Dynamics of sulphur-cycling microbiomes and potential role of viruses in cadmium- contaminated rice paddy soil during remediation

Microbial sulphur (S) transformations affect cadmium (Cd) mobility and bioavailability in soil. Viruses impact prokaryotic metabolisms and related ecological processes, but their influence on host metabolism and adaptability under Cd stress remains uncharacterized. Therefore, we investigated S-cycling microbial communities in the rhizosphere soil of rice and their potential functional profiles and interactions with viruses in response to Cd remediation via a Ca-Mg-Si soil amendment and during different rice growth stages. Microbial communities and S-cycling traits were significantly influenced by soil sulphate and available Cd concentrations. Genes associated with Cd resistance ( czcB , czcC ) and sulphate reduction ( cysC , sat , dsrB ) were enriched in amended relative to unamended soil, at the rice filling stage. Analysis of 67 bacterial metagenome-assembled genomes recovered from the rice heading to ripening stage revealed a widespread genomic capacity for coupling S-cycling potential and Cd resistance. Sulphate-reducing bacteria (SRB) potentially acquired an ABC transporter gene (encoding Cd efflux pump) via horizontal gene transfer. Rhizosphere soil microbial and viral community structures varied significantly among rice growth stages but were not influenced by soil amendment. Virus-host linkage indicated a significant decrease in abundance of lytic viruses of SRB in amended compared to unamended soil at rice maturity, and identification of temperate virus-encoded auxiliary metabolic genes suggesting a potential for viral-mediated effects on S-reduction process. In addition, our experimental results demonstrate that the virus-encoded ABC transporter gene is potential functional and contributes to improve host tolerance and growth under a relatively higher Cd stress (0.4 mg L⁻¹). This study underscores the importance of soil amendments in enhancing microbial S-cycling and Cd resistance potential, and advances our understanding of viral contributions to host adaptability and functioning during Cd-contaminated paddy soil remediation.