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Meena, M. Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture. Encyclopedia. Available online: (accessed on 07 December 2023).
Meena M. Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture. Encyclopedia. Available at: Accessed December 07, 2023.
Meena, Mukesh. "Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture" Encyclopedia, (accessed December 07, 2023).
Meena, M.(2021, December 02). Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture. In Encyclopedia.
Meena, Mukesh. "Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture." Encyclopedia. Web. 02 December, 2021.
Plant Growth-Promoting Rhizobacteria for Sustainable Agriculture

PGPR promotes plant growth indirectly by preventing phytopathogens by producing metabolites of antimicrobial nature; the production of enzymes such as chitinase, protease, and lipase, which enable lysis of pathogenic bacteria and fungi; and induction of systemic resistance. PGPR produces low molecular weight compounds possessing antimicrobial activity even at low concentrations. Due to these compounds, PGPRs are the first choice among biological control agents for sustainable agriculture.

plant growth-promoting rhizobacteria siderophore stress resistance enzyme phytohormone induced systemic resistance gene expression

1. Introduction

Indiscriminate use of agrochemicals led to deterioration of soils’ biotic communities, widespread environmental contamination by agrochemical residues, and significant negative impacts on public health [1][2], while combustion of fossil fuels and emissions of greenhouse gases are accelerating global climate changes [3]. Global climate change leads to the generation of abiotic stresses such as drought, salinity, and temperature extremes, which directly influence plants and result in decreased productivity. Abiotic stresses perplex plant growth and development and delay seed germination and enzyme activities [4][5]. Abiotic stresses also hinder soil microbial diversity and physicochemical properties of soil, resulting in lower productivity and yield loss [6]. To counteract the negative impacts of stress on crop plants, the agricultural policy is accentuating sustainable production systems with an emphasis on the use of beneficial soil microorganisms present in the rhizospheric region with multifaceted traits which promote plant growth and play a significant role in battling abiotic stress [7][8][9]. Rhizosphere, the layer of soil encasing the plant root, plays an important role in plant growth and development. It is the narrow zone surrounded by plant roots and the hot spot for microorganisms such as bacteria, fungi, nematodes, and algae. It is studied as one of the most complex ecosystems on earth [10][11]. Plant roots exude several metabolites with an abundant supply of carbon such as organic acids, sugars, vitamins, and amino acids which act as signals to attract microbial populations to bolster their proliferation [12][13][14][15]. The total microbial community present in the rhizosphere is called the rhizo-microbiome/rhizosphere microbiome and is divergent from the microbial community of the surrounding soil [16][17].
Within the rhizo-microbiome, a few soil bacteria called plant growth-promoting rhizobacteria (PGPR) colonize the surface of the root system and stimulate the growth and health of the plant by antagonistic and synergistic interactions [7][18][19][20]. Their diversity remains potent with a recurrent shift in community structure and species abundance. These PGPR could be free-living, symbiotic, parasitic, or saprophytic, and play potent roles in promoting plant growth and productivity. Free-living as well as associative and symbiotic rhizobacteria species belonging to the genus BacillusPseudomonasAzospirillumAzotobacterKlebsiellaEnterobacterAlcaligenesArthrobacterBurkholderia, and Serratia were reported as PGPR [21][22][23].
Based on their association with plant roots, PGPR can be classified into extracellular plant growth-promoting rhizobacteria (ePGPR) and intracellular plant-growth promoting rhizobacteria (iPGPR) [24][25]. ePGPR is the free-living rhizobacteria found in the rhizosphere, on the rhizoplane, or in the spaces between cells of the root cortex. AgrobacteriumSerratiaAzospirillumBacillusErwiniaMicrococcus, and Pseudomonas are examples of ePGPR [26]. iPGPR are the endophytic symbiotic bacteria that exist inside root cells, generally in specialized nodular structures, for example, MesorhizobiumRhizobium, and Frankia [27]. Actinomycetes such as Micromonospora sp., Streptomyces sp., Streptosporangium sp., and Thermobifida sp. which dominate the rhizospheric region are also reported to enhance plant growth and control fungal pathogens associated with the root [28].
PGPR promote plant growth by associative nitrogen fixation, phosphate solubilization, phytohormone production, and volatile organic compounds [29][30][31][32]. PGPR also neutralize stress in plants created by biotic and abiotic factors by boosting nutrient uptake, osmolyte accumulation, enhanced production of antioxidant enzymes, and metabolites [33][34][35]. Among several abiotic stresses, salinization of soil increasing continuously and degraded lands all over the globe causes food insecurity by reducing crop productivity [36]. High salt concentration in soils causes osmotic and ionic imbalances, reactive oxygen species (ROS) production, and water stress in plants. This review demonstrates the physiological, biochemical, and molecular mechanisms of salt-tolerant plant growth-promoting rhizobacteria (STPGPR) as emerging biological tools to counterbalance the harmful effects of high salt concentrations [37]. PGPR play an important role in bioremediation by detoxifying xenobiotics, heavy metals, and pesticides [12][38][39]. PGPR also revitalize the soil quality by increasing the soil organic content [40].
Numerous literature reviews have discussed the diverse beneficial traits of PGPR and their application as biocontrol agents, but their utilization in agriculture remains challenging worldwide. This may be due to the lack of research on understanding the mechanism of PGPR and plant interactions. The present review will thus attempt to shed more light on the mechanisms demonstrated by PGPR to enhance plant growth and its role in combating various types of abiotic stress to develop strategies for imminent agricultural sustainability. The review article will also delve into the triggers for PGPR colonization, molecular mechanisms, and the impact of PGPR on plant gene expression to elucidate some of the mechanisms by which PGPR enhances plant growth.

