Fig. 1

Microcosm experimental setup. Soil samples were collected from Cr-contaminated hotspots (Cr(VI), 665 mg/kg) and from clean areas around the site (Cr(VI), 0.09 mg/kg). Cr(VI) was added to the clean soil at concentrations of 0, 10, and 100 mg/kg (added as K₂Cr₂O₄) to create microcosm soil systems with different pollution levels. These soils were then sterilized three times using high-pressure sterilization. Using tangential flow filtration (TFF, membrane pore size 30 kDa), the microbiome (including prokaryotes and viruses) was enriched from both the clean and heavily Cr-polluted soils, abbreviated as CM and PM, respectively. These suspensions were then inoculated into sterilized soils of varying Cr(VI) concentrations to construct microcosm systems, named C-0, C-10, C-100, P-0, P-10, and P-100, which were incubated at room temperature for 35 days. Following incubation, DNA was extracted, and both long-read (MinION Nanopore) and short-read (Illumina Novaseq 6000) sequencing were performed