Contrasting microbial responses to polyethylene and paper-based cover residues in agricultural soil microcosms

Abstract Aims Agricultural cover materials can generate particulate residues in soil. Polyethylene covers may contribute persistent microplastic fragments, whereas paper-based covers may generate more degradable residues whose microbial effects remain less understood. However, microbial responses to these residues can be difficult to distinguish from natural time-driven community succession during incubation. Here, we compared polyethylene microplastics and paper-based microfragments in agricultural soil microcosms to determine how particle type and concentration influence bacterial and fungal communities relative to time-matched untreated controls. Methods Polyethylene microplastics and paper-based microfragments were applied at low and high concentrations to plant-free soil microcosms established with agricultural soil from the Fataca region, Portugal. Untreated controls were included at each sampling time to separate amendment-associated effects from incubation-driven microbial succession. Bacterial 16S rRNA gene and fungal ITS communities were characterized after two and six months of incubation using amplicon sequencing. Each incubated treatment was represented by six independent biological microcosms. Results Bacterial communities were mainly structured by incubation time. Untreated controls showed a marked richness and diversity decline after two months followed by recovery after six months, indicating a strong temporal baseline. Relative to these time-matched controls, polyethylene microplastics and paper-based microfragments produced comparatively modest bacterial shifts, including high-dose increases in Acidobacteriota after two months, increased relative abundance of Bradyrhizobium in polyethylene microplastic treatments, and reduced Bacilli/Bacillota across amended soils after six months. Fungal communities showed clearer amendment-associated responses. High paper-based microfragments reduced observed fungal richness by approximately 22% relative to the two-month control and by approximately 49% relative to the six-month control. This treatment also promoted high-dominance fungal communities, with early enrichment of Chytridiomycota and later dominance of Ascomycota, especially Sordariomycetes, Chaetomiaceae, and Parachaetomium . Conclusions Under plant-free microcosm conditions, bacterial responses were dominated by temporal succession, whereas fungal communities showed stronger amendment-associated responses, particularly under high paper-based microfragment addition. These results indicate that residues from plastic- and paper-based agricultural covers can affect soil microbial trajectories in different ways, and that particle type, concentration, and incubation time should be considered when evaluating cover-material residues.