Magnetic removal techniques using functionalized magnetic nanoparticles as adsorbents have been frequently tested for use in the removal of heavy metals in aqueous solution, but seldom in farmland soil. Here, a novel magnetic microparticle solid chelator (MSC) was employed as the adsorbent for magnetic removal and/or immobilization of Cd and Zn in a paddy soil (PS), an upland soil (US), and a paddy–upland rotation soil (RS) with different degrees of pollution. MSC was applied to 14 kg air-dried soil samples (PS, US, and RS) at the dosage of 1% (w/w), and then watered, and intermittently stirred. Finally, the MSC–metal complexes were retrieved using a magnetic device (MCR treatment) or not (MC treatment), and the removal efficiency of soil Cd and Zn in MCR treatment was evaluated. After magnetic separation of MSC–metal complexes, pot experiments were performed to investigate the impacts of the magnetic remediation process on rice growth, the phytoavailability of soil Cd and Zn, and the accumulation of Cd and Zn in rice plants. The MCR treatment exhibited recovery rates of 55.4%, 49.6%, and 19.0% for MSC–metal complexes in PS, US, and RS, respectively, which brought about removal efficiencies of 2.2–12.2% for Cd and 1.9–4.6% for Zn. The MC and MCR treatments substantially decreased the availability of soil Cd, but not soil Zn; this effect was more remarkable when using CaCl2 instead of DTPA as the extractant for determination of bioavailable metals. Furthermore, the CaCl2-extractable Cd and Zn had a more significant relationship with Cd and Zn concentrations in rice roots. The MC and MCR treatments led to dramatic reductions in rice grain Cd of 23.9–72.1% and 37.3–63.9%, respectively, in the three soils relative to the respective controls. The MC and MCR treatments also exhibited an inhibitory effects on rice grain Zn accumulation in US (10.6% and 4.3% decreases, respectively) and RS (9.3% and 19.5% decreases, respectively), but not in PS. Moreover, the grain yield was unaffected under the MCR treatment in the three soils, and significantly increased by 29.8% under the MC treatment in US. Our study suggests that MSC-based magnetic remediation technique can effectively immobilize and/or remove Cd and Zn in farmland soils, decreasing their uptake by rice plants, with no adverse effects on grain yield.
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