Short-lived detection of an introduced vertebrate eDNA signal in a nearshore rocky reef environment

Abstract

Environmental DNA (eDNA) is increasingly used to measure biodiversity of marine ecosystems, yet key aspects of the temporal dynamics of eDNA remain unknown. Of particular interest is in situ persistence of eDNA signals in dynamic marine environments, as eDNA degradation rates have predominantly been quantified through mesocosm studies. To determine in situ eDNA residence times, we introduced an eDNA signal from a non-native fish into a protected bay of a Southern California rocky reef ecosystem, and then measured changes in both introduced and background eDNA signals across a fixed transect over 96 hours. Foreign eDNA signal was no longer detected only 7.5 hours after introduction, a time substantially shorter than the multi-day persistence times in laboratory studies. Moreover, the foreign eDNA signal spread along the entire 38 m transect within 1.5 hours after introduction, indicating that transport and diffusion play a role in eDNA detectability even in protected low energy marine environments. Similarly, native vertebrate eDNA signals varied greatly over the 96 hours of observation as well as within two additional nearby fixed transects sampled over 120 hours. While community structure did significantly change across time of day and tidal direction, neither accounted for the majority of observed variation. Combined, results show that both foreign and native eDNA signatures can exhibit substantial temporal heterogeneity, even on hourly time scales. Further work exploring eDNA decay from lagrangian perspective and quantifying effects of sample and technical replication are needed to better understand temporal variation of eDNA signatures in nearshore marine environments.

Short‐term temporal variation of coastal marine eDNA

“…If the signal from eDNA is contemporary, such changes would be reflected in eDNA sampled on an hourly basis. With a few exceptions (e.g., Ely et al, 2021;Kelly et al, 2018;Sengupta et al, 2019), the influence of sampling eDNA at different times of day has been mostly neglected in aquatic eDNA studies, and broad inferences are often made without attention to sampling time.…”

“…If the signal from eDNA is contemporary, such changes would be reflected in eDNA sampled on an hourly basis. With a few exceptions (e.g., Ely et al, 2021; Kelly et al, 2018; Sengupta et al, 2019), the influence of sampling eDNA at different times of day has been mostly neglected in aquatic eDNA studies, and broad inferences are often made without attention to sampling time. As eDNA detections rely on stochastic observation processes, an ongoing challenge is to distinguish the signals arising from stochasticity (PCR, sequencing variation, and heterogeneous distribution of eDNA in the water) with those representing actual biological variation (e.g., diel species behavior).…”

“…While it has been established that eDNA composition changes with seasonal species turnover in fish communities (Sigsgaard, Nielsen, Carl et al, 2017; Stoeckle et al, 2017), there currently are very limited data on short‐term variation spanning hours to days (Bálint et al, 2018). Degradation time and transport of eDNA are not fully understood in natural aquatic environments, but several studies have documented rapid degradation over hours to days in temperate water samples (e.g., Andruszkiewicz et al, 2017; Ely et al, 2021; Sigsgaard, Nielsen, Bach et al, 2017; Strickler et al, 2015; Yamamoto et al, 2016). Because of rapid degradation, the general assumption is that sampling aquatic environments provides a contemporary picture of biodiversity at that site, but the exact temporal scale remains unknown.…”

eDNA captures depth partitioning in a kelp forest ecosystem

“…Degradation of eDNA signatures is relatively rapid in marine environments [8][9][10], with laboratory experiments showing degradation rates on the order of days [11][12][13]. However, in field conditions, detection of a specific eDNA point source can degrade beyond detection limits in only a few hours [14,15]. This evidence for rapid eDNA turnover rates suggests that eDNA signatures at a given location could be highly dynamic over time, particularly for species that are transitory.…”

A National Scale “BioBlitz” Using Citizen Science and eDNA Metabarcoding for Monitoring Coastal Marine Fish

“…Monuki et al (2021) found day to day variation in marine fish eDNA composition from the same site in consistency with known fish behavior. Ely et al (2021) shows that eDNA composition changed significant across time of day and that eDNA can display considerable heterogeneity, on an hourly basis. Jensen et al (2022) sampled eDNA at a coastal site every hour for 32 consecutive hours and found differences in species composition between samples taken only one hour apart, although the most significant difference was between samples collected at midday and those collected at midnight.…”