Molecular Approach to Study Soil Bacterial Diversity

Soil harbors planet earth’s most of the undiscovered biological diversity. Traditionally, the analysis of soil microbial communities has relied on culturing techniques using a variety of culture media designed to maximize the recovery of diverse microbial flora. Only a small fraction (<0.1 %) of microbial population has been accessible with this approach. The assessment of degree of biodiversity of natural microbial communities requires the analysis of their composition and structure, by determining the number and relative frequency of bacterial species in a community, the distribution of isolate within them, their physiological role in relation to environment as result of fluctuations in the environment. The advent of novel and advanced molecular techniques based on nucleic acids has revolutionized the studies of soil microbial flora which were previously limited by inability to culture most of the cells detected by direct microscopic observations. The amplification of ribosomal RNA (rRNA) and functional genes from nucleic acids extracted directly from environmental samples with subsequent analysis by fingerprinting methods or by sequencing and phylogenetic analysis. In this chapter, we aim to summarize the molecular techniques, which offer insight into phylogenetic and functional diversity of microbial assemblages along with the advantages and pitfalls of commonly used molecular methods.