Environmental DNA as a 'Snapshot' of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay, Sea of Japan.

T. Horiuchi ,Keita W. Suzuki,Michio Kondo ,Hideki Araki ,Masaki Miya,Hiroaki Murakami,Kohji Takahashi,Ayaka Fujiwara,Reiji Masuda,Kazushi Miyashita,Shunsuke Hidaka,Masamichi Hongo,Satsuki Tsuji,Toshifumi Minamoto,Kenji Minami,Jo Nishida,Atsushi Maruyama,Satoshi Yamamoto,Keiichi Fukaya,Hiroki Yamanaka,Hideki Sawada,Yuta Okugawa,Makoto Fukuda ,Hiroki Hashizume,Shou Kubonaga

doi:10.1371/journal.pone.0149786

Abstract

Recent studies in streams and ponds have demonstrated that the distribution and biomass of aquatic organisms can be estimated by detection and quantification of environmental DNA (eDNA). In more open systems such as seas, it is not evident whether eDNA can represent the distribution and biomass of aquatic organisms because various environmental factors (e.g., water flow) are expected to affect eDNA distribution and concentration. To test the relationships between the distribution of fish and eDNA, we conducted a grid survey in Maizuru Bay, Sea of Japan, and sampled surface and bottom waters while monitoring biomass of the Japanese jack mackerel (Trachurus japonicus) using echo sounder technology. A linear model showed a high R2 value (0.665) without outlier data points, and the association between estimated eDNA concentrations from the surface water samples and echo intensity was significantly positive, suggesting that the estimated spatial variation in eDNA concentration can reflect the local biomass of the jack mackerel. We also found that a best-fit model included echo intensity obtained within 10–150 m from water sampling sites, indicating that the estimated eDNA concentration most likely reflects fish biomass within 150 m in the bay. Although eDNA from a wholesale fish market partially affected eDNA concentration, we conclude that eDNA generally provides a ‘snapshot’ of fish distribution and biomass in a large area. Further studies in which dynamics of eDNA under field conditions (e.g., patterns of release, degradation, and diffusion of eDNA) are taken into account will provide a better estimate of fish distribution and biomass based on eDNA.

Highlights

Surveillance of fish species composition and biomass provides useful information for management and conservation of marine and freshwater ecosystems
Based on the two different data sets, we examined whether the environmental DNA (eDNA) concentration of the jack mackerel varied spatially in the bay, and whether the spatial variation of eDNA concentration was correlated to the biomass estimated by the acoustic survey
We found significant partial associations between spatial variation in estimated eDNA concentration from jack mackerel and echo intensity

Summary

Introduction

Surveillance of fish species composition and biomass provides useful information for management and conservation of marine and freshwater ecosystems. Echo sounder, which generates an acoustic pulse and detects echos from fish, allows one to survey large geographical areas in a short period of time, but it is inadequate for species identification and surveillance in environments with many obstacles such as coral reefs. In such environments, underwater visual censuses should be effective for fish counts and species identification, data from these methods may contain bias resulting from fish and diver (observer) behavior [9,10,11,12]. The numbers of fish species recovered by surveys with beach seines and bottom trawls are similar to those from underwater visual censuses [13], these surveys stress fish individuals and are not appropriate for threatened species

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