Jul 2026· Journal of Advances in Microbiology· Vol 26, pp. 193-209· 0 citations
TL;DR
It is concluded that endophytic microbes represent a scientifically mature but commercially underexploited resource for climate-resilient agriculture, and identifies where mechanistic understanding still needs to be reconciled with the variability of field performance.
Abstract
Endophytic microorganisms—bacteria and fungi that colonise internal plant tissues without inducing overt disease—are a functionally important and still partly hidden component of the plant microbiome. Advances in cultivation-independent methods and multi-omics technologies have, over the past two decades, turned endophyte research from a largely descriptive, taxonomy-led pursuit into a mechanistic science with real bearing on sustainable crop production. This review critically synthesises the literature on the biology, mechanisms, and agricultural relevance of plant-associated endophytic microbes. It examines how endophytes colonise host tissues, the routes by which they are transmitted within and between plant generations, and the ecological logic underlying host specificity and core microbiome assembly. The principal mechanisms through which endophytes promote plant growth—phytohormone biosynthesis, biological nitrogen fixation, phosphate solubilisation, siderophore-mediated iron acquisition, and modulation of ethylene via 1-aminocyclopropane-1-carboxylate deaminase—are discussed alongside indirect mechanisms of pathogen suppression, including antibiosis, competitive exclusion, and induced systemic resistance. Particular attention is paid to the role of endophytes in conferring tolerance to drought, salinity, heavy-metal contamination, and temperature extremes, and to specialised symbioses such as those formed by Serendipita indica, dark septate endophytes, and Epichloë species. The review then considers how this biology has been, or might be, translated into biofertilisers, biopesticides, biostimulants, seed-applied inoculants, and phytoremediation strategies, before evaluating the contribution of omics technologies and synthetic microbial communities to rational inoculant design. Persistent obstacles to field-scale reliability, formulation stability, and regulatory harmonisation are critically appraised. The review concludes that endophytic microbes represent a scientifically mature but commercially underexploited resource for climate-resilient agriculture, and identifies where mechanistic understanding still needs to be reconciled with the variability of field performance.
A review of endophytic Bacillus as a model for understanding how metabolically versatile and genomically plastic bacteria establish functional, but context-dependent, associations with plants extends the discussion beyond agricultural systems to consider the use of endophytic Bacillus in wild plant systems and ecological restoration.
Jefferson Brendon Almeida Dos Reis· Folia Microbiologica (Prague...· 0 citations
Horticultural crop improvement is moving from a plant-centred model toward a soil-plant-microbiome framework in which host genotype, root-zone biology and the production environment are considered together. Microbiome-assisted breeding (MAB) aims to select plant genotypes that recruit, accommodate or respond to microbial communities capable of improving nutrient acquisition, soil fertility, disease suppression, abiotic-stress resilience, fruit quality and post-harvest performance. This review synthesizes the current basis of holobiont engineering with a primary focus on soil and plant-associated microbes of horticultural crops. The rhizosphere, rhizoplane, root endosphere, seed, flower and fruit compartments are considered as connected but functionally distinct microbial habitats. Important microbial groups include arbuscular mycorrhizal fungi, plant-growth-promoting rhizobacteria, diazotrophs, phosphate-solubilizing bacteria and fungi, actinobacteria, Trichoderma, endophytes, yeasts and defined synthetic communities. Recent literature highlights three developments: regulation of rhizosphere microbiomes by host traits and management, microbiome-interactive traits as potential breeding targets, and rhizosphere hybridization or microbiome engineering to build climate-smart and disease-suppressive soils. However, microbial abundance alone is not evidence of function, and inoculants frequently perform inconsistently when they cannot establish within a compatible native community. A practical MAB pipeline should combine host genotyping, soil physicochemical analysis, 16S/ITS or shotgun sequencing, culturomics, metabolomics, causal inoculation, synthetic-community testing and multi-environment validation. The review proposes priority research pathways for fruit, vegetable, spice, ornamental and underutilized crops and emphasizes that plant genotype × microbiome × soil management interactions must be measured explicitly. MAB should therefore complement—not replace—conventional breeding, crop management, conservation and farmer knowledge.
J. Shankaraswamy· International Journal of Env...· 0 citations
Escalating crop losses caused by insect pests, together with pesticide resistance, environmental persistence, and increasing regulatory scrutiny of conventional agrochemicals, have intensified interest in biologically based pest-management strategies. Endophytic bacteria and fungi represent a promising avenue for crop protection because they can influence plant defense, pest performance, and multitrophic interactions within plant tissues. This review critically synthesizes the ‘landscape’ of endophyte-mediated pest resistance—the ‘journey’ of microbes from colonization to field protection—through direct antagonism by insecticidal metabolites and enzymes, immune priming, signaling crosstalk (i.e., jasmonic acid, salicylic acid, and ethylene pathways), volatile organic compound-mediated indirect defense, and microbiome restructuring. We further evaluate the strength of evidence across laboratory, greenhouse, and field studies, distinguishing well-supported mechanisms from responses that remain context-dependent or insufficiently validated under agronomic conditions. This implies that endophyte-based pest resistance will remain difficult to translate unless colonization stability, host specificity, ecological trade-offs, formulation performance, biosafety, and regulatory requirements are addressed together. Future progress will require standardized efficacy testing, multiomics-based mechanism validation, improved delivery systems, predictive strain-selection pipelines, and transparent biosafety frameworks. By linking mechanism, evidence strength, and deployment barriers, this review provides a translational framework for moving endophyte-mediated pest resistance from experimental promise toward field-ready crop protection.
