Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource‐conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes.     

Soil fungal community changes in response to long-term fire cessation and N fertilization in tallgrass prairie

In grasslands, fire management and fertilization are established drivers of plant community change, but associated soil fungal responses are less well defined. We predicted that soil fungal communities would change seasonally, that decades of fire cessation and nitrogen (N) fertilization would alter fungal distributions, and that plant and fungal community change would be correlated. Surface soils were sampled monthly for 1 y from a 30-y fire by fertilization experiment to evaluate fungal community dynamics and assess correlation with plant community heterogeneity. ITS gene community composition was seasonally stable, excepting increased arbuscular mycorrhizal fungal summer abundance in the burned, fertilized treatment. Long-term treatments affected soil fungal and plant communities, with correlated heterogeneity patterns. Despite woody encroachment in the fire cessation treatment, soil fungal communities did not resemble those of forests. This study provides evidence supporting the strength of feedbacks between fungal and plant community change in response to long-term grassland fire and N management changes.     

Linking symbiont community structures in a model arbuscular mycorrhizal system

? The influence of plant communities on symbiotic arbuscular mycorrhizal fungal (AMF) communities is difficult to study in situ as both symbionts are strongly influenced by some of the same soil and environmental conditions, and thus we have a poor understanding of the potential links in community composition and structure between host and fungal communities. ? AMF were characterized in colonized roots of thermal soil Mimulus guttatus in both isolated plants supporting AMF for only a few months of the growing season and plants growing in mixed plant communities composed of annual and perennial hosts. Cluster and discriminant analysis were used to compare competing models based on either communities or soil conditions. ? Mimulus guttatus in adjacent contrasting plant community situations harbored distinct AMF communities with few fungal taxa occurring in both community types. Isolated plants harbored communities of fewer fungal taxa with lower diversity than plants in mixed communities. Host community type was more indicative than pH of AMF community structure. ? Our results support an inherent relationship between host plant and AMF community structures, although pH-based models were also statistically supported.     

Fungal community composition in neotropical rain forests: the influence of tree diversity and precipitation

Plant diversity is considered one factor structuring soil fungal communities because the diversity of compounds in leaf litter might determine the extent of resource heterogeneity for decomposer communities. Lowland tropical rain forests have the highest plant diversity per area of any biome. Since fungi are responsible for much of the decomposition occurring in forest soils, understanding the factors that structure fungi in tropical forests may provide valuable insight for predicting changes in global carbon and nitrogen fluxes. To test the role of plant diversity in shaping fungal community structure and function, soil (0-20?cm) and leaf litter (O horizons) were collected from six established 1-ha forest census plots across a natural plant diversity gradient on the Isthmus of Panama. We used 454 pyrosequencing and phospholipid fatty acid analysis to evaluate correlations between microbial community composition, precipitation, soil nutrients, and plant richness. In soil, the number of fungal taxa increased significantly with increasing mean annual precipitation, but not with plant richness. There were no correlations between fungal communities in leaf litter and plant diversity or precipitation, and fungal communities were found to be compositionally distinct between soil and leaf litter. To directly test for effects of plant species richness on fungal diversity and function, we experimentally re-created litter diversity gradients in litter bags with 1, 25, and 50 species of litter. After 6?months, we found a significant effect of litter diversity on decomposition rate between one and 25 species of leaf litter. However, fungal richness did not track plant species richness. Although studies in a broader range of sites is required, these results suggest that precipitation may be a more important factor than plant diversity or soil nutrient status in structuring tropical forest soil fungal communities.     

The interactions between plant life form and fungal traits of arbuscular mycorrhizal fungi determine the symbiotic community

Arbuscular mycorrhizal (AM) fungi have traditionally been considered generalist symbionts. However, an increasing number of studies are pointing out the selectivity potential of plant hosts. Plant life form, determined by plant life history traits, seems to drive the AM fungal community composition. The AM fungi also exhibit a wide diversity of functional traits known to be responsible for their distribution in natural ecosystems. However, little is known about the role of plant and fungal traits driving the resultant symbiotic assemblages. With the aim of testing the feedback relationship between plant and fungal traits on the resulting AM fungal community, we inoculated three different plant life forms, i.e. annual herbs, perennial herbs and perennial semi-woody plants, with AM fungal communities sampled in different seasons. We hypothesized that the annual climate variation will induce changes in the mean traits of the AM fungal communities present in the soil throughout the year. Furthermore, the association of plants with different life forms with AM fungi with contrasting life history traits will show certain preferences according to reciprocal traits of the plants and fungi. We found changes in the AM fungal community throughout the year, which were differentially disrupted by disturbance and altered by plant growth form and plant biomass. Both plant and fungal traits clearly contributed to the resultant AM fungal communities. The revealed process can have implications for the functioning of ecosystems since changes in dominant plant life forms or climatic variables could influence the traits of AM fungal communities in soil and hence ecosystem processes.     

