Nanopore Sequencing Reveals Microbial Community Compositions on Microplastic in the Setun River of the Moscow Region

Microplastics introduced into freshwater environments create novel surfaces that select for specific microbial colonizers and exclude others. In urban rivers, these biofilms can act as reservoirs of antimicrobial resistance and contain potential enzymes for polymer degradation. We studied microbial communities associated with microplastics in the Setun River and examined how their composition changes during laboratory enrichment on plastic substrates. Native river specimen and cultures enriched on low-density polyethylene (LDPE) and polycaprolactone (PCL) were analyzed using mWGS and full-length 16S rRNA nanopore sequencing. Enrichment led to a pronounced shift toward nearly monoculture of Bacillota, more specifically Bacillus cereus, while native plastisphere communities were dominated by Pseudomonadota. Microscopy revealed clear degradation of PCL but not LDPE, and functional screening of native metagenomes uncovered a diverse resistome, including oqxAB efflux operons, mcr-3-like phosphoethanolamine transferases, various β-lactamases, and class 1 integron genes, demonstrating that the Setun River plastisphere already contained clinically relevant AMR determinants. These findings suggest that certain bacteria such as Bacillus cereus can thrive and dominate on plastic surfaces in urban rivers, while many other taxa cannot persist there, highlighting that microplastics strongly reshape plastisphere communities and emphasize the role of river-borne microplastics as potential vectors of antibiotic resistance.