The relationship between the distribution of common carp and their environmental DNA in a small lake.

Przemyslaw G. Bajer,Arga Chandrashekar Anil,Peter W. Sorensen,Jessica J. Eichmiller

doi:10.1371/journal.pone.0112611

Przemyslaw G. Bajer, Arga Chandrashekar Anil + Show 2 more

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https://doi.org/10.1371/journal.pone.0112611

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Abstract

Although environmental DNA (eDNA) has been used to infer the presence of rare aquatic species, many facets of this technique remain unresolved. In particular, the relationship between eDNA and fish distribution is not known. We examined the relationship between the distribution of fish and their eDNA (detection rate and concentration) in a lake. A quantitative PCR (qPCR) assay for a region within the cytochrome b gene of the common carp (Cyprinus carpio or ‘carp’), an ubiquitous invasive fish, was developed and used to measure eDNA in Lake Staring (MN, USA), in which both the density of carp and their distribution have been closely monitored for several years. Surface water, sub-surface water, and sediment were sampled from 22 locations in the lake, including areas frequently used by carp. In water, areas of high carp use had a higher rate of detection and concentration of eDNA, but there was no effect of fish use on sediment eDNA. The detection rate and concentration of eDNA in surface and sub-surface water were not significantly different (p≥0.5), indicating that eDNA did not accumulate in surface water. The detection rate followed the trend: high-use water > low-use water > sediment. The concentration of eDNA in sediment samples that were above the limit of detection were several orders of magnitude greater than water on a per mass basis, but a poor limit of detection led to low detection rates. The patchy distribution of eDNA in the water of our study lake suggests that the mechanisms that remove eDNA from the water column, such as decay and sedimentation, are rapid. Taken together, these results indicate that effective eDNA sampling methods should be informed by fish distribution, as eDNA concentration was shown to vary dramatically between samples taken less than 100 m apart.

Highlights

Methods to quantify the abundance of fish populations, such as mark-recapture and electrofishing, are costly and time-consuming
To determine whether fish distribution affects environmental DNA (eDNA) concentration and detection rate in lake water and sediment, we examined the distribution of carp eDNA in a small, shallow lake and compared it to known patterns of carp distribution, which had been monitored for several years
The present study showed that common carp distribution led to spatial patterns in both eDNA concentration and detection rate in a small, shallow lake

Summary

Introduction

Methods to quantify the abundance of fish populations, such as mark-recapture and electrofishing, are costly and time-consuming. Fish are often difficult to capture and detect at low densities, and capture methods themselves can lead to behavioral changes of the target species [1,2,3]. Molecular methods to detect the DNA released by aquatic organisms into their environment are non-invasive, rapid, and potentially more sensitive than traditional census techniques [4,5,6]. This environmental DNA (eDNA) is released through processes such as cell sloughage, mucus excretions, and defecation [7]. Next-generation sequencing approaches have successfully identified multiple species simultaneously [11,12]

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