Environmental DNA (eDNA) is a molecular surveillance tool that has been widely used for detection and monitoring of aquatic taxa. Species can be detected by amplifying the DNA collected in water samples that originated from discarded biological components of animals (e.g., skin cells, slime coat, and feces). Environmental DNA surveillance has been successfully used for detecting rare, cryptic, and invasive species. High-throughput sequencing (HTS) of eDNA (termed metabarcoding) can be used to detect hundreds of species simultaneously and can be used to address contemporary ecological questions, such as the characterization of communities and bioassessment of aquatic ecosystems. Although highly successful in many freshwater systems, eDNA has not been tested on biologically diverse aquatic systems, such as the Duck and Clinch rivers in Tennessee. I assessed the ability of eDNA surveillance to detect and delineate the distribution of single species, the pygmy madtom (Noturus stanauli) and the silver carp (Hypophthalmichthys molitrix), in the Duck and Clinch rivers. I also compared the community composition of fishes as measured by eDNA-metabarcoding with community composition data obtained by traditional sampling. Finally, I tested the effect of land use variables on fish community composition using both molecular and traditional measures of fish communities in the Duck and Clinch rivers.
Water samples (16-L) were collected and filtered from 14 sites in the Duck River in November 2017 and 10 sites in the Clinch River in January 2018. Custom de novo primers and probe were developed and used in tandem with end-point PCR (epPCR) and quantitative PCR (qPCR) for the detection and delineation of N. stanauli in the Duck and Clinch rivers. A previously published assay was used with qPCR to detect H. molitrix and help define the leading edge. Lastly, HTS on the Illumina Mi-Seq platform and bioinformatic analysis using a custom pipeline in the program mothur was used to characterize fish assemblages. Land-use variables were tested as environmental drivers of differences between fish assemblages, and were calculated from raster data as the percent coverage within a 1-km radius around each site. My results indicate that eDNA surveillance can be used to detect both single species and multiple species from bulk environmental samples. Detection can be limited by both environmental factors (e.g., discharge) and biotic factors (e.g., low population abundance). Each aquatic system is unique and eDNA surveillance efforts must be optimized for each system before robust conclusions can be made. Furthermore, eDNA coupled with traditional techniques may provide better detection rates than either technique alone.
|Advisor:||Hurt, Carla R.|
|Commitee:||Mattingly, Hayden T., Rogers, Mark E., Harrison, Michael, Boles, Jeffrey|
|School:||Tennessee Technological University|
|School Location:||United States -- Tennessee|
|Source:||DAI-B 81/2(E), Dissertation Abstracts International|
|Keywords:||Bioassessment, Bioinformatics, Environmental DNA, Freshwater fishes, Invasive species, Rare species|
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