A genetically engineered Citrobacter sp. XT1-2-2 modulates rhizosphere soil microbiome and induces root proteomic changes to reduce cadmium uptake in rice

This study systematically investigated the comprehensive effects of inoculating Citrobacter sp. XT1-2-2, Citrobacter sp. XT1-2-2-::APS and Citrobacter sp. XT1-2-2-::SiR in the pot experiment on the structure and diversity of the microbial community in rice rhizosphere soil, as well as the root proteome of rice. High-throughput sequencing technologies for 16 S rRNA and ITS were utilized to analyze the differences in rhizosphere bacterial and fungal communities. Additionally, TMT labeling combined with liquid chromatography-tandem mass spectrometry was employed for root proteomic analysis. The results showed that the soil samples inoculated with Citrobacter sp. XT1-2-2-::APS and Citrobacter sp. XT1-2-2-::SiR showed a significant reduction relative to the wild-type strain-inoculated in the available cadmium content in the soil at the maturity stage. Microbial analysis predicted significant differences in the community structure of bacteria and fungi in soil inoculated with over-expressed strains, leading to an increase in community abundance and diversity. The relative abundance of bacterial phyla including Bacillota , Bacteroidota , Pseudomonadota , Thermodesulfobacteriota and Acidobacteriota increased, whereas the fungal community was predominantly composed of Ascomycota , Chytridiomycota , Basidiomycota and unclassified fungi. Proteomic analysis predicted differential expressed proteins, mainly enriched in biosynthetic pathways, metabolic pathways, glutathione metabolism, cell wall organization, and antioxidant defense pathways. Understanding the over-expression of key reductase genes in XT1-2-2 effects on the endophytic microbiome and rice proteomics will help us better understand the complex interactions between rice and microorganisms. Furthermore, this provided theoretical support for the application of functional microorganisms in promoting rice growth and cadmium reduction. Not applicable.