Isolation, characterization and inoculation of Cd tolerant rice endophytes and their impacts on rice under Cd contaminated environment

Cadmium (Cd) contamination in paddy soil becomes increasingly prominent in recent years, which endangers the safe production of food crops. Cd-tolerant endophytes are ideal mediators for decreasing Cd content in rice plants, but their effects on the rice endophytic microbial community and gene expression profile have not yet been well elucidated. In this study, 58 endophytic bacteria from rice seeds were isolated and characterized. Five strains of them were selected based on their potential growth-promoting traits and strong Cd tolerance that could grow well under 4 mM Cd2+. By 16S ribosomal RNA (rRNA) identification, these five strains were designated as Enterobacter tabaci R2-7, Pantoea agglomerans R3-3, Stenotrophomonas maltophilia R5-5, Sphingomonas sanguinis R7-3 and Enterobacter tabaci R3-2. Pot experiments in relieving Cd stress in rice plants showed that the S. maltophilia R5-5 performed the strongest potential for reducing the Cd content in root and blade by 81.33% and 77.78%, respectively. The endophytic microbial community diversity, richness and composition were significantly altered in S. maltophilia R5-5 inoculated rice plants. Reverse-transcription qPCR (RT-qPCR) showed that the expression of Cd transporters, OsNramp5 and OsHMA2, were down-regulated in S. maltophilia R5-5-innoculated rice roots. The results indicate that the inoculation of endophytic bacteria S. maltophilia R5-5 provides a reference for alleviating the heavy metal contamination in paddy fields and can be a better alternative for guaranteeing the safe production of crops. Changes in the relative abundance of Cd-resistant microorganisms and the expression of Cd transporters might be the intrinsic factors affecting cadmium content in rice.