Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax)

Abstract

Background Anadromous rainbow smelt (Osmerus mordax) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples. Results Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8–13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems. Conclusions These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches.

Environmental DNA Detects Remaining Populations of Endangered Stream Salmon (Sichuan Taimen: Hucho bleekeri Kimura Salmonidae) in the Qinling Mountains

“…Interestingly, this period closely aligns with the peak eDNA concentration observed in June. Similar findings have been reported in other studies [26], indicating a positive relationship between eDNA concentration and breeding events [27][28][29]. These results suggest that directing sampling efforts toward the breeding season of target organisms may enhance the detection probabilities.…”

Temperature moderates eDNA–biomass relationships in northern pike

“…As the fish spawn, their activity and physical interactions increase (Lucas, 1992). Simultaneously, the spawning event itself leads to the release of sperm which becomes readily incorporated in the eDNA pool (Holmes et al, 2022; Tillotson et al, 2018; Tsuji & Shibata, 2021). The contribution of sperm could potentially be estimated by comparing ratios of nuclear and mitochondrial eDNA (Bylemans et al, 2017).…”

Temperature moderates eDNA-biomass relationships in northern pike

“…Simultaneously, the spawning event itself leads to the release of sperm which becomes readily incorporated in the eDNA pool (Tillotson et al 2018, Tsuji and Shibata 2021, Holmes et al 2022). The contribution of sperm could potentially be estimated by comparing ratios of nuclear and mitochondrial eDNA (Bylemans et al (2017).…”