On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation
- 681 Downloads
Environmental DNA (eDNA) analysis is an innovative tool for determining the distribution or abundance of aquatic macroorganisms. However, because eDNA degrades rapidly in water, long delays between sampling and analysis may hinder eDNA quantification. In the present study, we developed a portable filtration system that enables on-site (and on-the-road) filtration of water samples. Degradation rates of eDNA within 6 h were compared using water from an outdoor pond that was subjected to (1) on-site filtration, (2) transportation of water on ice, and (3) transportation of water at ambient temperature. Groups 2 and 3 were filtered in the laboratory 6 h after sampling. The concentration of eDNA was determined as the copy number of the mitochondrial cytochrome b gene of two fish species using real-time polymerase chain reaction. The portable filtration system offers the following benefits: (1) the eDNA concentration is preserved as is at the time of sampling, permitting higher accuracy of eDNA quantification, (2) use of a disposable sealed plastic bag reduces the risk of contamination and ensures on-the-road filtration, (3) time is saved because filtration can be accomplished when driving between sampling sites.
KeywordsDNA degradation Environmental DNA On-site filtration Reduce sample contamination Time-saving sampling
This work was supported by JSPS KAKENHI Grant 26840152 and 16K18610. This study was partially supported by the Environment Research and Technology Development Fund of the Ministry of the Environment (4RF-1302), the CREST program from the Japan Science and Technology Agency, and the Ryukoku University Technology Fund.
- Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55:611–622. doi: 10.1373/clinchem.2008.112797 CrossRefPubMedGoogle Scholar
- Miya M, Sato Y, Fukunaga T, Sado T, Poulsen JY, Sato K, Minamoto T, Yamamoto S, Yamanaka H, Araki H, Kondoh M, Iwasaki W (2015) MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R Soc Open Sci 2:150088. doi: 10.1098/rsos.150088 CrossRefPubMedPubMedCentralGoogle Scholar
- R Core Team (2013) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. http://www.R-project.org