Insights into structure and functioning of a soil microbial community amended with cattle manure digestate and sulfamethoxazole

Purpose: The present work aimed to fill some knowledge gaps on the effects on non-target natural soil microbial communities of the sulfamethoxazole (SMX) antibiotic potentially found in cattle manure digestate. Both soil prokaryotic and fungal community under different conditions were analyzed using molecular ecology methods. Methods: A previous microcosm experiment with a soil amended with a cattle manure digestate (3% dry mass) and spiked with SMX (20 mg/kg soil) was used for this in-depth study. Microbial live cell abundances were assessed by direct epifluorescence microscope methods. The microbial community structures were studied by DNA extraction and amplification using 16S rRNA primers targeting the V3-V4 region (for prokaryotes) and ITS1 (for fungi); Alpha-diversity indices (Chao1, Shannon and Evenness) were also estimated. Moreover, a prediction functional analysis was performed on prokaryotic 16S rRNA amplicon data with PICRUSt2 in order to predict possible variations in some microbial functioning. Results: Adding digestate to soil promoted both microbial abundance and some bacterial groups. The co-presence of SMX initially lowered these positive effects and decreased diversity. However, at day 61, the antibiotic was almost all removed and the microbial abundance and prokaryotic and fungal diversity showed increased values. Conclusion: The antibiotic detrimental effects on prokaryotic cells were transient and some resistant bacteria (e.g., Sphingomonas, Skermanella), presumably introduced into the soil with the digestate, were able to remove SMX. Moreover, the digestate long-term effect was to favor some fungal groups such as Basidiomycota. The presence of the genus Trichoderma (Ascomycota), able to transform antibiotics, does not exclude also as possible involvement of this fungus in SMX removal.