Wednesday, July 1, 2015

Microbes and Middle Schools

Fig.1. Students at Mills Park Middle School studying how dandelions recruit different microbial communities in various soil types (Credit: Laura Cochrane, Mills Park Middle School).

Editor’s Note: For our third installment in the International Year of Soils series, we spoke with Dr. Julia Stevens about her work with soil microbiology and connecting students to science. To learn more about her work with middle school students, click here.

For Julia Stevens, a challenging aspect of teaching microbiology to middle schoolers is the sheer scope of something so small.

“We’re talking about something that you can’t see, that the numbers are in the millions. The whole idea of both big and small is mind-boggling for people,” she said.

Stevens is a researcher at the North Carolina Museum of Natural Sciences whose work with host-microbe interactions requires students to get their hands a little dirty. She works with teachers to craft lesson plans for a citizen science project that asks students to study how different soils affect the growth of dandelions.

This project is an adaptation of her own research on how soil microbes affect - and are affected by - their host and the environment. The dandelion is an excellent research organism because it is so successful in good and bad soils, which means the microbes around their roots are extremely efficient in pulling in nutrients from nearby. This plant has the added benefit of being easily identifiable for her middle school groups, who send in samples of different soil types that had dandelions growing in them.

Stevens extracts DNA from each student's sample and barcodes specific sequences to create a picture of the microbial community. The overall shift in community composition from just soil to a full-grown dandelion shows how the plant recruits beneficial microbes from various soil types to aid its growth.

“Different types of soils host this different soil community of microorganisms. In each of these different soil types, you get different diversity of bacteria and fungi ... They’re not in completely different taxa, they’re just there in different abundances,” Stevens said.

Fig.2. Plate of microorganisms that were cultured from the soil (Credit: Julia Stevens).

Culturing the Unculturable

So why do soil microbes matter? Although microorganisms are often too small to be seen, they are vital in many natural processes, from fermentation to decomposition. A recent interest in microbial communities - along with improved techniques to study them on a genetic level - spurred research in how and why microbes do what they do. Stevens’ work with microbes that help invasive species grow is important to examine how these tiny organisms interact with their host and the soil around them. Unfortunately, there are some barriers to her research.

Even with the powers of modern genetic techniques, the ability to understand microbial function is limited. Genomes can be sequenced, but we can really only infer function when we recognize a gene. Additionally, the presence of a bacteria’s DNA in the soil does not mean that it is actively growing. That DNA may belong to microbes in cyst form, dormant, or even dead.

So Stevens looks to culturing bacteria in lab to see how they grow and what they need to grow. Even though only 1 percent of the entire bacterial community can be cultured, that small percentage can still inform how certain genes are characterized.

“Where are we seeing changes in community diversity and does that imply a change in function? Or is the function the same, it’s just a different actor in the role of a play,” Stevens said.

Fig.3. A teacher shows a recently picked dandelion from the citizen science project (Credit: Lea Shell, NCSU).

Reaching Students and Scientists

Ultimately the bacteria Stevens grows wind up in her culture collection of invasive species associated bacteria. This collection began during her dissertation on lionfish at the University of Alabama where she found a third of culturable bacteria on lionfish skin actually inhibited local fish pathogens. So far, Stevens has cultures from lionfish and dandelions, with plans to add microbial communities associated with an invasive planthopper species which recently appeared in Pennsylvania.

“It’s really creating the cultures and curating them and getting as much information as I can on them for my own research, but then also as a source for somebody who might be interested in another aspect of invasive species associated microbes,” Stevens said.

In addition to providing a resource for other researchers, this collection offers yet another way to engage students in science. Culture-based assays allow non-microbiologists, whether they are students or museum guests, to actually see the microbes active in soil. Stevens finds that once people go beyond their “microbes are gross” mindset, they can learn about how bacteria and fungi are essential to everyday processes.

“The big thing, working here at the museum, it’s not just outreach, but communicating science,” she said.

From citizen science to culture collections, Stevens hopes to connect people to the importance of soil microbiology, which is a hot topic for ongoing biomedical and agricultural research. The necessary lesson for both middle schoolers and scientists is that these tiny organisms have a big effect on the world around them.

Harris, J. (2009, July). Soil Microbial Communities and Restoration Ecology: Facilitators or Followers? Science, 31 (325): 573-574. doi: 101126/science.1172975

National Research Council (US) Committee on Metagenomics: Challenges and Functional Applications. (2007). The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet. Washington (DC): National Academies Press. Retrieved from


citizen science
Scientific research completed in large part through public participation, from data collection and analysis, to developing or testing technologies.
DNA barcoding
A technique used for characterizing species by sequencing just a short piece of DNA that acts as a genetic marker for that species. Different sequences are used for animals, plants, fungi, and bacteria.
A method used to multiply microorganisms by letting them grow and reproduce in or on a growth media which promotes the growth of only specific microbes.
culture collections
A repository of strains of microorganisms, which preserve microbial biodiversity and can provide material for research on particular strains.


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