Microbiology Resource of the Month: Student-Discovered Microbial Consortia

Feb. 27, 2020

This month, ASM features 2 recent studies as its microbial resources of the month, each collected, processed and analyzed by a team of student researchers.

Discovering new members of the microbial world has become more affordable and accessible in past years, thanks in part to the decreased cost of nucleic acid sequencing. Students at all levels can discover, culture, and sequence microbes from all environments and contribute to our understanding of microbial diversity.
Announcement: Draft Genome Sequences of 16 Halophilic Prokaryotes Isolated from Diverse Environments
Resource: Genomes of 16 salt-tolerant strains of bacteria and archaea
Robert Furrow and his colleagues at University of California, Davis, and University of Puerto Rico, Mayagüez, led a student-centered research project to uncover the microorganisms living in the salt flats of Cabo Rojo, Puerto Rico. Furrow and the team describe their research question and experiences with the project.

Announcement: Isolation and Whole-Genome Sequencing of 12 Mushroom-Associated Bacterial Strains: an Inquiry-Based Laboratory Exercise in a Genomics Course at the Rochester Institute of Technology
Resource: Genome sequences of 12 mushroom-associated bacterial strains
André Hudson and his colleagues at Rochester Institute of Technology led a student-centered research project to uncover the bacteria associated with mushrooms. Hudson describes the research question and student response to the project.
Hudson and Furrow (and Furrow’s team) offer insights into their research question and the processes they used to answer it.

What Was the Goal of Your Research Project?

Hudson (instructor, mushroom project): The overarching goal of the project was to provide undergraduate students with an inquiry-based laboratory exercise that was collaborative and fun. One of the goals was to emphasize communication and dissemination in the course.  My motto is, “it is not science until it is communicated,” and I thought it was imperative to take the students on a journey from conception to publication.
Alex Nord (co-instructor, salt flat project): The goal of this project was to give UC Davis undergraduate students the opportunity to do real research in a classroom setting. There is a growing belief that science education can have a much higher impact when students are exposed to research earlier in their academic careers. To be most effective, the research experience should be student-driven and have real-life impact.
With the cost of sequencing a microbial genome less than the cost of most genetics textbooks, we saw an opportunity to combine teaching principles of quantitative biology and genetics with giving the students the chance to do something new and contribute to the field of microbiology and microbial genetics. This project is the result of a team of undergraduates who put two quarters into culturing and analyzing the microbes.
I don't think it is a stretch to say that this experience was transformative, both for the students and for us as instructors. Reading the student names on the author list and knowing that each contributed to this team effort is one of my proudest moments of teaching.

One of the University of California Davis class cohorts who worked on the salt flat microbe project.
One of the University of California Davis class cohorts who worked on the salt flat microbe project.
Source: Photo courtesy R. Furrow

Matthew Kenaston (student, salt flat project): From an undergraduate perspective, I think there were 2 important benchmarks for whether the project would be successful. One, could we identify a diverse set of halophiles from diverse communities that could offer interesting ecological conclusions? Two, could you get a group of undergraduates to actually accomplish that? Luckily, the answer to both these questions was yes.

How Will These Genomes Be a Resource for Future Studies?

Hudson (instructor, mushroom project): I think there are many potential benefits to the scientific community and future studies. For example, mushroom/fungi are known to produce secondary metabolites that inhibit bacterial growth. The question of whether the isolated bacteria are endowed with the enzymatic machinery to degrade and or circumvent inhibitory compounds is very interesting.
In addition, one of the topics we discussed in the course pertains to how to be a good citizen as it relates to the science profession. We are willing to share the strains with anyone in the scientific community to facilitate future studies.
Students working on the mushroom-associated microbial project at Rochester Institute of Technology.
Students working on the mushroom-associated microbial project at Rochester Institute of Technology.
Source: Photo courtesy of A. Hudson

Hyunsoo Kim (graduate student TA, salt flat project): Generally speaking, halophiles are an interesting group of organisms to study because
  1. They are capable of survival and growth in a broad range of (often extreme) environmental conditions.
  2. Their distribution throughout the world is widespread and accessible.
  3. They have interesting and unique biochemistry.

For these organisms to survive in fluctuating and extreme conditions such as high salinity and solar radiation, as well as low water and nutrient availability, halophiles have evolved various cellular adaptations, some of which yield industrially relevant products. We believe that the availability of these halophilic genomes will allow the scientific community to better characterize life and halophilic mechanisms of survival in extreme environments, and will be a valuable contribution to systems biology, biotechnology, and evolutionary biology research.

What Was the Most Surprising Discovery?

Andre Hudson (instructor, mushroom project): I think the most surprising discovery was the number of uncultured Enterobacteriaceae species that were isolated (7 out of 12).

Rob Furrow (co-instructor, salt flat project): From an educational perspective, the biggest surprise was how naturally a smooth, collaborative workflow arose during the project. At the outset, research collaborators at the University of Puerto Rico collected samples. Then, UC Davis students took charge of culturing and isolating individual microbial strains as part of their coursework. After the first class sent off the purified DNA for sequencing, another class (with some overlap in students) took charge of performing genome assembly quality control and comparative genomic analyses.

In terms of biology, we were surprised to discover the broad diversity of microbes isolated from certain substrates. Student work also identified possible areas for revision in the phylogeny of the family Bacillaceae, which might provide insight into the evolution of halophilic adaptations in this family.

What Was the Student Reaction to Project Participation?

Andre Hudson (instructor, mushroom project): The students were really excited because they were involved in all aspect of the project from conception to publication. For many students, this was their first publication so they were really proud and happy.

Students at Rochester Institute of Technology working on the mushroom-associated microbe project.
Students at Rochester Institute of Technology working on the mushroom-associated microbe project.
Source: Photo courtesy of A. Hudson

Matt Kenaston (student, salt flat project): This project drew upon a diverse set of students from differing academic backgrounds. It proves to educators and students alike that, surprisingly, courses don’t have to start with knowing the outcome. Translating the unknown into the known is far more rewarding than I think most give it credit for.

Rob Furrow (co-instructor, salt flat project): This project was explicitly designed to draw students into a genuine process of exploration and discovery during a course-based research experience. It was thrilling to watch the students develop their abilities and draw new insights, and many are now pursuing additional research opportunities.

At the project’s conclusion students also specifically mentioned the value of using hands-on research as the framework for learning skills like programming and mathematical modeling; these skills can be intimidating for biology undergraduates in a traditional course setting.


Author: Julie Wolf, Ph.D.

Julie Wolf, Ph.D.
Dr. Julie Wolf is in science communications at Indie Bio, and is a former ASM employee.