Abstract
BackgroundHigh-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.ResultsResults 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).ConclusionsThe 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.
Highlights
High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and internal transcribed spacer (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
We 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 analysis of the bacterial operational taxonomic units (OTUs) data indicated a large degree of variability with the “Honey Crisp”/“M.M.111” samples exhibiting the lowest number of OTUs and the “Royal Gala”/“M.9” samples exhibiting the highest number of OTUs (Fig. 1b)
Summary
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 various attributes that contribute to disease resistance and size control, have not always been clearly elucidated, though specific genetic markers for various important traits in apple have been established [1,2,3,4]. Abdelfattah et al [8] noted that different portions of an apple fruit (stem-end, peel, wound, and calyx-end), surveyed at the point-ofpurchase (supermarket), possess a distinct microbiota and noted a predominance of yeast often associated with dermal disorders (rashes) in humans
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