Science You Can Use: Tipping the balance: Promoting beneficial fungi to keep a forest pathogen in check

Armillaria solidipes, a naturally occurring fungus, is responsible for one of the most widespread root diseases in western North American forests. Armillaria root disease affects a broad range of tree species, and by the time visible symptoms appear, significant damage has often already occurred. 

Advances in a field of DNA sequencing known as metagenomics are now helping researchers develop strategies to manage this disease using information that has been beneath their feet all along. 

Understanding soil microbial communities 

Photo Credit

USDA Forest Service photo by John W. Hanna

Basidiocarps of Armillaria solidipes on an alder at La Poel Point, Olympic National Park, Washington

Metagenomics is the study of microbial communities at the genetic level, revealing complex ecosystems in even the smallest soil samples. 

“We’re now able to see entire worlds within a teaspoon of soil,” said Ned Klopfenstein, a Research Plant Pathologist with the Forest Service’s Rocky Mountain Research Station. 

To develop novel management approaches for Armillaria root disease, Klopfenstein, fellow station Biological Science Technician John Hanna, and Research Plant Pathologist Mee-Sook Kim from the Pacific Northwest Research Station, partnered with Colorado State University professor Jane Stewart and her forest pathology team. Through preliminary metagenomic analyses, the team identified clear patterns in where A. solidipes occurred and where it did not. 

“There are several species of Armillaria in North America, but our research highlights a critical interaction between two in particular,” Kim said. “We observed that A. altimontana acts as a potential biological control against the pathogenic A. solidipes. Where these two species coexisted in northern Idaho and surrounding areas, A. altimontana was associated with reduced disease impact and significantly better tree growth.”

These protective effects may be region specific, as under certain environmental conditions A. altimontana can behave differently and may occasionally be associated with root disease. Still, the strong correlation is providing new options for land managers working in forests where A. solidipes is prevalent.

“It all comes down to avoiding disturbance of the beneficial fungi and bacteria while also determining how to encourage these beneficial soil microbes,” Klopfenstein said. 

Friendly fire

In 2024, the research team co authored a study examining how fire severity influences competition between Armillaria species. They found that the pathogenic A. solidipes dominated areas that experienced high-severity burns, while in low-severity burn areas, the beneficial A. altimontana was able to maintain its relative abundance. 

Sara Ashiglar, a co author on the study and Silviculturist on Idaho’s Nez Perce Clearwater National Forests, is already applying the findings. She pairs them with local knowledge about tree species susceptibility to A. solidipes to guide long term planning. 

“Almost everything we do on this forest is managing around Armillaria root disease,” Ashiglar said. “It’s pretty much everywhere.” Decades of logging, fire suppression, and white pine blister rust have shifted northern Idaho’s pine- and larch-dominated forests toward Douglas-fir and grand fir—species more vulnerable to root disease. As a result, forest damage from A. solidipes increased. 

Today, when using fire to prepare sites for planting, Ashiglar emphasizes keeping burn severity low. After wildfires, she prioritizes planting species that are less susceptible to root disease, such as western white pine and western larch, in severely burned areas. 

“We know it’s not going to happen overnight,” she said. “But understanding how to avoid increasing the risk of soil-borne pathogens while promoting healthy, disease-suppressive soils and resilient trees will go a long way in preserving Idaho’s forests.”