Assessing arthropod diversity metrics derived from stream environmental DNA: Spatiotemporal variation and paired comparisons with manual sampling
Background
Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods.
Methods
We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment.
Results
Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.
Citation Information
| Publication Year | 2023 |
|---|---|
| Title | Assessing arthropod diversity metrics derived from stream environmental DNA: Spatiotemporal variation and paired comparisons with manual sampling |
| DOI | 10.7717/peerj.15163 |
| Authors | Aaron Aunins, Sara J. Mueller, Jennifer A. Fike, Robert S. Cornman |
| Publication Type | Article |
| Publication Subtype | Journal Article |
| Series Title | PeerJ |
| Index ID | 70241955 |
| Record Source | USGS Publications Warehouse |
| USGS Organization | Fort Collins Science Center; Leetown Science Center |
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Metabarcode sequencing of aquatic environmental DNA from the Potomac River Watershed, 2015-2020
Biological indicator taxa have long been used for integrative assessments of water quality, particularly benthic invertebrate groups such as arthropods. While standardized protocols have been developed to calculate 'biological index' scores based on the abundances of these taxa, such systems are challenging to implement at large scales due to the sampling effort required, taxonomic expertise neede - Connect