Using biobeds for the treatment of fungicide-contaminated effluents from various agro-food processing industries: microbiome responses and mobile genetic element dynamics

Agro-food processing industries generate large amounts of pesticide-contaminated effluents that pose significant environmental threat if managed improperly. Biopurification systems like biobeds could be utilized for the depuration of these effluents although direct evidence for their efficiency are still lacking. We employed a column leaching experiment with pilot biobeds to (i) assess the depuration potential of biobeds against fungicide-contaminated effluents from seed-producing (SPIs) (carboxin, metalaxyl-M, fluxapyroxad), bulb-handling (BHIs) (thiabendazole, fludioxonil and chlorothalonil) and fruit-packaging (fludioxonil, imazalil) industries (FPIs), (ii) to monitor microbial succession via amplicon sequencing and (iii) to determine the presence and dynamics of mobile genetic elements (MGE) like intl1, IS1071, IncP-1 and IncP-1epsilon often associated with the transposition of pesticide-degrading genes. Biobeds could effectively retain and dissipate the fungicides that were contained in the agro-industrial effluents with 93.1 - 99.98 % removal efficiency in all cases. Lipophilic substances like fluxapyroxad (FLX) were mostly retained in the biobed while more polar substances like metalaxyl-M (MET-M) and carboxin (CBX) were mostly dissipated or showed higher leaching potential like MET-M. Biobeds supported a resilient bacterial and fungal community that was not affected by fungicide application but showed clear temporal patterns in the different biobed horizons. This was most probably driven by the establishment of microaerophilic conditions upon water saturation of biobeds, as supported by the significant increase in the abundance of facultative or strict anaerobes like Chloroflexi/Anaerolinae, Acidibacter and Myxococcota. Wastewater application did not affect the dynamics of MGE in biobeds whose abundance (intl1, IS1071, IncP-1epsilon) showed significant increases with time. Our findings suggest that biobeds could effectively decontaminate fungicide-contaminated effluents produced by agro-food industries and support a rather resilient microbial community. Further studies will focus on the role of MGEs in the evolution of pesticide catabolic pathways using shotgun metagenomics and plasmidome analysis.