Montana State University

MSU microbiologist earns doctorate studying microbes of Yellowstone and Hanford, Wash.

May 3, 2013 -- By Sepp Jannotta, MSU News Service

Microbiology doctoral student Kara De Leon, who graduates from Montana State University on Saturday, prepares a soil sample for transport in the laboratory of associate professor Matthew Fields. (MSU photo by Kelly Gorham).   High-Res Available

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BOZEMAN - In the hotpots of Yellowstone and the radioactive ground at the Hanford Nuclear Reservation, Kara De León's graduate work at Montana State University has put her on the front lines of a push to understand and harness the microorganisms known to researchers as biofilm.

The Nampa, Idaho, native looked to chart and correlate the interactions within biofilm communities in alkaline springs in Yellowstone National Park. She also focused on sequencing the chromium-loving bacteria the U.S. Department of Energy is hoping will ultimately protect the Columbia River and groundwater at Hanford, Wash.

De León, who graduates from MSU on Saturday, conducted the research for her doctoral dissertation through the lab of Matthew Fields at the Center for Biofilm Engineering. De León said she also developed skills in writing the computer code to support processing the data she collected.

"I think MSU is set up with the technology and professors to offer grad students a very competitive program, especially in biofilm," De León said. "This experience has given me the hard skills to do genetic sequencing (on microorganisms), as well as to write the (software) script that is essential to being able to manage the amount of data we can collect."

In addition, De León said her association with the CBE offered her an opportunity to teach a course in microbiology for non-majors, while working with a faculty mentor in shaping the course syllabus and exams. It also connected her with projects that are being carried out in collaboration with industry partners or, in the case of Hanford, the Department of Energy.

When she entered MSU as a graduate student through the Molecular Biosciences Program - an interdisciplinary platform for graduate study in basic and applied research - De León said she was not entirely certain which direction her career would take.

It took a bit of an introduction for her to know that she was fascinated by the ecology of microbial life.

"What I knew coming in was that I was blown away by the program," she said. "I'd never really thought of ecology on such a fine scale. As it turns out, that is where a lot of really interesting interactions are going on. And there are things that are happening that haven't been looked at before."

The timing for launching a doctoral inquiry into microbial ecology was good, De León said. MSU had just obtained the laboratory equipment needed to perform high-throughput genetic sequencing, a practice known as pyrosequencing.

The process being used at CBE now allows researchers to gather data on up to 200,000 unique DNA sequences in a sample, where prior methods and technology had enabled them to generate 1,000 sequences.

Along with other researchers in Fields' lab, De León traveled to Heart Lake in Yellowstone's backcountry to collect algae samples from the hot springs there. With a focus on some springs that were highly alkaline, the group hoped to promote research on so-called extremophile organisms that hold promise for, among other things, developing biofuels and remediating environmental disasters.

It was an assignment exotic enough given the area's remote location, which is notorious habitat for grizzly bears, but the uniqueness of the organisms they hoped to catalogue put it off the chart for pure research, De León said.

"If you're interested in things that haven't really been looked at before, this is an excellent place to go," she said.

Although the genetic sequencing and data processing was much the same, the work at Hanford addressed a more practical need - the mitigation of chromium contamination by stimulating groundwater and sediment microbes that "feed" on the heavy metal and reduce its ability to travel with the groundwater.

Through the DOE and a Lawrence Berkeley National Laboratory-based program called ENIGMA - Ecosystems and Networks Integrated with Genes and Molecular Assemblies - De León and other MSU scientists have been assisting an effort to use the microbes to keep groundwater laden with chromium from migrating into the Columbia River.

Along with others in Fields' lab, De León has been taking samples from test wells at Hanford and looking at changes that occur in biofilm and planktonic microorganisms after they are stimulated with carbon and other nutrients.

De León said her research findings show that the nutrients can help stimulate the chromium-loving microbes, which could have implications for how DOE's expensive mitigation program progresses at Hanford.

Fields said De León had made significant contributions to MSU's work for the ENIGMA program and toward the science of using biofilm for environmental cleanup.

"It is important because the better you understand something, the better you can control it," Fields said. "And it's exciting because as we start to understand what these microorganisms are doing when we stimulate them, then we'll be able understand how to apply the technology to other places with this kind of environmental contamination."

Fields said MSU has remained highly competitive as a research university because faculty have invested in equipment to allow for the high-throughput genetic sequencing that is propelling so much promising science.

"I think MSU is doing a good job with the multiple faculty members who are bringing genomics into their area of environmental inquiry," he said. "And Kara is a great example of the kind of scientist this university can turn out as a result."

De León is one of a cohort of seven CBE scientists who will graduate this spring from MSU with doctorates in microbiology or chemical and biochemical engineering. CBE is also graduating three students who have completed master's degrees and 10 with bachelor's degrees.

De León, who is still weighing her options for a post-doctoral placement, said she hopes to continue to advance the science of microbial ecology through academic research and teaching.

Phil Stewart, CBE director, said De León and CBE's other graduates have done a lot to help the institute advance the science of biofilm at MSU.

"I am amazed by the technical talent, initiative, teamwork and change-the-world outlook of this group of students," Stewart said. "They are going to make us proud."

Contact: Sepp Jannotta, (406) 994-7371 or