Summary
Feedback between plants and soil microbial communities can be a powerful driver of vegetation dynamics. Plants elicit changes in the soil microbiome that either promote or suppress ...conspecifics at the same location, thereby regulating population density‐dependence and species co‐existence. Such effects are often attributed to the accumulation of host‐specific antagonistic or beneficial microbiota in the rhizosphere. However, the identity and host‐specificity of the microbial taxa involved are rarely empirically assessed. Here we review the evidence for host‐specificity in plant‐associated microbes and propose that specific plant–soil feedbacks can also be driven by generalists. We outline the potential mechanisms by which generalist microbial pathogens, mutualists and decomposers can generate differential effects on plant hosts and synthesize existing evidence to predict these effects as a function of plant investments into defence, microbial mutualists and dispersal. Importantly, the capacity of generalist microbiota to drive plant–soil feedbacks depends not only on the traits of individual plants but also on the phylogenetic and functional diversity of plant communities. Identifying factors that promote specialization or generalism in plant–microbial interactions and thereby modulate the impact of microbiota on plant performance will advance our understanding of the mechanisms underlying plant–soil feedback and the ways it contributes to plant co‐existence.
There is increasing knowledge on the diversity of root-endophytic fungi, but limited information on their lifestyles and dependence on hosts hampers our understanding of their ecological functions. ...We compared diversity and biogeographical patterns of cultivable and noncultivable root endophytes to assess whether their occurrence is determined by distinct ecological factors.
The endophytic diversity in roots of nonmycorrhizal Microthlaspi spp. growing across Europe was assessed using high-throughput sequencing (HTS) and compared with a previous dataset based on cultivation of endophytes from the same root samples.
HTS revealed a large fungal richness undetected by cultivation, but which largely comprised taxa with restricted distributions and/or low representation of sequence reads. Both datasets coincided in a consistent high representation of widespread endophytes within orders Pleosporales, Hypocreales and Helotiales, as well as similar associations of community structure with spatial and environmental conditions. Likewise, distributions of particular endophytes inferred by HTS agreed with cultivation data in suggesting individual ecological preferences.
Our findings support that Microthlaspi spp. roots are colonized mostly by saprotrophic and likely facultative endophytes, and that differential niche preferences and distribution ranges among fungi importantly drive the assembly of root-endophytic communities.
Root‐colonizing fungi form species‐rich assemblages with key functions in principal ecosystem processes, making them prospectively important players in conservation and applied ecology. Harnessing ...the processes and services they drive requires a better understanding of their patterns of diversity and community structure, and how these link to function. Here, we search for possible adaptations to contrasting environmental and host conditions, indicative of participation in habitat‐specific processes. We surveyed heathland and grassland habitats across a latitudinal gradient in Western Europe, using a spatially explicit design to assess community variation at scales from centimeters, to thousands of kilometers. Root‐associated fungi assemble into strongly site‐specific communities irrespective of habitat type, shaped by environmental factors and spatial distance operating at different scales, but also by a high level of endemism, likely to be determined by local stochastic processes such as drift and dispersal limitation at short distances. Despite the high site specificity in communities, they are dominated everywhere by a core set of lineages with little preferences toward habitat conditions or host phylogeny. Our results suggest a convergent evolution across phylogenetically distant lineages toward the root‐colonizing habit, and a functional redundancy in strategies for habitat colonization and host interaction. Further efforts are needed to integrate functional trait composition in future community ecology studies of root‐colonizing fungi.
The plant-growth modulating effect of microbial volatile organic compounds (VOCs) has been demonstrated repeatedly. This has most often been performed by exposing plants to VOC released by microbes ...grown on nutrient rich media. Here, we used soil instead to grow fungi of the
genus and investigate how VOCs emitted by this system influenced the development of
plants. The volatile profiles of
strains grown in soil and malt extract were also compared. Our results demonstrate that distinct volatile signatures can be attributed to different
genetic clades but also highlight a major influence of the growth medium on volatile emission. Furthermore, all soil-grown
isolates increased primary root length in
by decreasing VOC concentrations in soil. This result represents a major paradigm shift in plant-microbe interactions since growth modulating effects have been attributed so far to the emission and not the consumption of volatile signals.
