Microplastics in agricultural soils alter bacterial and fungal communities: contrasting effects versus a paper-based alternative

Aims Soils are increasingly exposed to anthropogenic particles such as microplastics, particularly through fragmentation of agricultural plastic cover materials. However, their microbial impacts can be difficult to distinguish from natural time-driven community succession. This study compared the effects of microplastics and paper-based microfragments, proposed as an alternative cover material, on soil bacterial and fungal communities. Methods Microplastics and paper-based microfragments were applied at low and high concentrations in soil microcosms using soils from the Fataca region (Portugal), where plastic cover materials are widely used. Bacterial (16S rRNA gene) and fungal (ITS) communities were characterized after two and six months of incubation using amplicon sequencing. Results Bacterial communities showed strong temporal turnover during incubation, but both particle types produced taxon-specific deviations from time-matched controls. After two months, high-dose amendments increased the relative abundance of Acidobacteriota, while microplastic treatments also enriched Bradyrhizobium , a lineage associated with plant–microbe interactions. By six months, amended soils converged toward a shared bacterial pattern characterized by reduced Bacilli relative to controls. Fungal communities showed stronger and more persistent responses. High paper-based microfragments suppressed fungal diversity at both sampling times (observed features: 462 at two months; 598 at six months) and drove shifts from early Chytridiomycota enrichment toward Ascomycota dominance, particularly Sordariomycetes and Chaetomiaceae, including Parachaetomium . Microplastic amendments also altered fungal composition but produced weaker and less persistent changes. Conclusions Particulate residues from agricultural cover materials can alter soil microbial communities beyond natural temporal succession, with particularly strong fungal responses to high micropaper amendments.