Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation

Abstract

Background Plants are naturally associated with root microbiota, which are microbial communities influential to host fitness. Thus, it is important to understand how plants control root microbiota. Epigenetic factors regulate the readouts of genetic information and consequently many essential biological processes. However, it has been elusive whether RNA-directed DNA methylation (RdDM) affects root microbiota assembly. Results By applying 16S rRNA gene sequencing, we investigated root microbiota of Arabidopsis mutants defective in the canonical RdDM pathway, including dcl234 that harbors triple mutation in the Dicer-like proteins DCL3, DCL2, and DCL4, which produce small RNAs for RdDM. Alpha diversity analysis showed reductions in microbe richness from the soil to roots, reflecting the selectivity of plants on root-associated bacteria. The dcl234 triple mutation significantly decreases the levels of Aeromonadaceae and Pseudomonadaceae, while it increases the abundance of many other bacteria families in the root microbiota. However, mutants of the other examined key players in the canonical RdDM pathway showed similar microbiota as Col-0, indicating that the DCL proteins affect root microbiota in an RdDM-independent manner. Subsequently gene analysis by shotgun sequencing of root microbiome indicated a selective pressure on microbial resistance to plant defense in the dcl234 mutant. Consistent with the altered plant-microbe interactions, dcl234 displayed altered characters, including the mRNA and sRNA transcriptomes that jointly highlighted altered cell wall organization and up-regulated defense, the decreased cellulose and callose deposition in root xylem, and the restructured profile of root exudates that supported the alterations in gene expression and cell wall modifications. Conclusion Our findings demonstrate an important role of the DCL proteins in influencing root microbiota through integrated regulation of plant defense, cell wall compositions, and root exudates. Our results also demonstrate that the canonical RdDM is dispensable for Arabidopsis root microbiota. These findings not only establish a connection between root microbiota and plant epigenetic factors but also highlight the complexity of plant regulation of root microbiota.

The root microbiome: Community assembly and its contributions to plant fitness

“…For instance, mutant dcl234 , an Arabidopsis triple mutant with defects in the RNA‐directed DNA methylation (RdDM) pathway, had a reduced abundance of Aeromonadaceae and Pseudomonadaceae and an increased abundance of other families in the root microbial community. However, this regulation was independent of RdDM, and may have been caused by a series of modulations of cell‐wall components, root exudates, and plant defenses (Kaushal et al, 2021). Comparing the root microbiome of three rice mutants defective in histone methylation, researchers found that histone methylation may have modulated the microbiome structure and composition by affecting the abundance of hub species (Lv et al, 2021).…”

Rhizospheric microbial consortium of Lilium lancifolium Thunb. causes lily root rot under continuous cropping system

“…Microbiome samples were collected based on previous publications ( Lareen et al, 2016 ; Kudjordjie et al, 2019 ; Kaushal et al, 2021 ). Briefly: the rhizosphere substrates were collected from maize and tiger lily grown on Cambrian, Ordovician, and Silurian soil in Xiangxi prefecture, Hunan province, China.…”

“…DNA sample preparation and 16S rRNA gene sequencing were performed as previously described ( Kaushal et al, 2021 ), with minor modifications. Briefly, total DNA was extracted with the FastDNA ® SPIN Kit for Soil (MP Biomedicals, Solon, OH, USA) following the manufacturer’s instructions.…”

“…The composition of the rhizospheric bacterial community is affected by changes in environmental factors such as soil humidity, soil pH, and organic compounds content, which differ across soil types ( Cao et al, 2018 ; Lei et al, 2021 ; Khmelevtsova et al, 2022 ). In addition, the rhizospheric bacterial community is also affected by plant genotypes ( Jamalzadeh et al, 2021 ; Kaushal et al, 2021 ; He et al, 2022 ), implying a degree of host selectivity on the establishment of these communities.…”

The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant–microbe interactions

“…Phytohormone changes in plant physiology produce alterations in PRE composition and, therefore, in microbial communities, as reported for jasmonic acid (JA) [ 33 , 34 ]. Furthermore, using a triple mutant in Dicer-like genes involved in small RNAs biogenesis, Kaushal et al [ 87 ] found an altered PRE composition, which can partially explain the observed modifications in the root microbial community.…”