Soumik Dey Roy, Debamitra Chatterjee, Ritika Thakur et al.· Frontiers in microbiomes· 0 citations
Endophytes are diverse microorganisms inhabiting plant tissues that can promote plant growth, enhance stress tolerance, or suppress pathogens. However, the ecological roles of endophytes after host senescence and death remain poorly understood. This review examines how a subset of endophytes helps maintain ecosystem function in living plants, senescent tissues, litter, and associated microbial environments. Mechanisms of endophyte-mediated plant protection in living plants include pathogen inhibition, host regulation, nutrient acquisition, and abiotic stress tolerance. We also investigate post-senescence persistence and potential roles in litter decomposition and nutrient cycling via microbial and functional legacies, priority effects, extracellular enzyme activities, and community reassembly. Vertical transmission and horizontal dispersal can move microorganisms among stages, whereas host filtering acts after arrival to determine which microorganisms establish within host tissues. However, a full same-strain life-history loop has not been established. We propose an open, non-linear ecological continuum for selected endophytes that connects endophytic colonisation, saprotrophic persistence, and potential new-host establishment. In the future, longitudinal, strain-resolved, multi-omics, and synthetic-community studies will be conducted to verify the cross-stage connections and offer a microbial framework for plant protection, litter management, and ecological restoration.
Yu-Meng Sun, Xing-bing He, Yong-hui Lin et al.· Plants· 0 citations
Abstract Plant root microbial symbioses influence plant performance and ecosystem processes. Among these, dark septate endophyte (DSE) fungi are ubiquitous, non-mycorrhizal root endophytes with broad host ranges that facilitate nutrient acquisition, mitigate biotic and abiotic stress, and elicit positive, neutral, or negative plant growth responses depending on host and environmental context. Comparative genomic and transcriptomic analyses provide a robust framework for evaluating DSE lifestyles. Beyond their direct effects on plants, fungal endophytes contribute to soil microbiome networks, soil health, regenerative agriculture, and One Health. Integrating comparative genomics, transcriptomics, microbiome ecology, soil health, and agricultural studies, we present a systems-level synthesis of DSE biology that identifies key knowledge gaps and advances our understanding of DSE ecology and function. Comparative genomic, transcriptomic, and ecological evidence indicates that DSE share molecular and functional characteristics with ericoid mycorrhizal fungi, consistent with a hypothesized transition from saprotrophic toward specialized root-associated lifestyles. Their melanin production, extensive CAZyme repertoires, and broad ecological distribution suggest important roles in microbiome assembly, nutrient cycling, carbon dynamics, soil aggregation, and plant stress tolerance. We conclude by presenting an integrated framework linking plant–soil–fungus–environment interactions that defines core DSE competencies and highlights their importance for ecosystem functioning and sustainable agriculture.
K. Mandyam, A. Jumpponen· FEMS Microbiology Reviews· 0 citations
Plants produce a diverse range of secondary metabolites [SMs] such as alkaloids, terpenoids and phenolics, which play crucial roles in defense, signalling and human health applications like pharmaceuticals and nutraceuticals. Traditionally viewed as autonomous plant biosynthetic processes, several evidence reveals that profound influence of plant associated microbes (endophytes, rhizobacteria and phyllosphere communities) in engineering SM profiles. These microbes modulate SM biosynthesis through direct mechanism, including horizontal gene transfer of biosynthetic gene clusters, elicitation of stress responsive pathways via microbial elicitors (e.g. lipopolysaccharides), and metabolic cross feeding that supplies precursors or enzymes. Indirectly, they alter plant physiology by enhancing nutrient uptake, hormone signalling (e.g. auxins, jasmonate), and microbiome mediated priming against biotic/abiotic stresses. Recent metagenomic and metabolomic studies underscore microbiome -SM synergies in crop like rice and tomato, boosting yield of medicinally valuable compounds such as artemisinin in Artemisia annua. However, challenges persist in disentangling microbial causality from plant endogenous factors and scaling these interactions for agricultural biotechnology. This review synthesized multidisciplinary evidence on microbial engineering of plant SMs, highlighting molecular mechanisms, ecological contexts, and biotechnological prospects for sustainable crop improvement and novel drug discovery.
Priyanka Chauhan, P. Verma, A. Bhattacharya et al.· Discover Life· 0 citations
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