Vermicomposting Reshapes Microbial Communities and Functional Potential in Sewage Sludge: Insights from 16S and ITS Metabarcoding

Vermicomposting has been shown to be a cost-effective and sustainable approach for improving the environmental safety of sewage sludge, yet it remains comparatively understudied at the industrial scale. This study investigates how vermicomposting with the earthworm Eisenia andrei alters the taxonomic and functional diversity of bacterial and fungal communities in sewage sludge, including human-associated pathogens. Using 16S rRNA and ITS metabarcoding, we compared fresh sludge and sludge aged for 13 months without earthworms to vermicomposted sludge after 13 months. The study included one pilot-scale vermireactor and one control pilot-scale reactor with ten spatial subsamples per sampled layer (30 subsamples). Bioinformatic and statistical analyses showed that vermicomposting may produce significant shifts in taxonomic composition, reduce the abundance of baseline taxa, and enrich decomposer-associated bacteria and fungi. Both bacterial and fungal alpha diversity (e.g., Shannon) increased over time, while beta diversity (e.g., Bray–Curtis) analyses indicated heterogeneous changes in community structure across treatments and time points. Vermicomposting also seemed to activate the prediction of pathways associated with nitrogen metabolism, amino acid biosynthesis, and pollutant degradation, while reducing the prevalence of predicted antibiotic resistance. Human bacterial pathogens exhibited persistence but also temporal variation, suggesting compositional shifts during vermicomposting. Fungal communities transitioned from pathogen-associated taxa to predominantly saprotrophic and multifunctional groups, particularly in vermicompost. Overall, these findings suggest that vermicomposting may contribute to restructuring microbial communities in sewage sludge, with potential implications for the sustainability and safety of this biosolid.