The Art of Microbiology: an Agar Art Microbiology Lab CURE

Jeffrey Morris, University of Alabama at Birmingham
Sarah Adkins, saadkins@uab.edu, University of Alabama at Birmingham
Location: Alabama

Abstract

Students use agar art made with freshly isolated microbes as a source for developing their own novel research projects.

Student Goals

  1. Collaborate with teammates in using information from interdisciplinary sources to generate and test novel hypothesis.
  2. Collaboratively design and conduct experiments using appropriate measures and analyze and interpret data in order to support, refute, or refine hypotheses.
  3. Present conclusions of research orally and in writing.

Research Goals

  1. Discover novel microbial interactions in a variety of natural environments.
  2. Generate preliminary data for new microbial ecology research directions.

Context

This course was modified from an existing traditional cook-book microbiology class for undergraduate science majors, comprised primarily of upper-class students. Our students are required to have taken and passed Introductory Biology I, Introductory Biology II, and Genetics. The introductory sequences are survey courses which cover evolution, cell biology, molecular biology, plant biology, and physiology. At our institution, this 200-level semester-long introductory microbiology course has a required lecture component and lab which comprise 67% and 33% of a student's total grade, respectively. The microbiology lecture can seat 50 students, with up to 20 students in an accompanying lab section. The course is taught in a fourteen week semester where students meet in lab for about two hours twice a week.

Target Audience:Major
CURE Duration:A full term

CURE Design

The laboratory section of the course has students work in teams of 2-3 to develop and execute a novel research project based on observations of bacterial interactions in student made agar artwork. The main goal of our curriculum is for students to discover unexpected microbial interactions and behaviors that can lead to further experimentation. The curricular design is as follows:

1. Students isolate bacteria from a natural ecosystem (e.g. soil, seawater) into pure culture.
2. Students "pick their pallet" – i.e. they choose bacteria to paint with based on the aesthetic qualities of the microbes on agar plates.
3. Students use the pallet to create agar art based on a personalized design drawn on circular paper templates
4. Students analyze and observe agar art as it grows and changes over several weeks.
5. Meanwhile, students perform other experiments with their pallet, including biochemical tests (e.g. oxidase, catalase, catabolic range), environmental tolerances (e.g. pH, salt, temperature, UV), and 16S rRNA gene sequencing, gaining a broad understanding of the isolates' distinctive characteristics.
6. Students create testable microbial ecology hypotheses and propose methods and experiments based on petri dish art plate observations as well as the organisms' other characteristics.
7. Students execute their proposed experiments.
8. Students form conclusions and propose directions for further study, give short team-drawn poster presentations explaining their work and write a professional-style paper about their work.

The fundamental microbiology laboratory procedures in step 5 develop student skills and, along with instructor guidance, prepare students to form and execute their novel experimental designs. Student teams close the semester executing unique projects, each of which has different demands.

Teams have to read papers related to their chosen project, perform lab procedures appropriate to their experiment design, and learn the proper statistical methods to analyze their data. Importantly, each team will have quite different experiences, and the poster session at the end of the class gives them an opportunity to interact with many different kinds of experimental design, as well as to see that some hypotheses are supported and some are refuted, giving them a direct experience of the scientific method in action.

Using agar art as a platform for hypothesis creation has led to several student teams in our CURE studying the environmental cues regulating pigment expression in microbes as well as exploring a number of puzzling microbe-microbe interactions.

To some degree, this CURE represents the "fishing expedition" or exploratory style of research, which is generally a fatal flaw in a grant application to hypothesis-focused funding agencies like NSF. However, we believe that the study of microbe-microbe interactions is sufficiently underexplored that there are likely many unknown and interesting research directions students might stumble upon.

As an example of the promise of this CURE, one of our student teams discovered substantial variation in levels of cephalothin resistance amongst Bacillus isolates taken from soils on our campus, which might suggest a process of ongoing antibiotic resistance evolution. While brainstorming with these students, the possibility was raised that UAB's proximity to many hospitals might make the nearby area a "breeding ground" for resistance, and the hypothesis was suggested that one might see increasing levels of resistance as one got closer to the hospitals. The next semester, students followed up on that hypothesis by studying soil microbes collected along a transect radiating out from the hospitals in our city, to test the hypothesis that proximity to the hospitals correlates with the level of resistance in non-hospital associated, environmental bacteria. If born out, this would be an important and publishable finding, ultimately discovered because students became interested in understanding patterns of antibiotic production and resistance observed in their agar artworks. While this particular research direction is fairly specific to our urban medical campus, we expect that others who use this CURE will find their students pursue different but no less significant directions.

Core Competencies: Analyzing and interpreting data, Asking questions (for science) and defining problems (for engineering), Constructing explanations (for science) and designing solutions (for engineering), Planning and carrying out investigations, Using mathematics and computational thinking
Nature of Research:Informatics/Computational Research, Wet Lab/Bench Research

Tasks that Align Student and Research Goals

Research Goals →
Student Goals ↓
Research Goal 1: Discover novel microbial interactions in a variety of natural environments.
Research Goal 2: Generate preliminary data for new microbial ecology research directions.


