Soil Proteomics.

Soil is often referred to as a challenging ecosystem for application of omics approaches, such as metagenomics and metaproteomics. The reason that soil is so challenging is due to a combination of factors, including high microbial diversity and environmental heterogeneity. Both of these omics approaches also suffer from a deficiency of reference soil genomes in databases. Currently, these challenges are being addressed from several fronts. First, there is an increasing amount of soil metagenome data that is being generated using 2nd generation sequencing platforms. In addition, there have been several technical advances in methods for extraction of proteins from the soil matrix. We have tested and optimized several approaches for extraction of proteins from soil. For example, we spiked known quantities of the Gram-positive bacterium, Arthrobacter chlorophenolicus, into soil and after incubation used chemical reagents or pressure to lyse the cells. In addition, we first extracted bacterial cells from the soil matrix and then lysed the cells prior to protein purification and analysis. All of these methods were tested for the ability to assess the Arthrobacter proteome in soil. The cells were tagged with the gfp gene, encoding Green Fluorescent Protein (GFP) as an internal protein standard. The amount of GFP protein was compared to the concentration of the gfp gene determined by quantitative PCR, with good correlation between these measurements. In addition, the natural soil metaproteome was assessed. These results demonstrate that hundreds of proteins can be extracted from soil and pave the way for future experiments in soil metaproteomics.