Jul 2026· International Journal of Biological Macromolecules· Vol 375, pp.
153356
· 1 citation· 232 references
Medicine
TL;DR
The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.
Abstract
Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.
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.
Belshiya Rajan Grace, Sivakumar Karthikeyan, Rajeswari Ramanathan et al.· Genetics and Molecular Resea...· 0 citations
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
Abstract The microbiome is fundamental to plant performance in agroecosystems, influencing primary productivity and climate resilience. Microbiome modulation refers to the targeted manipulation (or steering) and optimization of microbiota features, including taxonomic structure, diversity, composition, assembly dynamics, stability, functional capacity, interactions, and network architecture. Here, we review the current state-of-the-art knowledge and strategies used for microbiome modulation, encompassing biological interventions such as bacteria, fungi, protists, nematodes, and phages, as well metabolites, compounds, and nutrients derived from plants. We further discuss emerging tools and strategies for next-generation microbiome modulation, including function-oriented, multitrophic defined microbial communities assembled based on ecological traits and interactions across multiple trophic levels to enable their establishment and function within the phytobiome; temperate phages; microbiome transplantation and breeding; and functional synbiotics, defined as combinations of beneficial microorganisms and compounds that improve microbiome health and function. In addition, we highlight key knowledge gaps and research priorities for advancing precision microbiome modulation. Addressing current challenges will require integrated frameworks combining experimental validation in planta and reductionist approaches with in silico modeling and multiomics analyses to better predict, design, and sustain beneficial plant-microbiome outcomes. Overall, microbiome modulation represents a paradigm shift in advancing sustainable and climate-resilient agri-food systems.
Malek Marian, Ioannis A. Stringlis, E. Rolli et al.· Sustainable 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
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
The rhizosphere is a key ecological niche where plants interact with microorganisms, and its health directly affects plant growth, development, and disease resistance. Existing theories have laid an important foundation for understanding plant-microbe interactions. Among them, the biological market theory interprets the mutualistic symbiosis between plants and microorganisms from the perspective of nutrient exchange, offering valuable insights into resource flow and interaction mechanisms within the rhizosphere. On this basis, this study further proposes the conceptual model of 'biological corporation' to integrate interaction mechanisms covering three dimensions: plant-dominated regulation, microbial functional differentiation, and signal network coordination. Within this theoretical framework, plants modulate the screening and colonisation of microbial communities via a dual-genome regulatory system. Microbial populations reshape community structure and drive functional differentiation through resource competition, cross-feeding symbiosis, and defensive strategies. Interkingdom and intrakingdom signal cascades further link the physiological and metabolic processes of plants and microorganisms, thereby facilitating the steady-state maintenance of the rhizosphere microecosystem. Based on this hierarchical symbiotic mechanism, we propose a three-step regulatory scheme for rhizosphere health restoration, and provide practical strategies including crop germplasm improvement, synthetic microbial consortium construction, and cross-kingdom signal engineering to mitigate combined biotic and abiotic stresses in farmland.
Wei Qiu, Xiufeng Tang, Qirong Shen et al.· Plant, Cell and Environment· 0 citations
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