Exploring microbial dysbiosis in orchards affected by little cherry disease

Abstract

The phytoplasma Candidatus phytoplasma pruni (CPP), a causative agent of little cherry disease (LCD), has become an increasing problem for sweet cherry growers in Washington state, which is the largest producer of cherries in the USA. The control of LCD currently relies on the identification and removal of infected trees, which has proven to be difficult because of the prolonged asymptomatic, but still contagious state of the disease, and the lack of reliable and economical tests. Thus, the development of new approaches for early detection of LCD will be an important step in the successful control of this tree fruit disease. To identify potential microbial indicators of CPP infection we evaluated the bacterial and fungal communities in the roots of cherry trees from two different orchards that were: (i) infected with CPP and symptomatic; (ii) infected with CPP but remained asymptomatic; and (iii) 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. 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 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.