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Shahrajabian, M.H.; Petropoulos, S.A.; Sun, W. Mechanisms of Microbial Biostimulant Action. Encyclopedia. Available online: https://encyclopedia.pub/entry/41438 (accessed on 05 December 2025).
Shahrajabian MH, Petropoulos SA, Sun W. Mechanisms of Microbial Biostimulant Action. Encyclopedia. Available at: https://encyclopedia.pub/entry/41438. Accessed December 05, 2025.
Shahrajabian, Mohamad Hesam, Spyridon A. Petropoulos, Wenli Sun. "Mechanisms of Microbial Biostimulant Action" Encyclopedia, https://encyclopedia.pub/entry/41438 (accessed December 05, 2025).
Shahrajabian, M.H., Petropoulos, S.A., & Sun, W. (2023, February 20). Mechanisms of Microbial Biostimulant Action. In Encyclopedia. https://encyclopedia.pub/entry/41438
Shahrajabian, Mohamad Hesam, et al. "Mechanisms of Microbial Biostimulant Action." Encyclopedia. Web. 20 February, 2023.
Mechanisms of Microbial Biostimulant Action
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This entry is adapted from the peer-reviewed paper 10.3390/horticulturae9020193

Sustainable farming of horticultural plants has been the focus of research during the last decade, paying significant attention to alarming weather extremities and climate change, as well as the pressure of biotic stressors on crops. Microbial biostimulants, including plant growth-promoting bacteria (PGPB) and arbuscular mycorrhizal fungi (AMF), have been proven to increase plant growth via both direct and indirect processes, as well as to increase the availability and uptake of nutrients, boosting soil quality, increasing plants’ tolerance to abiotic stress and increasing the overall quality attributes of various horticultural crops (e.g., vegetables, fruit, herbs). The positive effects of microbial biostimulants have been confirmed so far, mostly through symbiotic interactions in the plant–soil–microbes ecosystem, which are considered a biological tool to increase quality parameters of various horticultural crops as well as to decrease soil degradation. 

plant fungi biostimulants

1. Introduction

The mechanisms of action of microbial plant growth promoters are divided into direct and indirect ones. Direct mechanisms suggest that microbes are active in the synthesis of substances that can increase the uptake of nutrients, while indirect ones include, among others, zinc solubilization, siderophore production, indole acetic acid biosynthesis, phosphorus solubilization, ammonia and hydrogen cyanide production, antioxidant enzyme production, phytohormone production, and biological nitrogen fixation [1][2]. The negative impacts of environmental stresses could be mitigated by the application of microbial biostimulants such as fungi and bacteria via producing hormone-like stimulants with positive effects on plant growth [3]. Moreover, the protective effects of microbial biostimulants on plants against various stressors include the regulation of molecular processes that are involved in the interaction of plants with microorganisms and induce the biosynthesis of secondary metabolites [4]. The production of these protective molecules is achieved through the shikimate pathway that involves the enzyme Phenylalanine Ammonia Lyase (PAL) for the production of phenylpropanoids after microbial eliciting [5], which plants facilitate to cope with pressure from external factors and is known as induced systemic resistance (ISR) [6]. The main mechanisms addressed by microorganisms based on biostimulants are indicated in Figure 1. Figure 2 shows the impact of both foliar and soil on applications of various biostimulants such as humic substances, microorganisms, seaweed extract and protein hydrolysates on plant phenotype, cellular level, and molecular level.
Horticulturae 09 00193 g001 550
Figure 1. The principal mechanisms targeted by microorganisms based of different biostimulants.
Horticulturae 09 00193 g002 550
Figure 2. The most notable impacts of different biostimulants on plant phenotype, cellular level and molecular level.

