Exploring microbial dysbiosis in orchards affected by little cherry disease

Authors: Yurgel, Svetlana; SALLATO, BERNARDITA - Washington State University; CHEEKE, TANYA - Washington State University

Submitted to: Phytobiomes Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/23/2023
Publication Date: 2/23/2023
Citation: Yurgel, S., Sallato, B., Cheeke, T. 2023. Exploring microbial dysbiosis in orchards affected by little cherry disease. Phytobiomes Journal. https://doi.org/10.1094/PBIOMES-10-22-0072-R.
DOI: https://doi.org/10.1094/PBIOMES-10-22-0072-R

Interpretive Summary: Little cherry disease (LCD), caused by two viruses (Little Cherry virus 1 and 2) and the phytoplasma Candidus phytoplasma pruni (CPP) have become a significant threat to the Pacific Northwest sweet cherry production and sustainability. In 2020, more than 400 hectares were removed due to LCD, resulting in an estimated $30 million loss, mostly attributed to CPP. Effective disease abatement relies on early detection of infected trees and tree removal. Unfortunately, LCD symptoms are only present in mature trees and ripen fruit, which makes it impossible to identify disease presence when fruit are not present (nonbearing trees, or post-harvest), and there is a multi-year lag between the infection and symptom development, which leads to asymptomatic stage of the infection, which provides a silent host for LCD transmission and spread of the disease. Molecular tests appear effective, only when the infection is advanced, while not economically viable for growers. Thus, the development of new approaches for early detection of LCD, and CPP in particular, has become the highest priority for the sweet cherry industry, and an important step in successful control of the disease. One promising area of research for the early detection of tree fruit diseases is through microbiome analysis. A deviation in the community structure of the resident microbiomes of healthy versus infected individuals (i.e., dysbiosis) could provide important clues into the presence of the disease before symptoms appear. In this study we evaluated the dysbiosis associated with healthy and CPP infected trees, with and without symptoms of the disease.

Technical Abstract: Little cherry disease (LCD), caused in part by the phytoplasma Candidatus phytoplasma pruni (CPP), has become an increasing problem for sweet cherry growers in Washington state, the largest producer in USA. The control of LCD currently relies on the identification and removal of infected trees, which has proven to be difficult because of prolonged asymptomatic, while contagious stage, and lack of reliable and economic test. Thus, the development of new approaches for early detection of LCD is an important step in the successful control of this tree fruit disease. To identify potential microbial indicators of CPP, either as dysbiosis of the microbiome or by identifying microbial indicators that are enriched in one disease state or another, we evaluated the bacterial and fungal communities in the roots of cherry trees from two different orchards that were: (1) infected with CPP and symptomatic; (2) infected with CPP but remained asymptomatic; and (3) healthy, non-CPP infected trees. We found significant variation in the microbiomes between the two cherry orchards, with the location being a stronger driving factor determining the fungal compared to the bacterial community, indicating some uniqueness of the cherry tree root microbiome by orchard location. We also found that the fungal communities were less affected by the disease conditions compared to the bacterial microbiome. Overall, this study demonstrates feasibility of the microbiome approach for identification of indicator organisms capable to predict the disease status of the cherry trees for the early detection of LCD by CPP, but also demonstrates that more orchards need to be sampled as location was a stronger contributor to the microbiome of cherry tree roots than disease condition.