Genomic and transcriptomic analyses of the newly screened Bacillus sp. LX1 strain provide insights into its tolerance to Cd and enhancement of phytoextraction

Abstract

Background

Efficient microbe-assisted phytoremediation is urgently needed for coping with heavy metal-polluted environments.

Methods

In this study, a new strain of rhizobacteria from Cd-contaminated soil was screened, and its environmental adaptability, physiological characteristics, and effects on Cd phytoextraction were investigated. Furthermore, genomic sequencing and transcriptomic analysis were performed to explore the mechanisms underlying these functional characteristics.

Results

This strain, which was named Bacillus sp. LX1, was highly adaptable to Cd, pH, and temperature variations and exhibited typical plant growth-promoting characteristics. Inoculation with Bacillus sp. LX1 in rhizosphere improved Cd accumulation in mustard roots and shoots by 54.1% and 43.7%, respectively. These results can be attributed to increased plant growth, activated rhizospheric Cd bioavailability, and induced Cd transporter-encoding genes (e.g., HMA1, ZIP2, ZIP3, NRAMP3, and CAX2) in mustard roots. Integrated genomic and transcriptomic analyses provided molecular insights into its tolerance to Cd and enhancement of phytoextraction. The Bacillus sp. LX1 genome consists of a chromosome and a plasmid carrying a total of 5,934 genes with multiple functions. Under Cd (5 and 25 mg L⁻¹) stress, Bacillus sp. LX1 activated several important KEGG pathways, including quorum sensing, nucleotide excision repair, sulphur metabolism, and riboflavin metabolism, to resist Cd. Moreover, Cd regulated the synthesis of IAA, organic acids, siderophores, phosphatases, and extracellular polysaccharides, providing the material basis for Bacillus sp. LX1 to promote plant growth and increase soil Cd bioavailability.

Conclusion

This study greatly improves our understanding of the interactions among plants, rhizobacteria, and Cd.