**6.5 Agriculture**

Soil microbes play an important role in triggering the growth, stress responses and defense in plants. Understanding the relationship between the soil microbiota and plants using soil metagenomics will be very helpful in designing the crop systems. Metagenomics study of the soils supplemented with organic manures obtained from various farm animals would be very much helpful in formulating the fertilization strategies and reducing the dependence on inorganic fertilizers. For sustainable agricultural production, beneficial microbes of agricultural importance can serve as a crucial alternative. Metagenomics help in the prediction of microbial community structure and, therefore, can tackle and address fundamental scientific questions related to agriculturally important microorganisms. This approach has been successfully explored for the assessment of the diazotrophs belonging to the rhizosphere of native red kidney beans (RKB) of the Western Indian Himalaya by targeting *nifH* [89].
