Recent Advances in Functional Genomics and Proteomics of Plant Associated Microbes

Abstract

Research in soil microbiology has concerned the determination of the presence of gene sequences so as to assess microbial diversity rather than the determination of gene expression. Generally these molecular techniques are based on the specific amplification of the target nucleic acid by polymerase chain reaction (PCR) with either restriction analysis or separation by denaturing or conformational properties of the resulting amplicons (Lynch et al. 2004). On the other hand microbial activities in soil have been measured by classical techniques such as those for determining soil respiration, enzyme activities, N mineralization, adenylate energy charge, leucine and thymidine incorporation, etc., with no idea of gene expression. The rhizosphere effects on microbial diversity and activity are discussed in Chap. 14 of this book. Rapid progress in genomics has led to the availability of full genome sequences of hundreds of microorganisms, mostly bacteria (DeLong 2002). Combinations of new molecular methodology and genomics have been used successfully to link microbial phylogeny with function in several ecological studies and the same approach could provide significant insights into plant–microbe interactions in the rhizosphere. The functional genomics is based on a holistic or systemic approach with studying information flow within a cell and this requires the application of high throughput methods using automated technologies, which allow functional analysis of genome, proteome and metabolome of an organism (Wren 2000). In this way it is possible to get an insight on interplay of a large number of gene products and the relative consequences of this communication to the physiology of a cell. In contrast, molecular biologists have followed the reductionistic approach by studying single genes, and the individual actions of genes with a step-by-step characterization of metabolic pathways. Thus, an efficient DNA extraction with