Abstract
The environmental DNA (eDNA) method is a detection technique that is rapidly gaining credibility as a sensitive tool useful in the surveillance and monitoring of invasive and threatened species. Because eDNA analysis often deals with small quantities of short and degraded DNA fragments, methods that maximize eDNA recovery are required to increase detectability. In this study, we performed experiments at different stages of the eDNA analysis to show which combinations of methods give the best recovery rate for eDNA. Using Oriental weatherloach (Misgurnus anguillicaudatus) as a study species, we show that various combinations of DNA capture, preservation and extraction methods can significantly affect DNA yield. Filtration using cellulose nitrate filter paper preserved in ethanol or stored in a -20°C freezer and extracted with the Qiagen DNeasy kit outperformed other combinations in terms of cost and efficiency of DNA recovery. Our results support the recommendation to filter water samples within 24hours but if this is not possible, our results suggest that refrigeration may be a better option than freezing for short-term storage (i.e., 3–5 days). This information is useful in designing eDNA detection of low-density invasive or threatened species, where small variations in DNA recovery can signify the difference between detection success or failure.
Highlights
The past decade has seen a remarkable growth and interest in the use of the environmental DNA method as a tool for targeted species detection and biodiversity assessments
We found that the filtration method, combined with either ethanol or freezer storage, and extracted with either Qiagen’s DNeasy or MoBio’s PowerWater kit yielded better results compared to the precipitation method, which is consistent with previous studies [19, 21]
We found that environmental DNA (eDNA) yield was higher for samples extracted with the DNeasy kit compared to the PowerWater kit, this was not statistically significant in our study
Summary
The past decade has seen a remarkable growth and interest in the use of the environmental DNA (eDNA) method as a tool for targeted species detection and biodiversity assessments. While earlier research focused on the isolation of microbial DNA from environmental samples [1, 2], subsequent studies directed at isolating plant and animal DNA from such samples has opened up diverse fields of application of the method including surveillance of rare, threatened, or invasive species [3,4,5] and assessment of past and present biodiversity [6,7,8]. Many eDNA studies have been in aquatic ecosystems, and have proven effective in the detection of aquatic/semi-aquatic vertebrates and invertebrates [9,10,11,12,13,14]. The application of this non-invasive genetic technique is increasingly expected to influence environmental management [15], basic studies are encouraged to further explore its possibilities and limitations [16].
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