Adaptation of methanogenic microbial assemblages to antibiotics: The role of resistance genes and taxonomic composition

Antibiotics are omnipresent contaminants in aquatic systems and can impact key ecosystem processes. Methanogenesis by anaerobic Archaea is such a process that has gained attention because antibiotics can increase their methane (CH₄) production dynamics – a 28-fold more potent greenhouse gas than carbon dioxide. Since such effects may depend on assemblage composition and antibiotic resistance, we investigated antibiotic effects on methanogenesis in sediments from a negiglibly impacted site (reserve) and downstream of a wastewater treatment plant (WWTP). Prior to incubation, short-term pre-treatment with antibiotics aimed to stimulate adaptive responses. During incubation, antibiotics reduced methanogenesis speed in WWTP sediment (−7 %) but increased it in the reserve (10 %), with site-specific patterns linked to differences in prokaryotic assemblage composition and their gene expression. Methanomicrobia, a key methanogenic group, showed contrasting responses across sites, likely mediated by prokaryotic substrate dynamics, particularly within the acetate pathway. Pre-treatment effects on methanogenesis dynamics were minor (maximum Bayesian factor of 3.6), but subtle shifts in prokaryotic activity and composition were observed. Elevated antibiotic resistance gene expression in WWTP sediments reflected historical exposure but did not mitigate antibiotic impacts on methanogenesis. These findings show the vulnerability of methanogenic assemblages to antibiotics despite potential adaptations and emphasize the risks posed by pharmaceutical pollution to critical freshwater ecosystem functions.