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•Dispersal limitation, biotic interactions and environmental filters interact to drive plant and fungal community assembly, but their combined effects are rarely investigated. •This study examines how different heathland plant and fungal colonization scenarios realized via three biotic treatments ‐ addition of mature heathland derived sod, addition of hay and no additions ‐ affect soil fungal community development over six years along a manipulated pH gradient in a large‐scale experiment starting from an agricultural, topsoil removed state. •Our results show that both biotic and abiotic (pH) treatments had a persistent influence on the development of fungal communities, but that sod additions diminished the effect of abiotic treatments through time. Analysis of correlation networks between soil fungi and plants suggests that the reduced effect of pH in the sod treatment, where both soil and plant propagules were added, might be due to plant‐fungal interactions since the sod additions caused stronger, more specific, and more consistent connections compared to no addition treatment. •Based on these results, we suggest that the initial availability of heathland fungal and plant taxa, that reinforce each other, can significantly steer further fungal community development to an alternative configuration, overriding otherwise prominent effect of abiotic (pH) conditions.

Background and Aims Although soil-inhabiting fungi can affect tree health and biomass production in managed and pristine forests, little is known about the sensitivity of the plant-fungal associations to long-term changes in land use. We aimed to investigate how reforestation of farmlands change soil characteristics and affected the recovery of soil fungal functional guilds. Methods We examined edaphic conditions and fungal communities (Illumina Sequencing) in three land-use types: primary forests (PF), secondary forests (SF, established over two decades ago) and active farmlands during May, July and September in Wuying, China. Results Edaphic conditions and general fungal communities varied with land-use. Interestingly, overall fungal diversity was higher in soils at the farmland than at the forested sites, possibly as a result of recurring disturbances (tilling) allowing competitive release as described by the intermediate disturbance hypothesis. Although ectomycorrhizal fungal diversity and richness were marginally higher in PF than in SF, the latter still hosted surprisingly diverse and abundant ectomycorrhizal fungal communities. Conclusions Reforestation largely restored fungal communities that were still in transition, as their composition in SF was distinct from that in PF. Our results highlight the ability of fungi grown in previously strongly managed agricultural land to rapidly respond to reforestation and thus provide support for forest trees.

Fungi are the agents primarily responsible for the transformation of plant-derived carbon in terrestrial ecosystems. However, little is known of their responses to the seasonal changes in resource availability in deciduous forests, including photosynthate allocation below ground and seasonal inputs of fresh litter. Vertical stratification of and seasonal changes in fungal abundance, activity and community composition were investigated in the litter, organic and upper mineral soils of a temperate Quercus petraea forest using ergosterol and extracellular enzyme assays and amplicon 454-pyrosequencing of the rDNA-ITS region. Fungal activity, biomass and diversity decreased substantially with soil depth. The highest enzyme activities were detected in winter, especially in litter, where these activities were followed by a peak in fungal biomass during spring. The litter community exhibited more profound seasonal changes than did the community in the deeper horizons. In the litter, saprotrophic genera reached their seasonal maxima in autumn, but summer typically saw the highest abundance of ectomycorrhizal taxa. Although the composition of the litter community changes over the course of the year, the mineral soil shows changes in biomass. The fungal community is affected by season. Litter decomposition and phytosynthate allocation represent important factors contributing to the observed variations.

Plastic film mulching (PFM) is a widely used agricultural practice in the temperate semi-arid Loess Plateau of China. However, how beneficial soil microbes, arbuscular mycorrhizal (AM) fungi in particular, respond to the PFM practice is not known. Here, a field experiment was performed to study the effects of a 3-month short-term PFM practice on AM fungi in plots planted with spring wheat (Triticum aestivum L. cv. Dingxi-2) in the Loess Plateau. AM colonization, spore density, wheat spike weight, and grain phosphorus (P) content were significantly increased in the PFM treatments, and these changes were mainly attributable to changes in soil properties such as available P and soil moisture. Alkaline phosphatase activity was significantly higher in PFM soils, but levels of AM fungal-related glomalin were similar between treatments. A total of nine AM fungal phylotypes were detected in root samples based on AM fungal SSU rDNA analyses, with six and five phylotypes in PFM and no-PFM plots, respectively. Although AM fungal phylotype richness was not statistically different between treatments, the community compositions were different, with four and three specific phylotypes in the PFM and no-PFM plots, respectively. A significant and rapid change in AM fungal, wheat, and soil variables following PFM suggested that the functioning of the AM symbiosis had been changed in the wheat field under PFM. Future studies are needed to investigate whether PFM applied over a longer term has a similar effect on the AM fungal community and their functioning in an agricultural ecosystem.

Microbial symbionts inhabit tissues of all plants and animals. Their community composition depends largely on two ecological processes: (1) filtering by abiotic conditions and host species determining the environments that symbionts are able to colonize and (2) dispersal-limitation determining the pool of symbionts available to colonize a given host and community spatial structure. In plants, the above- and belowground tissues represent such distinct habitats for symbionts that we expect different effects of filtering and spatial structuring on their symbiont communities. In this study, we characterized above- and belowground communities of fungal endophytes—fungi living asymptomatically within plants—to understand the contributions of filtering and spatial structure to endophyte community composition. We used a culture-based approach to characterize endophytes growing in leaves and roots of three species of coastal beachgrasses in dunes of the USA Pacific Northwest. For leaves, endophyte isolation frequency and OTU richness depended primarily on plant host species. In comparison, for roots, both isolation frequency and OTU richness increased from the nutrient-poor front of the dune to the higher-nutrient backdune. Endophyte community composition in leaves exhibited a distance-decay relationship across the region. In a laboratory assay, faster growth rates and lower spore production were more often associated with leaf- than root-inhabiting endophytes. Overall, our results reveal a greater importance of biotic filtering by host species and dispersal-limitation over regional geographic distances for aboveground leaf endophyte communities and stronger effects of abiotic environmental filtering and locally patchy distributions for belowground root endophyte communities.

