined impacts on P. fremontii and their associated communities. We anticipate that (1) certain genotypes of P. fremontii will respond more favorably to the presence of Tamarix and to climatic change due to varying selection pressures to cope with competition and stress; (2) the ongoing evolution of Diorhabda's life cycle timing will continue to facilitate its expansion in North America, and will over time enhance herbivore impact to Tamarix; (3) defoliation by Diorhabda will reduce the negative impact of Tamarix on P. fremontii associations with mycorrhizal fungi; and (4) spatial variability in climate and climatic change will modify the capacity for Tamarix to survive episodic defoliation by Diorhabda, thereby altering the relationship between Tamarix and P. fremontii, and its associated mycorrhizal fungal communities. Given the complex biotic/abiotic interactions outlined in this review, conservation biologists and riparian ecosystem managers should strive to identify and conserve the phenotypic traits that underpin tolerance and resistance to stressors such as climate change and species invasion. Such efforts will greatly enhance conservation restoration efficacy for protecting P. fremontii forests and their associated communities.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change.

Convergence in mycorrhizal fungal communities due to drought, plant competition, parasitism, and susceptibility to herbivory: consequences for fungi and host plants

Plants and mycorrhizal fungi influence each other's abundance, diversity, and distribution. How other biotic interactions affect the mycorrhizal symbiosis is less well understood. Likewise, we know little about the effects of climate change on the fungal component of the symbiosis or its function. We synthesized our long-term studies on the influence of plant parasites, insect herbivores, competing trees, and drought on the ectomycorrhizal fungal communities associated with a foundation tree species of the southwestern United States, pinyon pine (Pinus edulis), and described how these changes feed back to affect host plant performance. We found that drought and all three of the biotic interactions studied resulted in similar shifts in ectomycorrhizal fungal community composition, demonstrating a convergence of the community towards dominance by a few closely related fungal taxa. Ectomycorrhizal fungi responded similarly to each of these stressors resulting in a predictable trajectory of community disassembly, consistent with ecological theory. Although we predicted that the fungal communities associated with trees stressed by drought, herbivory, competition, and parasitism would be poor mutualists, we found the opposite pattern in field studies. Our results suggest that climate change and the increased importance of herbivores, competitors, and parasites that can be associated with it, may ultimately lead to reductions in ectomycorrhizal fungal diversity, but that the remaining fungal community may be beneficial to host trees under the current climate and the warmer, drier climate predicted for the future.

The relative importance of rapid evolution for plant-microbe interactions depends on ecological context

Evolution can occur on ecological time-scales, affecting community and ecosystem processes. However, the importance of evolutionary change relative to ecological processes remains largely unknown. Here, we analyse data from a long-term experiment in which we allowed plant populations to evolve for three generations in dry or wet soils and used a reciprocal transplant to compare the ecological effect of drought and the effect of plant evolutionary responses to drought on soil microbial communities and nutrient availability. Plants that evolved under drought tended to support higher bacterial and fungal richness, and increased fungal : bacterial ratios in the soil. Overall, the magnitudes of ecological and evolutionary effects on microbial communities were similar; however, the strength and direction of these effects depended on the context in which they were measured. For example, plants that evolved in dry environments increased bacterial abundance in dry contemporary environments, but decreased bacterial abundance in wet contemporary environments. Our results suggest that interactions between recent evolutionary history and ecological context affect both the direction and magnitude of plant effects on soil microbes. Consequently, an eco-evolutionary perspective is required to fully understand plant-microbe interactions.

Climate relicts and their associated communities as natural ecology and evolution laboratories

Climate relicts, marginal populations that have become isolated via climate-driven range shifts, preserve ecological and evolutionary histories that can span millennia. Studies point to climate relicts as 'natural laboratories' for investigating how long-term environmental change impacts species and populations. However, we propose that such research should be expanded to reveal how climate change affects 'interacting' species in ways that reshape community composition and evolution. Biotic interactions and their community and ecosystem effects are often genetically based and driven by associations with foundation species. We discuss evolution in climate relicts within the context of the emerging fields of community and ecosystem genetics, exploring the idea that foundation relicts are also natural community and ecosystem laboratories and windows to future landscapes.

