Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Oct 12;4(1):ycae120.
doi: 10.1093/ismeco/ycae120. eCollection 2024 Jan.

Rhizospheric miRNAs affect the plant microbiota

Harriet Middleton  1   2 , Jessica Ann Dozois  2 , Cécile Monard  1 , Virginie Daburon  1 , Emmanuel Clostres  1 , Julien Tremblay  2 , Jean-Philippe Combier  3 , Étienne Yergeau  2 , Abdelhak El Amrani  1
Affiliations

Rhizospheric miRNAs affect the plant microbiota

Harriet Middleton et al. ISME Commun. .

Erratum in

Abstract

Small ribonucleic acids (RNAs) have been shown to play important roles in cross-kingdom communication, notably in plant-pathogen relationships. Plant micro RNAs (miRNAs)-one class of small RNAs-were even shown to regulate gene expression in the gut microbiota. Plant miRNAs could also affect the rhizosphere microbiota. Here we looked for plant miRNAs in the rhizosphere of model plants, and if these miRNAs could affect the rhizosphere microbiota. We first show that plant miRNAs were present in the rhizosphere of Arabidopsis thaliana and Brachypodium distachyon. These plant miRNAs were also found in or on bacteria extracted from the rhizosphere. We then looked at the effect these plants miRNAs could have on two typical rhizosphere bacteria, Variovorax paradoxus and Bacillus mycoides. The two bacteria took up a fluorescent synthetic miRNA but only V. paradoxus shifted its transcriptome when confronted to a mixture of six plant miRNAs. V. paradoxus also changed its transcriptome when it was grown in the rhizosphere of Arabidopsis that overexpressed a miRNA in its roots. As there were differences in the response of the two isolates used, we looked for shifts in the larger microbial community. We observed shifts in the rhizosphere bacterial communities of Arabidopsis mutants that were impaired in their small RNA pathways, or overexpressed specific miRNAs. We also found differences in the growth and community composition of a simplified soil microbial community when exposed in vitro to a mixture of plant miRNAs. Our results support the addition of miRNAs to the plant tools shaping rhizosphere microbial assembly.

Keywords: Variovorax; bacterial communities; plant miRNAs; rhizosphere; transcriptomics.

PubMed Disclaimer

Conflict of interest statement

The authors report no conflict of interest.

Figures

Figure 1
Figure 1
Experimental approach overview. Overview of the experiments leading to the identification of plant miRNAs in the rhizosphere and the confirmation of their effect on microbial communities. Created with BioRender.com
Figure 2
Figure 2
Plant miRNAs are present in the rhizosphere, roots, and bacteria and absent in unplanted soil. Relative abundance of the plant miRNAs found in the rhizosphere of (A) A. thaliana, (B) B. distachyon, (C) in the roots of A. thaliana, and (D) in or on rhizosphere bacteria while completely absent from unplanted soil.
Figure 3
Figure 3
Plant miRNAs affect the transcriptome of a rhizosphere bacterium. Gene expression of Variovorax paradoxus after (A) 20 min and (B) 120 min exposure to a mixture of six synthetic miRNAs (plant miRNAs compared to scrambled miRNAs), confocal microscopy images of (C) V. paradoxus and (D) B. mycoides after a 4-h exposure to ath-miR159a tagged with Cy5 and flow cytometry experiment showing (E) the percentage of active bacterial cells positive for Cy5 signal and (F) the median intensity of the Cy5 signal in active bacterial cells. Arrows in (C) and (D) indicate cells containing the fluorescent molecule. *: P < .05.
Figure 4
Figure 4
miPEP 159c shifts the expression of V. paradoxus. Expression of pri-miR159c in A. thaliana roots and V. paradoxus expression of CdsA, alpha-2-macroglobulin and LysR in the rhizosphere after exposure of the plant to miPEP159c vs. a water and a scrambled miPEP controls. ns: P > .05; *: P < .05, **: P < .01.
Figure 5
Figure 5
Plant miRNAs affect the bacterial community. (A) Phylum-level bacterial community composition and (B) Shannon diversity for different Arabidopsis mutants with impaired small RNAs pathways. (C) Phylum-level bacterial community composition for Arabidopsis plants inoculated with miPEP159a, miPEP159b, or miPEP159c. (D) Growth curve, (E) community composition at genus level, and (F) relative abundance of significantly affected ASVs for a simplified soil microbial community exposed to a mixture of synthetic plant or scrambled miRNAs. *: P < .05, **: P < .01. Different letters in (B) indicate significant differences (P<.05) in Tukey HSD tests.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Huang C-Y, Wang H, Hu P et al. Small RNAs—big players in plant–microbe interactions. Cell Host Microbe 2019;26:173–82. 10.1016/j.chom.2019.07.021 - DOI - PubMed
    1. Regmi R, Penton CR, Anderson J et al. Do small RNAs unlock the below ground microbiome-plant interaction mystery? Front Mol Biosci 2022;9:1017392. 10.3389/fmolb.2022.1017392 - DOI - PMC - PubMed
    1. Middleton H, Yergeau É, Monard C et al. Rhizospheric plant–microbe interactions: miRNAs as a key mediator. Trends Plant Sci 2021;26:132–41. 10.1016/j.tplants.2020.09.005 - DOI - PubMed
    1. Zhang T, Zhao Y-L, Zhao J-H et al. Cotton plants export microRNAs to inhibit virulence gene expression in a fungal pathogen. Nat Plants. 2016;2:16153. 10.1038/nplants.2016.153 - DOI - PubMed
    1. Cai Q, Qiao L, Wang M et al. Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes. Science 2018;360:1126–9. 10.1126/science.aar4142 - DOI - PMC - PubMed