RNA-based spray targets disease without disrupting potato microbiome

RNA-based crop protection has attracted growing interest as a potential alternative to conventional pesticides. However, its effects on the microorganisms living on plant surfaces remain poorly understood.

To investigate this, researchers at SLU, together with colleagues from The James Hutton Institute in the UK, studied how double-stranded RNA (dsRNA) sprays targeting Phytophthora infestans, the pathogen behind potato late blight, affect the bacterial and fungal communities living on potato leaves.

A closer look at potato leaf microbiomes

The study, accepted for publication in npj Biofilms and Microbiomes, examined how double-stranded RNA (dsRNA) sprays designed to control P. infestans affect the potato phyllosphere microbiome. P. infestans, the pathogen responsible for potato late blight, is one of the most destructive crop pathogens worldwide, causing billions of euros in annual losses and driving extensive fungicide use.

Using high-throughput sequencing, the researchers tracked bacterial and fungal communities on potato leaves following application of dsRNA molecules targeting genes essential for pathogen growth and infection.

Pathogen, not RNA treatment, drives microbiome changes

The results showed that dsRNA spraying had little impact on the dominant microbial communities naturally present on potato leaves. Core bacterial and fungal groups remained largely intact after treatment. By comparison, infection with P. infestans led to substantially greater shifts in microbiome composition.

– One key question for RNA-based crop protection is whether it affects beneficial microorganisms. Here, we show that the potato microbiome remains remarkably stable after dsRNA treatment, while the pathogen itself drives much larger changes, says Poorva Sundararajan.

RNA sprays preserve plant-beneficial microbes

The researchers also found that several bacterial groups associated with plant health and disease suppression persisted after treatment. Some potentially beneficial bacteria even increased in abundance when plants were challenged by the pathogen.

SIGS uses naturally occurring RNA molecules to selectively silence genes that pathogens need to grow and infect plants. Unlike conventional fungicides, RNA-based approaches can be designed to target specific pathogens with high precision, reducing the risk of unintended effects on other organisms.

– For any new crop protection technology, effectiveness alone is not enough. We also need to understand its environmental impact. Our findings show that SIGS can target the pathogen while largely preserving the beneficial microbial communities associated with the plant. This is an important step towards more precise and sustainable disease management, says Samrat Ghosh.

Promising results, but more field studies required

The findings contribute to a growing body of evidence supporting the environmental safety of RNA-based crop protection. As agriculture seeks alternatives to conventional pesticides and more sustainable approaches to disease control, understanding how these technologies interact with plant-associated microbial communities will be crucial.

– We still need more field studies across different potato varieties and growing conditions to confirm these results under field conditions. But overall, the study provides important evidence that RNA sprays can control the target disease without significantly disrupting the microbial communities that support plant health, says Ramesh Vetukuri.

The publication

Sundararajan, P. et al. Phyllosphere microbiome responses to spray-induced gene silencing targeting Phytophthora infestans in potato. Published in npj Biofilms and Microbiomes.
https://www.nature.com/articles/s41522-026-01040-5