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

• DOI: 10.1186/s40168-020-00966-y
• Publication Date: 2021-02-26T19:04:01Z
• Authors: Richa Kaushal; Li Peng; Sunil K. Singh; Mengrui Zhang; Xinlian Zhang; Juan I. Vílchez; Zhen Wang; Danxia He; Yu Yang; Suhui Lv; Zhongtian Xu; Rafael J. L. Morc...; Wei Wang; Weichang Huang; Paul W. Paré; Chun-Peng Song; Jian-Kang Zhu; Renyi Liu; Wenxuan Zhong; Ping Ma; Huiming Zhang
• Keywords: Callose

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