A quantitative analysis of vertebrate environmental DNA degradation in soil in response to time, UV light and temperature

Environmental DNA (eDNA) degradation influences the effectiveness of
eDNA-based biodiversity monitoring, but the factors that determine the
rate of decay of eDNA in terrestrial environments are poorly understood.
We assessed the persistence of vertebrate eDNA from a mock vertebrate
community created with soil from zoo enclosures holding ten target species
from different taxonomic classes (e.g. reptiles, birds and mammals) and of
different biomass (e.g. little penguin and giraffe). We examined species
detection rates resulting from eDNA metabarcoding, as well as relative
eDNA concentrations via qPCR, from soil samples over eight time points (0
to 12 weeks), during exposure to three ambient temperatures (10, 25 and 40
°C) and three levels of ultraviolet B (UV-B) radiation (0%, 50% and 100%
intensity). We recorded considerable variation in detectability between
species, independent of temperature and UV-B effects. Quantitative PCR
indicated degradation of eDNA over time for all temperature and UV
treatments, although it was still possible to detect eDNA from some
species after twelve weeks. Degradation rates were lowest for high UV-B
treatments, presumably due to UV-B reducing bacterial metabolism. The
temperatures investigated did not influence eDNA decay. Our results
indicate that eDNA in soil can persist under a range of temperatures and
high UV radiation for longer than expected. Sheltered sites with minimal
UV-B radiation, which have previously been considered ideal sites for
terrestrial eDNA collection, may not be optimal for eDNA persistence in
some cases due to microbial decay. A better understanding of eDNA
degradation in terrestrial environments is needed before eDNA
metabarcoding of soil can be used as a stand-alone method for accurate
surveying of terrestrial vertebrate communities.