SOIL AS A BIOLOGICAL SYSTEM AND THE ROLE OF OMICS APPROACHES

Department of Agrifood Production and Enviornmental Sciences
University of Firenze, Firenze, Italy

Abstract
Soil as a biological system is characterized by: i) the presence of a remarkable microbiological diversity; indeed 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 be 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.

The book “Omics in Soil Science” (Nannipieri et al 2014) presents the state-of-the-art of omics in soil science, a field that is advancing rapidly on many fronts. Omics (mainly metagenomics, metatranscriptomics, proteomics and proteogenomics) can provide useful information 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, etc. I shall discuss the role of soil proteomics to better understand and evaluate soil functioning and the present drawbacks in relative methods. Despite the various omics approaches hold much promise further refinement (for example, to compare omics approaches to methods that have become standards for soil microbiology research) is needed before they are ready for widespread adaptation. Each method to become standard should provide useful information quickly and inexpensively.