Chapter 2.6 - Recent Molecular Tools for Analyzing Microbial Diversity in Rhizosphere Ecosystem

Abstract

Rhizosphere is a repository of different micro-communities that can be used to isolate and exploration of microbes for use in agriculture, environments, and industries. Due to the fact that only a small portion of the microbial diversity is accessible through culture techniques, there is a lack of information regarding the dynamics and framework of micro-communities in various ecosystems. Microbiological research has provided a limited window for examining microbial flora due to the drawbacks of conventional enrichment methods and pure culture techniques. An evolutionary relationship-based natural taxonomic order was not found in the bacterial population as represented by the morphological and nutritional criteria. The genetic diversity of the rhizospheric micro-communities has not received much attention. Microbial taxonomists currently uses a variety of techniques to characterize and identify isolates up to the species level in order to study the genetic diversity and community framework of the rhizosphere microflora. A new field of biology known as “molecular microbial ecology” uses a molecular technique to study micro-communities and can offer detailed community structure as well as helpful phylogenetic data. The genomic age has led to the improvement of advanced molecular techniques for studying the diversity of culturable microbes, such as reverse sample genome probing, DNA–DNA hybridization, DNA base ratio (mole % G+C), and DNA microarray. Additionally, by using various molecular tools, some of which will be covered in this chapter, it is possible to characterize the nonculturable diversity of the rhizosphere ecosystem.