Significant host‐ and environment‐dependent differentiation among highly sporadic fungal endophyte communities in cereal crops‐related wild grasses

Abstract

Summary Endophytic fungi compose a significant part of plant microbiomes. However, while a small number of fungal taxa have proven beneficial impact, the vast majority of fungal endophytes remain uncharacterized, and the drivers of fungal endophyte community (FEC) assembly are not well understood. Here, we analysed FECs in three cereal crops‐related wild grasses – Avena sterilis, Hordeum spontaneum and Aegilops peregrina – that grow in mixed populations in natural habitats. Taxa in Ascomycota class Dothideomycetes, particularly the genera Alternaria and Cladosporium, were the most abundant and prevalent across all populations, but there was also high incidence of basidiomyceteous yeasts of the class Tremellomycetes. The fungal community was shaped to large extent by stochastic processes, as indicated by high level of variation even between individuals from local populations of the same plant species, and confirmed by the neutral community model and Raup‐Crick index. Nevertheless, we still found strong determinism in FEC assembly with both incidence and abundance data sets. Substantial differences in community composition across host species and locations were revealed. Our research demonstrated that assembly of FECs is affected by stochastic as well as deterministic processes and suggests strong effects of environment heterogeneity and plant species on community composition. In addition, a small number of taxa had high incidence and abundance in all of the 15 populations. These taxa represent an important part of the core FEC and might be of general functional importance.

Stem Endophytic Mycobiota in Wild and Domesticated Wheat: Structural Differences and Hidden Resources for Wheat Improvement

“…A. infectoria is associated with black point symptom or reduced grain quality [42,43], and has also been reported as an endophyte in non-wheat plants [44,45]. However, the very high incidence and abundance of A. infectoria in FECs from wheat-related wild plants that was observed in the current and a related study [2] argues that this fungus is part of the plants mycobiome rather than a pathogen.…”

“…DNA was extracted as described by Sun et al [2]. In brief, samples were lyophilized overnight and homogenized to a fine powder using a Geno/Grinder 2000 (OPS Diagnostics, Bridgewater, NJ, USA).…”

“…ITS amplicon libraries were produced from 596 DNA samples by the Environmental Sample Preparation and Sequencing Facility (ESPSF) at Argonne National Laboratory (as described by Sun et al [2]). Briefly, amplicon libraries targeting the fungal ribosomal ITS1 region were produced using ITS1f (5 -CTTGGTCATTTAGAGGAAGTAA-3 ) and ITS2r (5 -GCTGCGTTCTTCATCGATGC-3 ) primers [16].…”

“…In addition, incidence of each associated pairwise among sites and its accumulated rho (for positive and negative values, respectively) were also recorded. Considering the high stochasiticity in endophytic fungal communities of wild cereals [2], we assumed that the associated pairwise, which occurred in only one population, were probably caused by random factors and thus discarded them. Co-occurrence association networks visualized for each host combining all associated pairwise events that occurred at least twice.…”

“…sharonensis and T. dicoccoides. 3in [2] is the total relative variation within a given species (row) in all locations (entire set of the sampled plants of that species). For example, 0.702 is the total relative variation within species AS.…”