Browsing by Subject "eDNA"

Now showing 1 - 3 of 3
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    Modern Limnological and Paleolimnological Applications of Diatoms in Minnesota Lakes
    (2021-05) Burge, David
    The following chapters represent a continuity of diatom research in Minnesota lakes. In Chapter 2, the study on Upper and Lower Red Lakes demonstrates the use of well-established paleolimnological proxies to assess eco-limnological change in a pair of large shallow lakes and inform management of the lakes by the Red Lake Tribal Department of Natural Resources and the Minnesota Pollution Control Agency. Highlighted here was the use of diatoms using traditional morphological and geochemical approaches to reconstructing limnological history. In Chapter 3, I present a review on resurrection ecology as a new tool in the paleolimnological tool belt. This chapter highlights diatoms as prime candidates for resurrection ecology studies and the use of sediment eDNA to guide such studies. Chapter 4 uses the recommendations in Chapter 3 to leverage diatom microfossils and their DNA to examine the influence of 20th century dust deposition on productivity and community composition. This study highlights the first use of sediment DNA to characterize diatom assemblage changes in a North American lake, and furthermore highlights the beneficial uses of paired microfossil-DNA diatom proxies. In Chapter 5, I used sediment DNA to describe the genomic diversity of diatoms across lakes of Minnesota. The diatom diversity described here corresponds to the distribution of lake types across Minnesota that can be characterized by diatoms observed in light microscopy or by their DNA signatures. Furthermore, the paired use of diatom microfossils and sediment DNA showed similar limnological trends in the paleolimnological record of two lakes.
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    Predator to Prey to Poop: Bats as Microbial Hosts and Insectivorous Hunters
    (2020-09) Galey, Miranda
    Bat fecal samples are a rich source of ecological data for bat biologists, entomologists, and microbiologists. Feces collected from individual bats can be used to profile the gut microbiome using microbial DNA and to understand bat foraging strategies using arthropod DNA. We used eDNA collected from bat fecal samples to better understand bats as predators in the context of their unique gut physiology. We used high through- put sequencing of the COI gene and 16S rRNA gene to determine the diet composition and gut microbiome composition of three bat species in Minnesota: Eptesicus fuscus, Myotis lucifugus and M. septentrionalis. In our analysis of insect prey, we found that E. fuscus consistently foraged for a higher diversity of beetle species compared to other insects. We found that the proportional frequency of tympanate samples from M. septentrionalis and M. lucifugus was similar, while M. septentrionalis consistently preyed more often upon non-flying species. We used the same set of COI sequences to determine presence of pest species, rare species, and insects not previously observed in Minnesota. We were able to combine precise arthropod identification and the for- aging areas of individually sampled bats to observe possible range expansion of some insects. The taxonomic composition of the bat gut microbiome in all three species was found to be consistent with the composition of a mammalian small intestine. The gut community was dominated by microbes that subsist on mucins and simple sugars, mostly in the phyla Proteobacteria and Firmicutes. Lactic acid bacteria were proportionally more abundant than most other groups of bacteria across all host de- mographic variables measured. As high throughput sequencing costs continue to drop and bioinformatic techniques mature, studies such as this will become more valuable for evaluating ecological hypotheses in a holobiontic context. R code used in this thesis are provided in a supplementary PDF.
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    Seasonal influence on detection probabilities for multiple aquatic invasive species using environmental DNA
    (2023-12-14) Rounds, Christopher; Arnold, Todd W; Chun, Chan Lan; Dumke, Josh; Totsch, Anna; Keppers, Adelle; Edbald, Katarina; García, Samantha M; Larson, Eric R; Nelson, Jenna KR; Hansen, Gretchen JA; round060@umn.edu; Rounds, Christopher; University of Minnesota Fisheries Systems Ecology Lab
    Aquatic invasive species (AIS) are a threat to freshwater ecosystems. Documenting AIS prevalence is critical to effective management and early detection. However, conventional monitoring for AIS is time and resource intensive and is rarely applied at the resolution and scale required for effective management. Monitoring using environmental DNA (eDNA) of AIS has the potential to enable surveillance at a fraction of the cost of conventional methods, but key questions remain related to how eDNA detection probability varies among environments, seasons, and multiple species with different life histories. To quantify spatiotemporal variation in the detection probability of AIS using eDNA sampling, we surveyed 20 lakes with known populations of four aquatic invasive species: Common Carp (Cyprinus carpio), Rusty Crayfish (Faxonius rusticus), Spiny Waterflea (Bythotrephes longimanus), and Zebra Mussels (Dreissena polymorpha). We collected water samples at 10 locations per lake, five times throughout the open water season. Quantitative PCR was used with species-specific assays to determine the presence of species DNA in water samples. Using Bayesian occupancy models, we quantified the effects of lake and site characteristics and sampling season on eDNA detection probability. These results provide critical information for decision makers interested in using eDNA as a multispecies monitoring tool and highlight the importance of sampling when species are in DNA releasing life history stages.