Genotypic diversity in root‐endophytic fungi reflects efficient dispersal and environmental adaptation

Abstract

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.

Brassicaceous roots as an unexpected diversity hot-spot of helotialean endophytes

“…Just considering our isolates, all species with more than two isolates had representatives at separate locations over Europe, while often co-existing in the same site with isolates from other Cadophora species. This reproduces observations made by Grünig et al (2002) and Piercey et al (2004) on P. fortinii, who found individuals from separate locations to be more closely related to one another than were individuals collected a few meters apart, and also matches similar results with several lineages of dominant root endophytes (Glynou et al 2017). The mechanisms for this long distance dispersal are unknown, e.g., whether this is achieved via conidial dispersion or via transportation within plant material as microsclerotia or other diaspores (Currah et al 1993).…”

“…across western and southern Europe, as well as a number of other related phylotypes with a lower abundance and variable distribution breadths. In spite of their clustering in ITS-based phylotypes based on a 97 % pairwise sequence similarity threshold, isolates in these groups show a high within-phylotype variation in their ITS sequences, their morphology, and their pro les of secondary metabolites production as compared to other lineages of fungal endophytes (Glynou et al 2017;Maciá-Vicente et al 2018). Altogether, this variability suggests that these helotialean fungi do not constitute a homogeneous population of widespread and generalist endophytes, but rather comprise a fragmentary array of lineages that have undergone adaptations to local conditions.…”

Facultative root‐colonizing fungi dominate endophytic assemblages in roots of nonmycorrhizal Microthlaspi species

“…Mainly, we observed a stronger association of assemblages with soil characteristics and spatial effects than detected by cultivation (Glynou et al ., ). Our results indicate that most cultivable fungi have potentially wide niche breadths and cosmopolitan distributions (Glynou et al ., ), with occurrences likely associated with range‐wide variables such as climate. HTS revealed an important proportion of previously overlooked OTUs, endemic to restricted localities and that probably are sensitive to local shifts in their habitats (Poisot et al ., ).…”

Metabolomics‐based chemotaxonomy of root endophytic fungi for natural products discovery

“…In our collection, most helotialean isolates were Cadophora species or close relatives. They have a high genotypic diversity that contrasts with the relative homogeneity of dominant OTUs in Pleosporales and Hypocreales (Glynou et al ., ). It is plausible that such variability is reflected by their chemical profiles, suggesting a segregation of phylotypes into local sub‐populations with divergent phenotypes, as found elsewhere (Cheikh‐Ali et al ., ).…”

“…For instance, a few dominant species have been shown to be ubiquitous across large geographical areas but to follow different ecological patterns (Glynou et al ., ). Many isolates in these species appear to be rather genetically similar (Glynou et al ., ) but display divergent morphological and chemical traits and plant effects (Cheikh‐Ali et al ., ; Kia et al ., ). Therefore, our collection of isolates is suitable to assess patterns of variation in the secondary metabolome between/within fungal lineages, across geography and across ecological conditions.…”