**Abstract**

Soil is a living entity of the Earth, and considered as one of the main reservoir of microbial diversity. Studying the soil microbial diversity is very much necessary, as they play an important role in maintaining the health of soil by recycling the nutrients, creating soil structure and humus. However, the culture dependent approaches fail to provide clear estimates of the diversity and untapped resources. Hence, study of the microbial diversity using culture independent approaches become necessary. The field of metagenomics helps in studying the genomes of the diverse soil organisms collectively in their natural habitat which holds the promising for accessing novel genetic resources. Application of the metagenomics to the soil environment is very challenging due to several difficulties; one of which is co-extraction of humic acid with nucleic acids which hinder downstream high throughout processes. However, applying sequencing methods to soil microbial communities will help in uncovering the hidden resources like novel genes, biomolecules and other valuable products which are yet to be discovered or still unknown. Different culture independent techniques and applications of the metagenomics to study the abundant microflora of the complex and changing environment of soil discussed herein.

**Keywords:** soil microbiome, soil health, metagenomics, DGGE, 16S rDNA, metagenome sequencing
