Abstract
ABSTRACT 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. IMPORTANCE Members of the rhizosphere exhibit dynamic patterns of activity and dormancy. This study stresses the need to focus on active microbial communities to detect temporal changes in plant microbiomes. Additionally, the metabolic activity of microbes should be considered a key determinant of core microbiome membership. Parallel patterns in active community dynamics between fungal and bacterial communities provide a potentially generalizable rule of microbial community temporal dynamics in plant rhizospheres.
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Claims 8
Claim · model-written summary
Active bacterial and fungal root communities changed more over time than total communities.
- Taxon
- quaking aspen
Populus tremuloidese1 - Outcome
- rhizosphere bacterial and fungal communitiese0
- Direction
- more temporally dynamice0
- Comparator
- total communitiese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The active rhizosphere bacterial and fungal communities were more temporally dynamic than total communities”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Total communities responded more strongly to site-specific conditions.
- Taxon
- quaking aspenPopulus tremuloidese1
- Outcome
- total communitiese0
- Direction
- stronger responsee0
- Setting
- site-specific conditionse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“total communities exhibited a stronger response to site-specific conditions”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Some core microbiome members were often inactive, making the active core smaller.
- Taxon
- quaking aspenPopulus tremuloidese1
- Outcome
- smaller “active core” subsete0
- Direction
- smallere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“some core microbiome members were often inactive, yielding a smaller “active core” subset”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Hyaloscypha finlandica alone was present and active in every plot and timepoint.
- Taxon
- quaking aspenPopulus tremuloidese1
- Interactor
- Hyaloscypha finlandicaHyaloscypha finlandicae0symbiont
- Outcome
- Hyaloscypha finlandica was the only microbe that was both present and activee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“The fungal endophyte Hyaloscypha finlandica was the only microbe that was both present and active in all plots across all timepoints”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Soil temperature strongly influenced total and active community composition.
- Taxon
- quaking aspenPopulus tremuloidese1
- Outcome
- total and active community compositione0
- Setting
- Soil temperaturee0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Soil temperature strongly influenced both total and active community composition”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Eurotiomycetes abundance declined seasonally in a temperature-dependent way.
- Taxon
- quaking aspenPopulus tremuloidese1
- Interactor
- EurotiomycetesEurotiomycetese0symbiont
- Outcome
- Eurotiomycetes showing a temperature-dependent seasonal decline in abundancee0
- Direction
- declinee0
- Setting
- temperature-dependente0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the fungal class Eurotiomycetes showing a temperature-dependent seasonal decline in abundance”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Modulation of microbial activity is proposed as a mechanism for the aspen root holobiont response to environmental variation.
- Taxon
- quaking aspenPopulus tremuloidese1
- Outcome
- plant root holobiont responds to environmental variatione0
- Qualifier
- modulation of microbial activity levelse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“modulation of microbial activity levels is a key mechanism by which the plant root holobiont responds to environmental variation”
e1“roots of quaking aspen ( Populus tremuloides )”
Claim · model-written summary
Dominant symbionts may frequently remain dormant in the rhizosphere.
- Taxon
- quaking aspenPopulus tremuloidese1
- Outcome
- dominant symbionts may frequently persist in dormancye0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“even dominant symbionts may frequently persist in dormancy within the rhizosphere”
e1“roots of quaking aspen ( Populus tremuloides )”