Spatial factors and plant attributes influence soil fungal community distribution patterns in the lower reaches of the Heihe River Basin,Northwest China

Inland river basins include critical habitats and provide various ecosystem services in extremely arid lands. However, we know little about the distribution patterns of soil fungal communities in these river basins. We investigated the distribution patterns of soil fungal communities from the riparian oasis zone (ROZ) to the circumjacent desert zone (CDZ) at the lower reaches of the Heihe River. The results indicated that soil fungal communities were mainly dominated by the phyla Ascomycota and Basidiomycota across all samples. The dominant soil fungi taxa were significantly different between ROZ and CDZ habitats at both the phylum and genus levels. Fungal alpha diversity was mainly affected by spatial factors and plant functional traits, and Pearson correlation analysis revealed that fungal alpha diversity was more closely related to plant functional traits than soil properties. Furthermore, fungal community structure was best explained by spatial factors and plant attributes (including plant diversity and plant functional traits). Together, our findings provide new insights into the significance of spatial factors and plant attributes for predicting distributions of fungal communities in arid inland river basins, which will help us better understand the functions and services of these ecosystems.     

Comparisons of AM fungal spore communities with the same hosts but different soil chemistries over local and geographic scales

Arbuscular mycorrhizal (AM) fungi are ubiquitous and ecologically important microbes in grasslands. Both the host plant species and soil properties have been suggested as potentially important factors structuring AM fungal communities based on studies within local field sites. However, characterizations of the communities in relation to both host plant identity and soil properties in natural plant communities across both local and broader geographic scales are rare. We examined the AM fungal spore communities associated with the same C₄ grasses in two Eastern serpentine grasslands, where soils have elevated heavy metals, and two Iowa tallgrass prairie sites. We compared AM fungal spore communities among host plants within each site, looked for correlations between fungal communities and local soil properties, and then compared communities among sites. Spore communities did not vary with host plant species or correlate with local soil chemical properties at any site. They did not differ between the two serpentine sites or between the two prairie sites, despite geographic separation, but they did differ between serpentine and prairie. Soil characteristics are suggested as a driving force because spore communities were strongly correlated with soil properties when data from all four sites are considered, but climatic differences might also play a role.     

Fungal Growth and Biomass Development is Boosted by Plants in Snow-Covered Soil

Soil microbial communities follow distinct seasonal cycles which result in drastic changes in processes involving soil nutrient availability. The biomass of fungi has been reported to be highest during winter, but is fungal growth really occurring in frozen soil? And what is the effect of plant cover on biomass formation and on the composition of fungal communities? To answer these questions, we monitored microbial biomass N, ergosterol, and the amount of fungal hyphae during summer and winter in vegetated and unvegetated soils of an alpine primary successional habitat. The winter fungal communities were identified by rDNA ITS clone libraries. Winter soil temperatures ranged between -0.6°C and -0.1°C in snow-covered soil. We found distinct seasonal patterns for all biomass parameters, with highest biomass concentrations during winter in snow-covered soil. The presence of plant cover had a significant positive effect on the amount of biomass in the soil, but the type of plant cover (plant species) was not a significant factor. A mean hyphal ingrowth of 5.6 m g(-1) soil was detected in snow-covered soil during winter, thus clearly proving fungal growth during winter in snow-covered soil. Winter fungal communities had a typical species composition: saprobial fungi were dominating, among them many basidiomycete yeasts. Plant cover had no influence on the composition of winter fungal communities.     

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.     

