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

Antibiotics are used for the treatment or prevention of cattle infections. Antibiotic residues can be found in cattle manure due to the partial body metabolism in the animal treated. Cattle manure can be used for feeding anaerobic digestion plants and producing methane-rich biogas and digestate which can be used as a fertilizer. Sulfamethoxazole (SMX) is one of the most commonly prescribed and consumed sulfonamide antibiotic because it can inhibit both Gram-positive and Gram-negative bacteria. However, current knowledge about its environmental persistence and effects on terrestrial ecosystems are quite scarce. The aim of this work was to evaluate possible effects of adding SMX and a cattle manure digestate on a natural soil microbial community. For this purpose, a microcosm experiment was set up and both prokaryotic and fungal communities were studied in terms of structure and functioning including the nitrogen metabolism, oxidative stress and folic acid pathway. The evaluation of the microbial abundance (direct count in epifluorescence) and phylogenetic characterization (DNA extraction and amplification with Miseq Illumina with 16S rRNA primers targeting the V3-V4 region of prokaryotic and ITS1 of fungi) made it possible to evaluate how adding digestate induced a shift in the soil microbial community structure. An overall increase in organic carbon and nitrogen and in bacterial species involved in the nitrogen metabolism (e.g. some Alphaproteobacteria), was observed. The co-presence of SMX initially lowered some microbial groups; however, the detrimental antibiotic effect was transient, in line with its degradation. At the end of the experiment, an increase of live cells abundance was also found.