2. Modes of Action of Plant Growth-Promoting Rhizobacteria

Modes of action of plant growth-promoting rhizobacteria (PGPR) involve the induction of synthesis of biosurfactants and chelating factors, avermectins, secondary metabolities, fluorescent insecticidal toxins, beta-glucanases, and chitinases for disease resistance. Additionally, they may promote antioxidant activity and biosynthesis of phytochemicals, modulate the metabolism, synthesis and accumulation of anthocyanins, polyphenols and vitamin C, which finally results in quality improvement in the crop products. Other modes of action suggest the biosynthesis of cytokinins, ABA, ethylene, auxins, gibberlins, exopolysaccharides, organic acids and siderophores; the upregulation of stress-related genes; the expression of antioxidant enzymes activity; and the activation of growth promoting genes [7]. The application of plant growth-promoting bacteria may enrich soil with bacterial inoculums which improve nutrients’ supply (e.g., phosphate and potassium solubilizing bacteria), improve immunity against abiotic stressors through the induction of 1-aminocyclopropane 1-carboxylate (ACC) deaminase, amino acids, soluble sugars, and antioxidants like peroxidases (POD), catalases (CAT), superoxide dismutase (SOD), and ascorbate peroxidases (APX) [8][9]. The production of ACC deaminase, which catalyzes the conversion of ACC to α-ketobutyrate and ammonia, is also beneficial to plants when subjected to stress conditions since ACC is the precursor of ethylene which has adverse effects on plants [10]. Stress conditions are associated with oxidative stress and the induction of reactive oxygen species; therefore, plants accumulate antioxidant compounds such as phenolic compounds, organic acids, tocopherols, terpenoids, etc., or non-enzymatic antioxidants (e.g., proline, glycine-betaine) that help them to mitigate stress through scavenging of oxidative radicals [11][12][13].
In abiotic stress conditions such as drought, salinity, heavy metals, heat and cold stress, PGPR biostimulants lead to N2 fixation, P solubilization, the synthesis of volatile organic compounds (VOCs) and aminoacids, phytochrome modulation, and the production of siderophores and exopolysaccharides [8]. Moreover, they regulate phytohormone signaling via the synthesis of hormones such as TAA, cytokinin, gibberllins, ethylene, and ABA; induce antioxidant defense mechanisms, the accumulation of osmolytes, ROS scavenging, and lipid peroxidation inhibition; regulate the transcription and the expression of stress-related genes; or photosynthetical processes and morphological responses of plants to abiotic stress [8]. For example, Pellegrini et al. [14] reported that the application of Azospirillum brasilense, Gluconacetobacter diazotrophicus, Burkholderia ambifaria and Herbaspirillum seropedicae induced the production of plant hormones that had a positive role in solubilization and uptake of nutrients in onion plants. Similarly, Azospirillum brasilense (Sp7b and Sp245b) induced the production of substantial amounts of phytohormones such as IAA, and enhanced germination, root length, root weight, and vigor index of germinating seeds in cucumber, tomato and lettuce [15]; Bacillus pumilus, Bacillus Amyloliquefaciens, Bacillus mojavensis, and Pseudomonas putida induced the synthesis of indole-3-acetic acid N2-fixation and P solubilization, and improved growth, production and nutrient uptake of tomato plants [16].
Regarding the alleviation of pressure on plants from biotic stressors, the application of natural microbial biostimulants which are obtained from metabolites of soil micro-organisms is an appropriate technique, not only to increase crops’ performance but also to protect plants from various diseases [17][18]. The mode of action of Bacillus cereus (PX35), Serratia sp. XY21, and Bacillus subtilis SM21 against root-knot nematodes in tomato plants was to improve plant resistance via synergistic control [19]. On the other hand, the application of Pseudomonas aeruginosa LV improved resistance to bacterial stem rot in tomato plants via the accumulation of extracellular bioactive compounds such as proteins, defensins, phytoalexins, phenolics, and flavonoids [20]. In the case of ginger plants, Bacillus cereus, Bacillus subtilis BSP, and Bacillus BSV increased resistance against blister blight through the production of 1-ACC [21]; while both Bacillus safensis and Bacillus altitudinis increased resistance of cabbage to black rot via IAA production [22].

3. Modes of Action of Arbuscular Mycorrhizal Fungi

In the case of AMF, Rouphael et al. [12] concluded that the increase in biomass of crops after the application of two beneficial fungi, namely arbuscular mycorrhizal fungi (AMF) and Trichoderma koningii TK7, could be associated with the modulation of the multilayer phytohormone interaction network, as well as a potential increase in nitrogen use efficiency via the Glutamine Oxoglutarate Aminotransferase (GS-GOGAT) system. Moreover, Hashem et al. [13] reported that the adverse impacts of salt stress in cucumber were ameliorated by AMF inoculation that increased the activity of antioxidant enzymes which scavenged ROS and protected plant tissues from dehydration stress, including catalase, ascorbate peroxidase, and superoxide dismutase, plant biomass and the synthesis of pigments, proline, glycine betaine. Similarly, Shekoofeh et al. [23] reported that AMF inoculation protected Ocimum basilicum plants against salinity stress by increasing water use efficiency, and improved chlorophyll synthesis and mineral uptake. Balliu et al. [24] and Yuan et al. [25] also indicated that inoculation of tomato plants with AMF increased the contents of potassium, nitrogen, phosphorous and calcium in leaves, thus indicating an improved nutrients uptake and translocation, while the same practice may increase photosynthetic parameters such as net photosynthesis and stomatal conductance, also root growth, and result in improved nutrient uptake and water use efficiency [26]. Other examples of modes of action of AMFs include: the increased antioxidant activity and the accumulation of osmolytes [27]; the upregulation of proline biosynthesis [27][28]; and the accumulation of Mg, Ca and K which promoted chlorophyll production and increased the activity of enzymes [29][30]. Finally, regarding the mitigating effects of AMF against salinity stress, Estrada et al. [31] concluded that AMF inoculation restricted both accumulation and uptake of Na by adjusting the expression levels of AKT2, SOS1 and SKOR genes in roots which allowed them to retain the homeostasis of K+ and Na+. The recent advances in omics science has also helped to reveal that microbial biostimulants’ application involves great alterations in primary and secondary metabolites such as amino acids, lipids, phenolic acids and intermediates of the tricarboxylic acid (TCA) intermediates, as well as changes in protective mechanisms against stress that involve redox homeostasis, osmoregulation, stabilization of cell membranes, the production of energy through amino acid degradation and the increased expression of stress related genes [32][33].

