Metagenomics of Soil Bacteria

Drs. C. Titus Brown and James M. Tiedje, professors in the Department of Microbiology and Molecular Genetics, along with MSU postdoc Dr. Adina Howe, are using cutting-edge DNA sequencing technologies combined with high performance computing to explore the amazing diversity of bacteria in the soil.

In a kilogram of soil, there are as many bacteria as there are stars in our galaxy. These bacteria perform many important functions in the soil, including recycling nutrients, protecting against diseases, and aiding soil structure and water-holding capacity. The functions of these bacteria are encoded in DNA that can be extracted from the soil and sequenced, a process called metagenomics. Prior to sequencing, this DNA must be fragmented into shorter pieces. In a process called "assembly," Drs. Brown, Tiedje, and Howe rebuild the original DNA sequences from these fragments. The results help us better understand which bacteria are in various soils and what they are doing to affect soil ecology. Because of the millions of fragments of DNA generated from sequencing technologies, the large memory computers at HPCC combined with novel approaches are needed to complete the assemblies.

Once these assemblies are completed, researchers can compare the bacterial communities in various soils. Drs. Tiedje, Brown, and Howe compare the presence and functions of bacterial communities in stable, restored, and disturbed soils to better understand the effects of land management practices on soil ecology. These efforts will help to develop improved land management practices. Additionally, they study soils in the rhizosphere (near the roots) of biofuel plants to help improve the growth of these crops and better understand plant and microbe interactions. These approaches are not limited to soil and will be exciting to extend to other environments as well.