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.

QTL Analysis Revealed One Major Genetic Factor Inhibiting Lesion Elongation by Bacterial Blight (Xanthomonas oryzae pv. oryzae) from a japonica Cultivar Koshihikari in Rice

“…Rice ( Oryza sativa L.) is one of the most consumed foods in the world apart from wheat and maize, with 508.7 million tons produced during 2010–2021 [ 1 ]. As a staple food, rice feeds more than half of the human population [ 2 , 3 ]. Apart from being used as food, rice has great traditional and cultural importance in Asian countries.…”

Characterization of a Bacillus velezensis strain isolated from Bolbostemmatis Rhizoma displaying strong antagonistic activities against a variety of rice pathogens

“…The biological control mechanisms of Bacillus are mainly described as the production of direct antifungal substances such as volatile organic compounds (VOCs), non-volatile metabolites, and extracellular lytic enzymes. B. subtilis is the well-studied antagonist organism group in controlling rice blast, sheath blight, and bacterial leaf blight, which can produce mainly bacteriocin and lipopeptide compounds, organic acids, and chitinases to suppress pathogen either directly or through enhancing the plant defense mechanisms (Amruta et al, 2016;Kaspar et al, 2019;Doni et al, 2022). In addition to B. subtilis, other Bacillus spp.…”

“…Biological control, a sustainable and practical approach for plant disease management, is a promising alternative strategy in rice disease prevention and control ( Ab Rahman et al, 2018 ). So far, a variety of microorganisms, mainly including Bacillus , Pantoea , Streptomyces , Trichoderma , Clonostachys , Pseudomonas , Burkholderia , Lysobacter , and yeasts, have been shown to have the antagonistic ability against rice pathogens and some of which have been registered as the biopesticides used in controlling rice diseases in fields ( Qian et al, 2009 ; Limtong et al, 2020 ; Rani et al, 2021 ; Doni et al, 2022 ; Tan, 2022 ; Zhang H. J. et al, 2022 ).…”

“…Among the most commonly used antagonistic microorganisms, Bacillus is a prominent genus used as the biocontrol agents in rice production, with strong stress resistance and good environmental adaptability ( Doni et al, 2022 ). Bacillus is a large and heterogeneous collection of aerobic or facultatively anaerobic, rod-shaped, endospore-forming bacteria that are widely distributed throughout the environment ( Rabbee and Baek, 2020 ).…”

“…B . subtilis is the well-studied antagonist organism group in controlling rice blast, sheath blight, and bacterial leaf blight, which can produce mainly bacteriocin and lipopeptide compounds, organic acids, and chitinases to suppress pathogen either directly or through enhancing the plant defense mechanisms ( Amruta et al, 2016 ; Kaspar et al, 2019 ; Doni et al, 2022 ). In addition to B .…”