Environmental DNA (eDNA) is an emerging approach for detecting species, yet numerous methodological questions remain unanswered. Here we examined how time to filtration (0–48 h after collection) and sample storage (open vs. chilled in the dark) influenced detection and measured eDNA concentration. Water samples kept in the dark and chilled had no significant decrease in detection or eDNA concentration relative to those filtered immediately upon return from the field. Water samples exposed to light and ambient air temperature had non-detections beginning at 1 h, the majority of these samples were below the limit of detection (LOD) by 6 h, and eDNA was undetectable in these samples by 24 h. These results have important implications for eDNA research where immediate access to refrigeration is not available, or for fieldwork that requires extended sampling time (e.g., canoeing a river). Further, we report faster eDNA degradation times under ambient conditions than some previous aquaria or mesocosm studies, suggesting an ongoing need to study mechanisms related to eDNA persistence and sample storage.
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Carim KJ, Christianson KR, McKelvey KM, Pate WM, Silver DB, Johnson BM, Galloway BT, Young MK, Schwartz MK (2016) Environmental DNA marker development with sparse biological information: a case study on opossum shrimp (Mysis diluviana). PLoS ONE 11:e0161664. https://doi.org/10.1371/journal.pone.0161664
Cowart DA, Renshaw MA, Gantz CA, Umek J, Chandra S, Egan SP, Lodge DM, Larson ER (2018) Development and field validation of an environmental DNA (eDNA) assay for invasive clams of the genus Corbicula. Manage Biol Invasions 9:27–37. https://doi.org/10.3391/mbi.2018.9.1.03
Curtis AN, Larson ER (2020) No evidence that crayfish carcasses produce detectable environmental DNA (eDNA) in a stream enclosure experiment. Peer J 8:e9333. https://doi.org/10.7717/peerj.9333
Djurhuus A, Port J, Closek CJ, Yamahara KM, Romero-Maraccini O, Walz KR, Goldsmith DB, Michisaki R, Breitbart M, Boehm AB, Chavez FP (2017) Evaluation of DNA extraction methods for environmental DNA biodiversity assessments across multiple trophic levels. Front Mar Sci 4:314. https://doi.org/10.3389/fmars.2017.00314
Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4:423–425. https://doi.org/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. https://doi.org/10.1371/journal.pone.0022746
Hinlo R, Gleeson D, Lintermans M, Furlan E (2017) Methods to maximise recovery of environmental DNA from water samples. PLoS ONE 12:e0179251. https://doi.org/10.1371/journal.pone.0179251
Jo T, Murakami H, Masuda R, Sakata MK, Yamamoto S, Minamoto T (2017) Rapid degradation of longer DNA fragments enables the improved estimation of distribution and biomass using environmental DNA. Mol Ecol Resour 17:25–33. https://doi.org/10.1111/1755-0998.12685
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. https://doi.org/10.1007/s10201-015-0457-4
Pilliod DA, Goldberg CS, Arkle RS, Waits LP (2014) Factors influencing detection of eDNA from a stream-dwelling amphibian. Mol Ecol Resour 14:109–116. https://doi.org/10.1111/1755-0998.12159
Renshaw MA, Olds BP, Jerde CL, McVeigh MM, Lodge DM (2015) The room temperature preservation of filtered environmental DNA samples and assimilation into a phenol-chloroform-isoamyl alcohol DNA extraction. Mol Ecol Resour 15:168–176. https://doi.org/10.1111/1755-0998.12281
Schrader C, Schielke A, Ellerbroek L, Johne R (2012) PCR inhibitors-occurrence, properties and removal. J App Microbiol 113:1014–1026. https://doi.org/10.1111/j.1365-6762672.2012.05384.x
Spens J, Evans AR, Halfmaerten D, Knudsen SW, Sengupta MA, Mak SST, Sigsgaard EE, Hellström M (2016) Comparison of capture and storage methods for aqueous macrobial eDNA using an optimized extraction protocol: advantage of enclosed filter. Methods Ecol Evol 8:635–645. https://doi.org/10.1111/2041-210X.12683
Tsuji S, Ushio M, Sakurai S, Minamoto T, Yamanaka H (2017) Water temperature-dependent degradation of environmental DNA and its relation to bacterial abundance. PLoS ONE 12:e0176608. https://doi.org/10.1371/journal.pone.0176608
Yamanaka H, Motozawa H, Tsuji S, Miyazawa RC, Takahara T, Minamoto T (2016) On-site filtration of water samples for environmental DNA analysis to avoid DNA degradation during transportation. Ecol Res 31:963–967. https://doi.org/10.1007/s11284-016-1400-9
Yamanaka H, Minamoto T, Matsuura J, Sakurai S, Tsuji S, Motozawa H, Hongo M, Sogo Y, Kakimi N, Teramura I, Sugita M, Baba M, Kondo A (2017) A simple method for preserving environmental DNA in water samples at ambient temperature by addition of cationic surfactant. Limnology 18:233–241. https://doi.org/10.1007/s10201-016-0508-5
We are grateful to Aron Katz for ensuring that our water samples were not accidentally discarded by landscaping staff. We thank two reviewers and the handling editor for comments that improved this manuscript. This research was funded by Francis M. and Harlie M. Clark Research Grant to A.N. Curtis, U.S. Department of Agriculture National Institute of Food and Agriculture Hatch Project #1008988 to E.R. Larson, and P.I. allotment to M.A. Davis.
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The authors declare that they have no conflict of interest.
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Curtis, A.N., Larson, E.R. & Davis, M.A. Field storage of water samples affects measured environmental DNA concentration and detection. Limnology 22, 1–4 (2021). https://doi.org/10.1007/s10201-020-00634-y
- Sample handling
- DNA degradation
- Asian clam