A burgeoning world in a few grains of sand

Course on environmental-analysis techniques yields study co-authored by graduate students and undergrads

Diana Nemergut designed the course to teach technical skills in environmental microbiology. The course did much more; it also generated field research and a scholarly publication involving graduate students and even undergraduates.

Undergraduates do not typically co-author peer-reviewed journal articles, but those who do get turbocharged resumés.

Nemergut, associate professor of environmental studies at the University of Colorado Boulder, had designed a class to teach techniques useful in the job world, particularly at private environmental-consulting firms and for academic research labs.

In fall 2010, collecting and analyzing soil samples was one technique she began teaching. Shortly after the semester began, the Fourmile Fire erupted near Boulder. It burned for nearly two weeks, scorching 10 square miles and destroying 169 homes, making it the most expensive wildfire in Colorado to that date.

The fire disrupted both human and microbial life. Nemergut realized the catastrophic event created an opportunity to study how microbes in soil react to a fire. She and her students tested soils near the Wall Street Mill area in Fourmile Canyon.

“I thought this would be a great way to do experiments, to compare unburned soils and burned soils,” Nemergut said.

Graduate students sampled the burned soil areas four and weeks after the fire, and  undergraduates sampled the soil 16 weeks after. A team of researchers recorded the changing microbial diversity. The changes were initially guided by random forces but quickly became more influenced by selection. The surprising result: this happened within just 16 weeks.

Scott Ferrenberg, a doctoral candidate in ecology and environmental biology, was the only graduate student in Nemergut’s class, which presented its early results as a final exam that semester.

Nemergut asked Ferrenberg to continue working on the project and to serve as lead author on the peer-reviewed journal article that was then still taking shape. He and Nemergut collaborated with experts in microbes and fire disturbances from the Georgia Institute of Technology and the University of Montana.

Ultimately, the study drew in two other graduate students, Sean O’Neill and Joseph Knelman. It also included CU-Boulder faculty members Brett Melbourne, Alan Townsend, Steven Schmidt and Mark Williams.

What started primarily as a laboratory course intended to teach undergraduate and graduate students the newest techniques for studying microbial communities soon became a unique opportunity for students and faculty to collaborate on a novel, top-notch scientific study published this spring in the International Society of Microbial Ecology Journal, Ferrenberg said.

The journal consistently ranks among the top-ten ecological journals in the world.

Four then-undergraduate students are co-authors. They are 2011 alumnus Sam Duggan of molecular, cellular and developmental biology, 2011 alumnus Taylor Robinson of ecology and evolutionary biology, and 2012 alumni Bryan Todd and Daniel Bradley, both of ecology and evolutionary biology.

“In my career this far, I’ve never had an undergraduate co-author,” Nemergut said. That experience is especially valuable for students who want to pursue advanced degrees. In academe, Nemergut added, “papers (are) the currency.”

Duggan and Todd have since been accepted to graduate school.

People might not think of microbes as living in communities, but they do—in extraordinarily large numbers.

After the Fourmile Fire, just the few kilograms of soil the group collected from the forests near Boulder contained more than 4,000 unique species of bacteria, some of which were only found for brief periods after the fire.

That’s not quite the “world in a grain of sand” that the poet William Blake immortalized. But the sheer volume of microbial life in a little soil is staggering, Ferrenberg noted.

“The goal of understanding how organisms in these communities interact, and how natural communities come to be found together in the first place is a longstanding goal of biologists and the focus of the field known as ‘community ecology.’”

These questions have been pondered since Charles Darwin sailed on the HMS Beagle. “Despite this long history, ecologists still struggle to understand how communities assemble and how they respond to disturbances such as landslides or wildfires,” Ferrenberg stated.

But new knowledge and technology are rapidly broadening scientists’ understanding.

Such research is important, he said, because soil bacteria and fungi are “among the most important organisms on Earth.” Microbes in soil play enormous roles in nutrient cycles, plant growth and even atmospheric carbon dioxide levels. In fact, microbes play far-larger roles than the visible plants and animals typically thought of as dominating natural cycles.

While the presence and distribution of many plants and animals are clearly matched to the best habitat or “niche,” the research team found that soil microbial communities “reassemble” shortly after fire in a random manner, not in predictable patterns matched to the massive changes fire causes in the soil chemical environment, Ferrenberg said.

With time, however, the importance of the environment trumps the random nature of the community’s early start, and bacteria start to find their niches.

Nemergut compared microbial communities to human communities in the wake of a catastrophe such as hurricane Katrina. Right after Katrina, the population of New Orleans included a random mix of people who happened to be there and perhaps couldn’t get out.

Four months later, she said, the city was still reeling. But the types of people there were different and showed the role of selection. “You’d see construction people there, for instance. There’s a rationale with why certain people are there.”

Extending these microbial-diversity results beyond Boulder County’s soil might help scientists understand when to expect to see random communities versus niche-oriented communities, Ferrenberg said.

“This can have real implications for conservation and resource management where large amounts of money and time are spent trying to promote specific communities of organisms.”

The research was funded in part by a grant from the National Science Foundation.

Ferrenberg praised Nemergut for pursuing a novel research opportunity. “In my memory of being an undergrad in the ‘90s, this kind of thing wouldn’t have happened, where people would have thought of using a class to publish a paper.”

“I really applaud Diana for making it happen,” Ferrenberg said. “I think it’s a new model of education, and I’m just very appreciative to have been a part of it.”

Nemergut is pleased as well, partly because data from this study were used to write a grant proposal recently funded by the National Science Foundation. “That is something I didn’t predict.”