Aug 2026· Genetics and Molecular Research· 0 citations· 44 references
TL;DR
Functional multi-omics provides a transformative framework for bridging microbial diversity with ecosystem function, offering new opportunities to improve soil health, agricultural productivity and environmental sustainability.
Abstract
Sustainable agriculture requires a comprehensive understanding of the molecular mechanisms through which soil microorganisms regulate ecosystem functioning and plant productivity. While metagenomics has significantly advanced the characterization of microbial diversity and functional potential, it provides limited insight into the biological activities occurring under dynamic environmental conditions. Functional multi-omics, integrating metagenomics, metatranscriptomics, metaproteomics and metabolomics, overcomes this limitation by linking microbial genetic potential with active biological processes. This integrated systems biology approach provides unprecedented insights into plant-soil-microbiome interactions and their roles in nutrient cycling, disease suppression, abiotic stress tolerance and carbon sequestration. Advances in functional multi-omics have elucidated the molecular mechanisms governing microbial community assembly, rhizosphere communication and ecosystem functioning, enabling the identification of key microbial taxa, functional genes, proteins and metabolites associated with sustainable agricultural processes. These discoveries have accelerated the development of microbiome engineering strategies, microbiome informed crop improvement, synthetic microbial communities and next generation microbial biofertilizers aimed at enhancing nutrient-use efficiency, improving crop resilience and reducing dependence on synthetic agrochemicals. Despite these advances, challenges related to experimental standardization, multi-omics data integration, computational analyses, field scale validation and regulatory frameworks continue to constrain large scale agricultural implementation. Future integration of functional multi omics with artificial intelligence, precision agriculture, remote sensing and predictive ecological modelling is expected to facilitate site-specific microbiome management and climate-smart farming practices. Overall, functional multi-omics provides a transformative framework for bridging microbial diversity with ecosystem function, offering new opportunities to improve soil health, agricultural productivity and environmental sustainability.
Soil microbiomes are essential for nutrient cycling, plant health, stress resilience, and sustainable agriculture. Recent advances in high-throughput sequencing, multi-omics technologies, systems biology, and artificial intelligence (AI) have transformed our understanding of plant–microbiome interactions and enabled the development of innovative microbiome engineering strategies. This review provides a comprehensive overview of the mechanisms governing plant-associated soil microbiome assembly, microbial community functions, plant–microbe communication, and microbiome-mediated stress resistance in agricultural ecosystems. Current approaches to plant-associated soil microbiome manipulation and engineering, including microbial inoculants, synthetic microbial communities (SynComs), microbiome transplantation, rhizosphere steering, and synthetic biology-based interventions, are critically examined. The review further discusses the growing role of metagenomics, metabolomics, metatranscriptomics, machine learning (ML), and precision agriculture technologies in improving microbiome characterization, prediction, and management. Particular attention is given to the application of microbiome-based solutions for sustainable crop production, nutrient management, biological control, climate-smart agriculture, and ecosystem restoration. Despite significant progress, challenges related to field-scale variability, colonization stability, biosafety, regulatory frameworks, and data integration continue to limit large-scale implementation. Future advances in precision microbiome engineering are expected to combine ecological principles, multi-omics technologies, AI, and synthetic biology to develop predictive and resilient microbiome-based solutions for sustainable and climate-resilient agriculture.
A. Sadanov, G. Baimakhanova, B. Baimakhanova et al.· Microorganisms· 0 citations
The intricate relationship between soil microbiota and host plants plays a pivotal role in maintaining soil health and sustaining agricultural productivity. In this review, we examined current knowledge of these interactions, highlighting both their significance and the limitations in existing research. Although substantial progress has been made in elucidating the roles of diverse microbial communities in nutrient cycling, plant growth promotion, and disease suppression, several challenges remain. These include the complexity and diversity of microbial communities, as well as the dynamic nature of soil–plant interactions under varying environmental conditions. Furthermore, there is a need for greater integration of interdisciplinary approaches, encompassing molecular biology, microbiology, ecology, and agronomy, to effectively address these challenges. In this context, this study proposes future research directions aimed at advancing our understanding of soil microbiota-plant interactions and their implications for sustainable agriculture. These include the development and application of advanced omics techniques, such as metagenomics and metatranscriptomics, to comprehensively characterize microbial communities and their functional attributes. Furthermore, harnessing the potential of microbial inoculants and biofertilizers tailored to specific crops, soils, and environmental conditions represents a promising strategy for improving soil health, enhancing nutrient use efficiency, and ensuring sustainable crop production. Overall, addressing these research gaps and leveraging emerging technologies will deepen our understanding of soil microbiota-plant interactions and facilitate the development of innovative, science-based strategies to promote resilient and sustainable agricultural systems.
