Expanding Tiny Earth to genomics: a bioinformatics approach for an undergraduate class to characterize antagonistic strains

Optimization of Screening Media to Improve Antimicrobial Biodiscovery from Soils in Undergraduate/Citizen Science Research-Engaged Initiatives

Background/Objectives: Research-engaged academic institutions offer the opportunity to couple undergraduate education/citizen science projects with antimicrobial biodiscovery research. Several initiatives reflecting this ethos have been reported internationally (e.g., Small World, Tiny Earth, MicroMundo, Antibiotics Unearthed). These programs target soil habitats due to their high microbial diversity and promote initial screening with non-selective, nutrient media such as tryptic soy agar (TSA). However, evaluation of published outputs to date indicates that isolate recovery on TSA is consistently dominated by the genera Bacillus, Pseudomonas, and Paenibacillus. In this study, we evaluated the potential of soil extract agar to enhance soil isolate diversity and antibiosis induction outcomes in our undergraduate Antibiotics Unearthed research program. Methods: We comparatively screened 229 isolates from woodland and garden soil samples on both tryptic soy agar (TSA) and soil extract agar (SEA) for antimicrobial activity against a panel of clinically relevant microbial pathogens. Results: On one or both media, 15 isolates were found to produce zones of clearing against respective pathogens. 16S rRNA gene sequencing linked the isolates with three genera: Streptomyces (7), Paenibacillus (6), and Pseudomonas (2). Six of the Streptomyces isolates and one Pseudomonas demonstrated antimicrobial activity when screened on SEA, with no activity on TSA. Furthermore, incorporation of the known secondary metabolite inducer N acetyl-glucosamine (20 mM) into SEA media altered the pathogen inhibition profiles of 14 isolates and resulted in broad-spectrum activity of one Streptomyces isolate, not observed on SEA alone. In conclusion, SEA was found to expand the diversity of culturable isolates from soil and specifically enhanced the recovery of members of the genus Streptomyces. SEA was also found to be a superior media for antibiosis induction among Streptomyces isolates when compared to TSA. It was noted that Paenibacillus isolates' antibiosis induction demonstrated a strain-specific response with respect to the growth media used. Conclusions: The authors propose SEA inclusion of in soil screening protocols as a cost-effective, complementary strategy to greatly enhance outcomes in undergraduate/citizen science-engaged antimicrobial biodiscovery initiatives.

Draft Genome Sequences of Three Antibiotic-Producing Soil Bacteria, Staphylococcus pasteuri WAM01, Peribacillus butanolivorans WAM04, and Micrococcus yunnanensis WAM06, with Growth-Inhibiting Effects against Commensal Neisseria Strains

We report the isolation, identification, and assemblies of three antibiotic-producing soil bacteria ( Staphylococcus pasteuri , Peribacillus butanolivorans , and Micrococcus yunnanensis ) that inhibit the growth of Neisseria commensals in coculture. With pathogenic Neisseria strains becoming increasingly resistant to antibiotics, bioprospecting for novel antimicrobials using commensal relatives may facilitate discovery of clinically useful drugs.

Modeling-Guided Amendments Lead to Enhanced Biodegradation in Soil

Extensive use of agrochemicals is emerging as a serious environmental issue coming at the cost of the pollution of soil and water resources. Bioremediation techniques such as biostimulation are promising strategies used to remove pollutants from agricultural soils by supporting the indigenous microbial degraders. Though considered cost-effective and eco-friendly, the success rate of these strategies typically varies, and consequently, they are rarely integrated into commercial agricultural practices. In the current study, we applied metabolic-based community-modeling approaches for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Efficacy of biostimulants as enhancers of the indigenous degrader Paenarthrobacter was ranked through simulation and validated in pot experiments. A two-dimensional simulation matrix predicting the effect of different biostimulants on additional potential indigenous degraders (Pseudomonas, Clostridium, and Geobacter) was crossed with experimental observations. The overall ability of the models to predict the compounds that act as taxa-selective stimulants indicates that computational algorithms can guide the manipulation of the soil microbiome in situ and provides an additional step toward the educated design of biostimulation strategies. IMPORTANCE Providing the food requirements of a growing population comes at the cost of intensive use of agrochemicals, including pesticides. Native microbial soil communities are considered key players in the degradation of such exogenous substances. Manipulating microbial activity toward an optimized outcome in efficient biodegradation processes conveys a promise of maintaining intensive yet sustainable agriculture. Efficient strategies for harnessing the native microbiome require the development of approaches for processing big genomic data. Here, we pursued metabolic modeling for promoting realistic in terra solutions by simulation-based prioritization of alternative supplements as potential biostimulants, considering a collection of indigenous bacteria. Our genomic-based predictions point at strategies for optimizing biodegradation by the native community. Developing a systematic, data-guided understanding of metabolite-driven targeted enhancement of selected microorganisms lays the foundation for the design of ecologically sound methods for optimizing microbiome functioning.

