Skip to main content

Advertisement

SpringerLink
Log in

Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen, a critically endangered Asian salmonid

  • Research paper
  • Published:
Limnology Aims and scope Submit manuscript

Abstract

For field ecologists, detecting a target species in the wild is a severe bottleneck to understanding its distribution and population status. Recently, environmental DNA (eDNA) techniques have been developed as a noninvasive monitoring tool for aquatic organisms. While applications of eDNA techniques for biomass estimation have been proposed, little is known about an applicable size range of the organisms, which might affect relationships between biomass and eDNA concentration. Here, we investigated eDNA from Sakhalin taimen (Parahucho perryi), a giant salmonid species of northern Japan. This species is critically endangered and difficult to detect in the wild by conventional sampling methods. Using quantitative real-time PCR, we tested correlations between eDNA concentration and fish density using fish with a wide range of ages and body sizes in aquarium experiments. We found that our new primers and probe were truly species-specific, and that the eDNA concentration was significantly correlated with fish density and body size (p < 0.001). Furthermore, based on our calculation, the eDNA concentrations were rather constant among aquaria with fish in different age and size groups when their total weight was adjusted. These results suggest that eDNA concentrations can be an indicator of biomass of Sakhalin taimen, although further research is needed for its application in natural environments.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environ Sci Tech 48(3):1819–1827

    Article  CAS  Google Scholar 

  • Bellemain E, Harmony P, Gray T, Guegan F, Valentini A, Miaud C, Dejean T (2016) Trails of river monsters: detecting critically endangered Mekong giant catfish Pangasianodon gigas using environmental DNA. Glob Ecol Conserv 7:148–156

    Article  Google Scholar 

  • Brett JR, Glass NR (1973) Metabolic rates and critical swimming speeds of sockeye salmon (Oncorhynchus nerka) in relation to size and temperature. J Fish Res Board Can 30(3):379–387

    Article  Google Scholar 

  • Doi H, Inui R, Akamatsu Y, Kanno K, Yamanaka H, Takahara T, Minamoto T (2017) Environmental DNA analysis for estimating the abundance and biomass of stream fish. Freshw Biol 62(1):30–39

    Article  CAS  Google Scholar 

  • Eichmiller JJ, Bajer PG, Sorensen PW (2014) The relationship between the distribution of common carp and their environmental DNA in a small lake. PLoS One 9(11):e112611

    Article  PubMed  PubMed Central  Google Scholar 

  • Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL, Mahon AR, Pfrender ME, Lamberti GA, Lodge DM (2016) Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Res 16(1):29–41

    Article  CAS  Google Scholar 

  • Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett 4(4):423–425

    Article  PubMed  PubMed Central  Google Scholar 

  • Fukumoto S, Ushimaru A, Minamoto T (2015) A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan. J Appl Ecol 52(2):358–365

    Article  CAS  Google Scholar 

  • Fukushima M, Kameyama S, Kaneko M, Nakao K, Ashley SE (2007) Modelling the effects of dams on freshwater fish distributions in Hokkaido, Japan. Freshw Biol 52(8):1511–1524

    Article  Google Scholar 

  • Fukushima M, Shimazaki H, Rand PS, Kaeriyama M (2011) Reconstructing Sakhalin taimen Parahucho perryi historical distribution and identifying causes for local extinctions. Trans Am Fish Soc 140(1):1–13

    Google Scholar 

  • IUCN Red list (2015) IUCN species highlights. http://www.iucnredlist.org/news/2015-iucn-species-highlights

  • Jane SF, Wilcox TM, McKelvey KS, Young MK, Schwartz MK, Lowe WH, Letcher BH, Whiteley AR (2015) Distance, flow and PCR inhibition: eDNA dynamics in two headwater streams. Mol Ecol Resour 15(1):216–227

    Article  CAS  PubMed  Google Scholar 

  • Janosik AM, Johnston CE (2015) Environmental DNA as an effective tool for detection of imperiled fishes. Environ Biol Fish 98(8):1889–1893

    Article  Google Scholar 

  • Jerde CL, Mahon AR, Chadderton WL, Lodge DM (2011) “Sight-unseen” detection of rare aquatic species using environmental DNA. Conserv Lett 4(2):150–157

