Environmental DNA Advancing Our Understanding and Conservation of Inland Waters

Abstract

Aim: The aim of this chapter is to introduce the concepts and applications of environmental DNA (eDNA) for species detection and biomonitoring of freshwater ecosystems. Environmental assessment of inland waters is currently undergoing a revolution due to the increased utilization of eDNA and major advancements in molecular techniques. Several aspects of ecology and conservation biology across the academic, private and government sectors are already utilizing eDNA-based approaches with more applications being rapidly developed. Therefore, this chapter disseminates current fundamental understanding of the dynamics and applications of eDNA in freshwater environments. Main concepts covered: Environmental DNA (eDNA) is DNA extracted from environmental samples without targeting a particular organism or group of organisms. Within the realm of inland waters, eDNA samples typically include water, sediment or biofilm samples, though there is potential for other environmental sources. The ecology of eDNA (e.g., transport, degradation rate, molecular state) greatly affects the detectability of eDNA, as well as the interpretation of the results drawn from eDNA-based assessment. In particular, understanding the difference between eDNA detection dynamics in lotic (e.g., rivers and streams) versus lentic (e.g., ponds and lakes) environments is key to understanding and applying eDNA-derived information. Main methods covered: A major characteristic of eDNA-based research is the non-targeted aspect of species and community detection. It is therefore paramount that an understanding of the sampling and DNA extraction methods are outlined, and that concerns regarding potential inhibition (false negatives) and contamination sources (false positives) are addressed. The use of eDNA also requires additional experimental design considerations, particularly regarding replication and spatial resolution, due to the need to cross validate findings and the increased complexity of the data created compared to traditional taxonomic-based approaches. Currently, eDNA-based research can be divided into two main groups, population- and community-based analyzes. Population-based analyzes rely primarily on single-targeted (i.e., species) methods such as qPCR, which are lower cost and easier for smaller institutes or individuals to independently implement. Community-based approaches rely largely on high throughput sequencing (HTS) and require additional molecular and bioinformatics specialization and support, but result in greater potential for data generation and analytical power, given the proper study design. Future eDNA work will include applying PCR free-based methods to population analyzes and combining multi-dimensional environmental data for environmental community analyzes. Other advances in eDNA research may look to assess the transcriptional profiles of eDNA samples to assess functional community diversity. Conclusion/Outlook: This chapter provides an overview of current molecular and eDNA-based approaches for inland water assessment. There are many aspects of eDNA that are still largely unknown, but the ability to apply standardized non-invasive sampling with high throughput data is hard to ignore in the modern age.