An Alternative Approach to "Identification of Unknowns": Designing a Protocol to Verify the Identities of Nitrogen Fixing Bacteria

Increasing student interest with the Bacterial Unknown Identification Project: using mixed cultures to create real-world applications

Many introductory-level classes teach fundamental concepts, as they are prerequisites for upper-division courses. Therefore, the student body in these classes has diverse interests. To address this breadth of career trajectory, introductory-level laboratory courses often include experiments that demonstrate a wide range of microbiological techniques and processes. One of the experiments that is a standard component of many microbiology classes, the Bacterial Unknown Identification Project (BUIP), is often limited to isolated organisms or a specific environment. Here, we describe an updated method for the BUIP that incorporates the projected student career diversity through the implementation of multiple mixed cultures of microorganisms associated with different environments. This update can be utilized in any microbiology laboratory classroom. We maintained the learning objectives, including applying appropriate microbiological methods to analyze and interpret results, and effectively communicate scientific findings, while modifying the sample composition. Assessment of the modification demonstrated that upon completion of the BUIP, students felt that the project applied to their career and it did not take too much of their free time to complete.

Bacterial Unknown Project in the COVID-19 Era: Transition from In-Person Lab Experience to Online Environment

The eruption of the COVID-19 pandemic forced many universities to quickly transition traditional in-person laboratory courses to an online format for remote learning. Consequently, learning objectives focused on hands-on laboratory skills shifted to ones that assess skills that could be recapitulated in the online format. We have transitioned a staple experiment in most undergraduate microbiology labs, the Bacterial Unknown Project, for online delivery using the university Learning Management System. We maintained the learning objectives suited for online delivery, such as creating an experimental design for identifying an unknown bacterium and communicating scientific results, while replacing or modifying those which could not be replicated, such as demonstration of sterile techniques, with learning objectives that highlighted skills of collaboration, peer evaluation, and scientific communication. Assessment of these new and modified learning objectives demonstrated positive student learning. Additionally, an anonymous postproject survey asked students whether they perceived the online Bacterial Unknown Project had increased their skill level in the areas highlighted by the revised learning objectives. Results reflected that 80% of the students reported the Unknown Project had increased their skills in all areas evaluated.

The Bean Beetle Microbiome Project: A Course-Based Undergraduate Research Experience in Microbiology

Course-based undergraduate research experiences (CUREs) are an effective means of transforming the learning and teaching of science by involving students in the scientific process. The potential importance of the microbiome in shaping both environmental health and disease makes investigations of microbiomes an excellent teaching tool for undergraduate microbiology. Here, we present a CURE based on the microbiome of the bean beetle (Callosobruchus maculatus), a model system for undergraduate laboratory education. Despite the extensive research literature on bean beetles, little is known about their microbiome, making them an ideal system for a discovery-based CURE. In the CURE, students acquire microbiological technical skills by characterizing both culturable and unculturable members of the beetle gut-microbial community. Students plate beetle gut homogenates on different media, describe the colonies that are formed to estimate taxonomic diversity, extract DNA from colonies of interest, PCR amplify the16S rRNA gene for Sanger sequencing, and use the NCBI-nBLAST database to taxonomically classify sequences. Additionally, students extract total DNA from beetle gut homogenates for high-throughput paired-end sequencing and perform bioinformatic and statistical analyses of bacterial communities using a combination of open-access data processing software. Each activity allows students to engage with studies of microbiomes in a real-world context, to apply concepts and laboratory techniques to investigate either student or faculty-driven research questions, and to gain valuable experiences working with large high-throughput datasets. The CURE is designed such that it can be implemented over either 6-weeks (half semester) or 12-weeks (full semester), allowing for flexibility within the curriculum. Furthermore, student-generated data from the CURE (including bacterial colony phenotypic data, full-length 16S rRNA gene sequences from cultured isolates, and bacterial community sequences from gut homogenates) has been compiled in a continuously curated open-access database on the Bean Beetle Microbiome Project website, facilitating the generation of broader research questions across laboratory classrooms.

Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support

Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines. This review will go through the trends and patterns in inquiry-based undergraduate life science projects with particular emphasis on molecular biosciences-the research-aligned disciplines of biochemistry, molecular cell biology, microbiology, and genomics and bioinformatics. This will provide instructors with an overview of the model organisms, laboratory techniques and research questions that are adaptable for semester-long projects, and serve as starting guidelines for course-based undergraduate research.

Isolation and Characterization of Agrobacterium Strains from Soil: A Laboratory Capstone Experience

In this investigation, the students' goal was to isolate and characterize Agrobacterium strains from soil. Following selection and enrichment on 1A-t medium, putative Agrobacterium isolates were characterized by Gram stain reaction and biochemical tests. Isolates were further evaluated using polymerase chain reaction (PCR) with different primer sets designed to amplify specific regions of bacterial deoxyribonucleic acid (DNA). Primer sets included AGRH to identify isolates that were members of the Rhizobiaceae, BIOVAR1 primers to identify members of Agrobacterium biovar group I, and a third set, VIRG, to determine presence of virG (only present in pathogenic Agrobacterium strains). During the investigation, students applied previously learned techniques including serial dilution, use of selective/differential media, staining protocols, biochemical analysis, molecular analysis via PCR, and electrophoresis. Students also gained practical experience using photo documentation to record data for an eventual mock journal publication of the capstone laboratory experience. Pre- and post-evaluation of class content knowledge related to the techniques, protocols, and learning objectives of these laboratories revealed significant learning gains in the content areas of Agrobacterium-plant interactions (p ≤ 0.001) and molecular biology (p ≤ 0.01). The capstone journal assignment served as the assessment tool to evaluate mastery and application of laboratory technique, the ability to accurately collect and evaluate data, and critical thinking skills associated with experimental troubleshooting and extrapolation. Analysis of journal reports following the capstone experience showed significant improvement in assignment scores (p ≤ 0.0001) and attainment of capstone experience learning outcomes.