Antibiotic resistance genes in food wastes: diversity, dynamics, and interactions with prokaryotes and viruses in centralized biogas plants

Abstract

Anaerobic digestion (AD) is widely considered an effective approach for the treatment of food waste (FW). However, the diversity of antibiotic resistance genes (ARGs) in FW, together with ARG dynamics and their interactions with prokaryotes and DNA viruses during AD, remain insufficiently explored. This study performed metagenomic analyses of FW and digestate samples collected from 9 centralized biogas plants. The results showed that FW served as an important reservoir of ARGs. Although the distribution patterns of ARGs in FW and digestate differed, MLS, multidrug, tetracycline, aminoglycoside, and bacitracin were the five most abundant ARG types in both FW and digestate. While AD reduced the overall quantity of ARGs, its capacity to markedly decrease ARG abundance was limited. Procrustes analysis revealed associations between ARGs and prokaryotes and DNA viruses. Among the reconstructed prokaryotic metagenome-assembled genomes (180), 130 were identified as carrying ARGs. DNA viruses showed close associations with antibiotic-resistant bacteria (ARB), with viral-host relationships detected between 181 DNA viruses and 77 ARBs. Most of these viruses were temperate DNA viruses, which may indirectly influence ARG distribution by regulating ARB populations. Nevertheless, the contribution of DNA viruses to ARG dissemination appeared limited, given the small number of detected ARG-carrying viruses and the lack of high-risk ARGs.

Graphical abstract

Keywords

Anaerobic digestion / Food waste / Antibiotic resistance genes / DNA viruses / Prokaryotes

Highlight

	● FW and digestate are rich in ARGs, with widely shared ARGs present in both.
	● AD exerted a more pronounced reduction on ARG diversity than on ARG abundance.
	● ARGs distribution was related to both prokaryotic and DNA virus communities.
	● A large proportion of ARBs contained DNA viruses, primarily temperate viruses.
	● Only a small proportion of ARGs (less than 3%) was carried by DNA viruses.

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