Quantitative assessment of multiple fish species around artificial reefs combining environmental DNA metabarcoding and acoustic survey

Masaaki Sato,Tomohito Imaizumi,Ryogen Nambu,Naoki Furuichi,Nariaki Inoue,Masayuki Ushio

doi:10.1038/s41598-021-98926-5

Abstract

Since the early 1970s, many artificial reefs (ARs) have been deployed in Japanese coastal waters to create fisheries grounds. Recently, researchers began to use environmental DNA (eDNA) methods for biodiversity monitoring of aquatic species. A metabarcoding approach using internal standard DNAs [i.e., quantitative MiSeq sequencing (qMiSeq)] makes it possible to monitor eDNA concentrations of multiple species simultaneously. This method can improve the efficiency of monitoring AR effects on fishes. Our study investigated distributions of marine fishes at ARs and surrounding stations in the open oceanographic environment of Tateyama Bay, central Japan, using qMiSeq and echo sounder survey. Using the qMiSeq with 12S primers, we found higher quantities of fish eDNAs at the ARs than at surrounding stations and different fish species compositions between them. Comparisons with echo sounder survey also showed positive correlations between fish eDNA concentration and echo intensity, which indicated a highly localized signal of eDNA at each sampling station. These results suggest that qMiSeq is a promising technique to complement conventional methods to monitor distributions of multiple fish species.

Highlights

Artificial reefs (ARs) have been deployed worldwide to create fisheries grounds
The following were tested: (1) whether fish communities detected by environmental DNA (eDNA) metabarcoding match with the catch record of the coastal fishery, (2) whether the DNA quantities of multiple fish species calculated by the quantitative MiSeq sequencing (qMiSeq) decrease with increasing distance from an artificial reefs (ARs), 3) whether the spatial variation of fish DNA quantities correlates to the relative distribution estimated by the acoustic survey
We found that eDNA metabarcoding efficiently detected the fish assemblages around ARs of Tateyama Bay

Summary

Introduction

Artificial reefs (ARs) have been deployed worldwide to create fisheries grounds. Since the early 1970s, restrictions on overseas fishing have influenced high seas fisheries outside the exclusive economic zones (EEZ), and this situation led the Japanese government to implement a new fishery policy to develop and maintain coastal fisheries. This study showed that the estimated numbers of total and two dominant fish (Japanese anchovy and jack mackerel) DNA copies were significantly positively correlated with the numbers of DNA copies quantified by qPCR This method [i.e., quantitative MiSeq sequencing (qMiSeq)] can contribute to the quantitative assessment of multispecies fish eDNA. The qMiSeq with MiFish primer could be one of the most cost- and labor-effective approaches for the quantitative monitoring of multiple fish species in marine and coastal ecosystems, including ARs. Here, we investigated marine fish distributions around ARs in Tateyama Bay, central Japan, using eDNA metabarcoding, catch record of fishery, and echo sounder method. The qMiSeq using internal standard DNAs and MiFish primers was applied to assess whether the distribution of multiple fish species around ARs could be monitored based on the spatial variation in the estimated quantities of eDNA (i.e., identification of fish species and quantification of the number of fish eDNA copies simultaneously). The following were tested: (1) whether fish communities detected by eDNA metabarcoding match with the catch record of the coastal fishery, (2) whether the DNA quantities of multiple fish species calculated by the qMiSeq decrease with increasing distance from an AR, 3) whether the spatial variation of fish DNA quantities correlates to the relative distribution estimated by the acoustic survey

Methods

Results

Conclusion