Termination of belowground C allocation by trees alters soil fungal and bacterial communities in a boreal forest

The introduction of photosynthates through plant roots is a major source of carbon (C) for soil microbial biota and shapes the composition of fungal and bacterial communities in the rhizosphere. Although the importance of this process, especially to ectomycorrhizal fungi, has been known for some time, the extent to which plant belowground C allocation controls the composition of the wider soil community is not understood. A tree-girdling experiment enabled studies of the relationship between plant C allocation and microbial community composition. Girdling involves cutting the phloem of trees to prevent photosynthates from entering the soil. Four years after girdling, fungal and bacterial communities were characterized using DNA-based profiles and cloning and sequencing. Data showed that girdling significantly altered fungal and bacterial communities compared with the control. The ratio of ectomycorrhizal to saprobic fungal sequences significantly decreased in girdled treatments, and this decline was found to correlate with the fungal phospholipid fatty acid biomarker 18:2ω6,9. Bacterial communities also varied in the abundance of the two dominant phyla Acidobacteria and Alphaproteobacteria . Concomitant changes in fungal and bacterial communities suggest linkages between these two groups and point toward plant belowground C allocation as a key determinant of microbial community composition.     

Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: evidence from a continental‐scale study using massively parallel 454 sequencing

Aim The biogeography of arbuscular mycorrhizal (AM) fungi is poorly understood, and consequently the potential of AM fungi to determine plant distribution has been largely overlooked. We aimed to describe AM fungal communities associating with a single host‐plant species across a wide geographical area, including the plant’s native, invasive and experimentally introduced ranges. We hypothesized that an alien AM plant associates primarily with the geographically widespread generalist AM fungal taxa present in a novel range. Location Europe, China. Methods We transplanted the palm Trachycarpus fortunei into nine European sites where it does not occur as a native species, into one site where it is naturalized (Switzerland), and into one glasshouse site. We harvested plant roots after two seasons. In addition, we sampled palms at three sites in the plant’s native range (China). Roots were subjected to DNA extraction, polymerase chain reaction (PCR) and 454 sequencing of AM fungal sequences. We analysed fungal communities with non‐metric multidimensional scaling (NMDS) ordination and cluster analysis and studied the frequency of geographically widespread fungal taxa with log‐linear analysis. We compared fungal communities in the roots of the palm with those in resident plants at one site in the introduced range (Estonia) where natural AM fungal communities had previously been studied. Results We recorded a total of 73 AM fungal taxa. AM fungal communities in the native and introduced ranges differed from one another, while those in the invasive range contained taxa present in both other ranges. Geographically widespread AM fungal taxa were over‐represented in palm roots in all regions, but especially in the introduced range. At the Estonian site, the palm was colonized by the same community of widespread AM fungal taxa as associate with resident habitat‐generalist plants; by contrast, resident forest‐specialist plants were colonized by a diverse community of widespread and other AM fungal taxa. Main conclusions AM fungal communities in the native, invasive and experimentally introduced ranges varied in taxonomic composition and richness, but they shared a pool of geographically widespread, non‐host‐specific taxa that might support the invasion of a generalist alien plant. Our dataset provides the first geographical overview of AM taxon distributions obtained using a single host‐plant species.     

Host plant species effects on arbuscular mycorrhizal fungal communities in tallgrass prairie

Symbiotic associations between plants and arbuscular mycorrhizal (AM) fungi are ubiquitous in many herbaceous plant communities and can have large effects on these communities and ecosystem processes. The extent of species-specificity between these plant and fungal symbionts in nature is poorly known, yet reciprocal effects of the composition of plant and soil microbe communities is an important assumption of recent theoretical models of plant community structure. In grassland ecosystems, host plant species may have an important role in determining development and sporulation of AM fungi and patterns of fungal species composition and diversity. In this study, the effects of five different host plant species [Poa pratensis L., Sporobolus heterolepis (A. Gray) A. Gray, Panicum virgatum L., Baptisia bracteata Muhl. ex Ell., Solidago missouriensis Nutt.] on spore communities of AM fungi in tallgrass prairie were examined. Spore abundances and species composition of fungal communities of soil samples collected from patches within tallgrass prairie were significantly influenced by the host plant species that dominated the patch. The AM fungal spore community associated with B. bracteata showed the highest species diversity and the fungi associated with Pa. virgatum showed the lowest diversity. Results from sorghum trap cultures using soil collected from under different host plant species showed differential sporulations of AM fungal species. In addition, a greenhouse study was conducted in which different host plant species were grown in similar tallgrass prairie soil. After 4 months of growth, AM fungal species composition was significantly different beneath each host species. These results strongly suggest that AM fungi show some degree of host-specificity and are not randomly distributed in tallgrass prairie. The demonstration that host plant species composition influences AM fungal species composition provides support for current feedback models predicting strong regulatory effects of soil communities on plant community structure. Differential responses of AM fungi to host plant species may also play an important role in the regulation of species composition and diversity in AM fungal communities. Received: 29 January 1999 / Accepted: 20 October 1999     

