Efficacy of environmental DNA sampling to detect the occurrence of endangered coho salmon (Oncorhynchus kisutch) in Mediterranean‐climate streams of California's central coast

Abstract

Analysis of environmental DNA (eDNA) has emerged as an important tool for investigating the occurrence and distribution of fish and other species in aquatic environments. However, in lotic systems, uncertainty remains about how environmental factors influence the downstream transport, degradation, and dilution of eDNA, and hence how detection probability varies with distance from the eDNA source. We conducted cage experiments and paired eDNA and snorkel surveys to evaluate the potential for eDNA methods to detect endangered coho salmon in Mediterraneanclimate streams of the Santa Cruz Mountains, California. Juvenile coho salmon at two densities were placed in cages, and water samples were collected and analyzed (qPCR) at seven locations from 10 to 1,000 m downstream. Although we detected coho salmon eDNA up to 1,000 m downstream of the cage, the vast majority of detections were within 200 m, and detections at greater distances occurred only at the higher fish density. In field collections from 21 stream reaches across the Santa Cruz Mountains, eDNA methods and snorkeling produced identical outcomes in terms of reach-level detection of coho salmon. Probability of occurrence in a water sample and detection in a qPCR replicate both increased with observed fish density; however, even at the lowest densities, a protocol of three water samples and two qPCR replicates resulted in a >90% cumulative probability of detection. Overall, our studies suggest that detection probability decreased rapidly with distance in Santa Cruz Mountain streams, likely because low stream discharges, slow transport velocities, and strong interaction between the water column and stream substrate result in rapid degradation or settling of eDNA. Our findings thus support the use of eDNA methods for detecting rare species, but also indicate that local conditions strongly influence transport dynamics and hence need to be considered when developing survey designs.

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

“…Indeed, this notion was confirmed by Thalinger et al (2020) when they observed attenuation in caged fish eDNA signals with increasing stream discharge. Alternatively, low discharge may insufficiently transport eDNA to sampling locations before decay and settling mechanisms remove it from the system (Shogren et al, 2016; Spence et al, 2020).…”

“…A pilot study (data not shown) suggested that the eDNA signal from the hatchery itself (which is hydraulically connected to Scott Creek) is significantly attenuated before reaching the weir (20‐fold reduction, from ~200 copies/ml at the hatchery outflow to ~10 copies/ml at the weir), and a transport study in a nearby watershed suggest similar attenuation of caged O . kisutch eDNA at distance of 1 km (Spence et al, 2020).…”

“…Over 10,000 O. kisutch parr were released over the course of one day (November 21, 2019) in various locations throughout the Scott Creek watershed; unlike smolts, these fish were not expected to immediately migrate downstream (Quinn, 2018). A pilot study (data not shown) suggested that the eDNA signal from the hatchery itself (which is hydraulically connected to Scott Creek) is significantly attenuated before reaching the weir (20-fold reduction, from ~200 copies/ml at the hatchery outflow to ~10 copies/ml at the weir), and a transport study in a nearby watershed suggest similar attenuation of caged O. kisutch eDNA at distance of 1 km (Spence et al, 2020).…”

“…2020) when they observed attenuation in caged fish eDNA signals with increasing stream discharge. Alternatively, low discharge may insufficiently transport eDNA to sampling locations before decay and settling mechanisms remove it from the system(Shogren et al, 2016;Spence et al, 2020).The release of over 10,000 hatchery-origin O. kisutch parr into the watershed at the end of November 2019 was associated with an elevated eDNA signal for the remainder of the study. Because O. kisutch parr are not able to migrate to the ocean, it is expected that these fish redistributed throughout the Scott Creek watershed.…”

Ontogeny of eDNA shedding during early development in Chinook Salmon (Oncorhynchus tshawytscha)

“…Further, the detectability of DNA released from hatching eggs and sampled in the water column may differ between species that deposit eggs above the stream bed and species that construct redds. For example, detection of DNA from eggs deposited above the stream bed may follow a characteristic pattern where DNA concentrations are typically highest directly downstream of the source (Jane et al, 2015;Spence et al, 2021). In contrast, detection of DNA from redds may resemble species that are buried in stream beds, such as freshwater mussels, where peak DNA concentrations were found to be spatially shifted downstream The timing of life history events has important conservation implications for aquatic species and eDNA surveys can help identify when such events occur.…”