Soil bacteria protect wheat from pathogenic fungus

When inoculated into the soil, bacterial species altered the microbiome and protected plants from a fungus that causes root rot, reducing disease symptoms by up to 60%.

By André Julião  |  Agência FAPESP – Researchers from the Brazilian Agricultural Research Corporation (EMBRAPA) and the University of São Paulo (USP) described the role of three bacteria in suppressing a soil-borne wheat pathogen that causes root rot.

Their study, published in the journal NPJ Biofilms and Microbiomes, paves the way for the development of inoculants that can be used in agriculture.

“We selected three bacteria from a group we had isolated in a previous study that showed the greatest potential to improve plant growth and exert an antagonistic effect against the pathogen. When we grew wheat in soil containing the bacteria and the pathogen, the fungus Bipolaris sorokiniana, we observed a 60% reduction in disease symptoms compared to treatments with only the pathogen in the soil,” says Caroline Sayuri Nishisaka, who conducted the research as part of her doctoral studies with a FAPESP scholarship at the EMBRAPA Environment unit in Jaguariúna.

The study also involved researchers from the Center for Nuclear Energy in Agriculture (CENA) and the Luiz de Queiroz College of Agriculture (ESALQ), both at USP. The research is part of two projects supported by FAPESP (20/00469-2 and 25/11610-1).

“Perhaps the most interesting aspect of this study is that we didn’t observe the elimination of the pathogen, but rather how the presence of these bacteria protects the plant from it. The fungus remained present in similar quantities in the soil of both diseased and healthy plants. What changed was the outcome of the interaction. The plants inoculated with the bacteria built a kind of microbiological shield that prevented the fungus from causing the disease,” summarizes Rodrigo Mendes, a researcher at EMBRAPA Environment and project coordinator.

Mendes compares the action of the microbiome, a collection of microorganisms and their byproducts, to that of the human immune system. The immune system eliminates pathogens when the body is healthy, but it becomes vulnerable in situations such as autoimmune diseases and treatments that suppress immune function. “The presence of these beneficial bacteria reorganized the microbiome in such a way that the opportunistic fungus was kept under control,” he explains.

Ancestral wheat

The researchers selected three of the most promising bacterial species: Streptomyces virginiae, Paenibacillus ottowii, and Pseudomonas inefficax. Despite its name, the latter species was the most effective in controlling the pathogen.

P. inefficax performed best in the soil microbiome, significantly increasing root biomass. Along with S. virginiae, it exhibited the highest abundance of growth-promoting genes in terms of richness and diversity.

Additionally, treatments with either of these two bacteria increased biosynthetic gene clusters, which produce potentially beneficial plant compounds. P. inefficax restored microbiome functions linked to plant protection as well.

“We observed that the bacterium didn’t act directly on the pathogen but rather as an ecological engineer, altering the system’s ecology to strengthen the plant’s defenses. This represents an advance over established knowledge to date,” says Nishisaka, who is currently conducting postdoctoral research with a FAPESP fellowship at CENA-USP.

Top left: pathogen cultured alone, used as a control. Next: Streptomyces virginiae, Paenibacillus ottowii, and Pseudomonas inefficax inhibit fungal growth in vitro (photos: Caroline Sayuri Nishikata/EMBRAPA) 

The bacteria analyzed in the study were selected from a previous study by the group, in which the soil microbiome was surveyed from crops of ancestral wheat varieties and commercial cultivars. The species used in this study come from two landrace wheat varieties obtained from countries near the center of origin of wheat: one from Turkey and the other from Iran.

In another study, published in late 2025, the group showed that low soil microbiome diversity increases the severity of B. sorokiniana infection and that P. inefficax can suppress the pathogen.

The evaluated bacteria are part of EMBRAPA’s portfolio of assets and can be licensed by companies looking to develop products based on this research.    

The researchers are now seeking to understand which plant-produced metabolites support beneficial bacteria and are attempting to predict the metabolic pathways activated in this interaction. The results could facilitate the development of new technologies to control and prevent diseases in agricultural crops.

Root rot is one of the most common diseases affecting wheat, a cereal whose production totaled 7.87 million metric tons in Brazil in 2025, according to the National Supply Company (CONAB). Wheat is one of the most widely produced grains in the world, with more than 800 million metric tons harvested last year.

The article “Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat” can be read at www.nature.com/articles/s41522-026-01021-8.