    Article  Google Scholar 

  • Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinform 23(10):1289–1291

    Article  CAS  Google Scholar 

  • Lacoursière-Roussel A, Côté G, Leclerc V, Bernatchez L (2016) Quantifying relative fish abundance with eDNA: a promising tool for fisheries management. J Appl Ecol 53(4):1148–1157

    Article  Google Scholar 

  • Laramie MB, Pilliod DS, Goldberg CS (2015) Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol Conserv 183:29–37

    Article  Google Scholar 

  • 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(12):e114639

    Article  PubMed  PubMed Central  Google 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(7):150088

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pfleger MO, Rider SJ, Johnston CE, Janosik AM (2016) Saving the doomed: using eDNA to aid in detection of rare sturgeon for conservation (Acipenseridae). Glob Ecol Conserv 8:99–107

    Article  Google Scholar 

  • Pilliod DS, Goldberg CS, Arkle RS, Waits LP (2013) Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Can J Fish Aquat Sci 70(8):1123–1130

    Article  CAS  Google Scholar 

  • R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org

  • Rand PS (2006) Hucho perryi: IUCN (International Union for the Conservation of Nature) 2010 red list of threatened species, version 2010.3. IUCN. http://iucnredlist.org. Accessed Sept 2010

  • Sigsgaard EE, Carl H, Møller PR, Thomsen PF (2015) Monitoring the near-extinct European weather loach in Denmark based on environmental DNA from water samples. Biol Conserv 183:46–52

    Article  Google Scholar 

  • Spear SF, Groves JD, Williams LA, Waits LP (2015) Using environmental DNA methods to improve detectability in a hellbender (Cryptobranchus alleganiensis) monitoring program. Biol Conserv 183:38–45

    Article  Google Scholar 

  • Strickler KM, Fremier AK, Goldberg CS (2015) Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biol Conserv 183:85–92

    Article  Google Scholar 

  • Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z (2012) Estimation of fish biomass using environmental DNA. PLoS One 7(4):e35868

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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(8):e41732

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40(15):e115

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK (2013) Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 8(3):e59520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamashiro S (1965) Age and growth of the ito (Hucho perryi) in northeastern Hokkaido. B Jpn Soc Sci Fish 31:1–75

    Article  Google Scholar 

  • Zolotukhin SF, Semenchenko AU, Belyaev VA (2000) Taimen and lenok of Russian Far East. Khabarovskaya Kraevaya Tipografiya, Khabarovsk (in Russian with English summary)

    Google Scholar 

Download references

Acknowledgements

We thank S. Kamada, S. Namba and other members of the Animal Ecology Lab in the Faculty of Agriculture, Hokkaido University, for technical help, and M. Campbell for English correction and comments. We also thank K. Osanai, M. Kawahara and the other members of the Sarufutsu Itou Conservation Council for supporting our study. This study was funded by the Asahi Glass Foundation, JSPS KAKENHI grant numbers 26640136 and 17H03623 (HA). We declare that the experiments comply strictly with the current laws in Japan.

Author information

Authors and Affiliations

  1. Graduate School of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan

    Hiroki Mizumoto

  2. Hokkaido Research Organization, Salmon and Freshwater Fisheries Research Institute, Eniwa, Hokkaido, 061-1433, Japan

    Hirokazu Urabe

  3. Research Faculty of Agriculture, Hokkaido University, Kita-9, Nishi-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan

    Takashi Kanbe & Hitoshi Araki

  4. National Institute for Environmental Studies, Onogawa 16-2, Tsukuba, Ibaraki, 305-8506, Japan

    Michio Fukushima

Authors
  1. Hiroki Mizumoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hirokazu Urabe
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Takashi Kanbe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michio Fukushima
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hitoshi Araki
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Hitoshi Araki.

Additional information

Handling Editor: Toshifumi Minamoto

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 40 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mizumoto, H., Urabe, H., Kanbe, T. et al. Establishing an environmental DNA method to detect and estimate the biomass of Sakhalin taimen, a critically endangered Asian salmonid. Limnology 19, 219–227 (2018). https://doi.org/10.1007/s10201-017-0535-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10201-017-0535-x

Keywords

Search

Navigation