Data for: Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species
Data files
May 02, 2024 version files 67.08 KB
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README.md
2.56 KB
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storage_extraction_data.csv
39.41 KB
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template_volume_data.csv
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Abstract
Environmental DNA (eDNA) refers to genetic material released by organisms into their surrounding environment. Collecting and identifying eDNA has gained popularity for monitoring and surveillance of aquatic invasive species. Invasive species management is most successful when an invasion is identified early while population size is likely to be low, highlighting the importance of eDNA detection sensitivity. Various factors influence DNA yield recovered from environmental samples. Environmental DNA storage and extraction methods, for example, can be adjusted to maximize DNA yield, thereby improving detectability. In this study, we compared the performance of two eDNA storage and extraction methods in detecting three common aquatic invasive species (Bythotrephes longimanus, Dreissena polymorpha, and Faxonius rusticus) across five natural ecosystems of Minnesota, United States. One method involved storing filters in 95% ethanol (EtOH) and extracting DNA using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany), whereas the other method used cetyl trimethylammonium bromide (CTAB) for storage and a phenol–chloroform–isoamyl (PCI) procedure for DNA extraction. We also investigated the effect of DNA extract volume (1 μL relative to 3 μL) in qPCR reactions on eDNA detections for the commercial kit method. The CTAB‐PCI method yielded significantly more positive detections, across all three species, compared to the EtOH‐Qiagen method. Moreover, we found that using 1 μL of DNA extract in qPCR reactions was equally effective as using 3 μL. To improve detections of aquatic invasive species, we recommend that researchers store eDNA sample filters in CTAB or a similar lysis buffer such as Longmire's solution and extract with PCI when feasible, but note that lower extract volumes might be used without negative effect when either increasing technical replicates or repurposing samples for the detection of multiple species.
README: Data for "Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species"
https://doi.org/10.5061/dryad.r2280gbm8
Description of the data and file structure
File name: storage_extraction_data.csv
Overview of file: This file contains data used in statistical tests for the eDNA storage-extraction section of the manuscript.
Columns:
“Sample ID”: A unique identifier for each sample.
“Lake”: The lake or water body in which the sample was collected.
“Collection Date”: The date the sample was collected in month/day/year format.
“Point”: One of five sampling points (or locations) within the waterbody labeled as 1, 3, 5, 7, and 10.
“Replicate”: The numbered (1,2,3) field replicate taken at each sampling point.
“Preservation”: The filter preservation method as ETOH or CTAB.
“Extraction Method”: The DNA extraction method as Qiagen DNeasy Powersoil Pro Kit or phenol-chloroform-isoamyl
“Species”: The target species as rc for rusty crayfish, sw for spiny water flea, and zm for zebra mussel.
“Habitat”: Whether the sample was collected at a nearshore or offshore point in the waterbody.
“Detection”: Positive (1) or negative (0) detection of eDNA in the sample, where positive detection indicates at least one of three technical replicates amplified above the detection threshold.
File name: template_volume_data.csv
Overview of file: This file contains data used in statistical tests for the template volume section of the manuscript.
Columns:
“Sample ID”: A unique identifier for each sample.
“Lake”: The lake or water body in which the sample was collected.
“Collection Date”: The date the sample was collected in month/day/year format.
“Point”: One of five sampling points (or locations) within the waterbody labeled as 1, 3, 5, 7, and 10.
“Replicate”: The numbered (1,2,3) field replicate taken at each sampling point.
“Template volume”: The volume of eDNA template or extract used for qPCR as 1 = 1 μl and 3 = 3 μl.
“Species”: The target species as rc for rusty crayfish, sw for spiny water flea, and zm for zebra mussel.
“Habitat”: Whether the sample was collected at a nearshore or offshore point in the waterbody.
“Detection”: Positive (1) or negative (0) detection of eDNA in the sample, where positive detection indicates at least one of three technical replicates amplified above the detection threshold.