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Simplified capture, extraction, and amplification of cellular DNA from water samples

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Abstract

DNA analysis in water samples is attracting attention in various fields. However, conventional methods for DNA analysis require a work-intensive and time-consuming sample pre-treatment. In this study, a simplified pre-treatment method for analyzing DNA in water samples was evaluated. The process consists of filtration, DNA extraction, and amplification, which can be achieved within a short time. In the filtration process, two types of filters, firstly a tissue paper (Kimwipe) and then a glass filter (GF/F), were used in sequence. The first large pore size filter enabled a reduction in filtration time by removing large particulate matter impurities present in river water matrix. Cells spiked into 1 L of river water were recovered at more than 90% within approximately 5 min filtration time. Also, DNA was extracted from the captured cells directly on the surface of the filter in only 5 min. Thus, DNA collection and extraction from a water sample can be completed within about 10 min. Furthermore, PCR amplification was performed directly from DNA-attached filter sections, which greatly reduced the number of required pre-treatment steps. Finally, we succeeded in establishing a simple and fast on-site pre-treatment system by using a hand-driven syringe filtration method. This pre-treatment system is expected to offer the possibility for the future establishment of a rapid and easy DNA analysis method applicable to various types of water samples.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding authors on reasonable request.

References

  1. A. Martellini, P. Payment, R. Villemur, Use of eukaryotic mitochondrial DNA to differentiate human, bovine, porcine and ovine sources in fecally contaminated surface water. Water Res. 39, 541–548 (2005). https://doi.org/10.1016/j.watres.2004.11.012

    Article  PubMed  CAS  Google Scholar 

  2. C.M. Merkes, S.G. McCalla, N.R. Jensen, M.P. Gaikowski, J.J. Amberg, Persistence of DNA in carcasses, slime and avian feces may affect interpretation of environmental DNA data. PLoS ONE 9, e113346 (2014). https://doi.org/10.1371/journal.pone.0113346

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  3. K.M. Ruppert, R.J. Kline, M.S. Rahman, Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: a systematic review in methods, monitoring, and applications of global eDNA. Glob. Ecol. Conserv. 17, e00547 (2019). https://doi.org/10.1016/j.gecco.2019.e00547

    Article  Google Scholar 

  4. H.C. Rees, B.C. Maddison, D.J. Middleditch, J.R.M. Patmore, K.C. Gough, Review: the detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51, 1450–1459 (2014). https://doi.org/10.1111/1365-2664.12306

    Article  CAS  Google Scholar 

  5. P.F. Thomsen, E. Willerslev, Environmental DNA—an emerging tool in conservation for monitoring past and present biodiversity. Biol. Conserv. 183, 4–18 (2015). https://doi.org/10.1016/j.biocon.2014.11.019

    Article  Google Scholar 

  6. N. Daan, The IBTS database: a plea for quality control. (2001)

  7. P.F. Thomsen, J. Kielgast, L.L. Iversen, P.R. Møller, M. Rasmussen, E. Willerslev, Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7, e41732 (2012). https://doi.org/10.1371/journal.pone.0041732

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  8. A.D. Foote, P.F. Thomsen, S. Sveegaard, M. Wahlberg, J. Kielgast, L.A. Kyhn, A.B. Salling, A. Galatius, L. Orlando, M.T.P. Gilbert, Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7, e41781 (2012). https://doi.org/10.1371/journal.pone.0041781

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  9. P.F. Thomsen, J. Kielgast, L.L. Iversen, C. Wiuf, M. Rasmussen, M.T.P. Gilbert, L. Orlando, E. Willerslev, Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565–2573 (2012). https://doi.org/10.1111/j.1365-294X.2011.05418.x

    Article  PubMed  CAS  Google Scholar 

  10. C.S. Goldberg, A. Sepulveda, A. Ray, J. Baumgardt, L.P. Waits, Environmental DNA as a new method for early detection of New Zealand mudsnails (Potamopyrgus antipodarum). Freshw. Sci. 32, 792–800 (2013). https://doi.org/10.1899/13-046.1

