Soil as a Biological System and Omics Approaches

Abstract

Soil as a biological system is characterized by: i) the presence of a remarkable diversity since thousands of bacterial genomes can be present in one gram of soil. In addition microbial biomass is huge; ii) only a minor proportion of the available space is occupied by microorganisms in soil (microbiological space);  iii) soil colloids can adsorb important biological molecules such as proteins and nucleic acids. Nucleic acids can adsorbed and retain their biological activity; iv). soil components show enzyme-like activities. Unfortunately there is no methods to distinguish enzyme from enzyme-like reactions but these methods are needed to quantify both contributions; v) virus are more abundant than in other systems such as aquatic ones. A book “Omics in Soil Science” (Nannipieri et al 2014) has been recently published; it presents the state-of-the-art of omics in soil science, a field that is advancing rapidly on many fronts. The various omics (mainly metagenomics, metatranscriptomics, proteomics and proteogenomics) approaches hold much promise but also await further refinement before they are ready for widespread adaptation. One way to judge their readiness is to compare them to methods that have become standards for soil microbiology research. Methods become standards because they provide useful information quickly and inexpensively. There is no question that omics can provide useful information, some of which cannot be obtained with traditional techniques, and integration of omics methods may provide insights into ecosystem functioning. In particular, the potential for omics to provide comprehensive coverage of genes and genes products make them well-suited for the study of general soil microbiological phenomena, such as decomposition, response to water stress