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Microbial community assembly contributes to the restoration and rehabilitation of the disturbed ecosystems. However, the viral assembly mechanism and its difference from bacterial communities under soil contamination have not been previously reported. Here, clean, light and heavy chromium (Cr)-contaminated soils were collected from two Cr slag sites and adjacent soils in northwestern and southwestern China. Through metagenome and virome sequencing analysis, we found that the alpha diversity of bacterial genes (including overall genes and Cr detoxifying genes) showed no clear variance (p > 0.05) across soils, indicating the functional redundancy in the bacterial communities. The assembly of both the bacteria and virus taxa were primarily controlled by deterministic process across soils The assembly of bacterial genes turned from stochastic processes to deterministic processes when the Cr content increased in soils. By contrast, the assembly of viral genes altered from deterministic processes in clean soil into stochastic processes in Cr-contaminated soils. Virus-host linkage results showed that the niche breadth of bacteria and viruses was closely related. The normalized stochasticity ratio of viral functional assembly was positively correlated with the Simpson index of the bacteria (p < 0.05). The results suggested that the stochasticity of viral functional assembly was conducive to facilitating the functional redundancy of bacterial communities and their evolution toward the deterministic direction. [Display omitted] • Bacteria maintained functional redundancy under Cr exposure. • Deterministic process dominated the assemblies of bacterial and viral taxa. • Bacterial and viral genes were driven by distinct processes due to Cr exposure. • Viral communities facilitated the functional redundancy of host bacteria. [ABSTRACT FROM AUTHOR]