Bioaugmentation of manures by a tiamulin-degrading Sphingomonas as a mean to alleviate environmental dispersal of antibiotic residues

Several veterinary antibiotics (VAs) used in livestock farming deviate degradation by animals and they are excreted in faeces and from there in agricultural soils through the use of faecal material as organic fertilizers. Bioaugmentation of VA-contaminated faecal material with VA-degrading bacteria, is an environmentally friendly approach for reducing the environmental pressure posed by VAs. We explored the efficiency of a Sphingomonas isolate, able to actively degrade tiamulin (TIA), as bioaugmentation agent for the removal of TIA from pig faecal material fortified with TIA at two concentration levels (5 ug g-1 and 50 ug g-1). The efficiency of bioaugmentation was assessed comparatively with other practices currently used for the treatment of manures before their application in agricultural soils: stockpiling and anaerobic digestion. Bioaugmentation accelerated the dissipation of TIA (DT50 = 32.3 and 66.2 days) compared to anaerobic digestion (DT50 = 103 and 126.7 days) and stockpiling (DT50 = 95.38 and 113.8 days). Furthermore, we determined the impact of TIA on methane production and followed microbial succession during anaerobic digestion via amplicon sequencing. The lower concentration of TIA significantly stimulated biomethanation, driven by the increasing abundance of methanogens of the genus Methanosarcina which seemed to employ an aceticlastic biomethanation pathway. Our findings highlight (i) the potential of bioaugmentation of VA-contaminated faecal material as a mean to mitigate the dispersal of VA residues in agricultural settings (ii) the high risk of contamination of agricultural soils by the use of TIA-contaminated manures that have been stockpiled or anaerobically digest before their use in agricultural settings.