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.
Keywords: Agriculture, Bioinoculants, Bioremediation, Microbes, Metabolism, Soil.
