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Development of primer–probe sets for environmental DNA-based monitoring of pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon

  • Special Feature: Original Paper
  • Environmental DNA as a Practical Tool for Aquatic Conservation and Restoration
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Abstract

The pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon are economically important fishery resources in Japan. The catching of these fish species has decreased owing to environmental pollution and habitat loss caused by human impacts. We developed species-specific primer–probe sets to detect and quantify environmental DNA (eDNA) in these fish species. The primer–probe sets were specific to each target species with the detection limits of two (H. nipponensis) and one (S. microdon) copies per reaction, sufficient for eDNA analysis in the field. Using these assays, the eDNA was detected with a high probability (100% and 86% for H. nipponensis and S. microdon, respectively) at the sites where each fish species was captured by a cast net survey in the Hirata–Funagawa River (one of the inflowing rivers of Lake Shinji, Shimane Prefecture, Japan), where it was frequently detected without cast net capture. The eDNA was detected in S. microdon a little earlier than in H. nipponensis, and the eDNA concentrations of both species gradually decreased after peaking in July and reached negligible levels by October. The utility of the assays for estimating the seasonal appearances/disappearances of both species in this river was demonstrated. The species-specific primer–probe sets of the eDNA-based method represent a potentially useful monitoring tool that requires minimal labor and time and could be useful for managing H. nipponensis and S. microdon fisheries in the future.

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Acknowledgements

Ms. Mikie Fujii supported our research through personal donations. This research was supported by the Environment Research and Technology Development Fund (JPMEERF20164002) of the Environmental Restoration and Conservation Agency, Japan and by JST CREST (JPMJCR13A2), Japan. Kousuke Ikeda, Yusuke Ochiai, and Atsuko Kato (Pacific Consultants Co., Ltd.) provided samples for our research. We thank the Department of Molecular and Functional Genomics, Interdisciplinary Center for Science Research, Organization for Research and Academic Information, Shimane University, for providing the DNA facilities. The authors thank the faculty of Life and Environmental Sciences at Shimane University for providing financial support for publishing this report.

Funding

Environmental Restoration and Conservation Agency, JPMEERF20164002, Teruhiko Takahara, Core Research for Evolutional Science and Technology, JPMJCR13A2, Toshifumi Minamoto.

Author information

Author notes

  1. Masato Fujii: Deceased April 29, 2017.

Authors and Affiliations

  1. Faculty of Life and Environmental Sciences, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane, 690-8504, Japan

    Teruhiko Takahara & Masato Fujii

  2. Estuary Research Center, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane, 690-8504, Japan

    Teruhiko Takahara

  3. Inland Water Fisheries and Coastal Fisheries Division, Shimane Prefectural Fisheries Technology Center, 1659-1 Sono-cho, Izumo, Shimane, 691-0076, Japan

    Katsuya Fukui & Daisuke Hiramatsu

  4. Fisheries Division, Shimane Prefectural Government, 1 Tono-machi, Matsue, Shimane, 690-8501, Japan

    Daisuke Hiramatsu

  5. Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan

    Hideyuki Doi

  6. Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, Hyogo, 657-8501, Japan

    Toshifumi Minamoto

Authors
  1. Teruhiko Takahara
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  2. Katsuya Fukui
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  3. Daisuke Hiramatsu
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  4. Hideyuki Doi
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  5. Masato Fujii
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Corresponding author

Correspondence to Teruhiko Takahara.

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Conflict of interest

TM is an inventor of the patent for the use of BAC to eDNA preservation.

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Takahara, T., Fukui, K., Hiramatsu, D. et al. Development of primer–probe sets for environmental DNA-based monitoring of pond smelt Hypomesus nipponensis and Japanese icefish Salangichthys microdon. Landscape Ecol Eng 19, 11–19 (2023). https://doi.org/10.1007/s11355-022-00507-9

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  • DOI: https://doi.org/10.1007/s11355-022-00507-9

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