Biological and synthetic surfactant exposure increase anti-microbial gene occurrence in a freshwater mixed microbial biofilm environment

Aquatic habitats are particularly susceptible to chemical pollution from domestic, agricultural, and industrial sources. Antimicrobials are commonly used in medical and industrial environments to reduce harmful bacteria and biofilms. This has led to the rapid increase in the prevalence of antimicrobial resistant (AMR) genes. Alternate remedies to fight pathogenic bacteria and biofilms are in development including synthetic and biological surfactants such as sodium dodecyl sulphate (SDS) and rhamnolipids respectively. In the aquatic environment these surfactants are present as pollutants with potential to affect biofilm formation and AMR gene occurrence; however, there is limited research showing the actual environmental impact of such exposure. We tested the effects of rhamnolipid and SDS on natural aquatic biofilms in a freshwater stream in Northern Ireland. We grew biofilms on contaminant exposure substrata deployed within the stream over four weeks, and then carried out shotgun sequencing to determine microbial community composition, through 16s rRNA analyses (64,678 classifiable reads identified), and AMR gene occurrence (81 instances of AMR genes over 9 AMR gene classes) through a metagenomic analysis. There were no significant changes in community composition within all systems; however, biofilm exposed to rhamnolipid had a greater number of unique taxa as compared to our SDS treatments and controls. AMR gene prevalence was higher in surfactant-treated biofilms, with biofilm exposed to rhamnolipids having the highest presence of AMR genes and classes compared to the control or SDS treatments, in which genes encoding for rifampin resistance were detected. Our results suggest that the presence of rhamnolipid, and to a lesser extent SDS, encourages an increase in the prevalence of AMR genes in biofilms produced in mixed use water bodies.