Zoological applications for environmental DNA: detection, diversity, and health

Abstract

Environmental DNA (eDNA) monitoring has revolutionised the way biodiversity is surveyed over the past decade. There is now a myriad of eDNA protocols and techniques developed to improve eDNA isolation from environmental samples, greatly diversifying eDNA applications in the types of species surveillance that can now be undertaken. As the breadth of those applications increase and more studies show the promise of these tools to inform environmental management, there is greater impetus in the uptake by end-use agencies as part of routine monitoring. Indeed, the question is no longer if these eDNA methods work, but rather if reproducibility can be achieved to inform management decisions. There is now an increasing tendency to use the technology, either alone or in tandem with conventional techniques, in biodiversity assessments and in detection of single species such as threatened or invasive species. However, due to eDNA being an indirect form of detection, there are still uncertainties associated with eDNA monitoring and managers still struggle with how to use eDNA results in confident decision-making and management. In order for eDNA to become a routine tool for legislative requirements such as national State of the Environment (SoE) Reporting, there is a need to bridge the gap between research and management. In particular, stringent and highly scrutinised workflows are needed to deliver consistent and repeatable molecular results that can reliably inform management. In New Zealand, a number of studies have highlighted the potential for eDNA to be applied to a variety of different environments for a range of purposes. New Zealand also faces the same environmental pressures seen globally such as invasive species, habitat fragmentation, climate change, declining water quality as just a few examples. There is a great benefit for agencies to be adopting these eDNA tools as they can be more cost-effective, be widely distributed and enable greater consistency in the data received if applied appropriately. This special issue is a significant step forward in providing the necessary data that can inform the appropriate methods to apply for a particular purpose and to also understand some of the limitations and gaps that still need to be addressed before these tools are widely adopted. Readers looking to design their own eDNA studies would be well advised to consult some review papers discussing such aspects of eDNA studies as: experimental design e.g., (Goldberg et al. 2016), recording metadata e.g., (Nicholson et al. 2020); choice of DNA extraction method e.g. (Lear et al. 2018; Jeunen et al. 2019); selection of genome regions appropriate for the research question being asked e.g., (Drummond et al. 2015; Jeunen et al. 2019); reporting requirements for qPCR studies e.g. (Bustin et al. 2009); the pros and cons of the different techniques used in eDNA studies (Zaiko et al. 2018); limitations of eDNA studies (Kelly et al. 2019); and the tools needed before eDNA monitoring can be embedded within management programmes (Sepulveda et al. 2020). The use of DNA sourced directly from the environment as a means of understanding microbial diversity via metagenomics has been a technology with the longest history.