Studying community structure and dynamics of plant‐associated fungi is the basis for unravelling their interactions with hosts and ecosystem functions. A recent sampling revealed that only a few ...fungal groups, as defined by internal transcribed spacer region (ITS) sequence similarity, dominate culturable root endophytic communities of nonmycorrhizal Microthlaspi spp. plants across Europe. Strains of these fungi display a broad phenotypic and functional diversity, which suggests a genetic variability masked by ITS clustering into operational taxonomic units (OTUs). The aims of this study were to identify how genetic similarity patterns of these fungi change across environments and to evaluate their ability to disperse and adapt to ecological conditions. A first ITS‐based haplotype analysis of ten widespread OTUs mostly showed a low to moderate genotypic differentiation, with the exception of a group identified as Cadophora sp. that was highly diverse. A multilocus phylogeny based on additional genetic loci (partial translation elongation factor 1α, beta‐tubulin and actin) and amplified fragment length polymorphism profiling of 185 strains representative of the five dominant OTUs revealed a weak association of genetic differences with geography and environmental conditions, including bioclimatic and soil factors. Our findings suggest that dominant culturable root endophytic fungi have efficient dispersal capabilities, and that their distribution is little affected by environmental filtering. Other processes, such as inter‐ and intraspecific biotic interactions, may be more important for the local assembly of their communities.
Fungi are highly diverse organisms, which provide multiple ecosystem services. However, compared with charismatic animals and plants, the distribution patterns and conservation needs of fungi have ...been little explored. Here, we examined endemicity patterns, global change vulnerability and conservation priority areas for functional groups of soil fungi based on six global surveys using a high‐resolution, long‐read metabarcoding approach. We found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan, West‐Central Africa, Sri Lanka, and New Caledonia, with a negligible island effect compared with plants and animals. We also found that fungi are predominantly vulnerable to drought, heat and land‐cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests, and woodlands. We stress that more attention should be focused on the conservation of fungi, especially root symbiotic arbuscular mycorrhizal and ectomycorrhizal fungi in tropical regions as well as unicellular early‐diverging groups and macrofungi in general. Given the low overlap between the endemicity of fungi and macroorganisms, but high conservation needs in both groups, detailed analyses on distribution and conservation requirements are warranted for other microorganisms and soil organisms.
Using a long‐read metabarcoding approach, we found that the endemicity of all fungi and most functional groups peaks in tropical habitats, including Amazonia, Yucatan and West‐Central Africa, with a negligible island effect compared with plants and animals. Fungi are predominantly vulnerable to drought, heat and land cover change, particularly in dry tropical regions with high human population density. Fungal conservation areas of highest priority include herbaceous wetlands, tropical forests and woodlands.
Strains of an endophytic Exophiala sp. produced multiple metabolites similar to exophillic acid, with or without a β-d-glucopyranoside moiety, which presence was associated with the particular ...strain’s morphology. Display omitted
•We studied several strains of an endophytic Exophiala sp. with different geographical origins.•Two novel compounds and exophillic acid were isolated, and 18 related structures were identified.•Compounds in different strains either had or lacked a β-d-glucopyranoside moiety.•Chemical profiles were associated with the particular morphology of strains.
Members of the fungal genus Exophiala are common saprobes in soil and water environments, opportunistic pathogens of animals, or endophytes in plant roots. Their ecological versatility could imply a capacity to produce diverse secondary metabolites, but only a few studies have aimed at characterizing their chemical profiles. Here, we assessed the secondary metabolites produced by five Exophiala sp. strains of a particular phylotype, isolated from roots of Microthlaspi perfoliatum growing in different European localities. Exophillic acid and two previously undescribed compounds were isolated from these strains, and their structures were elucidated by spectroscopic methods using MS, 1D and 2D NMR. Bioassays revealed a weak activity of these compounds against disease-causing protozoa and mammalian cells. In addition, 18 related structures were identified by UPLC/MS based on comparisons with the isolated structures. Three Exophiala strains produced derivatives containing a β-d-glucopyranoside moiety, and their colony morphology was distinct from the other two strains, which produced derivatives lacking β-d-glucopyranoside. Whether the chemical/morphological strain types represent variants of the same genotype or independent genetic populations within Exophiala remains to be evaluated.
