Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks

Authors: LIU, JIA - Chongqing University; ABDELFATTAH, AHMED - Universitat Graz; WASSERMAN, BIRGIT - Universitat Graz; WISNIEWSKI, MICHAEL - Virginia Polytechnic Institution & State University; DROBY, SAMIR - Volcani Center (ARO); Fazio, Gennaro; MAZZOLA, MARK - Retired ARS Employee; WU, XUEHONG - China Agricultural University

Submitted to: Horticulture Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2021
Publication Date: 1/18/2022
Citation: Liu, J., Abdelfattah, A., Wasserman, B., Wisniewski, M., Droby, S., Fazio, G., Mazzola, M., Wu, X. 2022. Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks. Horticulture Research. 9. Article uhab013. https://doi.org/10.1093/hr/uhab013.
DOI: https://doi.org/10.1093/hr/uhab013

Interpretive Summary: Recently developed DNA sequencing technologies has allowed researchers to begin to explore microbial communities inhabiting the surface and interior of plants and is providing a wealth of new information. Plant roots recruit complex fungal and bacterial communities, and their composition is affected by host traits such as genotype, root type, root age, and environmental conditions. Based on our findings, it appears that apple rootstock-associated fungal communities were more strongly influenced by rootstock genotype than were bacterial communities. The composition of the fungal community was different in bulk soil, rhizosphere soil, and internal root tissue samples of different apple rootstocks. These communities also differed with the age or size of the root. Our studies indicate that apple rootstock genotype can significantly influence the selection and recruitment of fungal microbiota that may successively colonize larger roots and perhaps even aboveground plant organs. Thus, the differential microbial recruitment capabilities of the rootstocks may influence a variety of orchard production outcomes including fruit quality, by modifying water, nutrient and hormone fluxes in the scion, disease tolerance through selective enhancement of disease suppressive microorganisms, and plant fertility through superior ability to interact with mycorrhizal fungi that promote the uptake of nutrients. A deeper understanding of the interaction between rootstock genotype and the structure of its microbiome will provide novel approaches to influence and perhaps select for a wide range of economically important cultural traits.

Technical Abstract: The role of genotype on the composition of the endophytic microbiome of fruit trees remains an important question of practical significance, in regard to both breeding objectives and management practices. In the current study, the bacterial and fungal microbiota associated with four different apple rootstocks planted in the same soil environment were evaluated. Samples used to characterize the microbial taxa included bulk soil, rhizosphere, and endophytes present in fine roots (= 2 mm), intermediate roots (2 – 4 mm), and large roots (4 – 12 mm). Results demonstrated a clear impact of genotype and root size, especially for fungi, on microbial composition and diversity, but not abundance. Fungal and bacterial abundance was equal between different-sized roots, however, significantly higher microbial counts were detected in rhizosphere samples compared to root endosphere samples. The current study provides information that can be used to develop a comprehensive and readily-applicable understanding of the impact of genotype and environmental factors on the establishment of the plant microbiome, as well as its potential function and impact on host physiology. Additional studies will be required to develop the knowledge base required for the practical application of the microbiome to manipulate host disease resistance and physiology, as well as breeding objectives, in a directed, rather than empirical manner.