Abstract
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.
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References
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
Deiner K, Walser JC, Mächler E, Altermatt F (2015) Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol Conserv 183:53–63. doi:10.1016/j.biocon.2014.11.018
Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425. doi:10.1098/rsbl.2008.0118
Goldberg CS, Pilliod DS, Arkle RS, Waits LP (2011) Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders. PLoS One 6:e22746. doi:10.1371/journal.pone.0022746
Jerde CL, Mahon AR, Chadderton WL, Lodge DM (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv Lett 4:150–157. doi:10.1111/j.1755-263X.2010.00158.x
Maruyama A, Nakamura K, Yamanaka H, Kondoh M, Minamoto T (2014) The release rate of environmental DNA from juvenile and adult fish. PLoS One 9:e114639. doi:10.1371/journal.pone.0114639
Minamoto T, Naka T, Moji K, Maruyama A (2016) Techniques for the practical collection of environmental DNA: filter selection, preservation, and extraction. Limnology 17:23–32. doi:10.1007/s10201-015-0457-4
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
Piaggio AJ, Engeman R, Hopken MW (2014) Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA. Mol Ecol Resour 14:374–380. doi:10.1111/1755-0998.12180
Takahara T, Minamoto T, Doi H (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS One 8:e56584. doi:10.1371/journal.pone.0056584
R Core Team (2013) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. http://www.R-project.org
Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One 7:e41732. doi:10.1371/journal.pone.0041732
Yamanaka H, Minamoto T (2016) The use of environmental DNA of fishes as an efficient method of determining habitat connectivity. Ecol Indic 62:147–153. doi:10.1016/j.ecolind.2015.11.022
Acknowledgments
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.
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H. Yamanaka and H. Motozawa contributed equally to this work.
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Yamanaka, H., Motozawa, H., Tsuji, S. et al. On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation. Ecol Res 31, 963–967 (2016). https://doi.org/10.1007/s11284-016-1400-9
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DOI: https://doi.org/10.1007/s11284-016-1400-9