Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce

Abstract

The factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high-throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.

Fig. 1

Experimental design and sequencing output. A. Distribution of the four seed orchards (sites) across Southern Sweden. Pairs of sites depicted with the same shape (triangle or circle) contain the same sampled Norway spruce clones. Analyses were done separately for each pair of sites. B. Illustration of the sampling scheme within each site. Fifteen Norway spruce genotypes (clones) were selected and 10 vegetatively propagated biological replicates (ramets) from each clone were sampled, i.e. a total of 600 trees. From each ramet, 10 current year shoots were collected, and the needles were pooled prior to DNA extraction. The final dataset included 421 samples (Supplementary Table S1). In addition, 10 passive spore traps were placed evenly across each site and collected weekly from May to July to capture the composition of the deposited fungal spores. C. Barplot of the relative abundance of fungal classes in the needle mycobiome of each clone for each of the sites. Labels in x‐axis display each of the clones by site. G = Gåtebo, R = Runesten, L = Larslund, S = Söregärde. Dummy class refer to the dummy nodes that Protax creates to fill gaps in taxonomy annotations (Abarenkov et al., 2018). The exact proportions of each fungal class can be found in Supplementary Table S2. Although we display the fungal OTUs grouped by classes, all analyses of this study were done at OTU level.

Fig. 2

Alpha and beta diversity comparisons between clones across sites for the north–south (A,C,E) and the east–west (B,D,F) pairs of sites; (A–D) are ordination plots of a principal coordinate analysis of the needle mycobiome separated clone by site (A and B) and site (C and D). The main circles and bars represent the centroid and standard error of the samples for each of the sites or clones. The small circles represent each of the samples; (E and F) show differences in OTU richness and Shannon index for each clone on each site. The squares represent the mean values of OTU richness or Shannon index. The squares are connected by the same colour line to display differences in mean values across sites.

Fig. 3

Variation explained by clone, site and their interaction on the OTUs grouped by trophic mode and guilds for the (A) North–South and the (B) East–West pair of sites. Error bars indicate standard error.

Fig. 4

(A and C) Comparison of spore communities between sites and (B and D) association between spore communities and needle communities across sites; (A and C) are ordination plots of a principal coordinate analysis for each pair of sites. The main circles and bars represent the centroid and standard error of the samples from each site. The small circles represent each of the samples. The R ² and P values are based on a PERMANOVA analysis performed with the adonis2 function in R; (B and D) are correlations of fold changes in spore and needle communities across sites for the (B) north–south and (D) east–west pair of sites. Each circle represents an OTU that is coloured based on fungal classes. Dummy class refer to the dummy nodes that Protax creates to fill gaps in taxonomy annotations (Abarenkov et al., 2018).

Fig. 5

Association between genetic similarity and mycobiome composition for the five clones that had similar diameter at breast height between the two sites in the East–West pair. A. Dendrogram of the hierarchical clustering of all clones of the study based on the IBS distance matrix. The five clones selected for analyses are marked with coloured square. B. Ordination plot based on a principal coordinate analysis of the needle mycobiome. The main circles and bars represent the centroid and standard error of the samples for each of the clones averaged by site. The small circles represent each of the samples. Also shown are the correlations (r ² and P‐values from envfit function) of the scores of the five clones on the first and second axis of the PCA (Genetic PC1 and 2 vectors) performed on the IBS distance matrix (Supplementary Fig. S1).