Cotton swabs more effectively recover fungal DNA from Neotropical birds than polyester swabs

Abstract Birds interact with diverse fungal communities and may act as important, yet underrecognized, dispersal agents. Swabbing birds for external fungal DNA represents an emerging method to explore these ornithomycological interactions, yet the influence of swab material on DNA recovery has not been formally evaluated. In this study, we compared cotton and polyester swabs in their effectiveness at capturing fungal DNA from 162 birds of 47 species and 8 foraging guilds in southern Costa Rica. Birds were sampled in the field using paired cotton and polyester swabs on external surfaces (beak, feathers, and feet). We assessed differences in DNA detection, concentration, fungal richness, and community composition using quantitative assays and amplicon sequencing of the internal transcribed spacer 2 (ITS2) region of nuclear ribosomal DNA. Cotton swabs significantly outperformed polyester swabs across multiple metrics: DNA was detected more frequently, at higher concentrations, and yielded higher fungal read counts on cotton than polyester swabs. However, fungal richness and community composition did not differ between swab types, suggesting minimal bias in taxonomic representation. Regardless of swab type, the fungal family Aspergillaceae was most frequently detected across bird species. We recommend the use of cotton over polyester swabs for studies focused on external fungal DNA recovery from birds.