Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake

Christoph Hahn,Lori Lawson Handley,Rosetta Blackman,Harriet Johnson,Daniel S. Read,Rob Donnelly,Jianlong Li,Rose Wilcox,Amir Szitenberg,Ian J. Winfield,Bernd Hänfling,Helen Kimbell

doi:10.1002/edn3.5

Abstract

AbstractEnvironmental DNA offers great potential as a biodiversity monitoring tool. Previous work has demonstrated that eDNA metabarcoding provides reliable information for lake fish monitoring, but important questions remain about temporal and spatial repeatability, which is critical for understanding the ecology of eDNA and developing effective sampling strategies. Here, we carried out comprehensive spatial sampling of England's largest lake, Windermere, during summer and winter to (1) examine repeatability of the method, (2) compare eDNA results with contemporary gill‐net survey data, (3) test the hypothesis of greater spatial structure of eDNA in summer compared to winter due to differences in water mixing between seasons, and (4) compare the effectiveness of shore and offshore sampling for species detection. We find broad consistency between the results from three sampling events in terms of species detection and abundance, with eDNA detecting more species than established methods and being significantly correlated with rank abundance determined by long‐term data. As predicted, spatial structure was much greater in the summer, reflecting less mixing of eDNA than in the winter. For example Arctic charr, a deep‐water species, was only detected in deep, midlake samples in the summer, while littoral or benthic species such as minnow and stickleback were more frequently detected in shore samples. By contrast in winter, the eDNA of these species was more uniformly distributed. This has important implications for design of sampling campaigns, for example, deep‐water species could be missed and littoral/benthic species overrepresented by focusing exclusively on shoreline samples collected in the summer.

Highlights

Rapid monitoring of biodiversity for conservation, management, or assessing the impact of anthropogenic pressures is frequently difficult to achieve using established methods
Previous work has demonstrated that Environmental DNA (eDNA) metabarcoding provides reliable information for lake fish monitoring, but important questions remain about temporal and spatial repeatability, which is critical for understanding the ecology of eDNA and developing effective sampling strategies
We demonstrated that eDNA metabarcoding has huge potential for describing fish community structure in lakes (Hänfling et al, 2016)

Summary

Introduction

Rapid monitoring of biodiversity for conservation, management, or assessing the impact of anthropogenic pressures is frequently difficult to achieve using established methods. We found a strong spatial signal in the distribution of eDNA from species that prefer the more mesotrophic conditions of the lake's North Basin, compared to those that are associated with the more eutrophic conditions of the South Basin This indicates that eDNA provides a contemporary signal, at least to some extent, of the fish distribution, and that eDNA is promising for ecological assessment of water bodies. (1) how does eDNA distribution vary between seasons, (2) is shoreline sampling more effective than offshore sampling for species detection, and (3) how do abundance estimates from eDNA compare to those from established methods carried out at the same time? We explore each of these questions in this study, by adding data from summer and winter sampling campaigns on Windermere

Methods

Findings

Discussion

Conclusion