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ARS Home » Northeast Area » Kearneysville, West Virginia » Appalachian Fruit Research Laboratory » Innovative Fruit Production, Improvement, and Protection » Research » Publications at this Location » Publication #347296
Title: Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence

Author
item LIU, JIA - Chongqing University
item ABDELFATTAH, AHMED - University Of The Mediterranean
item Norelli, John
item Burchard, Erik
item SCHENA, LEONARDO - University Of The Mediterranean
item DROBY, SAMIR - Volcani Center (ARO)
item Wisniewski, Michael

Submitted to: Microbiome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2018
Publication Date: 1/27/2018
Citation: Liu, J., Abdelfattah, A., Norelli, J.L., Burchard, E.A., Schena, L., Droby, S., Wisniewski, M.E. 2018. Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence. BMC Microbiome. 6:18. https://doi.org/10.1186/s40168-018-0403-x.
DOI: https://doi.org/10.1186/s40168-018-0403-x

Interpretive Summary: There is growing interest in the role that the microbiome (the microbial microflora) plays in the physiology, metabolism, and health of the hosts they inhabit. This is especially true for the relationship between many human maladies and composition of the microbiome. In recent years, the term metaorganism has been used to describe a biological entity comprised of a host and its associated microbiome. In addition, the holobiont concept has been forwarded, which states that organisms and their associated microbiome have co-evolved to such a degree that they form a distinct co-evolving entity. In the current study, the endophytic microbiome of different apple scion cultivars, different rootstocks, and various rootstock/scion combinations were characterized. Results indicated that rootstocks and scions had a distinctly different microbiome. When different rootstock/scion combinations were characterized, it appeared that the rootstock had only a minor effect on the composition of the microbiome in the grafted scion wood. Interestingly, the non-dwarfing rootstock was enriched in genera of growth-promoting bacteria that were absent in the dwarfing rootstock. Furthermore, PCoA analysis indicated that the composition of the microbiome was similar in scions that were closely related (similar pedigree) in that they clustered together. In contrast, the microbiome of a scion with a pedigree distinctly different from the related cultivars, clustered independent from the clusters of the scions cultivars that had similar pedigrees. Therefore, the results of the study support the holobiont theory. Further studies are in progress to determine the effect of the microbiome on the physiology and metabolism of different cultivars.

Technical Abstract: The present study described the 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 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 have some influence on the microbiota of an associated scion, but the effect was not statistically significant. Additionally, pedigree had an impact on the endophytic microbiota where closely-related cultivars had similar microbial community compared to distantly-related scion cultivars. The more vigorous rootstock (‘M.M.111’) was observed to be richer in growth-promoting bacteria, compared to the dwarfing rootstock (‘M.9’). The mechanism by which the plant genotype, either rootstock or scion, has a determinant effect on the composition of microbial community is not known, but conforms to the “holobiont” concept in which metaorganisms (plants and their associated microbes) have co-evolved.