Journal Article
Taking eDNA underground: factors affecting eDNA detection of subterranean fauna in groundwater
van der Heyde, M., White, N.E., Nevill, P., Austin, A.D., Stevens, N., Jones, M. and Guzik, M.T.
Record Number:
6137
Year:
2023
Journal:
Molecular Ecology
Pages:
yy
Volume:
xx
Notes:
This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process which may lead to differences between this version and the Version of Record.
Abstract:
Stygofauna are aquatic fauna that have evolved to live underground. The impacts of
anthropogenic climate change, extraction and pollution on groundwater pose major threats to
groundwater health, prompting the need for efficient and reliable means to detect and monitor
stygofaunal communities. Conventional survey techniques for these species rely on
morphological identification and can be biased, labour intensive, and often indeterminate to
lower taxonomic levels. By contrast, environmental DNA (eDNA)-based methods have the
potential to dramatically improve on existing stygofaunal survey methods in a large range of
habitats and for all life stages, reducing the need for the destructive manual collection of
often critically endangered species or specialized taxonomic expertise. We compared eDNA
and haul-net samples collected in 2020 and 2021 from 19 groundwater bores and a cave on
Barrow Island, located north-west of Western Australia, and assessed how sampling factors influenced the quality of eDNA detection of stygofauna. The two detection methods were
complementary, eDNA metabarcoding was able to detect soft-bodied taxa and fish often
missed by nets, but only detected seven of the nine stygofaunal crustacean orders identified
from haul-net specimens. Our results also indicated that eDNA metabarcoding could detect
54-100% of stygofauna from shallow water samples and 82-90% from sediment samples.
However, there was significant variation in stygofaunal diversity between sample years and
sampling types. The findings of this study demonstrate that haul net sampling has a tendency
to underestimate stygofaunal diversity and that eDNA metabarcoding of groundwater can
substantially improve efficiency of stygofaunal surveys
Times Cited:
3