title: Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys.
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.
authors: Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima, Japan.
authors: Hideyuki
authors: H
authors: Doi
authors: Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima, Japan; Faculty of Pharmacy, Osaka Ohtani University, Tondabayashi, Japan.
authors: Kimiko
authors: K
authors: Uchii
authors: Graduate School of Integrated Arts and Sciences, Hiroshima University, Higashi-Hiroshima, Japan.
authors: Teruhiko
authors: T
authors: Takahara
authors: Institute for Sustainable Sciences and Development, Hiroshima University, Higashi-Hiroshima, Japan.
authors: Saeko
authors: S
authors: Matsuhashi
authors: Department of Environmental Solution Technology, Faculty of Science and Technology, Ryukoku University, Otsu, Japan.
authors: Hiroki
authors: H
authors: Yamanaka
authors: Graduate School of Human Development and Environment, Kobe University, Kobe, Japan.
authors: Toshifumi
authors: T
authors: Minamoto
mesh_terms: D000818:Animals; D018533:Biomass; D002347:Carps / Q000235:genetics / Q000254:growth & development; D004247:DNA / Q000032:analysis*; D004784:Environmental Monitoring / Q000379:methods*; D016133:Polymerase Chain Reaction; D060888:Real-Time Polymerase Chain Reaction
chemical_list: D004247:DNA