Unlocking Microbiome Potential for Tomato Disease Resistance

Bacterial speck disease poses a perennial challenge for tomato growers, often leading to reduced yields crucial for the processing industry. New research from Penn State offers promising insights into how a plant’s natural microbiome—the community of microorganisms living on and within it—could be harnessed to combat this pathogen.

The study, published in Environmental Microbiome, specifically investigated the phyllosphere microbiome, which refers to the microbial community residing on the above-ground parts of the tomato plant. Researchers compared the microbiomes of plants that naturally resisted bacterial speck with those that were susceptible to the disease.

A key finding was the presence of specific populations of Xanthomonas and Pseudomonas bacteria on plants that demonstrated resistance. This suggests these particular bacterial groups play a role in suppressing bacterial speck disease.

Dr. Kevin Hockett, associate professor of microbial ecology and lead author, highlighted the potential practical applications. “If we can learn more about which microbes are driving down the disease, it’s possible that we could isolate and combine them in the future for growers to use as a treatment,” he stated. He also noted that if this process proves effective for bacterial diseases, it could open doors for similar applications against widespread fungal diseases, expanding its potential impact on crop protection.

The research drew inspiration from observations in soil microbiomes, where repeated planting of a susceptible crop can, over time, lead to the soil’s microbial community shifting to suppress a specific pathogen. The team’s previous work confirmed that a plant’s above-ground microbiome can indeed adapt to suppress the bacteria causing bacterial speck. The current study aimed to pinpoint which specific microbes within this complex community were responsible for this disease suppression.

To achieve this, researchers employed a “passaging” technique. Tomato plants were first exposed to the bacterial speck pathogen. The microbiome from plants showing the least disease was then collected and transferred onto new, healthy plants, a process repeated nine times. This method allowed the scientists to progressively enrich for disease-suppressive microbes.

Now, with a better understanding of the composition of these disease-suppressive microbiomes, the next step is to identify the most crucial players. Hockett explained, “The first thing we want to do is go in and start pulling this community apart to identify who are really the important players for disease suppression.” This targeted approach aims to develop effective, naturally derived treatments for growers.

This collaborative study included contributions from Hanareia Ehau-Taumaunu, Terrence Bell, and Javad Sadeghi, and received support from various institutions and awards, underscoring the collective effort to advance plant health.

Sources : Penn State University, Environmental Microbiome

Reference: Ehau-Taumaunu, H., Bell, T.H., Sadeghi, J. et al. Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection. Environmental Microbiome 20, 77 (2025).

Full text: https://doi.org/10.1186/s40793-025-00734-1