Summary
Root endophytic fungi are found in a great variety of plants and ecosystems, but the ecological drivers of their biogeographic distribution are poorly understood. Here, we investigate the ...occurrence of root endophytes in the non‐mycorrhizal plant genus Microthlaspi, and the effect of environmental factors and geographic distance in structuring their communities at a continental scale. We sampled 52 plant populations across the northern Mediterranean and central Europe and used a cultivation approach to study their endophytic communities. Cultivation of roots yielded 2601 isolates, which were grouped into 296 operational taxonomic units (OTUs) by internal transcribed spacer sequencing of 1998 representative colonies. Climatic and spatial factors were the best descriptors of the structure of endophytic communities, outweighing soil characteristics, host genotype and geographical distance. OTU richness was negatively affected by precipitation, and the composition of communities followed latitudinal gradients of precipitation and temperature. Only six widespread OTUs belonging to the orders Pleosporales, Hypocreales and Helotiales represented about 50% of all isolates. Assessments of their individual distribution revealed particular ecological preferences or a cosmopolitan occurrence. Our findings support a strong influence of the local environment in determining root endophytic communities, and show a different niche occupancy by individual endophytes.
Cyclocybe aegerita
(synonym:
Agrocybe aegerita
) is a widely cultivated edible and reportedly almost cosmopolitan mushroom species that serves as a model fungus for basidiome formation and as ...producer of useful natural products and enzymes. Focusing on strains from different continents, here, we present a phylogenetic analysis of this species and some adjacent taxa that employs four phylogenetic markers. In addition, we tested the strains’ capability to fructify on agar media. Our analysis reveals that “
C. aegerita sensu lato
” splits up into the following two well-supported monophyletic geographic lineages: a European clade and an Asian clade. The European one is closely associated with the Chinese species
Cyclocybe salicaceicola
. In contrast, the Asian lineage, which we preliminarily designate as
Cyclocybe chaxingu
agg., may comprise several species (species complex) and clusters with the Pacific species
Cyclocybe parasitica
(New Zealand). In addition, fruiting properties differ across
C. aegerita
and its Asian and Pacific relatives; however, strains from the Asian clade and
C. parasitica
tend to form larger basidiomes with relatively big caps and long stipes and strains from the European clade exhibit a more variable fruiting productivity with the tendency to form more basidiomes, with smaller caps and shorter stipes. Moreover, some strains showed individual fruiting patterns, such as the preference to fruit where they were exposed to injuring stimuli. In conclusion, the delimitation of the newly delimited Asian species complex from our multilocus phylogeny of “
C. aegerita sensu lato
”, which is supported by phenotypic data, depicts an exemplary case of biogeographic diversity within a previously thought homogeneous species of near worldwide distribution.
Root‐associated fungi could play a role in determining both the positive relationship between plant diversity and productivity in experimental grasslands, and its strengthening over time. This ...hypothesis assumes that specialized pathogenic and mutualistic fungal communities gradually assemble over time, enhancing plant growth more in species‐rich than in species‐poor plots. To test this hypothesis, we used high‐throughput amplicon sequencing to characterize root‐associated fungal communities in experimental grasslands of 1 and 15 years of age with varying levels of plant species richness. Specifically, we tested whether the relationship between fungal communities and plant richness and productivity becomes stronger with the age of the experimental plots. Our results showed that fungal diversity increased with plant diversity, but this relationship weakened rather than strengthened over the two time points. Contrastingly, fungal community composition showed increasing associations with plant diversity over time, suggesting a gradual build‐up of specific fungal assemblages. Analyses of different fungal guilds showed that these changes were particularly marked in pathogenic fungi, whose shifts in relative abundance are consistent with the pathogen dilution hypothesis in diverse plant communities. Our results suggest that root‐associated fungal pathogens play more specific roles in determining the diversity–productivity relationship than other root‐associated plant symbionts.
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