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Deep, dark secrets: Research goes underground

June 08, 2010

This is spelunking with a twist. This is academic spelunking that is uncovering answers to questions. It is cave exploration that is helping sharpen the skills of tomorrow’s microbiologists.

Welcome to Todd Sandrin’s classroom. The associate director of the New College Division of Mathematical and Natural Sciences and his students, supported by a National Science Foundation (NSF) Microbial Observatories grant provided to the University of Arizona (Raina Maier, principal investigator), are exploring the microbes that dwell in Kartchner Caverns southeast of Tucson. They are hoping to gain insights into whether those microbes help form many of the magnificent cave structures, such as stalactites and stalagmites, in the caves. With funding from the NSF, the research has yielded what Sandrin believes are never before described bacteria from the caverns.

Sandrin says the work being done by his students is more than climbing and crawling and negotiating pitches and squeezes.

“This is important research because microorganisms perform many functions that larger organisms – humans, for example – rely on for their very existence,” says the associate professor, who joined the New College faculty at ASU’s West campus in 2008 from the University of Wisconsin-Oshkosh. “Microorganisms make oxygen, recycle wastes, clean up hazardous wastes. To understand how they perform these critically important tasks, we must be able to study them.”

Studying microorganisms in a controlled environment is one thing, but because as many as a whopping 99 percent of microorganisms in the natural environment fail to grow in a laboratory environment, Sandrin and company are taking it underground at Kartchner Caverns, an Arizona State park with more than two miles of pristine cave passages carved from limestone and filled with spectacular formations that have been growing for 50,000 years and even longer.

“Kartchner Caverns is widely recognized as a spectacular example of carbonate cave development,” says Sandrin. “The cave is one of the top 10 caves in the world in terms of mineralogical and speleothem development. The caverns represent an ideal, pristine habitat in which to study microbial community structure, function, dynamics and the role microorganisms play in speleothem formation.”

The research may also be groundbreaking.

“Our work has the potential to transform the current understanding of how caves and structures within them develop,” Sandrin says. “To my knowledge, my group, in collaboration with Dr. Raina Maier’s group at the University of Arizona, are the only ones in the world exploring microbial diversity in Kartchner. In addition to better understanding the development of cave structures, we also anticipate gaining insights into how microbes persist in this stressful, low-nutrient environment.”

While Sandrin’s legions seek insight into how carbon is cycled in cave environments and how microbes handle an unfriendly setting, they are also in the process of confirming the existence of previously undescribed bacteria. They are using gene (DNA) sequencing. The magnitude of the significance of such a find, he says, will be determined, in part, by the identity of the microbes and by what the microbes might be doing in the cave.

Susanne Rust, a senior in the life sciences degree program who is eyeing graduation in December, says the Kartchner Caverns research is feeding her interest in “the little guys” through the research opportunity provided by the Sandrin NSF grant.

“I became most fully engaged in microbiology after learning how important the little guys really are, and this research has exceeded my expectations beyond belief.

“It is so wonderful to be participating in the elucidation of knowledge and scientific understanding. It is really fun and exciting that we are trying to do something new and find out what is really living in Kartchner Caverns that we cannot see.”

Another student researcher, Nam Nguyen, graduated with a life sciences degree in 2009 and is currently applying to the master’s program in microbiology in ASU’s School of Life Sciences in the College of Liberal Arts and Sciences. A native of Vietnam who moved to the Valley in 1990 and graduated from Glendale High School in 2005, Nguyen dug into research after taking a Sandrin lecture on microbiology during the spring semester last year.

“I find Dr. Sandrin’s enthusiasm for his research to be infectious, and that got me interested,” says Nguyen. “I’ve learned a lot working in his research lab and have gained more experience in, and understanding of, the field of microbiology than I thought was possible.

“When someone asks me what the most rewarding part of my research is, I tell them that it is all rewarding. I gain valuable experience and insight through my daily lab activities and I believe that the results of my research will contribute to the body of knowledge in this field.”

When not caving at Kartchner, Sandrin and his students are exploring how microorganisms and the communities they compose cope with and flourish in stressful environments. Currently, his lab group is investigating fundamental chemical and molecular aspects of the toxicity of metals – research that could one day lead to the design of strategies to clean up – bioremediate – hazardous wastes in the environment. The work is enabled by a proteomics and functional genomics core facility at the West campus – a facility that student Rust is using to develop, optimize and refine methods of microbial fingerprinting.

“The core facility contains two key pieces of instrumentation – a MALDI-TOF mass spectrometer and a microarray scanner,” says Sandrin, who teaches such courses as “The Microbial Universe,” “Cell Biology Laboratory,” and individualized instruction for senior-year students. “Some of the equipment we are using for the Kartchner project is contained within the core facility.

“The West campus is truly one of a very fortunate few primarily undergraduate campuses in the nation that has this caliber life science research instrumentation available to students and faculty.”

He says students are the key in his research projects.  “Students are vital.  It is undergraduate students who, in part, allow the lab to be so productive. Working in consultation with and alongside me, they actually ‘do’ the work; they gather the data, they run the instruments.

“Clearly, the experience is helpful to them and many of my former students have gone on to secure outstanding jobs,” he adds, pointing to one who is currently working with J. Craig Venter, the internationally renowned biologist who sequenced the human genome.