The root–microbe–soil interface: new tools for sustainable plant production

Plant growth-promoting rhizobacteria (PGPR) are indispensable part of rhizosphere microbiota that grow in association with the host plants and stimulate the plant growth. PGPR microcosm establishes in soil ecosystem because of its adaptability in varied environments with faster growth rate and biochemical versatility. In recent years researches have emphasised the key role of PGPR in improving nutrition and productivity of important crops with therapeutic and industrial significance. Hence, therefore, the present chapter highlights PGPR-mediated acquired systemic resistance against phytopathogens and insect pests involving mechanisms of action. Field applications of PGPR-mediated results reflect their substantial role in inducing systemic resistance in crop plants.

Plants possess a range of active defense apparatuses that can be actively expressed in response to biotic stresses (pathogens and parasites) of various scales (ranging from microscopic viruses to phytophagous insect). The timing of this defense response is critical and reflects on the difference between coping and succumbing to such biotic challenge of necrotizing pathogens/parasites. If defense mechanisms are triggered by a stimulus prior to infection by a plant pathogen, disease can be reduced. Induced resistance is a state of enhanced defensive capacity developed by a plant when appropriately stimulated. Systemic acquired resistance (SAR) and induced systemic resistance (ISR) are two forms of induced resistance wherein plant defenses are preconditioned by prior infection or treatment that results in resistance against subsequent challenge by a pathogen or parasite. Selected strains of plant growth-promoting rhizobacteria (PGPR) suppress diseases by antagonism between the bacteria and soil-borne pathogens as well as by inducing a systemic resistance in plant against both root and foliar pathogens. Rhizobacteria mediated ISR resembles that of pathogen induced SAR in that both types of induced resistance render uninfected plant parts more resistant towards a broad spectrum of plant pathogens. Several rhizobacteria trigger the salicylic acid (SA)-dependent SAR pathway by producing SA at the root surface whereas other rhizobacteria trigger different signaling pathway independent of SA. The existence of SA-independent ISR pathway has been studied in Arabidopsis thaliana, which is dependent on jasmonic acid (JA) and ethylene signaling. Specific Pseudomonas strains induce systemic resistance in viz., carnation, cucumber, radish, tobacco, and Arabidopsis, as evidenced by an enhanced defensive capacity upon challenge inoculation. Combination of ISR and SAR can increase protection against pathogens that are resisted through both pathways besides extended protection to a broader spectrum of pathogens than ISR/SAR alone. Beside Pseudomonas strains, ISR is conducted by Bacillus spp. wherein published results show that several specific strains of species B. amyloliquifaciens, B. subtilis, B. pasteurii, B. cereus, B. pumilus, B. mycoides, and B.sphaericus elicit significant reduction in the incidence or severity of various diseases on a diversity of hosts.

The soilborne fungus Trichoderma virens secretes a small protein (Sm1) that induces local and systemic defenses in plants. This protein belongs to the ceratoplatanin protein family and is mainly present as a monomer in culture filtrates. However, Hypocrea atroviride (the telomorph form of Trichoderma atroviride) secretes an Sm1-homologous protein, Epl1, with high levels of dimerization. Nonetheless, the molecular mechanisms involved in recognition and the signaling pathways involved in the induction of systemic resistance in plants are still unclear. In this report, we demonstrate that Sm1 and Epl1 are mainly produced as monomer and a dimer, respectively, in the presence of maize seedlings. The results presented show that the ability to induce plant defenses reside only in the monomeric form of both Sm1 and Epl1, and we demonstrate for the first time that the monomeric form of Epl1, likewise Sm1, induces defenses in maize plants. Biochemical analyses indicate that monomeric Sm1 is produced as a glycoprotein, but the glycosyl moiety is missing from its dimeric form, and Epl1 is produced as a nonglycosylated protein. Moreover, for Sm1 homologues in various fungal strains, there is a negative correlation between the presence of the glycosylation site and their ability to aggregate. We propose a subdivision in the ceratoplatanin protein family according to the presence of the glycosylation site and the ability of the proteins to aggregate. The data presented suggest that the elicitor's aggregation may control the Trichoderma-plant molecular dialogue and block the activation of induced systemic resistance in plants.

