Fisheries Science

, Volume 85, Issue 2, pp 327–337 | Cite as

Dispersion and degradation of environmental DNA from caged fish in a marine environment

  • Hiroaki MurakamiEmail author
  • Seokjin Yoon
  • Akihide Kasai
  • Toshifumi Minamoto
  • Satoshi Yamamoto
  • Masayuki K. Sakata
  • Tomoya Horiuchi
  • Hideki Sawada
  • Michio Kondoh
  • Yoh Yamashita
  • Reiji Masuda
Original Article Biology


Environmental DNA (eDNA) consists of DNA fragments shed from organisms into the environment, and can be used to identify species presence and abundance. This study aimed to reveal the dispersion and degradation processes of eDNA in the sea. Caged fish were set off the end of a pier in Maizuru Bay, the Sea of Japan, and their eDNA was traced at sampling stations located at the cage and 10, 30, 100, 300, 600 and 1000 m distances from the cage along two transect lines. Sea surface water was collected at each station at 0, 2, 4, 8, 24 and 48 h after setting the cage, and again after removing the cage. Quantitative PCR analyses using a species-specific primer and probe set revealed that the target DNA was detectable while the cage was present and for up to 1 h after removing the cage, but not at 2 h or later. Among the 57 amplified samples, 45 (79%) were collected within 30 m from the cage. These results suggest that eDNA can provide a snapshot of organisms present in a coastal marine environment.


Detectability eDNA Quantitative PCR Species-specific primers and probe Striped jack Pseudocaranx dentex Transport 



We thank Yoshihito Ogura for navigating the boat and Masahiro Mukai and Aina Tanimoto (MFRS) for assisting with filtration procedures. This study was supported by CREST of JST (grant number: JPMJCR13A2) and the Sasakawa Scientific Research Grant from The Japan Science Society.

Supplementary material

12562_2018_1282_MOESM1_ESM.docx (223 kb)
Fig. S1 Observed flow velocities (a and b) and sea level (c) during the experiment. The length and angle of stick represent flow velocity and direction, respectively, recorded at NW (a) and NE (b) in Fig. 1. The eDNA sampling time points are represented by dotted lines


