The Microbial Connection to Sustainable Agriculture

Abstract

Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants' growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant-soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome's diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant-soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

Keywords: beneficial organisms; biocontrols; biofertilizer; microbiome; microbiome engineering; multidisciplinary omics technologies.

Figure 1

Interactions between plants and microorganisms in biotic and abiotic interactions. This diagram shows how abiotic and biotic stresses can be perceived by the plant, causing changes in cellular metabolism and affecting plant physiology, growth, and development. The stress management in plants, which is elicited by these stresses, is managed through crosstalk and interplay of hormones. In addition, there is crosstalk between signal molecules such as jasmonic acid and salicylic acid that regulate SAR and ISR, respectively. Both of these mechanisms induce a defense response in plants. On the left, we see how abiotic and biotic stresses affects plant physiology, growth, and development. These interactions result in negative impacts on susceptible varieties. Reactive oxygen species (ROS) are produced in response to these stresses. However, plants do possess mechanisms of homeostasis that keep the ROS at levels non-detrimental to the plant. On the right, we have the ISR and SAR, which are produced in response to crosstalk between signal molecules and hormones in plants. The SAR and ISR are instrumental in the defense and response of plants against current and future infiltration or associations by microorganisms, respectively.

Figure 2

A schematic diagram of several culture-dependent and non-culture-dependent methods that have been utilized extensively in the study of plant–soil microbiomes. The methods listed for the four omics technologies are the most commonly used techniques. The direct and indirect characterization of PGPB is also provided in this diagram. Legend: NMR—nuclear magnetic resonance; LC-MS—liquid chromatography–mass spectrometry; GC-MS—gas chromatography–mass spectrometry; RNA-Seq—RNA sequencing; DNA Seq—DNA sequencing.