Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol

Abstract

Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two‐step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.

Optimization and validation of a cost‐effective protocol for biosurveillance of invasive alien species

“…Contrary to eDNA metabarcoding of samples collected in ethanol (Zenker et al., 2020), our protocol was successful in generating high‐quality library preparations of the three targeted molecular markers for all of our samples. This validates that salt‐saturated solutions can act as a reservoir for eDNA in conventional trapping surveys (Young et al., 2020).…”

“…These results validate our modified protocol for detecting regulated bacterial and fungal taxa based on 16S and ITS and reinforce its utility for the identification of a wide variety of regulated taxa. However, whether or not some taxa are underrepresented in salt trap‐saturated solutions, as has been demonstrated for alcohol‐based collection fluids (Zenker et al., 2020), should be further evaluated.…”

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

“…In one of the first studies describing this non-destructive technique, DNA was isolated from mescal, a liquor containing the larva of the Agave butterfly, and a sequence from the family that includes the Agave butterfly was successfully recovered (Shokralla et al, 2010). The optimization of non-destructive DNA barcoding to identify single specimens and entire communities from sample preservative continues (Shokralla et al, 2010;Hajibabaei et al, 2012;Erdozain et al, 2019;Marquina et al, 2019;Gauthier et al, 2020;Zenker et al, 2020).…”

Metabarcoding Malaise traps and soil eDNA reveals seasonal and local arthropod diversity shifts

“…Metabarcoding environmental DNA (eDNA) studies are effective in assessing arthropod diversity in forests, either from soil 8 or using material collected by Malaise traps 9 . The use of eDNA present in soil, coined as the “biological engine of the earth” 10 and their invertebrate communities would be key to assess the forest belowground diversity.…”