A species-specific qPCR method to detect the giant jellyfish Nemopilema nomurai from environmental DNA

Abstract

The massive outbreaks of the giant jellyfish Nemopilema nomurai have caused serious problems in fisheries, and monitoring its distribution is necessary to predict its occurrence around Japan. In this study, we designed a primer/probe set of mitochondrial 16S for species-specific qPCR to detect N. nomurai. The utility of qPCR using environmental DNA (eDNA) was compared with conventional approaches (sight survey and net collection) in the Sea of Japan and the East China Sea in 2021–2023. The newly developed qPCR method showed an average 98.9% PCR efficiency (r²=0.9992). In the East China Sea, the highest copy numbers of the species were observed at stations using conventional methods to detect the maximum number of N. nomurai. The qPCR method also detected N. nomurai at stations that reported no observations using conventional methods in both sampling areas. Possible DNA degradation was observed in eDNA samples from the Sea of Japan in 2021, and the qPCR method detected N. nomurai at only a subset of the stations that reported the species using conventional methods. These results indicate that qPCR using eDNA can be an effective monitoring tool for N. nomurai; however, eDNA should be properly preserved and analyzed immediately to prevent its underestimation.