METHODS article
Front. Microbiol.
Sec. Microbe and Virus Interactions with Plants
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1609057
This article is part of the Research TopicMicrobial Symbionts of Lower PlantsView all 4 articles
Rhizosphere microbiomes of field-grown B. stricta exhibit minimal diel changes in microbial membership and protein synthesis potential
Provisionally accepted
- University of Wyoming, Laramie, United States
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The rhizosphere microbiome greatly affects plant health and fitness. Quantifying bacterial responses to fine-scale plant-mediated changes in the rhizosphere, such as those associated with diel cycling of host plant physiology, will increase our understanding of microbial community assembly patterns. Here, we used 16S rRNA biomarker gene (DNA) and transcript (RNA) sequencing to characterize changes in the rhizosphere community membership and PSP over short timescales in field-grown Boechera stricta plants. Microbial communities characterized by 16S-rRNA-transcripts, which serve as a proxy for microbial protein synthesis potential (PSP), showed greater sensitivity to fine-scale environmental changes than did communities characterized by 16S-rRNA biomarker gene sequencing, which reflects microbial presence/absence. Significant differences were seen between communities characterized by RNA vs. DNA, with RNA-derived communities showing greater alpha and beta diversity differences between the rhizosphere vs. control soil communities within phyla and in differential abundance analysis of genera. Communities reconstructed from RNA were also more sensitive to the effects of field block and collection timepoint. Differential abundance analysis revealed significant differences (p<0.05) between the pre-dawn (AM) and early afternoon (PM) timepoints for 5 genera based on 16S rRNA transcripts. This included the plant-associated genus Curtobacterium.However, when variance was partitioned between days of collection, the amplitude of the signal between diel timepoints was non-significant. In sum, community composition and protein synthesis potential was highly sensitive to abiotic factors expressed over the small spatial scale of field blocks and short 24-hr periods between collection days, but showed minimal to no diel patterning.
Keywords: rRNA (ribosomal RNA), 16S rRNA (16S rDNA), Plant Circadian Clock, rhizosphere bacteria, host microbiome interaction
Received: 09 Apr 2025; Accepted: 25 Aug 2025.
Copyright: © 2025 Ceretto and Weinig. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Alessandra Ceretto, University of Wyoming, Laramie, United States
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