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Simple extraction and analysis of environmental DNA using glass fibers in suspension form

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Abstract

A simple environmental DNA (eDNA) filtration and extraction method that can be implemented on-site from water sampling to analysis was developed. In suspended glass fiber (SGF) method, 10 mg of the SGF was added to 1 L of environmental water to adsorb eDNA. The glass fiber was then collected using gravity filtration only, and eDNA was extracted using a simple reagent. eDNA was extracted from 85 samples of aquarium water, agricultural water, and river water using the SGF and standard methods. Under the laboratory condition, the SGF method was able to recover more DNA in the water containing lambda DNA than in the standard eDNA filtration and extraction method using adsorption columns. The invasive aquatic bivalve Limnoperna fortunei was used as a target species for detection using qPCR analysis or loop-mediated isothermal amplification (LAMP) analysis, which is less sensitive to DNA amplification inhibitors. The results showed that the positivity rate of the SGF-extracted DNA in qPCR and LAMP analysis was comparable or higher than that of the standard method extraction-qPCR analysis. In particular, as LAMP analysis is less time consuming than qPCR analysis and the presence or absence of DNA amplification can be determined visually, it is considered suitable as a rapid, on-site eDNA analysis method. The SGF method combined with the LAMP analysis has the potential to be applied to eDNA surveys of various species.

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Acknowledgements

We would like to thank Toyota Land Improvement District, Japan Water Agency Aichi Canal General Management Office, and Japan Water Agency Toyogawa Canal Headquarters for their cooperation in collecting agricultural water. This work was supported by a grant from commissioned project study on “Development of management strategies for invasive alien species causing damage to agriculture” JPJ007966, Ministry of Agriculture, Forestry and Fisheries, Japan. The experiments in this study comply with current Japanese laws.

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  1. Aichi Agricultural Research Center, 1-1 Sagamine, Nagakute, Aichi, 480-1193, Japan

    Ryoji Suzuki, Kunio Kawamura & Yuko Mizukami

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  1. Ryoji Suzuki
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  2. Kunio Kawamura
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Correspondence to Ryoji Suzuki.

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Suzuki, R., Kawamura, K. & Mizukami, Y. Simple extraction and analysis of environmental DNA using glass fibers in suspension form. Limnology 24, 25–36 (2023). https://doi.org/10.1007/s10201-022-00705-2

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