Abstract
Course-based undergraduate research experience (CURE) courses incorporate high-impact pedagogies that have been shown to increase undergraduate retention among underrepresented minorities and women. As part of the Building Infrastructure Leading to Diversity program at the University of Detroit Mercy, a CURE metagenomics course was established in the winter of 2019. Students investigated the bacterial community composition in a eutrophic cove in Lake Saint Clair (Harrison Township, MI, United States) from water samples taken in the summer and winter. The students created 16S rRNA libraries that were sequenced using next-generation sequencing technology. They used a public web-based supercomputing resource to process their raw sequencing data and web-based tools to perform advanced statistical analysis. The students discovered that the most common operational taxonomic unit, representing 31% of the prokaryotic sequences in both summer and winter samples, corresponded to an organism that belongs to a previously unidentified phylum. This result showed the students the power of metagenomics because the approach was able to detect unclassified organisms. Principal Coordinates Analysis of Bray–Curtis dissimilarity index data showed that the winter community was distinct from the summer community [Analysis of Similarities (ANOSIM) r = 0.59829, n = 18, and p < 0.001]. Dendrograms based on hierarchically clustered Pearson correlation coefficients of phyla were divided into a winter clade and a summer clade. The conclusion is that the winter bacterial population was fundamentally different from the summer population, even though the samples were taken from the same locations in a protected cove. Because of the small class sizes, qualitative as well as statistical methods were used to evaluate the course’s impact on student attitudes. Results from the Laboratory Course Assessment Survey showed that most of the respondents felt they were contributing to scientific knowledge and the course fostered student collaboration. The majority of respondents agreed or strongly agreed that the course incorporated iteration aspects of scientific investigations, such as repeating procedures to fix problems. In summary, the metagenomics CURE course was able to add to scientific knowledge and allowed students to participate in authentic research.
Highlights
For over a quarter of a century, reports from science, technology, engineering and mathematics (STEM) advisory organizations have been calling for reform of undergraduate STEM curricula to focus on developing analytical skills instead of memorizing content (Project Kaleidoscope, 1991; Howard Hughes Medical Institute, 1996; National Research Council, 1996, 2003; National Science Foundation, 1996; Bauerle et al, 2009)
Metanalysis studies of 16S rRNA gene sequences obtained from diverse lakes on different continents have shown that freshwater lakes have an assemblage of prokaryotes that are distinct from marine and terrestrial habitats (Zwart et al, 2002; Newton et al, 2011)
The students were successful in isolating high quality environmental DNA (eDNA) from bacteria sampled from the frozen cove
Summary
For over a quarter of a century, reports from science, technology, engineering and mathematics (STEM) advisory organizations have been calling for reform of undergraduate STEM curricula to focus on developing analytical skills instead of memorizing content (Project Kaleidoscope, 1991; Howard Hughes Medical Institute, 1996; National Research Council, 1996, 2003; National Science Foundation, 1996; Bauerle et al, 2009) These same reports have called for teaching innovations that will increase the participation of underrepresented minority students in STEM. A study of oligotrophic versus eutrophic lakes in Greece showed greater species diversity in the eutrophic samples (Karayanni et al, 2019) These results suggest that trophic status can alter the freshwater prokaryote diversity, but a general rule on the relationship between nutrient level and prokaryote community diversity has not been established
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