Characterizing Staphylococcus aureus from Healthy Individuals: an Authentic Research Experience for Undergraduates

This article describes the implementation of the Staph Study, a sustainable, ongoing, scalable research study conducted with undergraduate students. The study characterizes Staphylococcus aureus specimens collected from the anterior nares of healthy members of our campus community. The ease with which we have been able to involve many students in the project has resulted in a significant increase in the research opportunities for undergraduates in our Science Department.

Connected while distant: Networking CUREs across classrooms to create community and empower students

Connections, collaborations, and community are key to the success of individual scientists as well as transformative scientific advances. Intentionally building these components into STEM education can better prepare future generations of researchers. Course-based undergraduate research experiences (CUREs) are a new and fast-growing teaching practice in STEM that can expand opportunities for undergraduate students to gain research skills. Because they engage all students in a course in an authentic research experience focused on a relevant scientific problem, CUREs provide an opportunity to foster community among students while promoting critical thinking skills and positively influencing their identities as scientists. Here, we review CUREs in the biological sciences that were developed as multi-institutional networks, and highlight the benefits gained by both students and instructors through participation in a CURE network. Throughout, we introduce Squirrel-Net, a network of ecology-focused and field-based CUREs that intentionally create connections among students and instructors. Squirrel-Net CUREs can also be scaffolded into the curriculum to form connections between courses, and are easily transitioned to distance-based delivery. Future assessments of networked CUREs like Squirrel-Net will help elucidate how CURE networks create community and how a cultivated research community impacts students' performance, perceptions of science, and sense of belonging. We hypothesize networked CUREs have the potential to create a broader sense of belonging among students and instructors alike, which could result in better science and more confident scientists.

Bridging Trade-Offs between Traditional and Course-Based Undergraduate Research Experiences by Building Student Communication Skills, Identity, and Interest

Undergraduate research plays an important role in the development of science students. The two most common forms of undergraduate research are those in traditional settings (such as internships and research-for-credit in academic research labs) and course-based undergraduate research experiences (CUREs). Both of these settings offer many benefits to students, yet they have unique strengths and weaknesses that lead to trade-offs. Traditional undergraduate research experiences (UREs) offer the benefits of personalized mentorship and experience in a professional setting, which help build students' professional communication skills, interest, and scientific identity. However, UREs can reach only a limited number of students. On the other end of the trade-off, CUREs offer research authenticity in a many-to-one classroom research environment that reaches more students. CUREs provide real research experience in a collaborative context, but CUREs are not yet necessarily equipping students with all of the experiences needed to transition into a research lab environment outside the classroom. We propose that CURE instructors can bridge trade-offs between UREs and CUREs by deliberately including learning goals and activities in CUREs that recreate the benefits of UREs, specifically in the areas of professional communication, scientific identify, and student interest. To help instructors implement this approach, we provide experience- and evidence-based guidance for student-centered, collaborative learning opportunities.

Real-World Ethical Dilemmas in Laboratory Safety for Microbiology Under-Resourced and Outreach Teaching

With modernization of safety standards for microbiology outreach teaching laboratories, ethical challenges arise in teaching microbiology for the public good without short-changing students in under-resourced situations, or when institutional support is subpar. Still, educators want students to engage using applied skills for inquiry, research-based microbial learning activities – safely. Following several United States microbial outbreaks, federal investigation traced sources back to teaching laboratories. Policy discussions ensued. The American Society for Microbiology (ASM) Task Force provides recommended but not mandated guidelines; however, guidelines are not amenable by all. Here, a real-world, ethical scenario of a university-level outreach microbiology laboratory course hosted at several locations provides context for under-resourced challenges in safety compliance. In this example of biomedical and public health ethical considerations, upper administration puts the onus on instructors to assure safe labs for their students and the general public. Temporarily hired instructors without curriculum or sufficient institutional support are put in precarious positions with often egregious practices to get the job done. This scenario is examined with different public health ethical frameworks and principles: non-maleficence, beneficence, health maximization, efficiency of policy regulations, respect for institutional and instructor autonomy, justice, and proportionality balancing stakeholder concerns. Sample curricular strategies are employed to mitigate these challenges. Taking a utilitarianism framework of the greatest good for the most benefit, this paper advocates for social justice supporting access to education as a moral duty. Administrations should ensure instructors are supported sufficiently to provide safe, authentic learning experiences. Solutions for under-resourced outreach teaching are needed for public trust.

