Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence

Abstract

Background: High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The objectives were to (1) determine if the microbiota differs in different rootstocks and apple varieties and (2) determine if specific rootstock-scion combinations influence the microbiota composition of either component.

Results: Results indicated that Ascomycota (47.8%), Zygomycota (31.1%), and Basidiomycota (11.6%) were the dominant fungal phyla across all samples. The majority of bacterial sequences were assigned to Proteobacteria (58.4%), Firmicutes (23.8%), Actinobacteria (7.7%), Bacteroidetes (2%), and Fusobacteria (0.4%). Rootstocks appeared to influence the microbiota of associated grafted scion, but the effect was not statistically significant. Pedigree also had an impact on the composition of the endophytic microbiota, where closely-related cultivars had a microbial community that was more similar to each other than it was to a scion cultivar that was more distantly-related by pedigree. The more vigorous rootstock (M.M.111) was observed to possess a greater number of growth-promoting bacterial taxa, relative to the dwarfing rootstock (M.9).

Conclusions: The mechanism by which an apple genotype, either rootstock or scion, has a determinant effect on the composition of a microbial community is not known. The similarity of the microbiota in samples with a similar pedigree suggests the possibility of some level of co-evolution or selection as proposed by the "holobiont" concept in which metaorganisms have co-evolved. Clearly, however, the present information is only suggestive, and a more comprehensive analysis is needed.

Keywords: Apple; Endophytic microbiota; Holobiont; Rootstock; Scion cultivar.

Fig. 1

Boxplot illustrating the differences in Shannon diversity measures of the fungal (a) and bacterial (b) communities in the tested apple cultivars and rootstocks

Fig. 2

Bar charts showing the relative abundance of most abundant (> 1%) fungal (a) and bacterial (b) genera detected across all samples

Fig. 3

Principle Coordinate Analysis (PCoA) based on Bray Curtis dissimilarity metrics, showing the distance in the fungal (a–d) and bacterial (e–h) communities between the same cultivars when grafted on different rootstocks, i.e., M.M.111 or M.9. The dissimilarity metrics are also presented for the “M.9” and “M.M. 111” ungrafted rootstocks (a, e)

Fig. 4

Stacked bar charts showing the relative abundance of most dominant fungal (a) and bacterial (b) phyla and classes and their distribution between M.9 and M.M.111 rootstocks using a cutoff of 0.1% across all samples

Fig. 5

A comparison of the relative abundance of the most abundant fungal (a) and bacterial (b) taxa (≥ 1%) in the three different scion cultivars, “Golden Delicious,” “Royal Gala,” and “Honey Crisp”

Fig. 6

Principle Coordinate Analysis (PCoA) based on Bray Curtis dissimilarity metrics, showing the distance in the fungal communities of all three scion cultivars (“Golden Delicious,” “Royal Gala,” and “Honey Crisp”) grafted on “M.9” or “M.M.111” rootstocks. Note that cultivars with a more closely related pedigree (“Golden Delicious” and “Royal Gala”) cluster closer to each other than the scion cultivar (“Honey Crisp”) with a less-related pedigree

Fig. 7

Pedigree of “Honey Crisp” and “Royal Gala” scion cultivars and “M.9” and “M.M.111” rootstocks. Note that “Royal Gala” is more closely related to “Golden Delicious” than “Honey Crisp.” The two rootstocks also appear to have little in common in their pedigree, although the exact pedigree of “M.9” has not been determined