Plant genetics and interspecific competitive interactions determine ectomycorrhizal fungal community responses to climate change

Although the importance of plant-associated microbes is increasingly recognized, little is known about the biotic and abiotic factors that determine the composition of that microbiome. We examined the influence of plant genetic variation, and two stressors, one biotic and one abiotic, on the ectomycorrhizal (EM) fungal community of a dominant tree species, Pinus edulis. During three periods across 16 years that varied in drought severity, we sampled the EM fungal communities of a wild stand of P. edulis in which genetically based resistance and susceptibility to insect herbivory was linked with drought tolerance and the abundance of competing shrubs. We found that the EM fungal communities of insect-susceptible trees remained relatively constant as climate dried, while those of insect-resistant trees shifted significantly, providing evidence of a genotype by environment interaction. Shrub removal altered the EM fungal communities of insect-resistant trees, but not insect-susceptible trees, also a genotype by environment interaction. The change in the EM fungal community of insect-resistant trees following shrub removal was associated with greater shoot growth, evidence of competitive release. However, shrub removal had a 7-fold greater positive effect on the shoot growth of insect-susceptible trees than insect-resistant trees when shrub density was taken into account. Insect-susceptible trees had higher growth than insect-resistant trees, consistent with the hypothesis that the EM fungi associated with susceptible trees were superior mutualists. These complex, genetic-based interactions among species (tree-shrub-herbivore-fungus) argue that the ultimate impacts of climate change are both ecological and evolutionary.

Conspecific plant-soil feedback scales with population size in Lobelia siphilitica (Lobeliaceae)

Plant-soil interactions directly affect plant success in terms of establishment, survival, growth and reproduction. Negative plant-soil feedback on such traits may therefore reduce the density and abundance of plants of a given species at a given site. Furthermore, if conspecific feedback varies among population sites, it could help explain geographic variation in plant population size. We tested for among-site variation in conspecific plant-soil feedback in a greenhouse experiment using seeds and soils from 8 natural populations of Lobelia siphilitica hosting 30-330 plants. The first cohort of seeds was grown on soil collected from each native site, while the second cohort was grown on the soil conditioned by the first. Our goal was to distinguish site-specific effects mediated by biotic and/or abiotic soil properties from those inherent in seed sources. Cohort 1 plants grown from seeds produced in small populations performed better in terms of germination, growth, and survival compared to plants produced in large populations. Plant performance decreased substantially between cohorts, indicating strong negative feedback. Most importantly, the strength of negative feedback scaled linearly (i.e., was less negative) with increasing size of the native plant population, particularly for germination and survival, and was better explained by soil- rather than seed-source effects. Even with a small number of sites, our results suggest that the potential for negative plant-soil feedback varies among populations of L. siphilitica, and that small populations were more susceptible to negative feedback. Conspecific plant-soil feedback may contribute to plant population size variation within a species' native range.

HSPRO controls early Nicotiana attenuata seedling growth during interaction with the fungus Piriformospora indica

In a previous study aimed at identifying regulators of Nicotiana attenuata responses against chewing insects, a 26-nucleotide tag matching the HSPRO (ORTHOLOG OF SUGAR BEET Hs1(pro)(-)(1)) gene was found to be strongly induced after simulated herbivory (Gilardoni et al., 2010). Here we characterized the function of HSPRO during biotic interactions in transgenic N. attenuata plants silenced in its expression (ir-hspro). In wild-type plants, HSPRO expression was not only induced during simulated herbivory but also when leaves were inoculated with Pseudomonas syringae pv tomato DC3000 and roots with the growth-promoting fungus Piriformospora indica. Reduced HSPRO expression did not affect the regulation of direct defenses against Manduca sexta herbivory or P. syringae pv tomato DC3000 infection rates. However, reduced HSPRO expression positively influenced early seedling growth during interaction with P. indica; fungus-colonized ir-hspro seedlings increased their fresh biomass by 30% compared with the wild type. Grafting experiments demonstrated that reduced HSPRO expression in roots was sufficient to induce differential growth promotion in both roots and shoots. This effect was accompanied by changes in the expression of 417 genes in colonized roots, most of which were metabolic genes. The lack of major differences in the metabolic profiles of ir-hspro and wild-type colonized roots (as analyzed by liquid chromatography time-of-flight mass spectrometry) suggested that accelerated metabolic rates were involved. We conclude that HSPRO participates in a whole-plant change in growth physiology when seedlings interact with P. indica.

The importance of individuals: intraspecific diversity of mycorrhizal plants and fungi in ecosystems

A key component of biodiversity is the number and abundance of individuals (i.e. genotypes), and yet such intraspecific diversity is rarely considered when investigating the effects of biodiversity of mycorrhizal plants and fungi on ecosystem processes. Within a species, individuals vary considerably in important reproductive and functional attributes, including carbon fixation, mycelial growth and nutrient utilization, but this is driven by both genetic and environmental (including climatic) factors. The interactions between individual plants and mycorrhizal fungi can have important consequences for the maintenance of biodiversity and regulation of resource transfers in ecosystems. There is also emerging evidence that assemblages of genotypes may affect ecosystem processes to a similar extent as assemblages of species. The application of whole-genome sequencing and population genomics to mycorrhizal plants and fungi will be crucial to determine the extent to which individual variation in key functional attributes is genetically based. We argue the need to unravel the importance of the diversity (especially assemblages of different evenness and richness) of individuals of both mycorrhizal plants and fungi, and the need to take a 'community genetics' approach to better understand the functional significance of the biodiversity of mycorrhizal symbioses.

