The function and resilience of aquatic ecosystems is reliant on microbes which are essential for key ecosystem processes and supplying food for higher trophic levels; however, aquatic microbiota worldwide are at risk from pharmaceutical pollution. Pharmaceuticals in waterways is an increasing area of concern due to the potential for the development of antimicrobial resistance (AMR), a global crisis, which may render the current suite of antibiotics ineffective for clinical treatment. Widespread and increasing pharmaceutical use results in continual supply to aquatic systems predominantly via waste water treatment plant (WWTP) effluent. Once in aquatic systems, pharmaceuticals, being a diverse suite of biologically active compounds, have the capacity to act on aquatic microbiota. Untangling the effects of pharmaceuticals on the environment is difficult due to synergistic and antagonistic interactions in complex mixtures of pollutants. The effect of pharmaceuticals on aquatic microbiota is often investigated via rates of ecosystem processes while community structure and genomics are often overlooked.
Our previous work demonstrated ciprofloxacin (antibiotic) exposure significantly decreases respiration in biofilm colonised in the Hudson River, New York, using contaminant exposure substrata (CES). Recent analysis shows ciprofloxacin decreased community diversity but abundance of WWTP-derived taxa increased. We investigated the abundance of antimicrobial resistant genes (ARGs) and biogeochemical functional genes (BFGs), even when rates of biogeochemical processes were unchanged, in order to enhance understanding of non-lethal effects of pharmaceuticals on aquatic microbiota. In some cases, no change in rate was observed for denitrification despite a decrease in denitrification-associated BFGs, which may indicate denitrification is currently occurring at sub-optimal rates due to pharmaceutical exposure. This study contributes to the understanding of the resistome and its importance for ensuring microbial function and ecosystem resilience to future stressors.