    Article  Google Scholar 

  11. A.J. Piaggio, R.M. Engeman, M.W. Hopken, J.S. Humphrey, K.L. Keacher, W.E. Bruce, M.L. Avery, 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 (2014). https://doi.org/10.1111/1755-0998.12180

    Article  PubMed  CAS  Google Scholar 

  12. T. Dejean, A. Valentini, C. Miquel, P. Taberlet, E. Bellemain, C. Miaud, Improved detection of an alien invasive species through environmental DNA barcoding: the example of the American bullfrog Lithobates catesbeianus. J. Appl. Ecol. 49, 953–959 (2012). https://doi.org/10.1111/j.1365-2664.2012.02171.x

    Article  Google Scholar 

  13. S. Creer, K. Deiner, S. Frey, D. Porazinska, P. Taberlet, W.K. Thomas, C. Potter, H.M. Bik, The ecologist’s field guide to sequence-based identification of biodiversity. Methods Ecol. Evol. 7, 1008–1018 (2016). https://doi.org/10.1111/2041-210X.12574

    Article  Google Scholar 

  14. D. Garlapati, B. Charankumar, K. Ramu, P. Madeswaran, M.V. Ramana Murthy, A review on the applications and recent advances in environmental DNA (eDNA) metagenomics. Rev. Environ. Sci. Biotechnol. 18, 389–411 (2019). https://doi.org/10.1007/s11157-019-09501-4

    Article  CAS  Google Scholar 

  15. C.R. Turner, M.A. Barnes, C.C.Y. Xu, S.E. Jones, C.L. Jerde, D.M. Lodge, Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods Ecol. Evol. 5, 676–684 (2014). https://doi.org/10.1111/2041-210X.12206

    Article  Google Scholar 

  16. B.P. Olds, C.L. Jerde, M.A. Renshaw, Y. Li, N.T. Evans, C.R. Turner, K. Deiner, A.R. Mahon, M.A. Brueseke, P.D. Shirey, M.E. Pfrender, D.M. Lodge, G.A. Lamberti, Estimating species richness using environmental DNA. Ecol. Evol. 6, 4214–4226 (2016). https://doi.org/10.1002/ece3.2186

    Article  PubMed  PubMed Central  Google Scholar 

  17. M.A. Barnes, C.R. Turner, The ecology of environmental DNA and implications for conservation genetics. Conserv. Genet. 17, 1–17 (2016). https://doi.org/10.1007/s10592-015-0775-4

    Article  CAS  Google Scholar 

  18. C.S. Goldberg, C.R. Turner, K. Deiner, K.E. Klymus, P.F. Thomsen, M.A. Murphy, S.F. Spear, A. McKee, S.J. Oyler-McCance, R.S. Cornman, M.B. Laramie, A.R. Mahon, R.F. Lance, D.S. Pilliod, K.M. Strickler, L.P. Waits, A.K. Fremier, T. Takahara, J.E. Herder, P. Taberlet, Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods Ecol. Evol. 7, 1299–1307 (2016). https://doi.org/10.1111/2041-210X.12595

    Article  Google Scholar 

  19. S. Yamamoto, K. Minami, K. Fukaya, K. Takahashi, H. Sawada, H. Murakami, S. Tsuji, H. Hashizume, S. Kubonaga, T. Horiuchi, M. Hongo, J. Nishida, Y. Okugawa, A. Fujiwara, M. Fukuda, S. Hidaka, K.W. Suzuki, M. Miya, H. Araki, H. Yamanaka, A. Maruyama, K. Miyashita, R. Masuda, T. Minamoto, M. Kondoh, Environmental DNA as a ‘snapshot’ of fish distribution: a case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan. PLoS ONE 11, e0149786 (2016). https://doi.org/10.1371/journal.pone.0149786

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  20. H. Yamanaka, H. Motozawa, S. Tsuji, R.C. Miyazawa, T. Takahara, T. Minamoto, 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