Moazma Batool, Sadam Hussain, Abdul Ghaffar Shar et al.· Frontiers in Microbiology· 0 citations
Plant-microbial partnerships and their underlying molecular mechanisms are indispensable, natural drivers of improved nutrient acquisition and stress tolerance in the face of climate-driven environmental challenges. Modern multi-omics tools, when coupled with artificial intelligence and synthetic biology, enable the precise design of targeted bioinoculants and synthetic microbial consortia. Translating these advanced microbiome-based strategies into scalable, field-level agricultural applications provides a sustainable path toward securing global food production while maintaining soil health. Global climate change imposes multifaceted abiotic and biotic stresses on crops, disrupting physiological and molecular processes and threatening agricultural productivity. Plant-associated microbes represent an underexplored yet powerful ally in enhancing crop resilience. This review presents current knowledge of plant–microbe interactions and the molecular mechanisms governing plant stress physiology, with an emphasis on climate-resilient and sustainable farming. Hence, ever-changing environmental cues pose a significant burden on agricultural productivity, and plant-associated microbial communities modulate a cascade of physiological and molecular responses, including production of phytohormones, signaling, regulation of reactive oxygen species homeostasis, and activation of plant immune responses to help plants withstand stress and enhance productivity. Moreover, root exudates, phytohormones, and quorum sensing mediate the central communication networks, facilitating plant–microbe cross talk. Additionally, the advances in OMICs approaches aid in disentangling the molecular underpinnings of these interactions by providing mechanistic insights and potential candidate gene targets for crop improvement and stress resilience. In the post-genomic era, integrating artificial intelligence and big data analysis to optimize microbiome-based strategies for sustainable agriculture is a new frontier for disentangling plant–microbe symbiosis to improve soil health, enhance crop yields, and improve stress tolerance. Thus, by integrating the ecological, physiological, and molecular perspectives, this review highlights the transformative potential of harnessing plant–microbe symbiosis for climate-resilient and sustainable agriculture. This review provides an up-to-date synthesis of plant–microbe interactions and their molecular roles in enhancing plant tolerance to multiple abiotic and biotic stresses under climate change scenarios. It integrates physiological, molecular, and omics-based perspectives across diverse microbial groups, including bacteria, fungi, archaea, and viruses. The review also highlights the potential of microbial symbiosis, together with emerging OMICS, AI, and Big Data approaches, to improve climate resilience and support sustainable agriculture.
Plant-associated microbiomes play a crucial role in environmental detoxification by influencing the degradation, immobilization, and resistance to toxins in polluted settings. The ecological and functional activity of endogenous microbial communities, such as rhizobacteria and endophytic microorganisms, is not well studied when examining contaminants and their environments, despite the fact that plant-mediated bioremediation has garnered a lot of research attention. The majority of previously published research focuses on a single biodegradation route or solitary plant-microbe interactions. Our knowledge of how the microbiome’s composition, functional diversity, and ecological stability of microbial communities work together to produce detoxifying results in practical applications is currently lacking. To advance understanding of how plant microbiomes cooperatively mediate environmental detoxification through metabolic interactions, adaptive responses, and host–microbiome communication, this review integrates insights from microbial ecology and functional microbiology. Its primary objective is to synthesize current knowledge on key microbial functions, including metal sequestration, xenobiotic degradation, redox regulation, and modulation of plant responses to biotic stress, while linking these functions to ecological processes such as host specificity, niche specialization, and community assembly. A distinctive aspect of this review is its ecosystem-level perspective, which shifts the focus from individual microbial taxa to the functional resilience of microbial communities in determining detoxification efficiency. The information provided in this review has a scope to provide framework to develop ecologically-sustaining, microbiome-based strategies for the detoxification of the environment and for conducting future bioremediation research.
S. Selim, K. Adhikary, Riya Sarkar et al.· Frontiers in Microbiology· 0 citations
Abstract Plants are best understood as evolutionary holobionts, in which the host and its associated microbiomes operate as an integrated unit to influence growth, health, and stress resilience. This comprehensive review synthesizes the most current knowledge of plant‐associated microbiomes across key ecological compartments, including the rhizosphere, endosphere, phyllosphere, and seeds, highlighting their assembly drivers, functional mechanisms, and translational potential. We dissect the molecular foundations of rhizobial and arbuscular mycorrhizal (AM) symbioses, the plant‐AM fungus‐bacterium continuum, alongside emerging concepts including the aerial root mucilagesphere, phyllosphere homeostasis, and the pathobiome. We further explore host genetic, metabolic, and environmental determinants of microbiome assembly, and present cutting‐edge methodologies ranging from quantitative profiling to artificial intelligence‐driven synthetic community design. Finally, we outline a strategic blueprint for harnessing standardized synthetic microbiomes and precision microbiome engineering to advance sustainable agriculture. This integrative framework bridges fundamental ecology with practical applications, delineating a path toward climate‐resilient crop production.
Mi Wei, Tengxiang Lian, Liying Chen et al.· iMeta· 0 citations
A comprehensive overview of recent advances in PGPM research is provided, with particular emphasis on next-generation microbial technologies, including synthetic microbial communities, advanced bioformulations, omics-based approaches, precision agriculture, and their contribution to the circular bioeconomy.
Danka Kiperović, Vera Karličić, Gordana Racić et al.· Agriculture· 0 citations
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