Availability and function of arbuscular mycorrhizal and ectomycorrhizal fungi during revegetation of dewatered reservoirs left after dam removal

Revegetation following dam removal projects may depend on recovery of arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) fungal communities, which perform valuable ecosystem functions. This study assessed the availability and function of AM and EM fungi for plants colonizing dewatered reservoirs following a dam removal project on the Elwha River, Olympic Peninsula, Washington, United States. Availability was assessed via AM fungal spore density in soils and EM root tip colonization of Salix sitchensis (Sitka willow) in an observational field study. The effect of mycorrhizal fungi from 4 sources (reservoir soils, commercial inoculum, and 2 mature plant community soils) on growth and nutrient status of S. sitchensis was quantified in a greenhouse study. AM fungal spores and EM root tips were present in all field samples. In the greenhouse, plants receiving reservoir soil inoculum had only incipient mantle formation, while plants receiving inoculum from mature plant communities had fully formed EM root tips. EM formation corresponded with alleviation of phosphorus stress in plants (lower shoot nitrogen:phosphorus). Thus, revegetating plants have access to AM and EM fungi following dam removal, and EM formation may be especially important for plant P uptake in reservoir soils. However, availability of mycorrhizal fungi declines with distance from established plant communities. Furthermore, EM fungal communities in recently dewatered reservoirs may not be as effective at forming beneficial mycorrhizae as those from mature plant communities. Whole soil inoculum from mature plant communities may be important for the success of revegetating plants and recovery of mycorrhizal fungal communities.     

Arbuscular mycorrhizal communities in tropical forests are affected by host tree species and environment

Arbuscular mycorrhizal (AM) fungi are mutualists with plant roots that are proposed to enhance plant community diversity. Models indicate that AM fungal communities could maintain plant diversity in forests if functionally different communities are spatially separated. In this study we assess the spatial and temporal distribution of the AM fungal community in a wet tropical rainforest in Costa Rica. We test whether distinct fungal communities correlate with variation in tree life history characteristics, with host tree species, and the relative importance of soil type, seasonality and rainfall. Host tree species differ in their associated AM fungal communities, but differences in the AM community between hosts could not be generalized over life history groupings of hosts. Changes in the relative abundance of a few common AM fungal species were the cause of differences in AM fungal communities for different host tree species instead of differences in the presence and absence of AM fungal species. Thus, AM fungal communities are spatially distinguishable in the forest, even though all species are widespread. Soil fertility ranging between 5 and 9 Mg/ha phosphorus did not affect composition of AM fungal communities, although sporulation was more abundant in lower fertility soils. Sampling soils over seasons revealed that some AM fungal species sporulate profusely in the dry season compared to the rainy season. On one host tree species sampled at two sites with vastly different rainfall, relative abundance of spores from Acaulospora was lower and that of Glomus was relatively higher at the site with lower and more seasonal rainfall.     

Long-lasting modification of soil fungal diversity associated with the introduction of rabbits to a remote sub-Antarctic archipelago

During the late nineteenth century, Europeans introduced rabbits to many of the sub-Antarctic islands, environments that prior to this had been devoid of mammalian herbivores. The impacts of rabbits on indigenous ecosystems are well studied; notably, they cause dramatic changes in plant communities and promote soil erosion. However, the responses of fungal communities to such biotic disturbances remain unexplored. We used metabarcoding of soil extracellular DNA to assess the diversity of plant and fungal communities at sites on the sub-Antarctic Kerguelen Islands with contrasting histories of disturbance by rabbits. Our results suggest that on these islands, the simplification of plant communities and increased erosion resulting from the introduction of rabbits have driven compositional changes, including diversity reductions, in indigenous soil fungal communities. Moreover, there is no indication of recovery at sites from which rabbits were removed 20 years ago. These results imply that introduced herbivores have long-lasting and multifaceted effects on fungal biodiversity as well as highlight the low resiliency of sub-Antarctic ecosystems.     

Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field‐based tree experiment

Exploring the link between above‐ and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well‐recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field‐based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant‐associated effects on soil fungal communities are largely guild‐specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness.     

