Overlooked eDNA contamination in human-influenced ecosystems: a call to manage large-scale false positives in biodiversity assessments

The use of environmental DNA (eDNA) has significantly revolutionized studies in biodiversity science. A crucial innovation of eDNA-based biodiversity assessment is the ability to detect species through genetic materials released by organisms into their environments, without the need for direct observation or capture (i.e., organisms remain “unseen”). The fact that organisms remain “unseen” has many pros and cons, many of which have been largely recognized and technically addressed or managed. However, two recent studies have both highlighted another critical issue regarding eDNA-based biodiversity assessments: the prevalence of overlooked eDNA contamination originating from human activities, such as the release of treated wastewater into aquatic ecosystems. Such eDNA contamination derived from human activities can lead to significant false positive errors in eDNA-based biodiversity assessments, particularly in human-disturbed ecosystems such as urban and coastal environments. Here I discuss the causes and consequences of eDNA contamination, stressing that this widespread but often neglected issue can substantially affect both eDNA-based theoretical studies and applied biodiversity management. Additionally, I propose several potential technical solutions to minimize its negative impacts, including well-designed sampling strategies, a deeper understanding of eDNA persistence and its spread in local waterbodies, and the use of environmental RNA (eRNA). Given that eDNA contamination can significantly impact ecosystems such as urban and coastal environments where biodiversity provides essential ecosystem services, I call for precautionary approaches and technical efforts to mitigate false positives derived from eDNA contamination in biodiversity assessments in these ecosystems.