Response of apple orchard microbiome to management and plant selective pressure

Authors: AJEETHAN, NIVETHIKA - Dalhousie University; ABBEY, LORD - Dalhousie University; ALI, SHAWKAT - Aafc Lethrdge Research Center; FULLER, KEITH - Aafc Lethrdge Research Center; Yurgel, Svetlana

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/17/2023
Publication Date: 3/24/2023
Citation: Ajeethan, N., Abbey, L., Ali, S., Fuller, K., Yurgel, S. 2023. Response of apple orchard microbiome to management and plant selective pressure. Microorganisms. 11(6). Article 1372. https://doi.org/10.3390/microorganisms11061372.
DOI: https://doi.org/10.3390/microorganisms11061372

Interpretive Summary: Washington state is the largest producer of apples in the United States and apple replant disease (ARD) is a well know challenge in areas with intensive tree fruit cultivation. ARD is characterized by poor health and a decline in productivity and fruit quality of newly introduced apple trees in old orchard soil. The etiology of ARD is complicated to define for several reasons, since it associated with a pathogen complex, which could include soil-borne pathogenic fungi (Cylindrocarpon and Rhizoctoni), oomycetes (Phytophthora and Pythium) and root lesion nematode (Pratylenchus penetrans). However, still ambiguity persists in the definition of the complex. This research was triggered by the hypothesis that the equilibrium between soil pathogenic microbial species accumulated during prolong life of apple trees and the beneficial microbiome in their roots might keep fruit trees healthy in old orchard soil. If this is true, the introduction of a synthetic microbial community composed of culturable endophytes isolated from mature healthy trees might be a way to “immunize” young trees and make them more resistant/tolerant to ARD. To test this hypothesis, we evaluated the soil and root associated microbiomes in established orchards, as well as in the uncultivated soil to survey the accumulation of pathogenic and beneficial taxa that can participate in this equilibrium. As a result, we identified a group of root endophytes that might be a target for isolation and testing for their potential to improve saplings adaptation to the soils affected by ARD.

Technical Abstract: The tree fruit industry in Nova Scotia is dominated by the apple (Malus domestica [Suckow] Borkh) sector, which is a major source of revenue for orchard owners. Apple replant disease (ARD) is a well-known problem in areas with intensive apple cultivation. The key to ARD adaptation is related to the suppression of soilborne plant pathogens through beneficial effect of plant growth promoting (PGP) microbes on the host-plant. This study employs 16S rRNA/ITS2/18S rRNA and 16S rRNA/ITS2 amplicon sequencing to study soil and root associated microbiomes respectively, from apple orchards and uncultivated soil in Nova Scotia. Our analysis indicated significant differences in soil microbial communities structure and composition between uncultivated and apple orchard soil. We identified an increase in the number of potential pathogens in the orchard soil compared to uncultivated soil, which either belong to the known ARD pathogenic complex or have the potential to facilitate ARD development. At the same time, we detected a significant increase in relative abundances of several potential plant-growth promoting or biocontrol microorganisms, as well as in non-fungal eukaryotes capable of promoting the proliferation of bacterial biocontrol agents in orchard soil. Additionally, apple root accumulated several potential PGP bacteria from Proteobacteria and Actinobacteria phyla, while the relative abundances of fungal taxa with the potential to contribute to ARD, such as Fusarium and Nectriaceae, were decreased in the apple root microbiome compared to the soil microbiome. This data suggested a more complex interaction between potential pathogenic and growth promoting microorganisms in soil and apple tree microbiome, which could support mature tree health.