Can DNA from wet, temperate soils be used for palaeoecological reconstruction?

Abstract

Sedimentary ancient DNA in well-dated contexts (sedaDNA) has great potential as a palaeoecological proxy. A few studies have attempted palaeoecological reconstructions using sedaDNA from soil; these studies have been mainly restricted to cold and/or dry soils. The study of soils from wet, temperate locations has been limited due to uncertainties surrounding the longevity and mobility of DNA in these environments. We addressed this knowledge gap with a novel field experiment that (i) tracked the movement and longevity of ‘exotic’ DNA applied to a wet, temperate soil and (ii) compared extant plant community structure with recent (decades old) environmental DNA (eDNA) data extracted from shallow (<20 cm deep) soil samples. We used DNA metabarcoding to detect the exotic DNA and reconstruct plant communities from soil eDNA at different depths. Dating control provided by layers of volcanic ash indicated that our oldest soil samples were formed ~100 years ago. Our findings indicated low survivability and limited (centimetre-scale or less) mobility of applied DNA. The reconstructed plant communities closely resembled extant vegetation cover. We concluded that sedaDNA would be suitable as a palaeo-proxy for vegetation in similar settings, albeit restricted to the most abundant taxa. Further work in more taxonomically and structurally diverse settings, preferably with different soil types, would be required to establish the broader use of soil sedaDNA as a palaeoecological proxy in wet, temperate soils.