Divergent phenologies may facilitate the coexistence of arbuscular mycorrhizal fungi in a North Carolina grassland

Interest in the diversity of arbuscular mycorrhizal (AM) fungal communities has been stimulated by recent data that demonstrate that fungal communities influence the competitive hierarchies, productivity, diversity, and successional patterns of plant communities. Although natural communities of AM fungi are diverse, we have a poor understanding of the mechanisms that promote and maintain that diversity. Plants may coexist by inhabiting disparate temporal niches; plants of many grasslands are either warm or cool season specialists. We hypothesized that AM fungi might be similarly seasonal. To test our hypothesis, we tracked the sporulation of individual AM fungal species growing within a North Carolina grassland. Data were collected in 1996 and 1997; in 1997, sampling focused on two common species. We found that AM fungi, especially Acaulospora colossica and Gigaspora gigantea, maintained different and contrasting seasonalities. Acaulospora colossica sporulated more frequently in the warm season, but Gi. gigantea sporulated more frequently in the cool season. Moreover, AM fungal species were spatially aggregated at a fine scale. Contrasting seasonal and spatial niches may facilitate the maintenance of a diverse community of AM fungi. Furthermore, these data may illuminate our understanding of the AM fungal influence on plant communities: various fungal species may preferentially associate with different plant species and thereby promote diversity in the plant community.     

Environmental filtering structures fungal endophyte communities in tree bark

The factors that control the assembly and composition of endophyte communities across plant hosts remains poorly understood. This is especially true for endophyte communities inhabiting inner tree bark, one of the least studied components of the plant microbiome. Here, we test the hypothesis that bark of different tree species acts as an environmental filter structuring endophyte communities, as well as the alternative hypothesis, that bark acts as a passive reservoir that accumulates a diverse assemblage of spores and latent fungal life stages. We develop a means of extracting high‐quality DNA from surface sterilized tree bark to compile the first culture‐independent study of inner bark fungal communities. We sampled a total of 120 trees, spanning five dominant overstorey species across multiple sites in a mixed temperate hardwood forest. We find that each of the five tree species harbour unique assemblages of inner bark fungi and that angiosperm and gymnosperm hosts harbour significantly different fungal communities. Chemical components of tree bark (pH, total phenolic content) structure some of the differences detected among fungal communities residing in particular tree species. Inner bark fungal communities were highly diverse (mean of 117–171 operational taxonomic units per tree) and dominated by a range of Ascomycete fungi living asymptomatically as putative endophytes. Together, our evidence supports the hypothesis that tree bark acts as an environmental filter structuring inner bark fungal communities. The role of these potentially ubiquitous and plant‐specific fungal communities remains uncertain and merits further study.     

Can fungal endophytes fast-track plant adaptations to climate change?

Rapid climate change threatens plant communities. While many studies address the impact of climate change on plants and mechanisms of their resilience to climate stressors, the role of the plant microbiome in aiding plants' adaptation to climate change has been less investigated. We argue here that fungal endophytes, an important constituent of the plant microbiome, may be key to the ability of plants to adapt to climatic stressors. The rapid adaptive response of endophytes coupled with their ability to ‘transfer’ resistance to their hosts may fast-track plants' adaptation to climate change. We briefly review the importance of Class 3 fungal endophytes of terrestrial plants and discuss how they may accelerate adaptations to climate change in crops and natural plant communities and call for efforts directed at improving the understanding of fungal endophyte-facilitated plant health. Such information could aid in devising improved strategies for mitigating climate change effects on plant communities.     

Higher host plant specialization of root‐associated endophytes than mycorrhizal fungi along an arctic elevational gradient

How community‐level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root‐associated fungi for plant species, asking whether the level of specialization varies with elevation. For this, we applied DNA barcoding based on the ITS region to root samples of five plant species equivalently sampled along an elevational gradient at a high arctic site. To assess whether the level of specialization changed with elevation and whether the observed patterns varied between mycorrhizal and endophytic fungi, we applied a joint species distribution modeling approach. Our results show that host plant specialization is not environmentally constrained in arctic root‐associated fungal communities, since there was no evidence for changing specialization with elevation, even if the composition of root‐associated fungal communities changed substantially. However, the level of specialization for particular plant species differed among fungal groups, root‐associated endophytic fungal communities being highly specialized on particular host species, and mycorrhizal fungi showing almost no signs of specialization. Our results suggest that plant identity affects associated mycorrhizal and endophytic fungi differently, highlighting the need of considering both endophytic and mycorrhizal fungi when studying specialization in root‐associated fungal communities.