Student Goal 1: Collaborate with teammates in using information from interdisciplinary sources to generate and test novel hypothesis.

Students isolate environment organisms and use the organisms to create unexpected interactions through agar art. Observations made from agar art form their hypothesis.

Students submit their hypothesis and artworks to be archived for future use and cryo-preserve their organisms.



Student Goal 2: Collaboratively design and conduct experiments using appropriate measures and analyze and interpret data in order to support, refute, or refine hypotheses.

Students design and conduct novel experiments to test their hypothesis using literature and basic statistics.

Student data and analysis are archived in spreadsheet format for future use.



Student Goal 3: Present conclusions of research orally and in writing.

Students explain their research in a professional style publication and in common language through hand-drawn poster.

Students write an informative abstract that is easily searchable including key meta-data about their study.


Instructional Materials

Instructional facilities should be compliant with BSL 2 requirements, which primarily differ from BSL 1 requirements in that equipment is designed to avoid aerosolization of cultures (e.g., during centrifugation and vortexing). Students should wear lab coats, glasses, and gloves at all times, and care should be taken not to contaminate items that will leave the teaching laboratory. This curriculum can be used with standard microbiology teaching laboratory access and supplies. In our course, students use PCR to amplify the 16S rRNA gene of their isolates, which requires purchase of primers, Taq polymerase (we use Promega GoTaq, which comes pre-packaged with loading buffer), and PCR purification kits, as well as access to a thermal cycler, gel electrophoresis equipment, and a mini-centrifuge. Additional equipment includes access to a DNA sequencing facility and online genomic analysis tools, and access to a spectrophotometer. At our institution, students pay a lab fee of $250.00 when they enroll in this course. A lab manual and notebook is provided to them.

Lab manual (Acrobat (PDF) 13MB Dec7 18)
Course syllabus (Microsoft Word 2007 (.docx) 128kB Dec7 18)

Assessment

Lab Manual Rubrics (Microsoft Word 2007 (.docx) 158kB Dec7 18)
Presentation Rubrics (Microsoft Word 2007 (.docx) 120kB Dec7 18)

Instructional Staffing

At our institution, the preparation for the CURE makes use of a full-time coordinator and/or graduate student lab assistant. They are tasked with preparing media, solutions, and maintaining equipment. When students create their own experiments, they turn in their media and equipment list to the instructor and the lab assistant fulfills the order so long as the request is reasonable. The lab instructor is ideally the professor or teacher interested in following the CURE protocol. Any graduate teaching assistants who replace the role of the professor should have close communication with the implementing professor.

Author Experience

Jeffrey Morris, University of Alabama at Birmingham

The American Society for Microbiology's agar art contest has proven to be very popular on the Internet. The creative output of the artists and scientists who contribute to the contest range from beautiful to profound to surreal. However, agar art can be used not only for aesthetic enjoyment, but also as an activity to create a living ecosystem that demonstrates microbial ecology in action. This CURE, in the spirit of the pioneer of the agar art, Alexander Fleming, invites students to not only become artists, but also to use their agar art to discover new facts about our microbial world.


Read full Instructor Story »

Advice for Implementation

One key issue to consider prior to using this CURE is that microbes isolated from the environment are considered BIOSAFETY LEVEL 2 opportunistic pathogens until shown to be otherwise. The American Society for Microbiology has provided a useful guideline for biosafety in BSL 2 teaching labs here: https://www.asm.org/index.php/education-2/22-education/8308-new-version-available-for-comment-guidelines-for-best-biosafety-practices-in-teaching-laboratories

Iteration

***********
Hypothesis creation and experimental design takes place gradually over the first ~2/3 of the course, with students refining their ideas as their understanding of the subject matter improves. Once the students begin their team-designed experiments, troubleshooting is common, and student teams often come up with innovative fixes for problems they run into. In fact, extra time is built into the time table for the course. Students are allowed into the lab any time so long as they sign-in with their teacher. Many students take advantage of these opportunities.

Using CURE Data

***********
Students are encouraged to present their results as a poster at the UAB Undergraduate Research Expo. Some students also request to continue working on their projects after the semester ends, and so far we have been able to accommodate all of these requests. Any student who contributes to a project that results in a publication will be offered the opportunity to be a co-author.

Resources

***********
For Faculty:
Adkins SJ, Rock RK, Morris JJ. Interdisciplinary STEM education reform: dishing out art in a microbiology laboratory. FEMS microbiology letters. 2017 Nov 15;365(1):fnx245.

Charkoudian LK, Fitzgerald JT, Khosla C, Champlin A. In living color: bacterial pigments as an untapped resource in the classroom and beyond. PLoS biology. 2010 Oct 5;8(10):e1000510




Comment? Start the discussion about The Art of Microbiology: an Agar Art Microbiology Lab CURE