The shared performance of different COI regions increases the niche breadth detectable from bat guano eDNA
Marcele Laux1, Ana Cláudia Jardelino2,3, Santelmo Vasconcelos1,4
1Instituto Tecnológico Vale, Belém, PA, Brazil.
Genetics and Molecular Biology
|August 10, 2026
Summary
Using multiple DNA barcode primers improves arthropod detection in bat guano. Combining primers like UEA2-UEA3, UEA3-UEA4, and UEA5-UEA6 provides a more comprehensive view of dietary niches than a single primer alone.
Area of Science:
- Molecular Ecology
- Genetics
- Bioinformatics
Background:
- Cytochrome c oxidase subunit I (COI) is a standard DNA barcode for Metazoa.
- Different regions of the COI gene show varying levels of genetic variation.
- Dietary niche analysis using environmental DNA (eDNA) can be biased by primer choice.
Purpose of the Study:
- To evaluate the effectiveness of combining three arthropod-specific primer pairs for detecting dietary niches in bat guano.
- To compare the performance of individual primer pairs (UEA2-UEA3, UEA3-UEA4, UEA5-UEA6) in terms of arthropod recovery and taxonomic resolution.
Main Methods:
- Bat guano samples were collected from the Amazon and Caatinga biomes in Brazil.
- DNA metabarcoding targeting the COI gene was performed using three primer pairs.
- Sequence data were analyzed to assess arthropod proportions, unassigned reads, non-target sequences, taxonomic coverage, richness, and diversity.
Main Results:
- Primer pairs recovered distinct proportions of Arthropoda (10-57%) and varied in non-target sequences (10-61%).
- UEA2-UEA3 showed highest taxonomic coverage for Arthropoda, while UEA3-UEA4 and UEA5-UEA6 exhibited higher alpha-diversity.
- UEA5-UEA6 identified the most unique arthropod genera, predominantly Lepidoptera, while UEA3-UEA4 also favored Lepidoptera and Diptera.
Conclusions:
- Employing multiple primer pairs is essential for comprehensive arthropod detection in eDNA studies.
- Relying on a single primer pair can lead to biased dietary niche assessments.
- Primer selection is a critical factor influencing the accuracy of eDNA metabarcoding, particularly in complex matrices like bat guano.
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