Detection, movement and persistence of invertebrate eDNA in groundwater

Abstract

Sampling groundwater biodiversity is difficult because of limited access and issues with species identification. Environmental DNA (eDNA) provides a viable alternative to traditional sampling approaches, however limited knowledge of the abundance and fate of DNA in groundwater hinders the interpretation of data from these environments. Groundwater environments are dark and have lower oxygen concentrations and microbial activity than surface waters. Consequently, assumptions about DNA fate in surface ecosystems may not apply to groundwaters. Here, we test the longevity and transport of eDNA in groundwater within a static microcosm and a flow-through mesocosm. A variety of invertebrates were placed within a mesocosm and microcosm to enable DNA shedding, and then removed. DNA persisted for up to 5 weeks after their removal in the static experiment and was detected between 9 and 33 days in the flow-through experiment. Sediments and water both proved important for eDNA detection. Crustacean DNA was detected sporadically and unpredictably, whereas non-crustacean DNA was detected more frequently despite their lower densities. We suggest that detecting crustaceans poses a challenge to utilising eDNA approaches for stygofauna monitoring. This is confounded by the scarcity of sequences for stygofauna in reference databases. Further research is needed before eDNA alone can be routinely employed for stygofauna detection.Analysis of environmental DNA (eDNA) is rapidly changing the way in which ecology is studied and the depth of understanding of biodiversity and ecosystem functioning. eDNA based detection methods may be more time and resource efficient, logistically more feasible and less invasive than traditional ecological sampling and survey methods 1. One environmental sample can be used to detect new and rare species 2-4 , characterise entire communities 5-7 describe food webs and community networks 8,9 , establish connectivity between ecosystems 10 , detect invasive species 11 and understand evolution and relatedness of species 7 . DNA metabarcoding allows the identification of taxa in a sample without the need for time-consuming morphological examination, which is of particular advantage in environments, such as groundwaters, where few taxa are formally described, or cryptic species are common 12 . The application of this technology in ecology and conservation has the potential to change the way ecosystems are managed 4 .Despite its many advantages, there are several challenges with using eDNA [13][14][15][16] , particularly when it is the sole method for characterising and/or monitoring some ecological communities [15][16][17][18] . Well-documented concerns with eDNA metabarcoding include issues with reference databases [18][19][20] , challenges with polymerase chain reaction (PCR), primer and metabarcoding biases 15,18 , difficulties amplifying specific taxa due to fragmentation 12,21 , estimating taxon abundances 12,22,23 and limited knowledge of the persistence and transport of DNA in the environment 9,17 . Such is...