Biochar is a product of carbon rich mass produced through the pyrolysis of organic wastes. Several reviews have been published demonstrating the effects of biochar on soil health, plant productivity and on the amelioration of adverse effects of climate. Depending upon the type of biomass and pyrolysis conditions maintained, biochar acquire specific characteristics like cation exchange capacity, pore size, surface area, mineral contents, energy density and adsorption capacity and help in serving a prime role in agriculture, climate change and waste management. Biochar significance also stems from its ability to sequester significant amount of carbon and reducing the efflux of greenhouse gas emission in the environment. Biochar is an important ecological niche for microbes, as biochar porous structure and high surface area, if maintained, helps in proliferation of microbes (plant growth-promoting rhizobacteria (PGPR) and mycorrhization). Biochar amendment has multiple effects on biological and biochemical properties, e.g. retention of nutrients (N, P, K), organic matter (C), water holding capacity and soil respiration, ultimately improving crop yield. In addition, it facilitates in providing tolerance against different abiotic and biotic stresses. Surface modification of biochar with nanomaterial is a promising strategy affecting its sorption capacity for contaminant removal. This review focuses on evaluating the role of biochar alone and in combination with PGPR on soil health, plant productivity under stress, enhancement of systemic resistance in plants and waste management. Further, this review demonstrates the modulation of functional characteristics of biochar as affected by nanomaterial in concert.

Increasing concerns over excessive agrochemical use, the emergence of resistant phytopathogens, and the impacts of climate variability on crop productivity have increased interest in plant growth promoting rhizobacteria (PGPR) as promising biological alternatives for sustainable crop production. Pseudomonas spp. are among the most extensively studied PGPR due to their remarkable metabolic diversity, strong rhizosphere colonization, and multifunctional roles in enhancing plant nutrition, improving stress tolerance, and suppressing plant diseases. These Gram-negative bacteria enhance plant growth through diverse direct and indirect mechanisms, including biological nitrogen fixation or stimulation of nitrogen fixation inco-existingdiazotrophs, phosphate solubilization, siderophore-mediated iron acquisition,nutrient and nichecompetition with pathogens, secretion of antimicrobial metabolites, and activation of induced systemic resistance in plants. Recent advances in omics technologies have improved understanding of the mechanisms underlying Pseudomonas mediated plant nutrition and biocontrol. However, these insights remain fragmented across the literature, limiting a comprehensive understanding of Pseudomonas-plant interactions. This review synthesizes current knowledge on nutrient mobilization, siderophore activity, antimicrobial metabolite production, and induced plant defense responses associated with beneficial Pseudomonas spp. Emphasis is placed on how these mechanisms collectively enhance plant productivity, stress tolerance, and disease resistance, highlighting the potential of Pseudomonas spp. as sustainable biofertilizers and biopesticides.

 As the world’s population is increasing rapidly, there is an urgent need to increase crop production. To achieve this goal, an eco-friendly alternative to chemical fertilizers and pesticides is required. Several types of microbes have been identified inhabiting the plant rhizosphere, such as nitrogen-fixing bacteria, plant growthpromoting rhizobacteria, fungi, proteobacteria, mycoparasitic and mycorrhizal fungi. These microorganisms not only influence the growth and development of plants but also suppress pathogenic microbes near plant roots through several different mechanisms. Non-symbiotic microbes play a crucial role in the biogeochemical cycling of organic and inorganic phosphorus (P) near the root zone via solubilization and mineralization of P from total soil phosphorus. Additionally, some non-pathogenic microbes have also been reported to induce systemic resistance in plants, which is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). The present review summarizes the latest knowledge on the role of non-pathogenic strains of microbiomes residing in the rhizosphere and their commercial applications.

