Complementary role of environmental DNA for line-transect bird surveys: A field test in a Japanese rice landscape

Abstract

• More bird species were detected by line-transect surveys than eDNA metabarcoding. • Terrestrial birds were not detected by eDNA metabarcoding. • Nocturnal aquatic bird species were detected by eDNA metabarcoding. • Both methods should be used to detect a whole bird community. Monitoring and conserving bird biodiversity in rice landscapes is a global challenge. Although environmental DNA (eDNA) metabarcoding can potentially provide a sensitive and comprehensive assessment of bird biodiversity in farmlands, there is a lack of research on the usefulness of eDNA samples from paddy water as sources of information on the species richness and abundance of birds. Hence, in this study, we conducted eDNA metabarcoding during the breeding seasons of birds in 2021 and 2022 in central Japan and evaluated its accuracy and comprehensiveness by comparing its performance with that of the conventional line-transect survey. More bird species (18) were detected by conducting the line-transect survey than by performing eDNA metabarcoding (8 bird species). Twelve bird species were detected only by the line-transect survey; meanwhile, two aquatic bird species, including nocturnal species, were detected by performing eDNA metabarcoding alone. The frequency of occurrence of each species among the water sample replicates was positively associated with species biomass. In addition, the frequency of occurrence was higher in aquatic birds than in terrestrial birds probably because aquatic birds intensively breed and forage in flooded rice fields, resulting in higher amounts of DNA deposition. Overall, our results suggest that although conventional bird surveys are superior to eDNA metabarcoding using paddy water samples for monitoring terrestrial bird diversity, eDNA metabarcoding plays a complementary role in assessing aquatic bird diversity.

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