Metagenomic comparison of effects of mesophilic and thermophilic manure anaerobic digestion on antimicrobial resistance genes and mobile genetic elements

Abstract

This study evaluated the long-term effects of mesophilic (MAD) and thermophilic (TAD) anaerobic digestion on the fate and evolution of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in cattle manure following a metagenomic approach. The results indicated that MAD and TAD lowered ARG levels in fresh cattle manure by over 50 % and MGEs by over 65 %. However, no statistically significant difference was observed between the MAD and TAD processes in terms of their ability to reduce ARG and MGE. Co-occurrence analysis suggested facultative anaerobic species belonging to the Bacillota and Actinomycetota phyla as the primary potential hosts of ARGs and MGEs. Analyses of co-assembled contigs revealed the presence of transposon and toxin-antitoxin systems in close proximity to ARGs typically found in anaerobic digesters. The identification of these systems near ARGs is particularly significant, as it highlights a potential mechanism for the persistence and spread of ARGs in such environments. Overall, the results indicated that digested cattle manure (whether under mesophilic or thermophilic conditions) would pose a much lower risk of dissemination of antimicrobial resistance than untreated manures. Since TAD did not outperform MAD at reducing ARGs and MGEs, thermophilic temperatures may not be necessary to improve ARG reduction rates in cattle manure AD. These valuable insights could help develop strategies to reduce the dissemination of antibiotic resistance due to manure treatment and disposal.

Keywords

• Resistome
• Mobilome
• Microbiome
• Waste management
• Livestock