Use of Droplet Digital PCR for Estimation of Fish Abundance and Biomass in Environmental DNA Surveys
Citation
Doi H, Uchii K, Takahara T, Matsuhashi S,
Yamanaka H, Minamoto T (2015) Use of Droplet
Digital PCR for Estimation of Fish Abundance and
Biomass in Environmental DNA Surveys. PLoS ONE
10(3): e0122763. doi:10.1371/journal.pone.0122763
Summary
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 [...]
Summary
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.
