Metabarcoding of fungal assemblages in Vaccinium myrtillus endosphere suggests colonization of above-ground organs by some ericoid mycorrhizal and DSE fungi

Abstract

Plants harbor in their external surfaces and internal tissues a highly diverse and finely structured microbial assembly, the microbiota. Each plant compartment usually represents a unique ecological niche hosting a distinct microbial community and niche differentiation, which may mirror distinct functions of a specialized microbiota, has been mainly investigated for bacteria. Far less is known for the fungal components of the plant-associated microbiota. Here, we applied a metabarcoding approach to describe the fungal assemblages in different organs of Vaccinium myrtillus plants (Ericaceae) collected in a subalpine meadow in North-West Italy, and identified specific taxa enriched in internal tissues of roots, stems, leaves and flowers. We also traced the distribution of some important fungi commonly associated with plants of the family Ericaceae, namely the ericoid mycorrhizal (ErM) fungi and the dark septate endophytes (DSE), both playing important roles in plant growth and health. Operational taxonomic units attributed to established ErM fungal species in the genus Hyaloscypha and to DSE species in the Phialocephala-Acephala applanata complex (PAC) were found in all the plant organs. Mycorrhizal fungi are thought to be strictly associated with the plant roots, and this first observation of ErM fungi in the above-ground organs of the host plant may be explained by the evolutionary closeness of ErM fungi in the genus Hyaloscypha with non mycorrhizal fungal endophytes. This is also witnessed by the closer similarities of the ErM fungal genomes with the genomes of plant endophytes than with those of other mycorrhizal fungi, such as arbuscular or ectomycorrhizal fungi.

Figure 1

Beta-diversity of the fungal assemblages associated with the different plant organs. The beta-diversity among the different organs was estimated by a NMDS analysis based on Bray–Curtis dissimilarities, with the following parameters: taxonomic level: feature, statistical method: PERMANOVA, experimental factor: organ. Fi = Flowers, Fo = Leaves, Fu = Stems, R = Roots. C1-C5: samples.

Figure 2

Description of the fungal diversity associated with different plant organs: relative abundance of fungal classes.

Figure 3

Heat tree matrix depicting the different taxa abundance among the plant organs, for all orders in the dataset. The size of the nodes in the gray cladogram (right) represents the number of OTUs identified at that taxonomic level. The small cladograms show the pairwise comparisons among the organs: a yellow node indicates a higher abundance of the taxon in the organ indicated in yellow than in the organ indicated in green. A green node indicates the opposite. Taxa identified as differently represented, statistically supported by the Wilcoxon test (p < 0.05), are tagged with a white asterisk.

Figure 4

OTU distribution in the different samples and fungal genera in the core OTUs. (a) Venn diagram of the OTUs from the different plant organs; (b) relative abundance of the genera within the 214 core OTUs.

Figure 5

Distribution of reads from the mycorrhizal species O. maius, H. gryndleri and H. hepaticicola, and the core OTU716 assigned to the DSE P. fortinii (PAC) in the V. myrtillus organs (double clustering based on average linkage algorithm and Pearson correlation). Numbers in the matrix represent the absolute reads supporting the OTUs. The color key represents the log scale of the number of reads.