Minnesota Mississippi Metagenome Project

Michael Sadowsky, director of the BioTechnology Institute, aims to answer at least part of that big question with help from some very little friends. Starting this winter he’ll be leading a project to gather genetic information from the microbes that teem in the river’s headwaters at the Itasca Biological Station and Laboratories and, eventually, at various spots downstream. The study will yield valuable insights into how human activity alters the river along its path Perhaps more important, it will provide CBS students an appetite-whetting taste of metagenomics—an emerging discipline that involves studying the combined genetic material of microorganisms harvested from a natural setting rather than examining single species of organisms grown in the lab.

Known as the Minnesota Mississippi Metagenome Project—M3P for short—the initiative started as an inspiration CBS Dean Robert Elde had after following the forays of genomics guru Craig Venter, who extracted microbial genes from ocean water as a way to explore a new dimension of marine biodiversity and search for unknown organisms with traits beneficial to humans.

Minnesota may not boast an ocean, but we do host the first 600 miles of America’s most-storied river. Put that together with the BTI’s high-throughput genomic screening facilities, and you have a one-of-a-kind education and research experience just waiting to happen. Elde applied for and received $400,000 in federal stimulus money to set up a program in which students learn the logistics of metagenomics while improving understanding of the river’s micro-ecosystem.

“The purpose of the whole project is to start looking at what’s in the Mississippi River,” says CBS education specialist Jane Phillips, who is heading up the academic aspects of the project. “We are so connected to the Mississippi here on campus. … It kind of runs through our blood.”

With Sadowsky at the helm, students will create two types of genomic libraries from Mississippi microbes. One, a collection of ribosomal DNA, can be used to assess the biodiversity within the sample. The other, made up of stretches of Mississippi microbe DNA that have been inserted into E. coli, provides a massive collection of genes that can be evaluated for their function. Using these libraries, students will assess biodiversity and look for traits such as antibiotic and heavy metal resistance and toxin-degrading enzymes that tell them something about the environment in which the organisms evolved.

“It’s not those experiments in science class when you already know the answer,” Sadowsky says. “Everything the students find will be new.”

Sadowsky’s hope is to use the two-year project to leverage additional funding that would bring in other CBS researchers and extend sampling to other stretches of the Mississippi River. By comparing results of samples from different places, he says, we can get a better understanding of human influences on the river and how they vary with time and location.

“The possibilities are endless,” he says. — Mary Hoff