Divergence in ectomycorrhizal communities with foreign Douglas-fir populations and implications for assisted migration

Assisted migration of forest trees has been widely proposed as a climate change adaptation strategy, but moving tree populations to match anticipated future climates may disrupt the geographically based, coevolved association suggested to exist between host trees and ectomycorrhizal fungal (EMF) communities. We explored this issue by examining the consistency of EMF communities among populations of 40 year-old Douglas-fir (Pseudotsuga menziesii var. menziesii) trees in a common-garden field trial using four provenances from contrasting coastal climates in southwestern British Columbia. Considerable variation in EMF community composition within test sites was found, ranging from 0.38 to 0.65 in the mean similarity index, and the divergence in EMF communities from local populations increased with site productivity. Clinal patterns in colonization success were detected for generalist and specialist EMF species on only the two productive test sites. Host population effects were limited to EMF species abundance rather than species loss, as richness per site averaged 15.0 among provenances and did not differ by transfer extent (up to 450 km), while Shannon's diversity index declined slightly. Large differences in colonization rates of specialist fungi, such as Tomentella stuposa and Clavulina cristata, raise the possibility that EMF communities maladapted to soil conditions contributed to the inferior growth of some host populations on productive sites. The results of the study suggest locally based specificity in host-fungal communities is likely a contributing factor in the outcome of provenance trials, and should be a consideration in analyzing seed-transfer effects and developing strategies for assisted migration.

Coral-associated marine fungi form novel lineages and heterogeneous assemblages

Coral stress tolerance is intricately tied to the animal's association with microbial symbionts. The most well-known of these symbioses is that between corals and their dinoflagellate photobionts (Symbiodinium spp.), whose genotype indirectly affects whether a coral can survive cyclical and anthropogenic warming events. Fungi comprise a lesser-known coral symbiotic community whose taxonomy, stability and function is largely un-examined. To assess how fungal communities inside a coral host correlate with water temperature and the genotype of co-occurring Symbiodinium, we sampled Acropora hyacinthus coral colonies from adjacent natural pools with different water temperatures and Symbiodinium identities. Phylogenetic analysis of coral-associated fungal ribosomal DNA amplicons showed a high diversity of Basidiomycetes and Ascomycetes, including several clades separated from known fungal taxa by long and well-supported branches. Community similarity did not correlate with any measured variables, and total fungal community composition was highly variable among A. hyacinthus coral colonies. Colonies in the warmer pool contained more phylogenetically diverse fungal communities than the colder pool and contained statistically significant 'indicator' species. Four taxa were present in all coral colonies sampled, and may represent obligate associates. Messenger RNA sequenced from a subset of these same colonies contained an abundance of transcripts involved in metabolism of complex biological molecules. Coincidence between the taxonomic diversity found in the DNA and RNA analysis indicates a metabolically active and diverse resident marine fungal community.

Molecular characterization of pezizalean ectomycorrhizas associated with pinyon pine during drought

Recent studies using molecular analysis of ectomycorrhizas have revealed that ascomycete fungi, especially members of the order Pezizales, can be important members of ectomycorrhizal (EM) fungal communities. However, little is known about the ecology and taxonomy of many of these fungi. We used data collected during a wet and a dry period to test the hypothesis that pezizalean EM fungi associated with pinyon pine (Pinus edulis) responded positively to drought stress. We also assessed the phylogenetic relationships among six, unknown pezizalean EM fungi, common to our study sites, using rDNA sequences from the internal transcribed spacer and large subunit (LSU) regions of the ribosomal DNA. Sequences of these fungi were then compared to sequences from known taxa to allow finer-scale identification. Three major findings emerged. First, at two sites, pezizalean EM were 44-95% more abundant during a dry year than a wetter year, supporting the hypothesis that pezizalean EM fungi respond positively to dry conditions. Second, four of the six unknown pezizalean EM fungi associated with P. edulis separated from one another consistently regardless of site or year of collection, suggesting that they represented distinct taxa. Third, comparison with LSU sequences of known members of the Pezizales indicated that these four taxa grouped within the genus Geopora of the family Pyronemataceae. Our results provide further evidence of the importance of pezizalean fungi in the ectomycorrhizal symbiosis and demonstrate high local abundance of members of the genus Geopora in drought-stressed pinyon-juniper woodlands.