The Problem of Acquired Physiological Immunity in Plants

Root-knot nematodes (RKN; Meloidogyne incognita) cause severe losses in tomato production, driving the need for sustainable control strategies. Methyl thiobutyrate (MTB), a volatile organic compound produced by the biocontrol bacterium Bacillus cereus Bc-cm103, was investigated for its nematicidal activity and underlying modes-of-action (MoAs). MTB exhibits direct contact toxicity, with a 12-h median lethal concentration (LC₅₀) of 48 μg mL-1 against second-stage juveniles (J2) and a median effective concentration (EC₅₀) of 89 μg mL-1 for inhibiting egg hatching. In pot assays, soil drenching with MTB at 100 μg mL-1 reduced gall formation by 89.8%, whereas application at 20 μg mL-1 achieved 84.6% control efficacy. Additionally, when applied as a volatile fumigant without direct root contact, MTB provided 41.7% control efficacy. Furthermore, split-root and foliar spray assays revealed that MTB triggers plant defense responses suggestive of induced systemic resistance in tomato plants, achieving control efficacies of 60.5% and 45%, respectively. Mechanistic studies revealed that MTB disrupts nematode cell membrane integrity and induces apoptotic-like morphological changes associated with upregulation of MI-asp1. Transcriptome analysis of MTB-treated tomato roots showed significant enrichment of defense-related pathways, including plant hormone signal transduction (SA/JA/ET), MAPK signaling and phenylpropanoid biosynthesis, providing molecular evidence for the observed systemic resistance. MTB controls RKN through a dual MoA involving direct contact toxicity, fumigant activity and the induction of systemic resistance in plants. This multifaceted activity highlights MTB's significant potential as an eco-friendly nematicide for integrated nematode management. © 2026 Society of Chemical Industry.

<i>Bacillus amyloliquefaciens</i> strain <scp>BaNCT02</scp>: An antagonist with multiple mechanisms of action against <i>Meloidogyne incognita</i>

Tobacco is a critical cash crop globally, contributing significantly to government revenues. However, its production is severely threatened by tobacco mosaic virus (TMV), which causes substantial yield and quality losses, leading to economic damage. Given the limited efficacy of chemical controls, biological control methods have gained prominence. Bacillus spp. are recognized as effective agents for plant disease management. In prior research, Bacillus velezensis HN-2 demonstrated promising traits for inducing plant resistance. This study revealed that the total protein extract from B. velezensis HN-2 triggers the production of reactive oxygen species, upregulates antioxidant enzymes, activates immune-related protein genes, and induces systemic resistance in plants. Its effectiveness surpassed that of benzothiadiazole and Dufulin in delaying TMV invasion. Further analysis identified a specific hydrolase protein within the total protein extract that plays a key role in the observed antiviral activity. Exogenous expression and functional assays confirmed that this hydrolase, designated P1, is the primary active protein in B. velezensis HN-2 responsible for delaying TMV infection. Hydrolase protein P1 acts as an elicitor to induce systemic resistance in the tobacco plant against TMV Infection. These findings provide an experimental foundation for the application of B. velezensis HN-2 in biological control strategies and offer theoretical insights into the use of Bacillus-derived proteins for TMV management. © 2025 Society of Chemical Industry.

Resistance to plant disease is often specific and metabolites and receptors contributing to this specificity may have specific structures. However, simple, structurally-unrelated compounds induce systemic resistance in unrelated plants to diverse pathogens including fungi, bacteria and viruses. Both resistance and induced systemic resistance (ISR) are associated with the rapid accumulation of the same structurally unrelated putative defense compounds that have diverse functions. It has been suggested that cultivar (race)-specific resistance is initiated by the specific interaction of a pathogen product (or pathogen induced product) and a plant receptor. However, restricted infection by pathogens can result in ISR and many different compounds can cause ISR. It is thus evident that there are both specific and non-specific routes to the master switch for ISR and there may be more than one master switch. Are reactive oxygen species and free radicals regulating the master switch(es) via both routes? It is also evident there are many switches, other than the master switch. Adding to the complexity of resistance and ISR are the observations that different compounds and pathways may mediate different biochemical resistances. Activation of one of the pathways may antagonize or enhance the activation or effectiveness of another. The review will address these complexities and questions and propose directions of research which require high priority. Factors which encourage and suppress the application of ISR in agriculture will also be addressed.

A new family of synthetic, membrane-active, ultrashort lipopeptides composed of only four amino acids linked to fatty acids was tested for the ability to induce systemic resistance and defense responses in plants. We found that two peptides wherein the third residue is a d-enantiomer (italic), C16-KKKK and C16-KLLK, can induce medium alkalinization of tobacco suspension-cultured cells and expression of defense-related genes in cucumber and Arabidopsis seedlings. Moreover, these compounds can prime systemic induction of antimicrobial compounds in cucumber leaves similarly to the plant-beneficial fungus Trichoderma asperellum T203 and provide systemic protection against the phytopathogens Botrytis cinerea B05, Pseudomonas syringae pv. lachrimans, and P. syringae pv. tomato DC3000. Thus, short cationic lipopeptides are a new category of compounds with potentially high utility in the induction of systemic resistance in plants.

