PCR and LAMP detection of environmental DNA of the invasive clam Corbicula fluminea

Abstract

An environmental DNA (eDNA) detection technique using TaqMan qPCR and LAMP analysis was developed for the Asian clam Corbicula fluminea, which is causing alarm in Japan and worldwide as an invasive alien spe-cies. The qPCR primer and probe designed in this study specifically amplified C. fluminea DNA, but did not amplify C. sandai or C. japonica DNA, both native Japanese species. In contrast, LAMP analysis showed that C. sandai DNA also reacted, but with a delay after the amplification of C. fluminea DNA, and it was possible to specifically detect C. fluminea DNA by setting the LAMP analysis time to 30 min. Field surveys at three study sites with different habitat conditions for C. fluminea showed that eDNA detection using qPCR/LAMP analyses were consistent with C. fluminea distribution. The applicability of a simple filtration and concentration method for eDNA using glass fibers in suspension (SGF method) was verified, and the SGF method had a higher eDNA recovery capacity than the conventional aspiration method using glass fiber filter paper. eDNA extraction using the SGF method and eDNA analysis using qPCR/LAMP may be useful for qualitative and simple habitat estimation of C. fluminea in poor water quality environments.