  1. Barnes MA, Turner CR, Jerde CL, Renshaw MA, Chadderton WL, Lodge DM (2014) Environmental conditions influence eDNA persistence in aquatic systems. Environ Sci Technol 48:1819–1827CrossRefPubMedGoogle Scholar
  2. Deiner K, Altermatt F (2014) Transport distance of invertebrate environmental DNA in a natural river. PLoS One 9:e88786CrossRefPubMedPubMedCentralGoogle Scholar
  3. 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 62:30–39CrossRefGoogle Scholar
  4. 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:e112611CrossRefPubMedPubMedCentralGoogle Scholar
  5. Evans NT, Olds BP, Renshaw MA, Turner CR, Li Y, Jerde CL, Lodge DM (2016) Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour 16:29–41CrossRefPubMedGoogle Scholar
  6. Ficetola GF, Miaud C, Pompanon F, Taberlet P (2008) Species detection using environmental DNA from water samples. Biol Lett UK 4:423–425CrossRefGoogle Scholar
  7. 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 52:358–365CrossRefGoogle Scholar
  8. 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 15:216–227CrossRefPubMedGoogle Scholar
  9. 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 27:25–33Google Scholar
  10. Kelly RP, Port JA, Yamahara KM, Crowder LB (2014) Using environmental DNA to census marine fishes in a large mesocosm. PLoS One 9:e86175CrossRefPubMedPubMedCentralGoogle Scholar
  11. Klymus KE, Richter CA, Chapman DC, Paukert C (2015) Quantification of eDNA shedding rates from invasive bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix. Biol Conserv 183:77–84CrossRefGoogle Scholar
  12. Lance RF, Klymus KE, Richter CA, Guan X, Farrington HL, Carr MR, Thompson N, Chapman DC, Baerwaldt KL (2017) Experimental observations on the decay of environmental DNA from bighead and silver carps. Manag Biol Invasion 8:343–359CrossRefGoogle Scholar
  13. 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:e114639CrossRefPubMedPubMedCentralGoogle Scholar
  14. Masuda R (2008) Seasonal and interannual variation of subtidal fish assemblages in Wakasa Bay with reference to the warming trend in the Sea of Japan. Environ Biol Fish 82:387–399CrossRefGoogle Scholar
  15. Masuda R, Matsuda K, Tanaka M (2012) Laboratory video recordings and underwater visual observations combined to reveal activity rhythm of red-spotted grouper and banded wrasse, and their natural assemblages. Environ Biol Fish 95:335–346CrossRefGoogle Scholar
  16. Minamoto T, Fukuda M, Katsuhara KR, Fujiwara A, Hidaka S, Yamamoto S, Takahashi K, Masuda R (2017) Environmental DNA reflects spatial and temporal jellyfish distribution. PLoS One 12:e0173073CrossRefPubMedPubMedCentralGoogle Scholar
  17. Miwa H, Ikeno H (2007) Three dimensional analysis of flow field and water environment in Maizuru Bay with consideration of density distribution. B Maizuru Natl Coll Tec 42:47–58 (In Japanese) Google Scholar
  18. Miya M, Sato Y, Fukunaga T, 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 2:150088CrossRefPubMedPubMedCentralGoogle Scholar
  19. Moyer GR, Díaz-Ferguson E, Hill JE, Shea C (2014) Assessing environmental DNA detection in controlled lentic systems. PLoS One 9:e103767CrossRefPubMedPubMedCentralGoogle Scholar
  20. Murphy HM, Jenkins GP (2010) Observational methods used in marine spatial monitoring of fishes and associated habitats: a review. Mar Freshw Res 61:236–252CrossRefGoogle Scholar
  21. O’Donnell JL, Kelly RP, Shelton AO, Samhouri JF, Lowell NC, Williams GD (2017) Spatial distribution of environmental DNA in a nearshore marine habitat. PeerJ 5:e3044CrossRefPubMedPubMedCentralGoogle Scholar
  22. Piaggio AJ, Engeman RM, Hopken MW, Humphrey JS, Keacher KL, Bruce WE, Avery ML (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 14:374–380CrossRefPubMedGoogle Scholar
  23. Pilliod DS, Goldberg CS, Arkle RS, Waits LP, Richardson J (2013) Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples. Can J Fish Aquat Sci 70:1123–1130CrossRefGoogle Scholar
  24. Rees HC, Bishop K, Middleditch DJ, Patmore JRM, Maddison BC, Gough KC (2014) The application of eDNA for monitoring of the great crested newt in the UK. Ecol Evol 4:4023–4032CrossRefPubMedPubMedCentralGoogle Scholar
  25. Sansom BJ, Sassoubre LM (2017) Environmental DNA (eDNA) shedding and decay rates to model freshwater mussel eDNA transport in a river. Environ Sci Technol 51:14244–14253CrossRefPubMedGoogle Scholar
