eDNA analysis of yard waste samples reveals taxonomical diversity, sequence database limitations, and consistencies across sequencing platforms

J Insect Sci. 2026 Jul 1;26(4):ieag062. doi: 10.1093/jisesa/ieag062.

ABSTRACT

Timely identification of biological species is often needed for various purposes, including economic reasons, and advances in DNA sequencing technologies have greatly augmented the ability to identify species through the application of DNA barcoding. One such method examines environmental DNA (eDNA) to sample the presence of organisms in an environment without necessarily having direct access to the whole organisms. In recent years, multiple high-throughput sequencing platforms have emerged, and there are differences in the efficiency, effectiveness, and economics across these platforms. In this report, we examine the application of two platforms, from PacBio and Oxford Nanopore Technologies, to sequence COI amplicons from nine barcoded yard waste samples that we previously studied for a different purpose. Here, we observed consistencies across the platforms in the identification of operational taxonomical units (OTUs) from broad swaths of life, most prominently including Bacteria, Amoebozoa, Fungi, Arthropoda, Nematoda, Spiralia, and Viridiplantae. Other taxonomical groupings were also tentatively identified. However, limitations in coverage of the diversity of COI sequences in the public databases rendered species-level identification impossible for many of the OTUs. Insect species were the best represented across all barcoded samples, and both sequencing platforms regarding percentage identity to the best BLAST hits in the databases. Following this, we took an in-depth look at the knowledge of the presence of highly matched species in the locality from where the eDNA samples were derived. Strengths and limitations of this approach in the analysis of eDNA are discussed.

PMID:42417135 | PMC:PMC13342719 | DOI:10.1093/jisesa/ieag062