Abstract

Sustainable farming is an emerging trend in recent decades to improve ecosystem health. However, little is known about to what extent and how this process affects the taxonomic diversity and functional capacities of above-ground microbes. Consequently, a metagenomics approach was applied to investigate how agricultural management practices, including organic, and conventional management, govern the structure and function of soil microbial communities. In a metagenome analysis, farming practices are strongly influenced by taxonomic and functional microbial diversity, and interactions of microbes. In agricultural soil, the most complex microbial network was observed that can be used for bioinoculant production and their applications for bioremediation of contaminated agricultural soil, indicating a strong resilience of the microbial community to withstand environmental stresses.

The metagenomics of soils can provide an assessment of the largely untapped genetic resources of soil microbial communities independent of cultivation for bioinoculant production. Novel biomolecules and genes have been identified by this approach. It also helps to study the metabolism of microorganisms that change in response to different environmental conditions. This chapter describes the use of these novel tools in the exploration of soil microbiota and its use to innovate new farming practices for a sustainable environment.

Soil microbial communities are the most complex of any other microbial communities. Methods based on sequencing remain the most effective way to analyze soil metagenomes. Future strategies to overcome this difficulty include comparative sequence analysis using soil metagenome sequences to identify microbial enzymes and novel bioactivities. The Metagenomics approach provides benefits over the restrictions of culture-dependent procedures along with the study of the community structure and function of microbes in the soil.