Antibiotic resistance of Daphnia microbiomes across different catchment types

Abstract :

Antibiotic resistance is a growing global concern, threatening the efficacy of antibiotics essential for both human and veterinary medicine. This study examines the prevalence of antibiotic-resistant bacteria within the microbiomes of Daphnia collected from freshwater lakes across different catchment types: urban, farm, and natural. Antibiotic resistance was assessed using bacterial culturing on antibiotic-supplemented agar and PCR-based detection of resistance genes. Plating results indicated that ampicillin resistance was detected exclusively at a farm site, suggesting a potential association with agricultural antibiotic use. Kanamycin resistance was particularly prevalent in farm and urban locations, while chloramphenicol resistance was widespread across all environments. Tetracycline resistance remained consistently low but was detected only in farm and urban catchments. Without antibiotic exposure, microbial levels remained high across all site types and environments. PCR amplification of known resistance genes, yielded minimal or insignificant results, suggesting a low prevalence of antibiotic resistance genes within the Daphnia microbiome despite phenotypic resistance observed in plating experiments. The discrepancy between genetic detection and plating results suggests that resistant bacteria, though present at low genetic frequencies, can proliferate and outcompete non-resistant bacteria under selective pressure. These findings suggest environmental antibiotic exposure in shaping microbial community dynamics and that anthropogenic activities, such as agricultural runoff and wastewater exposure, contribute to the dissemination of antibiotic resistance in aquatic ecosystems. This study emphasizes the need for continued surveillance of antibiotic resistance in freshwater environments and calls for the integration of metagenomic analyses and long-term monitoring to better understand resistance mechanisms and their ecological impacts.