Received: 18 January 2019 | Revised: 7 June 2019 | Accepted: 10 June 2019 DOI: 10.1111/1755‐0998.13055 RESOURCE ARTICLE A comparison of droplet digital polymerase chain reaction (PCR), quantitative PCR and metabarcoding for species‐specific detection in environmental DNA Susanna A. Wood1 | Xavier Pochon1,2 | Olivier Laroche1,3 | Ulla von Ammon1,2 | Janet Adamson1 | Anastasija Zaiko1,2 1Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand Abstract 2Institute of Marine Science, University of Targeted species‐specific and community‐wide molecular diagnostics tools are Auckland, Auckland, New Zealand being used with increasing frequency to detect invasive or rare species. Few studies 3Department of Oceanography, School of Ocean and Earth Science and have compared the sensitivity and specificity of these approaches. In the present Technology, University of Hawaii at Manoa, study environmental DNA from 90 filtered seawater and 120 biofouling samples Honolulu, HI, USA was analyzed with quantitative PCR (qPCR), droplet digital PCR (ddPCR) and meta‐ Correspondence barcoding targeting the cytochrome c oxidase I (COI) and 18S rRNA genes for the Susanna A. Wood, Coastal and Freshwater Group, Cawthron Institute, Nelson, New Mediterranean fanworm Sabella spallanzanii. The qPCR analyses detected S. spallan‐ Zealand. zanii in 53% of water and 85% of biofouling samples. Using ddPCR S. spallanzanii was Email:
[email protected] detected in 61% of water of water and 95% of biofouling samples. There were strong Funding information relationships between COI copy numbers determined via qPCR and ddPCR (water New Zealand Government's Strategic 2 2 Science Investment Fund (SSIF) through R = 0.81, p < .001, biofouling R = 0.68, p < .001); however, qPCR copy numbers were the NIWA Coasts and Oceans Research on average 125‐fold lower than those measured using ddPCR.