Two-season urban-stream eDNA study finds qPCR detects otters missed by metabarcoding

Field sampling summarized in the journal abstract found that qPCR assays amplified Eurasian otters from the same April and October samples in which eDNA metabarcoding did not detect them, although traditional surveys confirmed the animals’ presence. Based on the number of positive samples in repetitions, otters were detected at 42.9% to 85.7% of sampling sites in April and at all sites in October. The authors interpreted this pattern as indicating a higher detection probability in October and suggested that it could reflect a potential expansion of their home range during that season.

The study examined environmental DNA from an urban stream and compared metabarcoding with species-specific qPCR for Eurasian otter detection. Fieldwork and literature reviews documented 13 mammal species, of which eDNA metabarcoding detected six, including Canis lupus, Felis silvestris and Mustela sibirica. The failure of metabarcoding to register otters in both sampling months, despite their confirmed presence and successful amplification by qPCR, led the authors to identify qPCR as the more effective method for investigating otter distribution in the urban setting.

Metabarcoding results for fish were similar to those of traditional surveys. At the family level, Cyprinidae represented 54.57% of fish species in April and 43.58% in October, followed by Gobiidae at 16.90% and 22.88%, respectively. Pseudorasbora parva was the dominant fish species at the species level in Saetgang, accounting for 5.68% and 6.35% of relative abundance in April and October. The authors described this prey availability as potentially supporting opportunistic feeding by Eurasian otters, rather than presenting the metabarcoding results as direct evidence of otter diet.

The reported evidence is limited to one urban stream, two sampling months and the findings available in the abstract, so it does not establish year-round seasonal patterns or generalizability to other waterways. Within that scope, the study supports choosing qPCR for otter detection and metabarcoding for describing the surrounding fish assemblage. The authors concluded that the suitable eDNA analysis method depends on the research purpose.

Subject of Research: Comparison of metabarcoding and qPCR for seasonal Eurasian otter eDNA detection in an urban stream

Article Title: Optimising eDNA analysis for urban otter monitoring: seasonal patterns, detection strategies and prey availability

Article References: Kang, Y., Han, S., & Song, Y. (2024). Optimising eDNA analysis for urban otter monitoring: seasonal patterns, detection strategies and prey availability. Metabarcoding and Metagenomics, 8, Article e115512. https://doi.org/10.3897/mbmg.8.115512

Image Credits: AI Generated

DOI: 10.3897/mbmg.8.115512

Keywords: environmental DNA, Eurasian otter, metabarcoding, qPCR, urban stream, seasonal monitoring, fish prey, Pseudorasbora parva, Optimising, eDNA, analysis, urban