Kyoto, Japan -- Beneath the forest floor extends a vast ecosystem where a diverse array of microorganisms inhabit soil and root systems. Here, fungi and bacteria play particularly pivotal roles in processes such as nutrient cycling and carbon sequestration. Within these microbial communities may exist a keystone species , which exerts a disproportionately large influence on the entire structure and function of such an ecosystem.
While scientists often associate a keystone species with conspicuous predators, pollinators, and plants, there is also a belief that the myriad microorganisms inhabiting the soil include 'hidden' key species. These may be crucial to understanding the dynamics of a complex ecological community, but identifying them within microbial environments is particularly daunting, as experimentally assessing the impact of any one particular species is impossible in a system as vast as a forest.
Fortunately, recent developments in DNA analysis technology have made it possible to capture the diversity of forest microorganisms as large-scale datasets. A team of researchers at Kyoto University was inspired to use this data to identify the masterminds hiding beneath the forest floor.
"Even a single plant root measuring less than one millimeter in diameter harbors a diverse array of coexisting microorganisms," says first author Mikihito Noguchi. "By identifying a keystone species, we aim to elucidate the mechanisms underlying the formation and maintenance of the microbial communities that support forest ecosystems from below."
The team collected 1,270 root samples from a cool-temperate forest in Sugadaira, Nagano prefecture, and analyzed DNA data from fungi and bacteria residing there. With this, they represented the microbial communities as one landscape by modeling the compositions they tend to adopt. This allowed the researchers to develop a theoretical framework to identify species that may be capable of dramatically altering the structure of the landscape: a resulting algorithm was fed to a supercomputer. Finally, the scientists compared their data from Nagano to a large dataset of forests in Europe to verify their findings across vast geographical distances.
Their results point toward a group of fungi known as endophytes , which symbiotically inhabit plant tissue and may play a key role in reshaping the symbiotic relationships between plants and microorganisms in the roots and soil. Endophytes had previously received little attention for their effect on forest ecosystems, but this study has revealed that these hidden masterminds significantly influence the landscape structure of fungal communities.
Further, the novel methods developed in this study serve as a versatile framework for identifying the crucial microorganisms that underpin the dynamics of other complex microbiomes, and have the potential for application in ecosystems far beyond the forest. In the future, these methods are expected to lead to management techniques that consider the ecosystem as a whole, including microbial communities.
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The paper "Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes" appeared on 28 October 2026 in Nature Communications , with doi: 10.1038/s41467-026-78401-3
About Kyoto University
Kyoto University is one of Japan and Asia's premier research institutions, founded in 1897 and responsible for producing numerous Nobel laureates and winners of other prestigious international prizes. A broad curriculum across the arts and sciences at undergraduate and graduate levels complements several research centers, facilities, and offices around Japan and the world. For more information, please see: http://www.kyoto-u.ac.jp/en
Nature Communications
Observational study
Not applicable
Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes
28-Oct-2026
HT is a founder and director of Sunlit Seedlings Ltd. Other authors declare no competing interests.