  26. Sassoubre LM, Yamahara KM, Gardner LD, Block BA, Boehm AB (2016) Quantification of environmental DNA (eDNA) shedding and decay rates for three marine fish. Environ Sci Technol 50:10456–10464CrossRefPubMedGoogle Scholar
  27. Strickler KM, Fremier AK, Goldberg CS (2015) Quantifying effects of UV-B, temperature, and pH on eDNA degradation in aquatic microcosms. Biol Cons 183:85–92CrossRefGoogle Scholar
  28. Takahara T, Minamoto T, Yamanaka H, Doi H, Kawabata Z (2012) Estimation of fish biomass using environmental DNA. PLoS One 7:e35868CrossRefPubMedPubMedCentralGoogle Scholar
  29. Takahara T, Minamoto T, Doi H (2013) Using environmental DNA to estimate the distribution of an invasive fish species in ponds. PLoS One 8:e56584CrossRefPubMedPubMedCentralGoogle Scholar
  30. Thomsen PF, Kielgast J, Iversen LL, Møller PR, Rasmussen M, Willerslev E (2012a) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS One 7:e41732CrossRefPubMedPubMedCentralGoogle Scholar
  31. Thomsen PF, Kielgast J, Iversen LL, Wiuf C, Rasmussen M, Gilbert MTP, Willerslev E (2012b) Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol 21:2565–2573CrossRefPubMedGoogle Scholar
  32. Thomsen PF, Møller PR, Sigsgaard EE, Knudsen SW, Jørgensen OA, Willerslev E (2016) Environmental DNA from seawater samples correlate with trawl catches of subarctic, deepwater fishes. PLoS One 11:e0165252CrossRefPubMedPubMedCentralGoogle Scholar
  33. 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:e0176608CrossRefPubMedPubMedCentralGoogle Scholar
  34. Turner CR, Barnes MA, Xu CCY, Jones SE, Jerde CL, Lodge DM (2014) Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods Ecol Evol 5:676–684CrossRefGoogle Scholar
  35. Turner CR, Uy KL, Everhart RC (2015) Fish environmental DNA is more concentrated in aquatic sediments than surface water. Biol Conserv 183:93–102CrossRefGoogle Scholar
  36. Ushio M, Murakami H, Masuda R, Sado T, Miya M, Sakurai S, Yamanaka H, Minamoto T, Kondoh M (2018) Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. MBMG 2:e23297Google Scholar
  37. Valentini A, Taberlet P, Miaud C, Civade R, Herder J, Thomsen PF, Dejean T (2016) Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol 25:929–942CrossRefPubMedGoogle Scholar
  38. Wilcox TM, McKelvey KS, Young MK, Lowe WH, Schwartz MK (2015) Environmental DNA particle size distribution from brook trout (Salvelinus fontinalis). Conserv Genet Resour 7:639–641CrossRefGoogle Scholar
  39. Wilcox TM, McKelvey KS, Young MK, Sepulveda AJ, Shepard BB, Jane SF, Schwartz MK (2016) Understanding environmental DNA detection probabilities: a case study using a stream-dwelling char Salvelinus fontinalis. Biol Conserv 194:209–216CrossRefGoogle Scholar
  40. Yamamoto S, Minami K, Fukaya K, Takahashi K, Sawada H, Murakami H, Tsuji S, Hashizume H, Kubonaga S, Horiuchi T, Hongo M, Nishida J, Okugawa Y, Fujiwara A, Fukuda M, Hidaka S, Suzuki K.W, Miya M, Araki H, Yamanaka H, Maruyama A, Miyashita K, Masuda R, Minamoto T, Kondo M (2016) Environmental DNA as a ‘snapshot’ of fish distribution: a case study of Japanese jack mackerel in Maizuru Bay, Sea of Japan. PLoS One 11:e0149786CrossRefPubMedPubMedCentralGoogle Scholar
  41. Yamamoto S, Masuda R, Sato Y, Sado T, Araki H, Kondoh M, Minamoto T, Miya M (2017) Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci Rep 7:40368CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Japanese Society of Fisheries Science 2019

Authors and Affiliations

  • Hiroaki Murakami
    • 1
    Email author
  • Seokjin Yoon
    • 2
  • Akihide Kasai
    • 2
  • Toshifumi Minamoto
    • 3
  • Satoshi Yamamoto
    • 4
  • Masayuki K. Sakata
    • 3
  • Tomoya Horiuchi
    • 1
  • Hideki Sawada
    • 1
  • Michio Kondoh
    • 5
  • Yoh Yamashita
    • 1
  • Reiji Masuda
    • 1
  1. 1.Maizuru Fisheries Research Station, Field Science Education and Research CenterKyoto UniversityMaizuruJapan
  2. 2.Faculty of Fisheries SciencesHokkaido UniversityHakodateJapan
  3. 3.Graduate School of Human Development and EnvironmentKobe UniversityKobeJapan
  4. 4.Department of Zoology, Graduate School of ScienceKyoto UniversityKyotoJapan
  5. 5.Graduate School of Life SciencesTohoku UniversitySendaiJapan

Personalised recommendations