Uncovering Putative Bacterial Pathogens in Lakes in Aotearoa New Zealand Using Environmental DNA

The emergence of aquatic diseases poses significant risks to ecological, social, cultural and economic values. Aquatic environments are intricately linked to human and animal health, as water can facilitate the spread and transmission of pathogens and waterborne diseases. We conducted an environmental DNA survey of 287 lakes across Aotearoa New Zealand, spanning a broad gradient of natural and human-influenced conditions. Using a curated bacterial pathogens database, we detected 412 potentially pathogenic taxa-250 detected only in water and 162 found in both water and sediment; none were exclusive to sediment. Dominant groups included <i>Pseudomonas</i>, <i>Acinetobacter</i>, <i>Clostridium</i>, <i>Afipia</i> and Burkholderiaceae. Putative pathogens were ubiquitous in all lakes, including remote alpine sites with minimal human impact. Pathogen communities were associated with the extent of high-productivity exotic grassland in the catchment and elevated nutrient levels, although richness was not linked to environmental drivers. Our findings show that eDNA can be a cost-effective, broad-spectrum screening tool that complements targeted diagnostics. The widespread occurrence of potential pathogens in lakes underscores the need for improved understanding of their ecological dynamics and the environmental conditions that promote disease outbreaks, supporting freshwater biosecurity, ecosystem management and public and animal health.