Monitoring of mammal and bird species in an urban ecological park using environmental DNA metabarcoding

Abstract

Monitoring species distribution and abundance accurately and efficiently are vital for conservation efforts. Next-generation sequencing and DNA metabarcoding using environmental DNA (eDNA) allow for the simultaneous identification of multiple species in one sample, enabling swift biodiversity assessment in complex ecosystems. However, most eDNA studies focus on aquatic organisms and ecosystems.This study’s main objective was to use eDNA metabarcoding to monitor mammal and bird species in an urban ecological park. The chosen study site was Gildong Ecological Park, Seoul, South Korea, with a total area of 80,000 m² divided into three marsh area, a forested mountain area, and a rural experience learning center. Water sampling occurred five times from August to September, yielding 65 samples from three park sections. We employed MiMammal and MiBird primers targeting mitochondrial 12 S to investigate mammals and birds, serving as pivotal biological indicators within urban ecosystems.Metabarcoding revealed the presence of 73% (11/15) and 67% (represented 67% of the total 6268 individual) of the dominant mammalian and avian species, respectively, known to inhabit the park, compared to the results of traditional surveys. The mountain samples (1.51) and marsh samples (2.32) had significantly different median read counts when including all species; however, the same comparison within each taxonomic group yielded no statistically significant differences. Though we detected species differences using eDNA across summer, autumn, and winter monitoring, no statistically significant differences were found among seasons within the park. However, the park’s area is relatively small for detecting variations in eDNA. This might be because there is a lot of animal activity throughout the study site and/or a limited influence of microhabitats. These results could provide valuable insights for using eDNA to monitor animals in urban ecological parks.