Premise of the study: Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities. Methods: Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of five North American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska). Key results: Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, reflecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences reflected climate factors more strongly than geographic distance alone. Conclusions: Our study provides a first evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition reflect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specificity, metabolic capability, and comparative genomics.

Endophytic fungi play an important role in the life of grapevine, either as beneficial microorganisms or as pathogens. Many surveys concerning the fungal grapevine community have been conducted. Nevertheless, exactly how the fungal community arises within the plant and develops from young shoots to mature vines is still unknown. Therefore, it was the aim of this study to investigate the early development of endophytic fungal communities in healthy grapevine branches from 2 months to 8 years old. More than 3800 fungi belonging to 86 operational taxonomic units (OTUs) were isolated from wood samples and assigned to eight age groups. The community composition within the age groups changed and significant differences between young (≤ 1 year) and old (> 1 year) branches were found. The former were primarily dominated by ubiquitous, fast-growing fungi like Alternaria spp., Aureobasidium pullulans, Cladosporium spp., or Epicoccum nigrum, while communities of perennial branches additionally harbored many grapevine trunk disease (GTD)-associated fungi such as Diplodia seriata or Eutypa lata. This work gives an insight into the early development of fungal communities in grapevine, the nature and composition of primary settlers and core communities, as well as the emergence of GTD-associated fungi in perennial wood. This information may help grapevine growers to better estimate the risk in relation to the applied training system, producing mainly old branches or young shoots.

There is consensus that plant species richness enhances plant productivity within natural grasslands, but the underlying drivers remain debated. Recently, differential accumulation of soil-borne fungal pathogens across the plant diversity gradient has been proposed as a cause of this pattern. However, the below-ground environment has generally been treated as a ‘black box’ in biodiversity experiments, leaving these fungi unidentified. Using next generation sequencing and pathogenicity assays, we analysed the community composition of root-associated fungi from a biodiversity experiment to examine if evidence exists for host specificity and negative density dependence in the interplay between soil-borne fungi, plant diversity and productivity. Plant species were colonised by distinct (pathogenic) fungal communities and isolated fungal species showed negative, species-specific effects on plant growth. Moreover, 57% of the pathogenic fungal operational taxonomic units (OTUs) recorded in plant monocultures were not detected in eight plant species plots, suggesting a loss of pathogenic OTUs with plant diversity. Our work provides strong evidence for host specificity and negative density-dependent effects of root-associated fungi on plant species in grasslands. Our work substantiates the hypothesis that fungal root pathogens are an important driver of biodiversity-ecosystem functioning relationships.

The rhizosphere microbiome is regulated by plant genotype, root exudates and environment. There is substantial interest in breeding and managing crops that host root microbial communities that increase productivity. The eudicot model species Arabidopsis has been used to investigate these processes, however a model for monocotyledons is also required. We characterized the rhizosphere microbiome and root exudates of Brachypodium distachyon, to develop it as a rhizosphere model for cereal species like wheat. The Brachypodium rhizosphere microbial community was dominated by Burkholderiales. However, these communities were also dependent on how tightly they were bound to roots, the root type they were associated with (nodal or seminal roots), and their location along the roots. Moreover, the functional gene categories detected in microorganisms isolated from around root tips differed from those isolated from bases of roots. The Brachypodium rhizosphere microbiota and root exudate profiles were similar to those reported for wheat rhizospheres, and different to Arabidopsis. The differences in root system development and cell wall chemistry between monocotyledons and eudicots may also influence the microorganism composition of these major plant types. Brachypodium is a promising model for investigating the microbiome of wheat.

Arbuscular mycorrhizal fungi (AMF) were surveyed for species richness and abundance in sporulation in six distinct land uses in the western Amazon region of Brazil. Areas included mature pristine forest and sites converted to pasture, crops, agroforestry, young and old secondary forest. A total of 61 AMF morphotypes were recovered and 30% of them could not be identified to known species. Fungal communities were dominated by Glomus species but Acaulospora species produced the most abundant sporulation. Acaulospora gedanensis cf., Acaulospora foveata, Acaulospora spinosa, Acaulospora tuberculata, Glomus corymbiforme, Glomus sp15, Scutellospora pellucida, and Archaeospora trappei sporulated in all land use areas. Total spore numbers were highly variable among land uses. Mean species richness in crop, agroforestry, young and old secondary forest sites was twice that in pristine forest and pasture. fungal communities were dominated in all land use areas except young secondary forest by two or three species which accounted for 48% to 63% of all sporulation. Land uses influenced AMF community in (1) frequency of occurrence of sporulating AMF species, (2) mean species diversity, and (3) relative spore abundance. Conversion of pristine forest into distinct land uses does not appear to reduce AMF diversity. Cultural practices adopted in this region maintain a high diversity of arbuscular mycorrhizal fungi.