Microbe to Microbiome: A Paradigm Shift in the Application of Microorganisms for Sustainable Agriculture

Abstract

Light, water and healthy soil are three essential natural resources required for agricultural productivity. Industrialization of agriculture has resulted in intensification of cropping practices using enormous amounts of chemical pesticides and fertilizers that damage these natural resources. Therefore, there is a need to embrace agriculture practices that do not depend on greater use of fertilizers and water to meet the growing demand of global food requirements. Plants and soil harbor millions of microorganisms, which collectively form a microbial community known as the microbiome. An effective microbiome can offer benefits to its host, including plant growth promotion, nutrient use efficiency, and control of pests and phytopathogens. Therefore, there is an immediate need to bring functional potential of plant-associated microbiome and its innovation into crop production. In addition to that, new scientific methodologies that can track the nutrient flux through the plant, its resident microbiome and surrounding soil, will offer new opportunities for the design of more efficient microbial consortia design. It is now increasingly acknowledged that the diversity of a microbial inoculum is as important as its plant growth promoting ability. Not surprisingly, outcomes from such plant and soil microbiome studies have resulted in a paradigm shift away from single, specific soil microbes to a more holistic microbiome approach for enhancing crop productivity and the restoration of soil health. Herein, we have reviewed this paradigm shift and discussed various aspects of benign microbiome-based approaches for sustainable agriculture.

Keywords: cover crop; microbial consortia; mycorrhiza; rhizobacteria; rhizosphere.

FIGURE 1

A schematic comparison between individual microorganism-based reductionist approach and microbial community-based holistic approach.

FIGURE 2

Responsiveness as the% gain in plant fitness attribute in response to symbiosis over un-colonized cohorts. This figure illustrates a hypothetical situation wherein genotype A loses less biomass (–20%) in response to soil nutrient limitation than does genotype B (–40%). However, if genotype B for its inherently associated rhizosphere microbiome responds optimally to a mycorrhizal symbiont, then it may be that it loses the least biomass (–10%) due to soil nutrient limitation, if the symbiont is present.% denotes loss in biomass due to soil nutrient limitation.