Environmental DNA complements monitoring and occupancy estimation of urban terrestrial species

Background/Question/Methods

Environmental DNA (eDNA) metabarcoding can accurately and non-invasively detect unknown organisms. The potential applications of eDNA to detect species and taxa have been recognized. Furthermore, eDNA can contribute to a spatially unbiased assessment of biodiversity occupancy. Here, we applied eDNA to detect terrestrial species in urban green spaces on a regional scale. We evaluated eDNA effectiveness in three different urban green structures (forests, ecological corridors, and parks) in Gwanggyo New Town, Suwon, South Korea. From July 30, 2019 to June 03, 2020, we installed 67 artificial water tanks (in 23 forests, 20 ecological corridors, and 24 parks) containing distilled water by the type of urban green space. We used a camera trap to check the contact between the water tank and terrestrial species (drinking water, bathing, etc.) and verify the eDNA. We filtered 30–60 ml of water in each tank using a 0.45 μm Sterivex filter. We extracted DNA in an aseptic laboratory using the method proposed by Ushio et al. (2017). We applied the MiMammal-U 12s rRNA universal primer in the PCR process to amplify the terrestrial species sequence. Finally, we used a conservative sequence cut-off process to detect optimal molecular operational taxonomic units (MOTUs) and terrestrial species.

Results/Conclusions

We identified 4,986,596 terrestrial species sequence reads in 67 samples. After bioinformatics analysis, the final “filtered” dataset included 21 terrestrial species (13 forests, 14 ecological corridors, and five parks; ANOVA, F(2, 69) = 2.147, p=0.125). We newly identified four small terrestrial species, including Muridae, through eDNA, as many terrestrial species have been identified in forests. In particular, eDNA was detected by clearly distinguishing between summer (Eurystomus orientalis) and winter (Fringilla montifringilla) migratory birds.As eDNA has been increasingly applied as the next-generation technology of species monitoring, we successfully monitored terrestrial species according to urban ecosystem greenery type through the comparison of eDNA, camera traps, and field surveys. We were able to detect the majority of the reported 37 terrestrial species (18 mammals and 19 birds) in only seven days in an urban ecosystem. However, we identified significant inconsistencies between terrestrial species detected by eDNA, camera trap, and field methods, and only 11 (28.94%) species were detected by all survey methods. We still consider field survey to be a powerful monitoring technique due to differences in life history (tunnel, flight, etc.) of urban terrestrial species. To achieve time- and cost-effective species monitoring, a combination of survey methods must be used.