A Microcosm Study of Surface Sediment Environmental DNA: Decay Observation, Abundance Estimation, and Fragment Length Comparison

Abstract

Interpretation of environmental DNA (eDNA) is a major problem hindering the application of this emerging technology for environmental monitoring. The decay characteristics and bioabundance estimation of different DNA fragment lengths are largely unknown, especially for eDNA captured from surface sediments. An estuarine amphipod, Grandidierella japonica, was used as the target species in this study. We conducted a lab-scale experiment using DNA extraction to clarify the effect of bacteria on eDNA decay. We also conducted a microcosm experiment using amphipods to clarify interpretations of information regarding eDNA decay and bioabundance estimation by using two fragments with different lengths (126 and 358 bp). It was found that the bacteria concentration accelerated eDNA decay, and long fragments were more susceptible to bacteria, thus decaying faster, than short fragments in the exponential decay period. The fresh eDNA (collected within 24 h of removing the amphipods) was more indicative of bioabundance than old eDNA (collected 240−480 h after removing amphipods), and short fragments better reflected bioabundance than long fragments. Finally, we compared the half-life of eDNA in surface sediment with that in a water sample and found that the temporal scales of surface sediment and water are similar (days to weeks). Our results suggest that surface sediment also has the potential to monitor the environment at a temporal scale similar to water.

Variation of Environmental DNA in Sediment at Different Temporal Scales in Nearshore Area of Tokyo Bay

“…In another word, the resolution of surface sediment eDNA was more than one month based on the results obtained from this study. It was also consistent with our previous kinetic study [37] of eDNA which pointed out that eDNA from surface sediment has the potential to indicate the water environment at a certain present temporal scale.…”

Sedimentary eDNA provides different information on timescale and fish species composition compared with aqueous eDNA

“…Therefore, the estimation of abundance by using eDNA metabarcoding needs careful interpretation. Wei et al (2018) observed two phases in the sedimentary eDNA decay process: a fast-decay phase (until 72 hr after removal of individuals), followed by a slow-decay phase (until 480 hr). However, we F I G U R E 5 Number of fish species detected by eDNA metabarcoding.…”

“…Most eDNA studies on macro-organisms analyzed eDNA in water samples (Goldberg, Strickler, & Fremier, 2018;Ishige et al, 2017;Minamoto et al, 2012;Miya et al, 2015;Ushio et al, 2018;Valentini et al, 2016); however, several recent studies have targeted eDNA in underwater sediments (Buxton, Groombridge, & Griffiths, 2018;Shaw et al, 2016;Turner, Uy, & Everhart, 2015;Wei, Nakajima, & Tobino, 2018). To date, comparison of the basic properties between sample types (i.e., water/sediment) has been performed only for fish eDNA.…”

Influence of sediment and stream transport on detecting a source of environmental DNA

“…There are fewer studies measuring eDNA decay or degradation in sediment, but Sakata et al [54] also found lower rates of decay in sediment than in water, with rates in sediment even a magnitude lower than our findings (k = 0.0003) for two fish species. Interactive factors that affect rates have been identified, including biochemical oxygen demand and initial concentration of eDNA present [21] and bacterial activity [55], as well as protection from other adverse conditions (e.g., enzymatic degradation by binding to clay or organic fractions) [22,56]. Sediment has been long recognized for its protective characteristics that extend survival of microbes [22,53].…”