18 - Function-driven microbial genomics for ecofriendly agriculture

Abstract

Present agricultural research is focused on addressing dual issues of food security and environmental sustainability in the wake of changing climate. While intensive agricultural practices have managed to achieve food security, they are also associated with negative effects of environmental damage, biodiversity loss and land degradation. The negative effects highlight issues of loss in functional diversity of agricultural lands. Thus, necessitate changes in land management practices like inclusion of integrated and organic nutrient management for achieving long term ecological balance. These ecofriendly land management practices make positive impacts on soil microbiome which in turn benefit plant metabolic processes and bio-geo chemical cycles. Problems of low crop yields due to biotic and abiotic factors can be overcome by optimizing plant–microbe interactions. Microbes are generally studied using traditional techniques and are being utilized in the form of biofertilizers, bioremediation/biocontrol agents and biostimulants for decades. However, only handful of microbes’ functionalities are known (as less than 1% are cultivable in lab) and majority of microbes are largely uncharacterized. Microbial genomics is set of cultivation-independent methods accompanied by reductions in cost, technical advances in sequencing technologies and new computational developments which have markedly increased our knowledge on functionality of microbial communities in variety of environments. Genomic analyses are yielding unprecedented insights into microbial evolution, diversity and ecosystem services. Elucidation of the functions of entire genome sequences to understand the inner workings of an organism and give biochemical, physiological, and ecological meaning to the information present in sequences. Microbial genomic tools are being used to study functional characterization of genome sequences, horizontal gene transfers to understand different evolutionary lineages and for functional annotation by reconstruction of metabolic pathways to shed light on role of microbes in plant nutrition and biogeochemical cycles. Recent genomic studies are beginning to reveal the specific microbial strains that contain metabolic pathways favorable for plant nutrition. Rhizosphere microbiome research describes the communities and their dynamics due to changes in environmental conditions. The understanding of microbiome functionality by using the highly promising genomic approaches is helping in exploring promising microbial candidates for sustainable crop production.