Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding

Abstract

Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity directly or can be invasive and therefore problematic. This is especially the case when threatened fish populations are the study subject, such as the Arctic charr (Salvelinus alpinus L.) populations in Windermere (Cumbria, UK). Arctic charr populations have been studied in this lake since the 1940s, and the locations and characteristics of spawning grounds have been described in detail using techniques such as hydroacoustics, as well as physical and visual surveys of the lake bottom. Here, in conjunction with established netting surveys, we added an environmental DNA (eDNA) metabarcoding approach to assess the spatial distribution of Arctic charr in the lake throughout the year to test whether this tool could allow us to identify spawning locations and activity. Sampling was carried out between October 2017 and July 2018 at three locations in the lake, covering putative and known spawning sites. eDNA metabarcoding provided accurate spatial and temporal characterisation of Arctic charr spawning events. Peaks of Arctic charr read counts from eDNA metabarcoding were observed during the spawning season and at specific locations of both putative and known spawning sites. Net catches of mature Arctic charr individuals confirmed the association between the Arctic charr spawning activity and the peaks of eDNA metabarcoding read counts. This study demonstrates the ability of eDNA metabarcoding to effectively and efficiently characterize the spatial and temporal nature of fish spawning in lentic systems.

Inferring species interactions from co-occurrence networks with environmental DNA metabarcoding data in a coastal marine food-web

“…For example, herring will consume juvenile cod, but adult cod will also consume herring, which may skew correlation trends when age-class cannot be distinguished (Lynam et al, 2017). Spawning events may additionally result in increased peaks in eDNA abundances which could further bias interactions towards those incorporating early life stages, since the presence of DNA derived from gametes may not reflect the occurrence of trophic interactions in the same way as for older age classes (Di Muri et al, 2022;Valsecchi et al, 2021).…”

12S Gene Metabarcoding with DNA Standard Quantifies Marine Bony Fish Environmental DNA, Identifies Threshold for Reproducible Amplification, and Overcomes Distortion Due to Non-Fish Vertebrate DNA

“…For example, in Shelton et al, 2022b, in analyzing fish eDNA with MiFish-U F/R primers, outliers were cartilaginous species, which are known to amplify poorly with this primer set, while teleost taxa amplification was relatively uniform. Recent reports demonstrate good correlation between relative reads and relative organism abundance, which implies that even without internal standards, metabarcoding correctly reports relative eDNA abundance in some settings (Afzali et al, 2020;Di Muri et al, 2022;Ershova, Wangensteen, Descoteaux, Barth-Jensen, & Praebel, 2021;Klymus, Marshall, & Stepien, 2017) The reverse MiFish primer overlaps with the forward Riaz primer, which might mean there is less difference in amplification efficiency between these primer sets than one would otherwise expect. PCR bias could be further evaluated by testing both primer sets on samples containing eDNA of other species and on mock communities, calibrating modified MiFish primers with protocols similar to those here, and comparing NGS copies to results with single-species qPCR or ddPCR assays.…”

Environmental DNA reveals fine scale spatial and temporal variation of prey species for marine mammals in a Scottish marine protected area

“…One of the biggest limitations of using eDNA metabarcoding to explore predator-prey dynamics is the inability to distinguish between different age classes (Hansen et al, 2018), as predators often preferentially target prey of certain sizes (Robinson et al, 2023;Visser et al, 2021). In particular, spawning events have been observed to increase the abundance of read counts retrieved in eDNA studies, but larval forms are unlikely to be suitable prey for piscivorous marine mammals (Di Muri et al, 2022;Ratcliffe et al, 2021). However, eDNA can provide information about where and when to carry out more intensive surveys to retrieve parameters such as the age-class structure of fishes present.…”