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