Tiny Microbes Turn Out To Be Global Players

Holly Simon adjusts the bioreactor

11/09/07 Portland, Ore. 

In the rapidly evolving field of molecular biology, where computational techniques are enabling new discoveries almost daily, a few years can seem like an eternity. As recently as 1992, for example, Crenarchaeota were thought to be a relatively obscure group of microorganisms occupying highly specific ecological niches--extremely hot, highly sulfuric hot springs, for example, or undersea hydrothermal vents.

What a difference 15 years can make. Today, researchers like Dr. Holly Simon are making careers out of studying the critical roles played by some crenarchaeotes--since discovered to be the most abundant archaea in the ocean--in global biogeochemical cycles.

"Recent research suggests that the activities of non-thermophilic crenarchaeotes--those that live in moderate or cold temperatures--have a major impact on global carbon and nitrogen cycles," says Simon, Ph.D., an assistant professor in environmental and biomolecular systems at Oregon Health & Science University's School of Science & Engineering, "Fifteen years ago, scientists didn't have any idea of the role they played in either process."

For example, Simon points out, one strain of chrenarchaeotes oxidizes ammonia to provide energy for carbon fixation when oxygen is present. That reaction is the first step in the nitrification process--previously believed to be carried out exclusively by bacteria--which in turn is an important part of the nitrogen cycle.

Simon's enthusiasm for the tiny organisms--and her expertise in studying soil-based crenarchaeotes--goes a long way towards explaining her recently received five-year, nearly $800,000 grant from the National Science Foundation (NSF). Simon plans to study crenarchaeotes in riverine sediments, hypothesizing that they may possess other novel metabolic characteristics. As part of the project, Simon's lab will attempt to isolate and grow pure strains of crenarcheaotes from Columbia River sediments in a lab environment--a goal that so far has proved extremely difficult for scientists.

In fact, only one crenarchaeote--the marine-based Nitrosopumilus maritimus--has been successfully cultivated in the lab. Part of the difficulty, says Simon, is the time it takes for these crenarchaeotes to become enriched in laboratory culture: six months, in some cases, as opposed to the rapid overnight growth of well-studied bacteria like E. coli.

In addition, Simon notes that crenarchaeotes, when they oxidize ammonia, can become victims of their own success in metabolizing elements. In nature, they are part of complex microbial communities, with other organisms helping to metabolize toxic by-products--such as nitrite--that they produce. When crenarchaeotes are isolated from those communities in the laboratory, however, such toxic substances may accumulate to levels where they poison the crenarchaeotes themselves.

Simon's NSF proposal was based in part on her work growing soil Crenarchaeota in the lab. Although she has not yet isolated a particular strain, she has successfully used a semi-continuous batch system--in a device called a bioreactor--to grow microbial communities with clear genetic and structural evidence of Crenarchaeota. The NSF grant will allow Simon to apply similar techniques to growing microorganisms collected from riverine sedimentary core samples, with the goal of determining the composition and metabolic processes of those microbial communities and, she hopes, enabling isolation and cultivation of the crenarchaeotes.

Simon will be supported in her research by James Nurmi, staff scientist and Professor Paul Tratnyek, professor of environmental and biomolecular systems, who will use microelectrodes to examine the chemical properties of microbial microhabitats. Their focus is on understanding the environmental influences and constraints on the organisms and, secondarily, translating that understanding into successful laboratory-grown cultures.

The NSF CAREER award also provides support for Dr.Simon's educational aims, including development of a new graduate degree program and curriculum, guided experiences in genomics for undergraduate students, and mentoring of high school researchers. The undergraduate genomics program is being developed with the support of Associate Professor Jon Schnorr of Pacific University. In total, the project will support one Ph.D. student, up to ten undergraduate students, and as many as five high school students from the Portland-based Saturday Academy.

"NSF CAREER grants are highly sought-after awards," said Brad Tebo, Ph.D., head of the Department of Environmental and Biomolecular Systems, "and Dr. Simon's project exemplifies our department's commitment to bridging research and education. We're very excited to see our microbial program expanding in this way, especially as it complements other projects like those supported by the Center for Coastal Margin Observation & Prediction." CMOP--an NSF-supported Science & Technology Center based at the School of Science & Engineering--focuses on developing environmental observation techniques that span scales, from molecules to ecosystems.

The National Science Foundation's Faculty Early Career Development (CAREER) program was established in recognition of the critical roles played by faculty members in integrating research and education. It is the NSF's most prestigious award for junior faculty members, and is designed to provide support that will enable awardees to develop careers as outstanding teacher-scholars.