Nature Communications· 2026Q1
Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes
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- 2026year
Short summary
A new statistical framework identifies keystone fungal taxa (Phialocephala, Oidiodendron) that reorganize forest root microbiome assembly, linked to shifts in mycorrhizal symbiosis.
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Key points
- A novel statistical framework identifies keystone taxa that reorganize microbiome assembly.
- Endophytic fungi Phialocephala and Oidiodendron were identified as key drivers of root microbiome assembly changes in a Japanese forest.
- These fungal taxa are linked to shifts in mycorrhizal symbiosis, confirmed by independent European data.
- Prokaryotic communities transition between states associated with specific bacterial taxa (Candidatus Udaeobacter) and fungi.
AI-generated from the title and abstract; the full text is not read.
Abstract
Root-associated fungi and bacteria play pivotal roles in terrestrial ecosystem processes. However, identifying keystone taxa driving below-ground microbial assembly remains a major challenge. Here, we present a statistical framework for identifying microbes that reorganize microbiome assembly. Using 1,270 root samples collected from a cool-temperate forest in Japan, we reconstruct assembly landscapes describing the probabilistic structure of community states. We then find that several endophytic fungi (e.g., Phialocephala and Oidiodendron) are strongly associated with the reorganization of assembly landscape topography along abundance gradients, coinciding with shifts in mycorrhizal symbiosis. Independent datasets from Europe confirm that the highlighted genera are significantly associated with changes in mycorrhizal colonization patterns. Prokaryotic communities exhibit transitions among states characterized by core taxa, Pseudomonadota, or Actinomycetota, strongly associated with abundance gradients of Candidatus Udaeobacter and several endophytic fungi. These findings provide a scalable framework for prioritizing candidate keystone taxa and linking microbiome assembly to ecosystem-scale processes.
The authors' abstract, as published at the source. Nature Communications, 2026 · DOI ↗
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Field: Plant Science
Plant ScienceAgricultural and Biological Sciences