Comparison of next-generation DNA sequencing to traditional morphological identification for environmental monitoring

Project ID: 1831
Principal Investigator: Sherri Pucherelli
Research Topic: Invasive Species
Funded Fiscal Years: 2018 and 2019
Keywords: None

Research Question

This research will help determine the benefits, limitations, and accuracy of next-generation DNA sequencing in comparison to traditional taxonomic methods. Many Reclamation projects require environmental monitoring, as the impact of invasive species, construction, water treatments, habitat restoration, and other habitat manipulations can be determined by observing the change in local species richness and abundance. Some commonly studied organisms include, macroinvertebrates, zooplankton, and bacteria. Traditional methods for monitoring these communities require specialized sampling procedures, sample processing, and expertise on taxonomic identification, which require a significant amount of time and funds. Traditional methods also require that specimen are euthanized for identification, which is not ideal when sampling for native, threatened and endangered species. Next-generation sequencing is a new technology that may be used to replace some traditional sampling methods at a lower cost while potentially providing more precise data output and reveal hidden diversity. An additional benefit of the technology is that it does not require the sacrifice of native, exotic, or threatened organisms. The technology does have limitations and the goal of this research study is to determine how best to utilize this technology for a variety of Reclamation projects. RESEARCH STRATEGY: This project includes a literature review of the current research in the field to determine how to structure the study to make sure it builds upon the current research. Macroinvertebrate samples collected from wetlands in Folsom, CA, that were previously identified by a taxonomist, will be analyzed by next-generation sequencing (NGS). DNA will be extracted from both the isopropanol supernatant, used as the fixative and storage media for the samples, and from pooled and macerated macroinvertebrate tissue. Polymerase chain reaction (PCR) will be used to amplify a fragment of DNA from both the media a

Need and Benefit

The results of this study will help determine how next-generation sequencing can be used to benefit Reclamation projects that require environmental monitoring in response to construction activities, invasive species, habitat restoration, and water treatment. The Reclamation Detection Laboratory for Exotic Species (RDLES) has had at least 5 requests for this analysis and many collaborators in the regions have expressed interest. Reclamation has limited taxonomic identification capabilities, and many of the regional offices contract out this work for significant costs. This research may provide a new option for completing this work at a reduced cost. Next-generation sequencing is a relatively new technology that still requires project specific research, therefore this work has potential for a peer review journal publication.

This study will provide a cost-benefit analysis of next-generation sequencing compared to traditional methods that will be Reclamation specific. We will determine if the data produced by the method are more or less informative as traditional methods. This research will determine which Reclamation projects would benefit most from this technology and managers of those projects throughout the regions will be briefed on the technology and Reclamations capabilities.

Next-generation sequencing is a powerful tool and rapidly evolving field, and Reclamation will be required to utilize this technology. When this analysis is requested we will have to incorporate this research into real-world jobs which significantly limits our ability to understand the technology and is unfair to our client's limited budget.

Contributing Partners

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Research Products

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Last Updated: 4/4/17