Arabidopsis multiomics reveals the role of autophagy in root microbiome assembly

iMetaOmic

10.1002/imo2.28

Plant autophagy is an intracellular degradation and material dynamic recycling system that is involved in leaf senescence, nutrient recycling and plant stress resistance. However, whether plant autophagy regulates root microorganisms is unknown. We applied amplicon-based (16S) and metagenomics approaches to investigate how autophagy affects the assembly and ecological functions of plant-related microbiomes. Root proteomics and metabolomics were used to evaluate the effects of autophagy on plants in detail. We determined that autophagy had a markedly stronger effect on the diversity and composition of the endosphere microbial community. And autophagy also causes functional shifts in the root microbiome, which are mainly related to metabolism and signal transduction. Notably, the physiological changes in roots of autophagy mutants, such as a decreased cellulose content, the accumulation of monosaccharides related to the cell wall composition, and an increased secretion of carbohydrates and lipids, confirmed that autophagy alters the cell wall. Our results show that autophagy shapes the root microbial community through three aspects: plant cell wall, defense and root exudates.