Soil microbes contribute significantly to nutrient cycling and nitrogen availability in agricultural soils. My research focuses on how crop management strategies impact the native soil microbial communities and the influence cropping systems have on the nitrogen and carbon dynamics. In an effort to understand these effects, we are employing molecular techniques to quantify and identify microbes including bacteria, fungi, archaea and nematodes important in nutrient cycling in agricultural soils. We are also analyzing changes in the abundance of genes required for certain microbial functions such nitrogen cycling. By analyzing the functional genes, such as the gene encoding ammonia monooxygenase which catalyzes the first step of the conversion of ammonia to nitrite, we can make assumptions on how management strategies such as crop rotation or nitrogen fertilization impact microbial ammonia oxidation.
The molecular biology capabilities are new to the USDA-ARS microbiology program at Pendleton and currently include DNA/RNA extraction, gel electrophoresis, PCR (polymerase chain reaction), quantitative PCR, T-RFLP (for determining changes in microbial diversity, terminal restriction fragment length polymorphism), DNA sequencing and DNA/RNA quantification using fluorescence or a Bioanalyzer.