Microbial Contributions for Rice Production: From Conventional Crop Management to the Use of 'Omics' Technologies

Abstract

Rice, the main staple food for about half of the world's population, has had the growth of its production stagnate in the last two decades. One of the ways to further improve rice production is to enhance the associations between rice plants and the microbiome that exists around, on, and inside the plant. This article reviews recent developments in understanding how microorganisms exert positive influences on plant growth, production, and health, focusing particularly on rice. A variety of microbial species and taxa reside in the rhizosphere and the phyllosphere of plants and also have multiple roles as symbiotic endophytes while living within plant tissues and even cells. They alter the morphology of host plants, enhance their growth, health, and yield, and reduce their vulnerability to biotic and abiotic stresses. The findings of both agronomic and molecular analysis show ways in which microorganisms regulate the growth, physiological traits, and molecular signaling within rice plants. However, many significant scientific questions remain to be resolved. Advancements in high-throughput multi-omics technologies can be used to elucidate mechanisms involved in microbial-rice plant associations. Prospectively, the use of microbial inoculants and associated approaches offers some new, cost-effective, and more eco-friendly practices for increasing rice production.

Keywords: microbiome; plant–microbe interactions; rice; sustainable agriculture; symbiosis.

Figure 1

SRI methods produce more robust plant growth and health (right) than conventional grown plant (left). This is due to the SRI agroecosystems providing a more supportive environment for microbes to grow and to benefit rice plants, while conventional methods limit microbes’ growth and inhibit their effects. If this model is transposed to the larger scale of an SRI rice field, it is understandable why SRI plants achieve higher growth performance and yield as well as more resistance to biotic and abiotic stresses. In SRI rice fields, many and diverse microbes exist and interact with rice plants. Subsequently, this synergetic relationships between SRI methods and microbes affected the rice plant growth, physiological processes, yield, and patterns of gene expression.

Figure 2

Excessive use of biocides and chemical fertilizers resulted in the severe outbreaks of various rice diseases in Selangor, Malaysia: (a) Rice plants infected by Pantoea spp. with a yellowish leaf blight disease lesion on the leaves that leads to unfilled, empty, and discolored grains (photo courtesy of Muhammad Nazri Ishak), (b) Close-up view of the infected leaf with a lesion at the edge (adapted from Doni et al. [16], the journal does not require permission to use materials), (c) Typical field symptoms of bacterial panicle blight caused by Burkholderia glumae with discoloration and sterility of grain as well as rotting and panicle blanking, (d) A close look at the severely infected panicle. The panicle remains upright rather than bending down with the weight of the grain (photo courtesy of Nurul Shamsinah Mohd Suhaimi). Therefore, the use of beneficial microorganisms for the biological control of plant diseases needs to be encouraged and promoted as a powerful solution to replace toxic chemical biocides.

Figure 2

Excessive use of biocides and chemical fertilizers resulted in the severe outbreaks of various rice diseases in Selangor, Malaysia: (a) Rice plants infected by Pantoea spp. with a yellowish leaf blight disease lesion on the leaves that leads to unfilled, empty, and discolored grains (photo courtesy of Muhammad Nazri Ishak), (b) Close-up view of the infected leaf with a lesion at the edge (adapted from Doni et al. [16], the journal does not require permission to use materials), (c) Typical field symptoms of bacterial panicle blight caused by Burkholderia glumae with discoloration and sterility of grain as well as rotting and panicle blanking, (d) A close look at the severely infected panicle. The panicle remains upright rather than bending down with the weight of the grain (photo courtesy of Nurul Shamsinah Mohd Suhaimi). Therefore, the use of beneficial microorganisms for the biological control of plant diseases needs to be encouraged and promoted as a powerful solution to replace toxic chemical biocides.

Figure 3

Microbes that are residing in, on, and inside the rice plants affected rice plant growth, physiological, biochemical, and molecular processes. Thereby, they increase rice plant growth, development, and yield as well as more resistance to biotic and abiotic stresses.