Open AccessWater pre-filtration methods to improve environmental DNA detection by real-time PCR and metabarcoding
Author(s) -
Kazuto Takasaki,
Hiroki Aihara,
Toshinobu Imanaka,
Takahiro Matsudaira,
Keita Tsukahara,
Atsuko Usui,
Sora Osaki,
Hideyuki Doi
Publication year - 2021
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0250162
Subject(s) - environmental dna , biomonitoring , turbidity , filtration (mathematics) , polymerase chain reaction , biology , water quality , real time polymerase chain reaction , environmental chemistry , chemistry , environmental science , ecology , gene , genetics , biodiversity , statistics , mathematics
Environmental DNA (eDNA) analysis is a novel approach for biomonitoring and has been mostly used in clear water. It is difficult to detect eDNA in turbid water as filter clogging occurs, and environmental samples contain various substances that inhibit the polymerase chain reaction (PCR) and affect the accuracy of eDNA analysis. Therefore, we applied a pre-filtration method to better detect the fish species (particularly pale chub, Opsariichthys platypus ) present in a water body by measuring eDNA in environmental samples containing PCR inhibitors. Upon conducting 12S rRNA metabarcoding analysis (MiFish), we found that pre-filtration did not affect the number or identities of fish species detected in our samples, but pre-filtration through pore sizes resulted in significantly reduced variance among replicate samples. Additionally, PCR amplification was improved by the pre-filtration of environmental samples containing PCR inhibitors such as humic substances. Although this study may appear to be a conservative and ancillary experiment, pre-filtration is a simple technique that can not only improve the physical properties of water, such as turbidity, but also the quality of eDNA biomonitoring.