Conservation Genetics Resources

, Volume 8, Issue 3, pp 231–234 | Cite as

Using environmental DNA to detect an endangered crayfish Cambaroides japonicus in streams

  • Kousuke Ikeda
  • Hideyuki Doi
  • Kazunori Tanaka
  • Tadashi Kawai
  • Junjiro N. Negishi
Technical Note


The freshwater crayfish, Cambaroides japonicus, is endangered in Hokkaido, Japan and inhabits burrows. Here, we applied environmental DNA (eDNA) method for evaluating the species distributions with comparing hand-capture method in the headwater streams. We detected the eDNA of C. japonicus from all sites, where we collected C. japonicus, and confirmed that eDNA can be applied to detect burrowing aquatic freshwater crayfish without disturbing their habitats.


Species-specific primers Real-time PCR Lotic system Species detection 



We thank to Takashi Mitsuzuka, and Atsuko Kato for their assistances for the sampling. We wish to appreciate Itsuro Koizumi, Toru Suzuki, Toshifumi Minamoto, Teruhiko Takahara, Hitoshi Araki, Masanori Nunokawa, and Ryota Kawanishi, who kindly provide their comments on this study.


  1. Bustin SA, Benes V, Garson JA et al (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55(4):1–12. doi: 10.1373/clinchem.2008.112797 CrossRefGoogle Scholar
  2. Deiner K, Walser J-C, 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 CrossRefGoogle Scholar
  3. Dejean T, Valentini A, Miquel C et al (2012) 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. doi: 10.1111/j.1365-2664.2012.02171.x CrossRefGoogle Scholar
  4. Doi H, Uchii K, Takahara T et al (2015) Use of droplet digital PCR for estimation of fish abundance and biomass in environmental DNA surveys. PLoS ONE 10:e0122763. doi: 10.1371/journal.pone.0122763 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Foote AD, Thomsen PF, Sveegaard S et al (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7:e41781. doi: 10.1371/journal.pone.0041781 CrossRefPubMedPubMedCentralGoogle Scholar
  6. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Kawai T, Nakata K, Hamano T (2002) Temporal changes of the density in two crayfish species, the native Cambaroides japonicus (De Haan) and the alien Pacifastacus leniusculus (Dana), in natural habitats of Hokkaido, Japan. Freshw Crayfish 13:198–206Google Scholar
  8. Lodge DM, Turner CR, Jerde CL et al (2012) Conservation in a cup of water: estimating biodiversity and population abundance from environmental DNA. Mol Ecol 21:2555–2558. doi: 10.1111/j.1365-294X.2012.05600.x CrossRefPubMedPubMedCentralGoogle Scholar
  9. Minamoto T, Yamanaka H, Takahara T et al (2012) Surveillance of fish species composition using environmental DNA. Limnology 13:193–197CrossRefGoogle Scholar
  10. R Core Team (2015) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
  11. Schmidt BR, Kéry M, Ursenbacher S, Hyman OJ, Collins JP (2013) Site occupancy models in the analysis of environmental DNA presence/absence surveys: a case study of an emerging amphibian pathogen. Methods Ecol Evol 4:646–653. doi: 10.1111/2041-210X.12052 CrossRefGoogle Scholar
  12. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  13. Thomsen PF, Kielgast J, Iversen LL et al (2012a) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573. doi: 10.1111/j.1365-294X.2011.05418.x CrossRefPubMedGoogle Scholar
  14. Thomsen PF, Kielgast J, Iversen LL et al (2012b) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS ONE 7:e41732. doi: 10.1371/journal.pone.0041732 CrossRefPubMedPubMedCentralGoogle Scholar
  15. Tréguier A, Paillisson J-M, Dejean T et al (2014) Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds. J Appl Ecol 51:871–879. doi: 10.1111/1365-2664.12262 CrossRefGoogle Scholar
  16. Uchii K, Doi H, Minamoto T (2016) A novel environmental DNA approach to quantify the cryptic invasion of non-native genotypes. Mol Ecol Resour 16:415–422. doi: 10.1111/1755-0998.12460 CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Kousuke Ikeda
    • 1
  • Hideyuki Doi
    • 2
  • Kazunori Tanaka
    • 3
  • Tadashi Kawai
    • 4
  • Junjiro N. Negishi
    • 1
  1. 1.Graduate School of Environmental ScienceHokkaido UniversitySapporoJapan
  2. 2.Graduate School of Simulation StudiesUniversity of HyogoKobeJapan
  3. 3.Research Group of Regional Sciences, Graduate School of LettersHokkaido UniversitySapporoJapan
  4. 4.Wakkanai Fisheries Research InstituteWakkanaiJapan

Personalised recommendations