    Article  CAS  Google Scholar 

  21. The eDNA Society, Environmental DNA sampling and experiment manual. https://ednasociety.org/en/manuals/. Accessed 2023-10-09

  22. S.R. Jangam, D.H. Yamada, S.M. McFall, D.M. Kelso, Rapid, point-of-care extraction of human immunodeficiency virus type 1 proviral DNA from whole blood for detection by real-time PCR. J. Clin. Microbiol. 47, 2363–2368 (2009). https://doi.org/10.1128/jcm.r00092-09

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. G. Cananzi, I. Gregori, F. Martino, T. Li, E. Boscari, E. Camatti, L. Congiu, I.A.M. Marino, M. Pansera, A. Schroeder, L. Zane, Environmental DNA metabarcoding reveals spatial and seasonal patterns in the fish community in the Venice Lagoon. Front. Mar. Sci. (2022). https://doi.org/10.3389/fmars.2022.1009490

    Article  Google Scholar 

  24. M.M. AlShahni, K. Makimura, T. Yamada, K. Satoh, Y. Ishihara, K. Takatori, T. Sawada, Direct colony PCR of several medically important fungi using Ampdirect® plus. Jpn. J. Infect. Dis. 62, 164–167 (2009). https://doi.org/10.7883/yoken.JJID.2009.164

    Article  PubMed  CAS  Google Scholar 

  25. H. Doi, R. Inui, Y. Akamatsu, K. Kanno, H. Yamanaka, T. Takahara, T. Minamoto, Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshw. Biol. 62, 30–39 (2017). https://doi.org/10.1111/fwb.12846

    Article  CAS  Google Scholar 

  26. Biomere, Inc., The Biomere Platform. https://biomeme.com/. Accessed 2023-10-09

  27. H. Doi, T. Watanabe, N. Nishizawa, T. Saito, H. Nagata, Y. Kameda, N. Maki, K. Ikeda, T. Fukuzawa, On-site environmental DNA detection of species using ultrarapid mobile PCR. Mol. Ecol. Resour. 21, 2364–2368 (2021). https://doi.org/10.1111/1755-0998.13448

    Article  PubMed  CAS  Google Scholar 

  28. H. Aoki, H. Tao, Label- and marker-free gene detection based on hybridization-induced conformational flexibility changes in a ferrocene–PNA conjugate probe. Analyst 132, 784–791 (2007). https://doi.org/10.1039/B704214K

    Article  ADS  PubMed  CAS  Google Scholar 

  29. H. Aoki, M. Torimura, T. Nakazato, 384-channel electrochemical sensor array chips based on hybridization-triggered switching for simultaneous oligonucleotide detection. Biosens. Bioelectron. 136, 76–83 (2019). https://doi.org/10.1016/j.bios.2019.04.047

    Article  PubMed  CAS  Google Scholar 

  30. H. Aoki, T. Sukegawa, M. Torimura, T. Nakazato, Nonlabeling and nonexternal indicator DNA sensing based on ferrocene-terminated probes immobilized on gold film electrode arrays with plasma and acid treatments. Sens. Mater. 32, 1079–1090 (2020). https://doi.org/10.18494/Sam.2020.2640

    Article  Google Scholar 

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Acknowledgements

DC gratefully acknowledges financial support through Keio University internal research funding schemes. HA gratefully acknowledges financial support through AIST internal research funding schemes. We are grateful to Yukiko Kumakura of AIST for her cooperation in with data acquisition.

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Authors and Affiliations

  1. Department of Applied Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa, 223-8522, Japan

    Mai Kawaguchi, Hiroki Kamo, Kazuki Miura, Yuki Hiruta, Siro Simizu & Daniel Citterio

  2. Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki, 305-8569, Japan

    Hiroshi Aoki

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  1. Mai Kawaguchi
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Kawaguchi, M., Aoki, H., Kamo, H. et al. Simplified capture, extraction, and amplification of cellular DNA from water samples. ANAL. SCI. 40, 501–510 (2024). https://doi.org/10.1007/s44211-023-00482-7

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  • DOI: https://doi.org/10.1007/s44211-023-00482-7

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