Arbuscular mycorrhizal (AM) fungi influence the expression of defence-related genes in roots and can cause systemic resistance in plants probably due to the induced expression of specific defence proteins. Among the different groups of defence proteins, plant food allergens were identified. We hypothesized that tomato-allergic patients differently react to tomatoes derived from plants inoculated or not by mycorrhizal fungi. To test this, two tomato genotypes, wild-type 76R and a nearly isogenic mycorrhizal mutant RMC, were inoculated with the AM fungus Glomus mosseae or not under conditions similar to horticultural practice. Under such conditions, the AM fungus showed only a very low colonisation rate, but still was able to increase shoot growth of the wild-type 76R. Nearly no colonisation was observed in the mutant RMC, and shoot development was also not affected. Root fresh weights were diminished in AM-inoculated plants of both genotypes compared to the corresponding controls. No mycorrhizal effects were observed on the biomass and the concentration of phosphate and nitrogen in fruits. Real-time quantitative polymerase chain reaction analysis revealed that six among eight genes encoding for putative allergens showed a significant induced RNA accumulation in fruits of AM-colonised plants. However, human skin reactivity tests using mixed samples of tomato fruits from the AM-inoculated and control plants showed no differences. Our data indicate that AM colonisation under conditions close to horticultural practice can induce the expression of allergen-encoding genes in fruits, but this does not lead necessarily to a higher allergenic potential.

Diaphorina citri, an important pest and insect vector that can transmit the pathogenic bacteria Candidatus Liberibacter asiaticus, causing Huanglongbing disease, is one of many challenges in citrus agriculture. Integrated pest management by utilizing microorganisms is a wise and efficient alternative without damaging the environment. Utilization of Plant Growth Promoting Rhizobacteria (PGPR), such as Bacillus cereus and B. velezensis, is a potential strategy for the biological control of plant diseases or insect vectors. By inducing systemic resistance in plants, PGPR can enhance plant defense against diseases and insect pests while activating molecular and physiological changes in plants. This research aimed to determine the effect of B. cereus and B. velezensis on the plant growth and feeding behavior of D. citri. The height and volume of the plant canopy were observed periodically for 6 months, while the feeding behavior of D. citri was monitored using the Electrical Penetration Graph (DC-EPG). The results showed increased height and volume of the citrus plant canopy treated with B. cereus, indicating that B. cereus could act as a PGPR. The application of B. cereus and B. velezensis to citrus seedlings affected the feeding behavior of D. citri. D citri showed difficulty in penetrating the phloem tissue of citrus plants.

Crop plants are subjected to different kinds of stresses, and as a result, their growth is adversely affected. Different mechanisms may be used by crop plants to tolerate the stress including the morphological and physiological ones. However, the efficiency of such mechanisms differs in sensitive and tolerant crop species, and the tolerant species can utilize such mechanisms more efficiently. The other important aspect of stress tolerance in crop plants is related to their interactions with the soil microbes. A wide range of soil microbes including arbuscular mycorrhizal (AM) fungi, plant growth-promoting rhizobacteria (PGPR), and endophytic bacteria as well as their interactions can affect stress tolerance in crop plants. Such a topic is among the most important research subjects and can greatly affect the efficiency of crop plants under stress. Mycorrhizal fungi are soil fungi, developing a symbiotic association with their nonspecific host plants, and increase their growth by enhancing the uptake of water and nutrients. PGPR are soil bacteria, which can enhance the growth of their host plant by different mechanisms through developing a nonsymbiotic association. The endophytic microbes are able to colonize the inner parts of their host plant and affect its growth under different conditions including stress. The interactions of soil microbes in most cases can positively affect the growth of the host plant under different conditions including stress. The important point, which deserves investigation, is the interaction of mycorrhizal fungi, PGPR, and the endophytic bacteria, which reside in plant roots affecting plant growth and yield production. Such details will be useful for the production of more tolerant microbial inoculums, which are more efficient under different conditions including stress. Some of the most important and recent findings related to the growth of crop plants under stress, as affected by the interactions of soil microbes, along with the future perspectives are presented, reviewed, and analyzed.