Analysis of a coastal North Sea fish community: Comparison of aquatic environmental DNA concentrations to fish catches

Judith D L Van Bleijswijk,Johannes Ij Witte,Julia C Engelmann,Henk W Van Der Veer,Harry J Witte,Lise Klunder

doi:10.1002/edn3.67

Judith D L Van Bleijswijk, Johannes Ij Witte + Show 4 more

Open Access

https://doi.org/10.1002/edn3.67

Copy DOI

Abstract

AbstractAnalyses of environmental DNA have the potential to become an integrated tool in fish research and management. We performed a pilot study during the spring migration of fishes from the North Sea into the Wadden Sea and present comparative results from daily fyke catches (20 mm mesh) in the Marsdiep tidal inlet on two locations and results from weekly fish eDNA analyses on three locations, all within 2 km distance.Fish catches did not differ significantly between the two locations, whereas the eDNA composition showed a significant location effect. However, when eDNA analysis was restricted to species that were caught with the fykes, differences among locations became insignificant. Over ten weeks, from late April to early July, presence–absence calls of fishes based on weekly eDNA sampling significantly agreed with calls based on seven days of fyke fishing 1 km westwards. Fish eDNA compositions differed significantly among sample days and months but not between tides. Over the season, patterns in eDNA concentration (12S rRNA gene copies/L) inferred from quantitative PCR and Illumina HiSeq community composition corresponded to patterns in wet mass for the eight most abundant fish species in the fyke (>6 weeks present) despite changes in water temperature and changes in fish size class. Small sandeel and gobies, which are important prey for large fishes and birds, were typically missed with the fyke but contributed up to 25%–40% of the fish eDNA depending on the sample location.

Highlights

The shallow Dutch Wadden Sea, part of Europe's largest estuarine area, is known as an important nursery and feeding area for bottom-dwelling and pelagic fishes (Bergman et al, 1989; DickeyCollas, Bolle, Van Beek, & Erftemeijer, 2009; Zijlstra, 1972, 1983)
The aims of this study were to test the applicability of fish environmental DNA (eDNA) analyses by (a) comparing the presence–absence calls of fish species based on eDNA to fish catches; (b) evaluating the effects of eDNA sampling time, with respect to tide, on presence–absence calls; (c) investigating relationships between in situ eDNA concentration and fish mass or fish counts extracted from the fyke results; and (d) comparing seasonal patterns in eDNA abundance of the dominant fish species to the patterns found in the fyke catches
Since fyke fishing is a laborious and invasive method, we tested whether an alternative method based on eDNA sampling from the accessible NIOZ jetty in the Marsdiep would give similar results

Summary

| INTRODUCTION

The shallow Dutch Wadden Sea, part of Europe's largest estuarine area, is known as an important nursery and feeding area for bottom-dwelling and pelagic fishes (Bergman et al, 1989; DickeyCollas, Bolle, Van Beek, & Erftemeijer, 2009; Zijlstra, 1972, 1983). The rate of eDNA degradation is mainly dependent on environmental factors, of which the most important are probably temperature (Strickler, Fremier, & Goldberg, 2015; Tsuji, Ushio, Sakurai, Minamoto, & Yamanaka, 2017) and microbial phosphate limitation (Salter, 2018) It may already be possible for well-characterized systems to predict fish species abundance from eDNA surveys using multivariate models incorporating biotic and abiotic variables (Tillotson et al, 2018). We test whether eDNA sampled from the NIOZ jetty can provide an easy and complete “fingerprint” of the fish community in the highly dynamic coastal North Sea–Wadden Sea area by comparing eDNA results with daily fyke catches. The aims of this study were to test the applicability of fish eDNA analyses by (a) comparing the presence–absence calls of fish species based on eDNA to fish catches; (b) evaluating the effects of eDNA sampling time, with respect to tide, on presence–absence calls; (c) investigating relationships between in situ eDNA concentration (copies per liter Marsdiep water) and fish mass or fish counts extracted from the fyke results; and (d) comparing seasonal patterns in eDNA abundance of the dominant fish species to the patterns found in the fyke catches

| MATERIALS AND METHODS

| DISCUSSION

Findings

| CONCLUSIONS