High‐frequency and long‐term observations of eDNA from imperiled salmonids in a coastal stream: Temporal dynamics, relationships with environmental factors, and comparisons with conventional observations

Abstract

A greater understanding of eDNA behavior in the environment is needed before it can be employed for ecosystem monitoring applications. The objectives of this study were to use autonomous sampling to conduct long‐term, high‐frequency monitoring of the eDNA of native salmonid species in a Californian coastal stream, describe temporal variation of eDNA on multiple scales and identify environmental factors that drive this variation, and evaluate the ability of the eDNA datasets to detect rare species and represent organismal abundance. Using high‐throughput autonomous environmental sample processors (ESPs) and qPCR, we enumerated eDNA concentrations from 674 water samples collected at subdaily intervals over 360 days at a single site. We detected eDNA from two imperiled salmonids (coho salmon Oncorhynchus kisutch and steelhead/rainbow trout O. mykiss) in most samples; O. kisutch eDNA was generally in lower concentration and more variable than O. mykiss eDNA. High‐frequency (i.e., subdaily and daily) variability in salmonid eDNA concentrations showed occasional patchiness (i.e., large differences between consecutive samples), while seasonal differences were observed consistent with the ecology of the species at this site. Salmonid eDNA concentrations were significantly associated with creek discharge, photoperiod, and whether the creek mouth was open or closed by a seasonal sandbar. The release of hatchery‐origin O. kisutch parr into the stream was associated with a significant increase in eDNA concentration for the remainder of the study. We compared eDNA signals with fish abundance data collected from traps located at the site. Fish were detected more often by eDNA than from trapping. Significant positive associations between fish abundance and eDNA concentrations were observed for O. mykiss; however, no such associations were observed for O. kisutch. This study adds to our knowledge on the occurrence and behavior of fish eDNA in lotic systems and informs future biomonitoring efforts using automated sampling technology.

Environmental DNA of Antarctic krill (Euphausia superba): Measuring DNA fragmentation adds a temporal aspect to quantitative surveys

“…Species‐specific environmental DNA survey methods are becoming more accessible and are increasingly incorporated into biodiversity surveys and management practices (Brys et al, 2021; Rees et al, 2014; Searcy et al, 2022; Zaiko et al, 2018). Beyond recording the presence or absence of a species, quantification of eDNA can also be linked to species abundance (Lacoursière‐Roussel et al, 2016; Rourke et al, 2022; Spear et al, 2021; Stoeckle et al, 2021), which is invaluable information for management purposes.…”

Putting eDNA to the test: A field comparison of eDNA metabarcoding to established protocols for assessing biodiversity in Missouri's Ozark Highland streams

“…Recent studies have focused on the distribution of eDNA in lotic environments and have consistently found a relationship between discharge and detection (Curtis et al, 2021;Searcy et al, 2022;Wood et al, 2021).…”

High frequency environmental DNA metabarcoding provides rapid and effective monitoring of fish community dynamics

“…Although, Searcy et al. (2022) employed higher frequency daily sampling across a year. High frequency sampling strategies have, for example, detected clear diel changes in marine fish community composition (sampling hourly across 32 h: Jensen et al., 2022), as well as significant variation in eDNA concentrations in the context of a dynamic biological event, such as salmon spawning (sampling daily for 1 month using qPCR: Tillotson et al., 2018).…”

“…Existing time-series studies of eDNA have applied a range of short-term, high frequency sampling e.g., hourly across days (Ely et al, 2021;Jensen et al, 2022), to longer-term sampling, with less frequency e.g., weekly or fortnightly across 5 to 18 months (Djurhuus et al, 2020;Sigsgaard et al, 2017;Stoeckle et al, 2017;Ushio et al, 2018) and up to 3 years (Di Capua et al, 2021), to twice monthly for 2 years (Ushio et al, 2023). Although, Searcy et al (2022) employed higher frequency daily sampling across a year. High frequency sampling strategies have, for example, detected clear diel changes in marine fish community composition (sampling hourly across 32 h: Jensen et al, 2022), as well as significant variation in eDNA concentrations in the context of a dynamic biological event, such as salmon spawning (sampling daily for 1 month using qPCR: Tillotson et al, 2018).…”