Next-generation Microbial Technologies for Sustainable Agriculture: A Critical Review of Advances in Plant–microbe Interactions, Biofertilisers and Microbiome Engineering
Jul 2026· Journal of Advances in Microbiology· Vol 26, pp. 99-119· 0 citations
TL;DR
The synthesis shows that the conceptual foundations of the field, including community assembly, host filtering and the holobiont perspective, are comparatively secure, whereas the translation of these principles into dependable agronomic tools is not, and priorities are proposed to move the field from descriptive potential towards demonstrated agronomic value.
Abstract
Microbial technologies are increasingly promoted as a route to lower the environmental burden of crop production while sustaining yields, yet the distance between mechanistic promise and reliable field performance remains substantial. This critical narrative review examines the current state of three interlinked domains: the ecology of plant–microbe interactions, the development of biofertilisers and microbial inoculants, and the emerging practice of microbiome engineering. The literature was identified and verified through Crossref Metadata Search and the international Digital Object Identifier resolution system, complemented by citation tracing of recent reviews, with an emphasis on peer-reviewed evidence published between 2011 and 2026. The synthesis shows that the conceptual foundations of the field, including community assembly, host filtering and the holobiont perspective, are comparatively secure, whereas the translation of these principles into dependable agronomic tools is not. Mechanisms of plant growth promotion such as phytohormone modulation, nutrient mobilisation and induced systemic resistance are well characterised under controlled conditions, but their expression in the field is strongly modulated by soil context, host genotype, resident community resistance and formulation quality. The evidence for engineered associative nitrogen fixation in cereals, host-mediated microbiome selection and synthetic community design is mechanistically compelling yet largely confined to proof-of-concept studies. Recurrent weaknesses include short experimental horizons, geographical concentration of trials, inconsistent reporting and a scarcity of independent replication, which together sustain an efficacy–reproducibility gap. The most defensible near-term gains lie in resident-aware inoculant design, standardised multi-site trialling and the integration of microbiome phenotypes into crop breeding, while the ecological and biosafety implications of deliberate microbiome manipulation require structured assessment. Confidence in current conclusions is calibrated accordingly, and priorities are proposed to move the field from descriptive potential towards demonstrated agronomic value.
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
Microbial bioinoculants are increasingly positioned as key technological enablers of sustainable and climate-resilient agriculture, offering biological routes to enhance nutrient use efficiency, suppress pathogens, and improve crop tolerance to abiotic stress while reducing dependence on synthetic agrochemicals. Despite substantial advances in molecular microbiology, plant-microbe interaction research, and microbial biotechnology, the agronomic performance of commercial bioinoculants remains inconsistent across soils, climates, and cropping systems. This persistent variability reflects a structural disconnect between mechanistic understanding at the molecular scale and the largely empirical design of formulation and delivery technologies. In this review, we argue that next-generation bioinoculants should be reconceptualized as engineered biological systems in which microbial traits are rationally designed and explicitly integrated with advanced formulation architectures. We review recent progress in molecular engineering of plant-associated microbes, including synthetic gene circuits, stress tolerance engineering, metabolic rewiring, and signal-responsive regulatory pathways, and integrate these advances with developments in encapsulation, stimuli-responsive carriers, shelf-life stabilization, and smart delivery matrices. We propose a unifying framework in which formulations function as ecological and physiological interfaces that gate microbial survival, activation, and functional expression in complex agroecosystems. By bridging synthetic biology, materials science, and rhizosphere ecology, this integrated design paradigm provides a pathway toward predictable, high-performance biofertilizers and biopesticides suitable for scalable agricultural deployment.
