Vertebrate and Macroinvertebrate metabarcoding results from pilot water sampling
Harestone Moss Limited
Description
Results from metabarcoding analysis of eDNA water disk filters performed by NatureMetrics. Only records for taxa matched to taxonomic rank of family and higher are included in this dataset.
Data quality
Please note that the abundance of taxa cannot be directly inferred from the proportion of total sequence reads. While the proportion of sequence reads is a consequence of abundance, it is also impacted by biomass, activity, surface area, condition, distance from the physical sample, primer bias, and species-specific variation in the genome.
Methods
DNA from each filter was extracted using a commercial DNA extraction kit with a protocol modified to increase DNA yields.
Vertebrate sampling: purified DNAs were amplified with PCR for a hypervariable region of the 12S rRNA gene to target vertebrates as part of the eDNA survey.
Macroinvertebrate sampling: purified DNAs were amplified with PCR for a hypervariable region of the COI rRNA gene to target macroinvertebrates as part of the eDNA survey.
Analysis includes 12 replicate PCRs per sample.
Consensus taxonomic assignments were made for each OTU using sequence similarity searches against two reference databases for the macroinvertebrate analyses (NCBI nt (GenBank) and Barcode of Life Database (BOLD)) and NCBI nt (GenBank) reference database for the vertebrate analyses. The GBIF taxonomic backbone was used for consistency between databases. Results from all searches were combined and assignments made to the lowest possible taxonomic level where there was consistency in the matches. Conflicts were flagged and resolved manually. Minimum similarity thresholds of 98%, 95%, and 92% were used for species-, genus- and higher-level assignments respectively. Assigned taxa were checked against GBIF occurrence records for presence in the United Kingdom and elevated to higher taxonomic levels if there were no occurrences.
Citation
Harestone Moss Ltd ([Insert download year]). Vertebrate and Macroinvertebrate metabarcoding results from pilot water sampling. Occurrence dataset on the NBN Atlas
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Digitised records
Looking up... the number of records that can be accessed through the NBN Atlas. This resource was last checked for updated data on 18 Sep 2023. The most recent data was published on 18 Sep 2023.
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