Molecular tools in rhizosphere microbiology-from single-cell to whole-community analysis

It is the aim of this chapter to present an overview of new, molecular tools that have been developed over recent years to study individual, single cells and composite, complex communities of microorganisms in the rhizosphere. We have carefully focused on culture-independent assays and selected methodologies that have already been or will soon be applicable for rhizosphere microbiology. Emphasis is placed on rhizosphere bacteria and the review first describes a number of the new methodologies developed for detection and localization of specific bacterial populations using modern electron and fluorescence microscopy combined with specific tagging techniques. First half of the chapter further comprises a thorough treatise of the recent development of reporter gene technology, i.e. using specific reporter bacteria to detect microscale distributions of rhizosphere compounds such as nutrients, metals and organic exudates or contaminants. Second half of the chapter devoted to microbial community analysis contains a thorough treatise of nucleotide- and PCR-based technologies to study composition and diversity of indigenous bacteria in the natural rhizosphere. Also included are the most recent developments of functional gene and gene expression analyses in the rhizosphere based on specific mRNA transcript or transcriptome analysis, proteome analysis and construction of metagenomic libraries.