MicroMundo@UPorto: an experimental microbiology project fostering student's antimicrobial resistance awareness and personal and social development

Antimicrobial resistance (AMR) is a global societal challenge requiring the contribution of professionals along with general community citizens for their containment. Portugal is one of the European countries where a lack of knowledge on the correct use of antimicrobials and AMR problematic is preeminent. Moreover, youth demotivation to pursue science careers is emerging. To address these problems an innovative experimental service-learning pedagogical strategy, MicroMundo@UPorto, was implemented in Portugal during 2018 through University of Porto as a partner of the global Citizen Science project 'Tiny Earth' responding to the AMR crisis. In this first edition of MicroMundo@UPorto, university students (n = 41; Pharmaceutical Sciences and Nutrition Sciences) organized in eight teams tutored by university professors/researchers (n = 13) on Microbiology and AMR theoretical and practical aspects as well on communication skills to enable their guidance of younger school students (n = 140/3 schools) in experiments to discover antimicrobial-producing microorganisms while exploring the soil microbial diversity. Post-survey-based evaluation revealed that this project allowed university students to acquire diverse personal, social and scientific skills while increasing AMR awareness, in the One-Health perspective, and interest for science in school students. This University to Society approach can be successfully extended across Portugal and for education in Microbiology in general, with benefits for the future generations contributing to socially responsible and scientifically-literate citizens.

Is Community Relevance Enough? Civic and Science Identity Impact of Microbiology CUREs Focused on Community Environmental Justice

Course-based undergraduate research experiences (CUREs) often involve a component where the outcomes of student research are broadly relevant to outside stakeholders. We wanted to see if building courses around an environmental justice issue relevant to the local community would impact students' sense of civic engagement and appreciation of the relevance of scientific research to the community. In this quasi-experimental study, we assessed civic engagement and scientific identity gains (N = 98) using pre- and post-semester surveys and open-ended interview responses in three different CUREs taught simultaneously at three different universities. All three CURES were focused on an environmental heavy metal pollution issue predominantly affecting African-Americans in Birmingham, Alabama. While we found increases in students' sense of science efficacy and identity, our team was unable to detect meaningful changes in civic engagement levels, all of which were initially quite high. However, interviews suggested that students were motivated to do well in their research because the project was of interest to outside stakeholders. Our observations suggest that rather than directly influencing students' civic engagement, the "broadly relevant" component of our CUREs engaged their pre-existing high levels of engagement to increase their engagement with the material, possibly influencing gains in science efficacy and science identity. Our observations are consistent with broader community relevance being an important component of CURE success, but do not support our initial hypothesis that CURE participation would influence students' attitudes toward the civic importance of science.

Bringing Real-World Microbiology Experiences to Undergraduate Students in Resource-Limited Environments

Undergraduate microbiology curriculum should be amenable to periodic changes to incorporate new developments and ideas. The curriculum should be used not merely as a way to disseminate facts but also as a way to allow students to experience the process of science. In the context of undergraduate microbiology education in Osmania University (Hyderabad, India), existing curriculum does not explicitly allow students to engage in deeper understanding of concepts and understanding of the process of science, both in lecture and laboratory courses. The assessment methods that are currently used are limited in scope as they only test factual recall and superficial understanding of the subject and very minimally assess critical thinking skills. Another factor hampering innovation in the broader context of undergraduate education is the unavailability and inaccessibility to adequate resources. To address the issue of resource-limitations in implementing activities that expose undergraduate students to real-world microbiology experiences, a collaboration between a research institute and two teaching colleges was formed. This collaboration involved teacher and student workshops on exploring microbial diversity using 16S rRNA analysis with a view of blending novel research questions with technical skills in the undergraduate microbiology lab. This effort is an example of educators providing students with authentic experiences and, helping them gain critical knowledge and research skills in microbiology even under resource constraints, and students demonstrating motivation to participate in similar activities in the future. The collaborative effort described here can be a broadly sustainable model to improve overall undergraduate education in relatively resource-limited environments.

Microbiomes for All

Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.