Anaerobic Storage Completely Removes Suspected Fungal Pathogens but Increases Antibiotic Resistance Gene Levels in Swine Wastewater High in Sulfonamides

Wastewater storage before reuse is regulated in some countries. Investigations of pathogens and antibiotic resistance genes (ARGs) during wastewater storage are necessary for lowering the risks for wastewater reuse but are still mostly lacking. This study aimed to investigate pathogens, including harmful plant pathogens, and ARGs during 180 d of swine wastewater (SWW) storage in an anaerobic storage experiment. The contents of total organic carbon and total nitrogen in SWW were found to consistently decrease with the extension of storage time. Bacterial abundance and fungal abundance significantly decreased with storage time, which may be mainly attributed to nutrient loss during storage and the long period of exposure to a high level (4653.2 μg/L) of sulfonamides in the SWW, which have an inhibitory effect. It was found that suspected bacterial pathogens (e.g., Escherichia–Shigella spp., Vibrio spp., Arcobacter spp., Clostridium_sensu_stricto_1 spp., and Pseudomonas spp.) and sulfonamide-resistant genes Sul1, Sul2, Sul3, and SulA tended to persist and even become enriched during SWW storage. Interestingly, some suspected plant fungal species (e.g., Fusarium spp., Ustilago spp. and Blumeria spp.) were detected in SWW. Fungi in the SWW, including threatening fungal pathogens, were completely removed after 60 d of anaerobic storage, indicating that storage could lower the risk of using SWW in crop production. The results clearly indicate that storage time is crucial for SWW properties, and long periods of anaerobic storage could lead to substantial nutrient loss and enrichment of bacterial pathogens and ARGs in SWW.