4. Indirect Effects of Microbial Biostimulants

Apart from the direct effects on molecular processes, the eliciting with microbial biostimulants is associated with morphological changes such as the increase in root surface and changes in root morphology after inoculation with AMFs that both facilitate increased water and nutrient’s uptake, thus helping plants to cope with the negative effects of stressors [34]. The same changes in roots have also been suggested as a mechanism of action for PGPR-based biostimulants, being regulated through hormonal activities such as indole-3-acetic acid that regulates cell elongation and division, the development of new roots and the formation of hairy roots [35]. Glick [10] also mentioned that plant growth-promoting bacteria interact with plants in different ways, such as Rhizospheric (binding to root or seed surface), Endophytic (typical in tissues inside the plant), Symbiotic (typically in root nodules), and Phyllospheric (binding to leaf or stem surfaces). Certain microbial biostimulant may protect plants against freezing and cold stress, like Paraburkholderia phytofirmans for grapevine, through the production of ACC [36]; Pseudomonas fluorescens A506 protected pear and apple trees through competition with bacteria producing INA+; Pseudomonas fragi, Pseudomonas proteolytica, Brevibacterium frigoritolerans, Pseudomonas fluorescens, and Pseudomonas chlororaphis that were beneficial to bean plant through scavenging of reactive oxygen species (ROS) and inhibition of lipid peroxidation [37]; Pantoea dispersa 1A, Pseudomonas spp. and S. marcescens SRM that protected wheat plants via production of ACC and IAA [38]. Some microbial biostimulants can also protect crops against heat stress, such as Pseudomonas sp. AKMP6 and Pseudomonas putida AKMP7 through the reduction in reactive oxygen species (ROS), the increment in content sugar, protein, starch, proline, chlorophyll, and amino acid, and the production of phytohormones [39][40]; Glomus sp. protected tomato plants through the enhanced scavenging activity of ROS in the leaves and roots and the reduction in peroxidation of lipids and the production of H2O2 [41]; Bacillus aryabhatthai SRBO2 for soybean via the production of abscisic acid [42]; Bacillus amyloliquefaciens, and Azospirillum brasilense for wheat via the reduction in reactive oxygen species (ROS) and heat shock proteins pre-activation [43]; and Paraburkholderia phytofirmans for potato plants through the decrease in H2O2 and the production of ACC [44]. In apple and pear, competition with ice nucleating activity by Pseudomonas fluorescence A506 occurs to protect the crops from cold and frost [45]. Burkholderia phytofirmans strain PsJN, increased Co2 fixation and O2 evolution, and significantly boosted the levels of proline, phenolics and starch of the grapevine plantlets to resist cold stress [46]. Regarding water stress, Lim and Kim [47] observed that inoculation of Bacillus licheniformis strain K11 with pepper plants tolerated water shortage stress more effectively than un-inoculated plants, while Saia et al. [48] suggested that although different strains of AMF and Trichoderma koningii in greenhouse lettuce (Lactuca sativa L.) grown under water stress increased mineral components including Ca, Cu, Mg, P, Mn, Fe, and Zn, and different phenolic acids, the impacts of biostimulants were targeted in modulation of the biosynthesis of secondary compounds rather than improving nutrient uptake. Moreover, the inoculation of water-stressed plants with Phoma glomerata, Penicillium sp., Exophiala sp., Glomus intraradices, and Paecilomyces formosus may lead to greater soil exploration by roots or fungal hyphae with significantly improved root conductivity [49][50]. Finally, microbial inoculation may lead to increased hormone production such as Indole-3-acetic acid (Pseudomonas chlororaphis TSAU13 and Funneliformis mosseae) in tomato, cucumber and orange, and abscisic acid in soybean [51]. The most important protective mechanisms related to the application of various microbial biostimulants against both abiotic and biotic stresses are indicated in Table 1.
Table 1. The most important protective mechanisms related to the application of different microbial biostimulant in regards to both biotic and abiotic stresses.
Stresses Type of Stresses Protective Mechanisms References
Abiotic stress      
Water stress *Drought
*Flooding		 *Osmolite production
*Increase in antioxidant activity
*Phytohormone level modulation
*Secretion of Extracellular Polymeric Substances (EPS)		 [46][47][48]
Thermal stress *Extreme heat
*Freezing		 *Emission of volatile organic compounds
*Photohormone level modulation
*Ice-nucleatin activity antagonism
*Osmo and thermal protection
*Delay of senescence		 [37][38][39][40]
Nutrient stress   *Increased soil exploration
*Mineral nutrients solubilization		 [35][36]
Biotic stress   *Induced system resistance
*Phytohormone level modulation
*Direct antagonism with pathogens		 [8][14][15][16][17]

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