Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys

Hideyuki Doi; Kimiko Uchii; Teruhiko Takahara; Saeko Matsuhashi; Hiroki Yamanaka; Toshifumi Minamoto

doi:10.1371/journal.pone.0122763

Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys

PLoS One. 2015 Mar 23;10(3):e0122763. doi: 10.1371/journal.pone.0122763. eCollection 2015.

Authors

Hideyuki Doi¹, Kimiko Uchii², Teruhiko Takahara³, Saeko Matsuhashi¹, Hiroki Yamanaka⁴, Toshifumi Minamoto⁵

Affiliations

¹ Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima, Japan.
² Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima, Japan; Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Japan.
³ Graduate School of Integrated Arts and Sciences, Hiroshima University, Higashi-Hiroshima, Japan.
⁴ Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, Otsu, Japan.
⁵ Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.

Abstract

An environmental DNA (eDNA) analysis method has been recently developed to estimate the distribution of aquatic animals by quantifying the number of target DNA copies with quantitative real-time PCR (qPCR). A new quantitative PCR technology, droplet digital PCR (ddPCR), partitions PCR reactions into thousands of droplets and detects the amplification in each droplet, thereby allowing direct quantification of target DNA. We evaluated the quantification accuracy of qPCR and ddPCR to estimate species abundance and biomass by using eDNA in mesocosm experiments involving different numbers of common carp. We found that ddPCR quantified the concentration of carp eDNA along with carp abundance and biomass more accurately than qPCR, especially at low eDNA concentrations. In addition, errors in the analysis were smaller in ddPCR than in qPCR. Thus, ddPCR is better suited to measure eDNA concentration in water, and it provides more accurate results for the abundance and biomass of the target species than qPCR. We also found that the relationship between carp abundance and eDNA concentration was stronger than that between biomass and eDNA by using both ddPCR and qPCR; this suggests that abundance can be better estimated by the analysis of eDNA for species with fewer variations in body mass.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Biomass*
Carps / genetics
Carps / growth & development
DNA / analysis*
Environmental Monitoring / methods*
Polymerase Chain Reaction*
Real-Time Polymerase Chain Reaction

Substances

DNA

Grants and funding

This study was supported by the Environment Research and Technology Development Fund (4RF-1302) of the Ministry of the Environment, Japan, JST-CREST. Additional funding was provided in part by the Industry-University Collaboration Grant for Young Scientists in Hiroshima University to Teruhiko Takahara. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.