Suvendu Das, P. Verma, Pil Joo Kim et al.· Microbiology Research· 0 citations
Microbial innovations are increasingly recognized as important components of sustainable agriculture because of their potential to improve nutrient availability, soil health, crop protection and plant resilience while reducing dependence on resource-intensive agricultural inputs. This review synthesizes recent advances in agricultural microbiomes and beneficial microorganisms, with particular emphasis on plant growth-promoting rhizobacteria, endophytes, mycorrhizal fungi, actinomycetes and microbial consortia. Their roles in biological nitrogen fixation, nutrient solubilization, nutrient cycling, pathogen suppression, modulation of plant defense and enhancement of tolerance to drought, salinity and other environmental stresses are examined. The review further evaluates emerging approaches, including microbiome engineering, synthetic microbial communities, synthetic biology, multi-omics and artificial intelligence, that are enabling more targeted and function-oriented microbial interventions. Despite substantial advances, translation from laboratory and controlled-environment studies to consistent field performance remains constrained by environmental variability, poor microbial establishment and persistence, formulation and shelf-life limitations, scale-up challenges, biosafety concerns and regulatory uncertainty. An integrated crop-soil-microbiome approach, supported by ecologically adapted strains or consortia, improved delivery systems, multi-location validation, standardized quality control and data-driven microbial selection, is therefore essential for reliable field application. Future microbial technologies should be evaluated not only for biological efficacy but also for agronomic performance, economic feasibility, environmental safety and compatibility with existing crop-management practices. Such integration can strengthen the contribution of microbial biotechnology to resource-efficient, climate-resilient and environmentally sustainable agricultural production.
M. Kanimozhi, Vijay Kumar, Laxmi Rawat et al.· Genetics and Molecular Resea...· 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
Indigenous fermented biological formulations are increasingly used in natural, organic and low-external-input farming, particularly in South Asia. Preparations such as Jeevamrit, Ghanjeevamrit, Beejamrit and Panchagavya contain complex mixtures of microorganisms, organic substrates, nutrients and fermentation-derived metabolites, and are commonly proposed to stimulate soil biological activity and improve crop performance. Yet the central ecological question remains unresolved: whether these preparations reproducibly restructure the rhizosphere microbiome through direct microbial inoculation, indirect biostimulation of resident communities, plant-mediated recruitment, or combinations of these processes. This critical narrative review evaluates the evidence linking indigenous biological formulations with rhizosphere microbial abundance, diversity, community assembly, functional potential, nutrient cycling and soil-plant feedbacks. Particular attention is given to recent culture-independent studies, multi-omics characterisation of formulations, field comparisons of natural and conventional management, and mechanistic evidence from broader soil microbial ecology. The evidence consistently indicates that preparation methods strongly influence the microbial and metabolite composition of fermented inputs. Field studies frequently report higher culturable microbial populations, microbial biomass and enzyme activities under formulation-based or natural-farming treatments, whereas sequencing studies show context-dependent shifts in bacterial and fungal communities. Evidence for durable transfer or engraftment of formulation-derived taxa into the rhizosphere is much weaker; ecological filtering by soil conditions, plant genotype, root exudation, crop stage and co-management practices appears to be decisive. General organic-amendment literature supports a strong biostimulatory role for added carbon and nutrients, complicating attribution of observed responses to introduced microorganisms. Methodological limitations include bundled treatment packages, limited source tracking, reliance on relative-abundance sequencing, sparse longitudinal sampling and inadequate nutrient mass balances. A more defensible interpretation is therefore that indigenous formulations function as variable ecological inputs whose effects emerge from interactions among their microbial consortia, metabolites, substrates and the receiving soil-plant system. Future progress requires factorial multi-site trials, strain-resolved source tracking, absolute microbial quantification, integrated metagenomic-metatranscriptomic-metabolomic measurements, nutrient-budget assessment and explicit biosafety quality control.
Anurag Saikia, Ira Sarma, A. Sarmah et al.· Asian Journal of Soil Scienc...· 0 citations
Plant–microbe interaction is an essential component of sustainable agriculture which promotes plant growth, improves nutrient assimilation, and enhances plant resistance to various environmental stress conditions. Beneficial microbes, such as rhizobacteria, mycorrhizal fungi, and endophytes, boost plant functions using molecular signaling, phytohormone modification, systemic resistance induction, and pathogen antagonism. The use of new multi-omics techniques has uncovered complicated communication systems mediated by root exudates, recognition via receptors and microbial community functioning. In this review, the current understanding of the molecular basis of plant–microbe associations and their roles in combating drought, salinity, temperature, and heavy metals stresses is summarized. Special attention is paid to the promising approach based on microbiome engineering, synthetic communities and next generation biofertilizers for climate-smart agriculture. The main difficulties associated with environmental fluctuations, host specificity, inconsistency at field scale, and the lack of omics and bioinoculant validation guidelines are also highlighted.
Bishal Sarkar, Saumendu Deb Roy· Discover Plants· 0 citations
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