Characterization of Proteolytic Microbes and Their Activities in Soils

This chapter deals with the characterization of proteolytic microbes and their activities in soils. It discusses in detail the methods to assess proteolysis, tools to study the gene and transcript pool of proteolytic organisms, and the investigation of proteolysis in terrestrial ecosystems. Proteolytic activity is usually detected by either following the decrease of initial substrate or more often measuring the increase of amino acids or peptides released during the incubation period. Methods to study organisms involved in proteolysis are based on the isolation of proteolytic microorganisms on special selective media. To estimate the number of proteolytic bacteria/fungi, plate counting and most probable number (MPN) techniques have been applied. The MPN-polymerase chain reaction (PCR) method focuses on the quantification of gene fragments at the end of amplification and requires post-PCR steps to ensure the visualization of the generated products. Real-time PCR techniques allow a detection of the product once linear amplification is achieved and do not require post-PCR procedure. The presence of the target gene in complex communities can be simply demonstrated by the hybridization of the DNA/cDNA recovered from soil to the specific labeled probe. Metagenomics represent a new approach in a genomic analysis. The chapter outlines a study of the temporal variations of proteolytic activities along with a variation of proteolytic bacteria at different soil sites.