The need for robust qPCR-based eDNA detection assays in environmental monitoring and species inventories

Abstract

Considerable promise and excitement exist in the application of environmental DNA (eDNA) methods to environmental monitoring and species inventories as eDNA can provide cost-effective and accurate biodiversity information. However, considerable variation in data quality, rigor, and reliability has eroded confidence in eDNA application and is limiting regulatory and policy uptake. Substantial effort has gone into promoting transparency in reporting and deriving standardized frameworks and methods for eDNA field workflow components, but surprisingly little scrutiny has been given to the design and performance elements of targeted eDNA detection assays which, by far, have been most used in the scientific literature. There are several methods used for eDNA detection. The most accessible, cost-effective, and conducive to standards development is targeted real-time or quantitative real-time polymerase chain reaction (abbreviated as qPCR) eDNA analysis. The present perspective is meant to assist in the development and evaluation of qPCR-based eDNA assays. It evaluates six steps in the qPCR-based eDNA assay development and validation workflow identifying and addressing concerns pertaining to poor qPCR assay design and implementation; identifies the need for more fulsome mitochondrial genome sequence information for a broader range of species; and brings solutions toward best practices in forthcoming large-scale and worldwide eDNA applications, such as at-risk or invasive species assessments and site remediation monitoring.