Metagenomics as a Tool to Explore Mycorrhizal Fungal Communities

Fungi are important inhabitants of soil communities and help in providing nutrition to plants in symbiont form, act as decomposers and also harm the plants playing the role of monstrous pathogens. Arbuscular mycorrhizal fungus (AMF) is a heterogeneous group of fungal species associated with the roots of over 90% of higher plant species. The exploration and study of AMF diversity in ecosystems is carried out for many different reasons. The most fundamental reason is to find out more about the basic ecology of AMF. New knowledge about AMF ecology has being successfully uncovered with the application of metagenomics and has added to our knowledge of the vast pool of microbes. Metagenomics assess the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. It has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. DNA pyrosequencing along with metabarcoding is being extensively used in investigating the prokaryotic and eukaryotic assemblages in soil ecosystems. The aim of this chapter is to focus on the role of metagenomic analysis in exploring the AMF which is the most widespread symbionts in agri ecosystems worldwide.