Environmental DNA shedding and decay rates from diverse animal forms and thermal regimes

Abstract

Environmental DNA (eDNA) analysis from water samples is a promising new method to identify both targeted species and whole communities of aquatic organisms. However, the current literature regarding eDNA shedding rates primarily focuses on fish and most decay rate constants are reported for warm sunlit waters. Here, we conducted experiments to investigate how eDNA shedding differs between animal forms and how long eDNA can persist in waters of varying temperature and light conditions. We designed quantitative PCR assays for one fish (mummichog, Fundulus heteroclitus), one crustacean (grass shrimp, Palaemon spp.), and two scyphomedusae (moon jelly, Aurelia aurita and nettle, Chrysaora spp.) to estimate eDNA shedding and decay rates. We found that shedding rates were highly variable for all organisms, but grass shrimp had the lowest shedding rate. We quantified eDNA decay rate constants at 6, 15, and 23°C and found that decay rate constants of mummichog and grass shrimp were larger at higher temperatures, while those of scyphomedusae did not show clear temperature dependence. We also found that higher‐order decay models with tails fit the data better than first‐order log‐linear models, suggesting temporal variability in eDNA decay rates. Results indicate that different animal forms shed different types of eDNA, impacting both shedding and decay rates. These findings fill critical knowledge gaps regarding variation in eDNA shedding and decay across animal forms under a range of realistic marine temperature conditions. These data will be useful for interpreting field studies that utilize eDNA to investigate ocean habitats that are otherwise difficult to access.

Environmental (e)RNA advances the reliability of eDNA by predicting its age

“…In summary, these results demonstrate how incorporating eRNA quantification into existing eDNA protocols can both increase detection probability by targeting highly concentrated rRNAs and improve interpretation of positive detections by modeling the ratio of eRNA:eDNA, or assessing detection of low abundant mitosisassociated mRNAs. The release and degradation relationships between genomic fragments found here might change due to physiological differences between life-histories 51 or between organisms 19 , and thus these genomic relationships should be investigated for other taxonomic groups. We found a significant decrease in the Ratio R:D over time, allowing us to predict the age of genomic material, and thus reduce error from legacy genomic signal.…”

“…The decay rates of the exponential decay models were estimated as dC′/dt = − kC′, where C′ = C t /C 0 was used to normalize eDNA/eRNA concentration. Previous decay studies have demonstrated biphasic eDNA decay 19,37 , and as such we analyze the log-linear decay rates over the initial 72-h. The decay rates were estimated by fitting a linear mixed-effect model with the values of log e (C t /C 0 ) as the response variable.…”

Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities

“…Instead, our findings strongly reinforce the conclusion that eDNA can discriminate communities at fine spatial scales as first established by Port et al 27 , even within habitats. Fish abundance estimated from eDNA data depends on several factors, including eDNA shedding, degradation and dispersion [45][46][47][48] . The persistence of eDNA can vary among aquatic organisms, but a growing body of evidence suggest that eDNA decay rates are faster in marine compared to freshwater environments and that once shed eDNA may only be detectable for hours to a few days [46][47][48] .…”

“…Fish abundance estimated from eDNA data depends on several factors, including eDNA shedding, degradation and dispersion [45][46][47][48] . The persistence of eDNA can vary among aquatic organisms, but a growing body of evidence suggest that eDNA decay rates are faster in marine compared to freshwater environments and that once shed eDNA may only be detectable for hours to a few days [46][47][48] . For instance, both Andruszkiewicz et al 47 and Collins et al 46 compiled previous findings on eDNA half-lives, showing they were relatively short in temperate marine environments, ranging from 6.9 h for the northern anchovy 45 to 63 h for the Maugean skate 49 .…”

“…The persistence of eDNA can vary among aquatic organisms, but a growing body of evidence suggest that eDNA decay rates are faster in marine compared to freshwater environments and that once shed eDNA may only be detectable for hours to a few days [46][47][48] . For instance, both Andruszkiewicz et al 47 and Collins et al 46 compiled previous findings on eDNA half-lives, showing they were relatively short in temperate marine environments, ranging from 6.9 h for the northern anchovy 45 to 63 h for the Maugean skate 49 . Another study found similar eDNA decay rates in anchovy, sardine, and mackerel, with first-order rate constants on the order of 10 −1 per hour 45 .…”