The plant microbiome, found in the rhizosphere, phyllosphere, and endosphere, is essential for nutrient acquisition, stress tolerance, and the overall health of plants. This review aims to update our knowledge of and critically discuss the diversity and functional roles of the rice microbiome, as well as microbiome engineering strategies to enhance biofertilization and stress resilience. Rice hosts various microorganisms that affect nutrient cycling, growth promotion, and resistance to stresses. Microorganisms carry out these functions through nitrogen fixation, phytohormone and metabolite production, enhanced nutrient solubilization and uptake, and regulation of host gene expression. Recent research on molecular biology has elucidated the complex interactions within rice microbiomes and the signalling mechanisms that establish beneficial microbial communities, which are crucial for sustainable rice production and environmental health. Crucial factors for the successful commercialization of microbial agents in rice production include soil properties, practical environmental field conditions, and plant genotype. Advances in microbiome engineering, from traditional inoculants to synthetic biology, optimize nutrient availability and enhance resilience to abiotic stresses like drought. Climate change intensifies these challenges, but microbiome innovations and microbiome-shaping genes (M genes) offer promising solutions for crop resilience. This review also discusses the environmental and agronomic implications of microbiome engineering, emphasizing the need for further exploration of M genes for breeding disease resistance traits. Ultimately, we provide an update to the current findings on microbiome engineering in rice, highlighting pathways to enhance crop productivity sustainably while minimizing environmental impacts.

The fungal species belonging to the genus Trichoderma has been globally recognized as a potential candidate of biofertilizer and biocontrol agent to prevent devastating soil-borne fungal pathogens and enhance growth and productivity of agricultural crops. The antagonistic activity of Trichoderma to pathogenic fungi is attributed to several mechanisms including antibiosis and enzymatic hydrolysis, which are largely associated with a wide range of metabolites secreted by the Trichoderma species. Besides suppressing target pathogens, several metabolites produced by Trichoderma species may act against non-pathogenic beneficial soil microbial communities and perform unintended alterations within the structures and functions of microbial communities in the crop rhizosphere. Multiple microbial interactions have been shown to enhance biocontrol efficacy in many cases as compared to bioinoculant employed alone. The key advances in understanding the ecological functions of the Trichoderma species with special emphasis on their associations with plant roots and other microbes exist in the crop rhizosphere, which are briefly described here. This review focuses on the interactions of metabolites secreted by Trichoderma species and plant roots in the rhizosphere and their impacts on pathogenic and non-pathogenic soil microbial communities. The complex interactions among Trichoderma–plants–microbes that may occur in the crop rhizosphere are underlined and several prospective avenues for future research in this area are briefly explored. The data presented here will stipulate future research on sustainably maximizing the efficiency of Trichoderma inoculation and their secondary metabolites in the crop soil ecosystem.

Illumina-MiSeq next-generation sequencing of ITS 5.8S rRNA gene demonstrated the transgenerational transmission of fungal seed-endophytes (mycobiome) across three consecutive wheat host generations under standard-control and drought conditions in the greenhouse. Drought-stressed plants experienced a positive shift in the seed mycobiome’s composition, moderated by the external acquisition of endophytic Penicillium (E+) at the seed level. Untreated (E−) and unstressed plants harbor a maximal fungal diversity of non-equilibrium ecological communities. While fungal composition in drought-stressed E− plants experienced important fluctuation, E+ plants maintained fungal ecological communities in phase equilibrium across generations. E+ plants hosted a relatively higher abundance of Ascomycota in the 2^nd and 3^rd seed generations of wheat, whereas higher abundance of Basidiomycota was detected in 1^st generation seeds. The dynamic response of ecological communities to environmental stress is conducive to E+ plants’ active recruitment of endosymbiotic consortia in seeds, benefiting host stress resilience and phenotype. In contrast, E− plants showed an erratic distribution of detected OTUs with an increased occurrence of phytopathogens and diminished plant performance under stress. The present study gives insight into the understanding of the seed-mycobiome composition and dynamics with the potential to improve plant host traits in an adverse environment.

Climate change and the increasing frequency and severity of drought events pose significant challenges for sustainable agriculture worldwide. Soil microorganisms, both beneficial and pathogenic, play a crucial role in mediating plant–environment interactions and shaping the overall functioning of agroecosystems. This review summarizes current knowledge on the adaptive mechanisms used by different groups of plant-beneficial soil microorganisms—rhizobacteria and arbuscular mycorrhizal fungi (AMF)—as well as phytopathogenic bacteria and fungi, in response to drought. The review focuses on identifying the commonalities and differences in the survival strategies of these groups of beneficial and pathogenic soil microorganisms under drought conditions. Additionally, it reviews and compares the plant defence mechanisms under drought conditions facilitated by rhizobacteria and AMF. Special attention is given to the genetic exchange between beneficial and pathogenic soil microorganisms through horizontal gene transfer (HGT), which allows them to exchange traits. It is observed that drought may favor enhanced genetic exchange and the spread of pathogenic traits in the soil microbiome. This review will be useful for a wide range of readers to better understand the dynamics of the soil microbiome under climate change and to apply this knowledge to sustainable agricultural practices.

Protecting food crops from viral pathogens is a significant challenge for agriculture. An integral approach to genome-editing, known as CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and CRISPR associated protein 9), is used to produce virus-resistant cultivars. The CRISPR/Cas9 tool is an essential part of modern plant breeding due to its attractive features. Advances in plant breeding programs due to the incorporation of Cas9 have enabled the development of cultivars with heritable resistance to plant viruses. The resistance to viral DNA and RNA is generally provided using the Cas9 endonuclease and sgRNAs (single-guide RNAs) complex, targeting particular virus and host plant genomes by interrupting the viral cleavage or altering the plant host genome, thus reducing the replication ability of the virus. In this review, the CRISPR/Cas9 system and its application to staple food crops resistance against several destructive plant viruses are briefly described. We outline the key findings of recent Cas9 applications, including enhanced virus resistance, genetic mechanisms, research strategies, and challenges in economically important and globally cultivated food crop species. The research outcome of this emerging molecular technology can extend the development of agriculture and food security. We also describe the information gaps and address the unanswered concerns relating to plant viral resistance mediated by CRISPR/Cas9.