Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

Nash, Jake; Tremble, Keaton; Schadt, Christopher Warren; Cregger, Melissa A.; Bryan, Corbin; Vilgalys, Rytas

doi:10.1128/msystems.00285-25

Time-series RNA metabarcoding of the active Populus tremuloides root microbiome reveals hidden temporal dynamics and dormant core members

Journal Article · Thu Nov 06 23:00:00 EST 2025 · mSystems

DOI:https://doi.org/10.1128/msystems.00285-25· OSTI ID:3001733

^[1]; Tremble, Keaton ^[1]; ^[2]; ^[2]; Bryan, Corbin ^[1]; Vilgalys, Rytas ^[1]

Duke Univ., Durham, NC (United States)
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

The rhizosphere is a critical interface between plant roots and soil, harboring diverse microbial communities that are essential to plant and ecosystem health. Although these communities exhibit stark temporal dynamics, their dormancy/activity transitions remain poorly understood. Such transitions may enable microbes to rapidly adjust functional contributions faster than community turnover alone would allow. Here, we used RNA metabarcoding to characterize the active fraction of microbial communities on the roots of quaking aspen (Populus tremuloides) in a time-series study across a natural environmental gradient. We explore cryptic temporal microbial community dynamics of rhizosphere communities at the ecosystem scale. The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities, while total communities exhibited a stronger response to site-specific conditions. Notably, some core microbiome members were often inactive, yielding a smaller “active core” subset. The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints. Soil temperature strongly influenced both total and active community composition, with the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance. Together, these results reveal that modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation, and that even dominant symbionts may frequently persist in dormancy within the rhizosphere.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 3001733

Journal Information:: mSystems, Journal Name: mSystems Vol. 10; ISSN 2379-5077

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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