Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes
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.
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BibTeX
@article{noguchi2026statistical,
title = {{Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes}},
author = {Mikihito Noguchi and Kenta Suzuki and Hiroaki Fujita and Hirokazu Toju},
journal = {Nature Communications},
year = {2026},
month = oct,
doi = {10.1038/s41467-026-78401-3},
url = {https://www.nature.com/articles/s41467-026-78401-3},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Statistical inference of keystone taxa reshaping the assembly rules of forest root microbiomes
AU - Mikihito Noguchi
AU - Kenta Suzuki
AU - Hiroaki Fujita
AU - Hirokazu Toju
PY - 2026
DA - 2026/10/28
JO - Nature Communications
DO - 10.1038/s41467-026-78401-3
UR - https://www.nature.com/articles/s41467-026-78401-3
AB - 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.
SN - 2041-1723
ER -