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[AOS12-P03] Comparison of species-specific qPCR and metabarcoding methods to detect small pelagic fish distribution from open ocean environmental DNA
Keywords:environmental DNA, fish distribution, Kuroshio Extension, small pelagic fish
Environmental DNA (eDNA) is increasingly used to non-invasively monitor aquatic animals in freshwater and coastal areas. Since full investigation of marine fish distributions is difficult due to huge volume of the ocean in addition to stormy weather, researchers also began to use eDNA methods for marine fish distribution survey. However, the use of eDNA in the open ocean (hereafter referred to OceanDNA) is still limited because of the sparse distribution of eDNA in the open ocean.
Small pelagic fish have a large biomass and are widely distributed in the open ocean. In this research, we chose small pelagic fish as targets and aimed to test the performance of two OceanDNA analysis methods—species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers when determining the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species (Sardinops melanostictus, Engraulis japonicus, Scomber japonicus, Scomber australasicus, Trachurus japonicus, and Cololabis saira) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure.
During the KS-18-5 cruise by Shinsei-Maru, seawater samples were collected at 19 stations in the Kuroshio Extension area. We collected the water samples from 5 to 300 m through Niskin bottles combined with Conductivity Temperature Depth (CTD) instrument, which measured water mass properties, and collected the surface water sample by a bucket from 0 m. The total sample number is 247. Water samples were filtered by Sterivex-GP pressure filter units (with a 0.22 μm pore size) and the filters were stored at -20 °C, then DNA was extracted from filter after the cruise.
We compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method. However, the reason of the different results between the qPCR and MiFish methods is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, we proposed a combined method to simultaneously determine the quantitative distribution of small pelagic fish species within the fish community structures.
Small pelagic fish have a large biomass and are widely distributed in the open ocean. In this research, we chose small pelagic fish as targets and aimed to test the performance of two OceanDNA analysis methods—species-specific qPCR (quantitative polymerase chain reaction) and MiFish metabarcoding using universal primers when determining the distribution of small pelagic fish in the open ocean. We focused on six small pelagic fish species (Sardinops melanostictus, Engraulis japonicus, Scomber japonicus, Scomber australasicus, Trachurus japonicus, and Cololabis saira) and selected the Kuroshio Extension area as a testbed, because distribution of the selected species is known to be influenced by the strong frontal structure.
During the KS-18-5 cruise by Shinsei-Maru, seawater samples were collected at 19 stations in the Kuroshio Extension area. We collected the water samples from 5 to 300 m through Niskin bottles combined with Conductivity Temperature Depth (CTD) instrument, which measured water mass properties, and collected the surface water sample by a bucket from 0 m. The total sample number is 247. Water samples were filtered by Sterivex-GP pressure filter units (with a 0.22 μm pore size) and the filters were stored at -20 °C, then DNA was extracted from filter after the cruise.
We compared the detection performance in each target fish between the using of qPCR and MiFish methods. A positive correlation was evident between the qPCR and MiFish detection results. In the ranking of the species detection rates and spatial distribution estimations, comparable similarity was observed between results derived from the qPCR and MiFish methods. In contrast, the detection rate using the qPCR method was always higher than that of the MiFish method. Amplification bias on non-target DNA and low sample DNA quantity seemed to partially result in a lower detection rate for the MiFish method. However, the reason of the different results between the qPCR and MiFish methods is still unclear. Considering the ability of MiFish to detect large numbers of species and the quantitative nature of qPCR, we proposed a combined method to simultaneously determine the quantitative distribution of small pelagic fish species within the fish community structures.