The Impact of Evolutionary and Metabolic Diverse Microbes in Soil is Stunning

Pivotal steps in local and global cycles of carbon, nitrogen and other biologically relevant elements are mediated largely or exclusively by microbes. Numbering approximately 10,000,000,000 per gram of soil and estimated to represent more than a million species, investigations of the composition and function of these microbial communities present formidable challenges. Current research is focused primarily on the subset of microbes involved in the production or consumption of greenhouse gases, although surveys of fungal, bacterial and viral diversity have been initiated by collaborators from several institutions.

Relating Community Structure and Function

Soil TestingLong-term monitoring of the flux of greenhouse gases at the KBS LTER revealed the dramatic detrimental impact of agriculture on the production and consumption of greenhouse gases. Soil is the largest methane sink on the planet, and conversion of forest to farm decreases the consumption of methane by methane-oxidizing bacteria in soil. We are using molecular surveys of functional genes in the methane oxidation pathway to investigate relationships between the diversity of methane-oxidizing bacteria and the rate of methane consumption. Preliminary findings reveal that increases in the diversity of methanotrophs are positively correlated with rates of methane oxidation, suggesting that agricultural practice destroy niches of these bacteria. Monitoring the diversity of denitrifiers across the KBS LTER landscape also reveals changes in denitrifier diversity that relate to fluxes of nitrous oxide – one of the end products during anaerobic respiration of nitrate.

Cultivation and Genomics of Novel Bacteria

More than half of bacterial phyla identified in molecular surveys of soil microbes have no cultured representatives. Using novel cultivation and screening methods (Stevenson et al. 2004) representatives of phylogenetically diverse bacteria have been cultivated from agricultural and native soils at the KBS LTER (Eichorst et al. 2007). Genome sequencing of individual isolates and metagenomic sequencing of the community has been initiated in an effort to understand variation in the genetic capacity of microbes and microbial communities across a gradient of landscapes.

Life History Traits of Soil Bacteria


Analysis of the growth characteristics of a collection of bacteria isolated from soil suggest that bacteria possessing multiple copies of the ribosomal RNA-encoding genes are more competitive when resource availability fluctuates, due to their ability to synthesize ribosomes rapidly, while those possessing few ribosomal RNA genes may be more efficient at growth under constant, low-nutrient conditions (Klappenbach et al., 2000). These results form the basis of a conceptual model that focuses on protein synthesis – the single largest metabolic expense in bacteria. The model provides a direct link between bacterial genomics and organismal ecology (Dethlesfsen and Schmidt, 2007) and is providing insights into the competitive success of microbes present in natural and managed terrestrial environments.

Selected Publications

  • Eichorst, S.A. J. A. Breznak and T. M. Schmidt. 2007. Taxonomy and ecology of newly isolated soil bacteria that define Terriglobus gen. nov., in the phylum Acidobacteria. Applied and Environmental Microbiology 73:2708-2717.
  • Dethlefsen, L. and T.M. Schmidt. 2007. The performance of the translational apparatus varies with the ecological strategies of bacteria. Journal of Bacteriology 189:3237-3245.
  • Stevenson, B.S, S.A. Eichorst, J.T. Wertz, T. M. Schmidt and J.A. Breznak. 2004. New strategies for cultivation and detection of previously uncultured microbes. Applied and Environmental Microbiology 70:4748-4755.
  • Buckley, D.H. and T.M. Schmidt. 2003. Diversity and dynamics of microbial communities in soils from agroecosystems. Environmental Microbiology 5:441-452.
  • Klappenbach, J., J.M. Dunbar and T.M. Schmidt. 2000. rRNA gene copy number predicts ecological strategies in bacteria. Applied and Environmental Microbiology 66:1328-1333.