The use of citizen science in fish eDNA metabarcoding for evaluating regional biodiversity in a coastal marine region: A pilot study

Abstract

To test the feasibility of a citizen science program for fish eDNA metabarcoding in coastal marine environments, we recruited six groups of voluntary citizens for a science education course at a natural history museum. We held a seminar on eDNA and a workshop for seawater sampling and on-site filtration using syringes and filter cartridges for the participants. After that, they selected single survey sites following the guidelines for conducting a safe field trip. They performed seawater sampling and on-site filtration at these sites during their summer holidays. The six selected sites unexpectedly included diverse coastal habitats within a 40 km radius, located at temperate latitudes in central Japan (~35°N). After the field trips, they returned filtered cartridges to the museum, and we extracted eDNA from the filters. We performed fish eDNA metabarcoding, along with data analysis. Consequently, we identified 140 fish species across 66 families and 118 genera from the six samples, with species richness ranging from 14 to 66. Despite its limited sample size, such a diverse taxonomic range of fish species exhibited spatial biodiversity patterns within the region, which are consistent with species distribution. These include north-south and urbanization gradients of species richness, geographic structure of the fish communities, and varying salinity preferences of the component species. This case study demonstrates the potential of fish eDNA metabarcoding as an educational and scientific tool to raise public awareness and perform large-scale citizen science initiatives encompassing regional, national, or global fauna.

Gravity filtration of environmental DNA: A simple, fast, and power-free method

“…The species richness (59 spp.) and composition of the fish communities were almost concordant with those of previous studies performed around the sampling area [ 11 , 12 ]. All the species detected at high frequencies were common in the region, and no species were included that were unnatural (Table S1), suggesting that the samples obtained by gravity filtration are of sufficient quality to be used for eDNA metabarcoding.…”

“…Three samples were gravity-filtered at a height of 2 m from 1 L of seawater obtained once a month between February and April 2022 from the coast of Tateyama, Chiba Prefecture, located along the Pacific coast of Japan. Libraries were prepared for three samples using MiFish primers [10] and subjected to MiSeq sequencing [11] . These sequences were subjected to taxon assignment [11] .…”

“…Libraries were prepared for three samples using MiFish primers [10] and subjected to MiSeq sequencing [11] . These sequences were subjected to taxon assignment [11] . We detected 27–38 fish species in the three samples, with a total of 59 species distributed across 32 families (Supplemental data; Table S1).…”

Prospects and challenges of environmental DNA (eDNA) metabarcoding in mangrove restoration in Southeast Asia

“…The benefits of involving local communities in restoration efforts and monitoring are three-fold (Schmitt and Duke, 2015;Miya et al, 2022): (1) shared ownership ensures multi-stakeholder support and continued protection of the site, (2) payment for restoration efforts contribute towards local livelihoods, and, (3) increased participation allows for more detailed data collection. However, the lack of taxonomic expertise and the need to maintain a standardised protocol present challenges to increase community involvement in restoration (Eger et al, 2022).…”

“…However, the lack of taxonomic expertise and the need to maintain a standardised protocol present challenges to increase community involvement in restoration (Eger et al, 2022). The use of eDNA metabarcoding addresses these limitations as community volunteers or employees are able to collect the eDNA metabarcoding sample with minimal training (Miya et al, 2022), and samples are then analysed by taxon experts and molecular researchers who can easily provide a comprehensive species list. This rapid assessment by local communities across a finer temporal and spatial scale (Agersnap et al, 2022) could also allow for early detection of invasive species (Larson et al, 2020) and changes in coastal communities or targeted species (Biggs et al, 2015).…”