Dataset Information

A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity.

ABSTRACT: Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of soil samples against confirmed species observations from a long-term (approx. 9-year) camera-trapping study. At the same time, we considered multiple experimental parameters, including two sampling designs, two DNA extraction kits and two metabarcodes of different sizes. All mammals regularly recorded with cameras were detected in eDNA. In addition, eDNA reported many unrecorded small mammals whose presence in the study area is otherwise documented. A long metabarcode (?220 bp) offering a high taxonomic resolution, achieved a similar efficiency as a shorter one (?70 bp) and a phosphate buffer-based extraction gave similar results as a total DNA extraction method, for a fraction of the price. Our results support that eDNA-based monitoring should become a valuable part of ecosystem surveys, yet mitochondrial reference databases need to be enriched first.

SUBMITTER: Leempoel K

PROVIDER: S-EPMC7003463 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity.

Leempoel Kevin K Hebert Trevor T Hadly Elizabeth A EA

Proceedings. Biological sciences 20200115 1918

Before environmental DNA (eDNA) can establish itself as a robust tool for biodiversity monitoring, comparison with existing approaches is necessary, yet is lacking for terrestrial mammals. Moreover, much is unknown regarding the nature, spread and persistence of DNA shed by animals into terrestrial environments, or the optimal experimental design for understanding these potential biases. To address some of these challenges, we compared the detection of terrestrial mammals using eDNA analysis of ...[more]

PMID: 31937227

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Project description:The application of high-throughput sequencing of the 16S rRNA gene has increased the size of microbial diversity datasets by several orders of magnitude, providing improved access to the rare biosphere compared with cultivation-based approaches and more established cultivation-independent techniques. By contrast, cultivation-based approaches allow the retrieval of both common and uncommon bacteria that can grow in the conditions used and provide access to strains for biotechnological applications. We performed bidirectional pyrosequencing of the bacterial 16S rRNA gene diversity in two terrestrial and seven aquatic Antarctic microbial mat samples previously studied by heterotrophic cultivation. While, not unexpectedly, 77.5% of genera recovered by pyrosequencing were not among the isolates, 25.6% of the genera picked up by cultivation were not detected by pyrosequencing. To allow comparison between both techniques, we focused on the five phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Deinococcus-Thermus) recovered by heterotrophic cultivation. Four of these phyla were among the most abundantly recovered by pyrosequencing. Strikingly, there was relatively little overlap between cultivation and the forward and reverse pyrosequencing-based datasets at the genus (17.1-22.2%) and OTU (3.5-3.6%) level (defined on a 97% similarity cut-off level). Comparison of the V1-V2 and V3-V2 datasets of the 16S rRNA gene revealed remarkable differences in number of OTUs and genera recovered. The forward dataset missed 33% of the genera from the reverse dataset despite comprising 50% more OTUs, while the reverse dataset did not contain 40% of the genera of the forward dataset. Similar observations were evident when comparing the forward and reverse cultivation datasets. Our results indicate that the region under consideration can have a large impact on perceived diversity, and should be considered when comparing different datasets. Finally, a high number of OTUs could not be classified using the RDP reference database, suggesting the presence of a large amount of novel diversity.

Project description:Several different techniques and methods are used to capture and study beetles (Coleoptera). One option is the use of window traps with various trapping liquids. However, these liquids used in comparative studies may have a biasing effect on the results. The effectiveness of the frequently used liquid baits, involving beer, wine, vinegar, and water as the reference liquid, was compared in this study. Twenty-four traps were assigned to two habitat categories (sunny and shady) and four kinds of bait: beer, wine, vinegar, and water. During the study from June to July 2021, a total of 29,944 invertebrates were captured; of these, 3,931 individuals belonged to Coleoptera. A total of 3,825 beetles were identified, belonging to 120 species and 36 families. The most abundant family was Nitidulidae, with 3,297 adults (86% of the total). The number of arthropods differed only in the trapping liquid, and the captures were similar between beer and wine and between vinegar and water. The trapping liquid had a more significant effect on beetle abundance and species richness. In contrast, exposure had a significant effect only on the number of beetle species and a higher ratio of beetles was found in the shade. Beer and wine were very attractive and collected similar beetle communities. However, the diversity (Shannon's index) was low due to the high abundance of several species. Traps with vinegar and water collected a similar composition and species richness. After removing sap beetles (Nitidulidae) from all traps, a significant difference was still recorded between trapping liquids in the number of individuals and species, and their communities were much more similar. Thus, at high abundances of sap beetles, it is possible to exclude them from analyses and obtain more accurate data when assessing environmental variables. The results showed that the type of trapping liquids used can have substantial effects on abundance and species composition captured beetles in traps especially for beer and wine. The beer and wine in traps can significantly influence the subsequent biodiversity assessment. We recommend the use of trapping liquids without the baiting effect to correctly assess the effect of environmental variables on beetle richness and abundance.

Dataset Information

A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity.

Publications

A comparison of eDNA to camera trapping for assessment of terrestrial mammal diversity.

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