Molecular Microbial Biodiversity Assessment in the Mycorrhizosphere

The mycorrhizosphere is an active and dynamic region with various types of organisms inhabiting this zone. While the most important player in the mycorrhizosphere may be the mycorrhizae, past research has indicated an equally important role for the bacterial community within this biosphere. The bacterial community interacts with the mycorrhizae and also with other communities and these interactions can either be direct or indirect and beneficial or non-beneficial. Exploring the immense diversity within this biosphere will require techniques that will best represent the microbial diversity and structure. This is especially important when a large number of these organisms are non-culturable or difficult to culture, therefore making the entire process of isolation, identification and characterization more difficult. Molecular microbial diversity assessment is a way forward for us to analyze the soil diversity in the mycorrhizosphere. This chapter will address the various PCR based and non PCR based molecular techniques that may be utilized to study the microbial diversity and structure within the mycorrhizosphere.