Relationships between the eDNA concentration obtained from metabarcoding and stream fish abundance estimated by the removal method under field conditions

Abstract

Estimating abundance or biomass using eDNA metabarcoding is a powerful emerging tool that may provide an alternative to conventional laborious methods for biological monitoring. However, inferring aquatic macroorganism abundance or biomass using eDNA concentrations remains challenging, especially in lotic environments, because of several potential confounding factors. In this study, we tested whether quantitative eDNA metabarcoding that uses internal standard DNA can be used to estimate the abundance of four fish species. We collected eDNA samples and concurrently estimated fish densities using the conventional removal method in small tributaries in four seasons during a year. The effects of potential confounding factors, including the body mass of the individuals, water temperature, and discharge volume, were assessed using an allometric scaling model. We found an increasing trend of eDNA concentration against the increase in abundance across all species. In the most abundant species, a significant increase in the precision of predicted abundance was achieved by considering confounding factors, such as season and discharge. Although this study successfully determined the relationships between eDNA concentration and fish abundance under lotic field conditions, it also identified several limitations of quantitative eDNA metabarcoding. The relationship between eDNA concentration and fish abundance in rare species showed significant variances in the regression. More sequencing depth may be necessary to detect rare species sufficiently. The eDNA concentration estimation error effect was significant, particularly among the samples that showed the same abundance figures by direct capture estimation. The utilization of quantitative eDNA metabarcoding may be suitable for organisms that are expected to have a substantial variation in their population density. More comparative studies with various conventional methods would be informative, especially in lotic field environments, to overcome these limitations and achieve wider applications of eDNA metabarcoding in future research and monitoring.

Regional‐scale effects of deer‐induced forest degradation on river ecosystem dynamics

“…This study revealed a strong correlation between eDNA concentrations and snorkeling counts of fishes, indicating the applicability of quantitative DNA metabarcoding method for investigating quantitative patterns in fish populations, as supported by previous studies (Di Muri et al, 2020; Nakagawa et al, 2022; Tsuji et al, 2022). Previous studies have identified various factors that can influence the estimation of population densities of river organisms based on eDNA concentrations (Nakagawa et al, 2022; Yates et al, 2021). To minimize the impact of seasonal changes in water temperature and body mass composition of individuals, we restricted the sampling periods to summer.…”

“…When the eDNA concentration exhibits a strong correlation with organism density in a habitat, this technique, known as “quantitative eDNA metabarcoding,” can facilitate large‐scale surveys of biological communities that are challenging to investigate using conventional methods. However, the use of eDNA concentrations to infer abundance of aquatic macro‐organisms remains controversial, particularly in lotic environments, due to various factors such as variations in river discharge and seasonal changes in mean body mass of individuals (Nakagawa et al, 2022; Yates et al, 2021). Therefore, when applying the quantitative eDNA metabarcoding technique to large‐scale surveys, such as inter‐catchment comparisons of stream communities, it is crucial to interpret the results carefully, using comparable data obtained from a well‐established conventional method.…”

Environmental DNA compliments traditional sampling for monitoring fish communities in a Texas estuary

“…The availability of eDNA targets in environmental water can also be affected by variation in initial particle size and decay, which can vary by species and across environmental conditions (Moushomi et al 2019; Yates et al 2019; Barnes et al 2020). Finally, differences in nucleotide composition and biomass across taxa can affect the rates of replication directly during PCR, with species that attain larger body sizes being better represented than smaller species (Nichols et al 2018; Nakagawa et al 2022).…”

State-of-the-art of data analyses in environmental DNA approaches towards its applicability to sustainable fisheries management

“…process-based models see point 3. e.g. Lacoursière-Roussel et al, 2016, Sepuĺveda et al, 2021Nakagawa et al, 2022), and the poor knowledge on the probability of detection in eDNA metabarcoding approaches (i.e. occupancy and process models, see point 3, e.g.…”