2. PGPR Mitigating Stress in Plants

According to Global Agricultural Productivity (GAP), the growth rate of agricultural production must increase by 1.75% annually for there to be enough food to supply the demand of 10 billion people in 2050 [41]. According to Nemecek and Gaillard [42], PGPR greatly influenced farming systems, pedo-climatic conditions, and management techniques. Abiotic factors such as salinity, temperature, drought, fertilizer application, pesticides, heavy metal contamination, and soil pH harm the productivity of crops [6]. Among the abiotic factors, salinization is being considered as the most hazardous stress condition for agricultural productivity [43][44]. Soil salinization has posed a serious threat to food security. It affects the physiological processes, such as aberration in reproductive physiology; the pattern of flowering and fruiting, which affects the crop biomass and yields; and soil processes such as residue decomposition, respiration, denitrification, nitrification, microbial activity, and soil biodiversity [45][46] (Figure 1).
Figure 1. Effect of salinity on plant growth and development.
Fertilizers containing high amounts of salt not only increase the salinity of the soil, but also induce osmotic stress in plants, which ultimately hampers plant growth [47][48][49][50]. Reclamation of such saline soils for agricultural activities is time consuming and not cost effective [51][52]. The commonly used methods to reclaim saline soils are by using physical (scraping, flushing, and leaching) and chemical (neutralizing agents such as gypsum and lime) processes [53] but these processes possess fewer efficacies in hypersaline soils [54]. Salt tolerant PGPR (ST-PGPR) have been reported to ameliorate salt stress in the plant by direct and indirect mechanisms [36][55][56]. PGPRs produce phytohormones such as cytokinins, auxins, and gibberellins [57], antioxidative enzyme ACC deaminase [58][56], exopolysaccharides [59][60], and osmolytes [61][62] (Figure 2). PseudomonasEnterobacterBacillusKlebsiellaStreptomycesAgrobacterium, and Ochromobacter are reported to improve the productivity of crops under salt stress [63][64]. Rajput et al. [65] reported the enhancement of growth and yield in wheat crop by an alkaliphilic bacterium Planococcus rifietoensis. ST-PGPR strain Bacillus licheniformis SA03 isolated from saline soil provided increased salt tolerance in Chrysanthemum [66]. A novel salt tolerant Pseudomonas sp. M30-35 isolated from the rhizosphere of Haloxylon ammodendron reported tolerance capabilities against drought and salt. Bacillus safensis VK isolated from an Indian desert showed salt tolerance capabilities of up to 14% NaCl [67]. Its genome deciphering revealed the presence of several genes which enabled it to function in drought, hypersaline, polyaromatic hydrocarbons (PAHs), and heavy metal contamination.
Figure 2. Mitigation of salt stress by STPGPR (salt-tolerant plant growth-promoting rhizobacteria) in plants.
ST-PGPR Klebsiella sp. IG3 tolerate salinity up to 20% by positively modulating the expression of the WRKY1 (transcription factor dealing with plants reaction to biotic stress) and rbcL (codes for the ribulose-1,5-bisphosphate carboxylase/oxygenase, RuBisCo) genes under saline conditions [68]. A halotolerant PGPR (Klebsiella sp. D5A) possessed salt tolerance genes and PGP traits such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, acetoin, siderophore production, 2,3-butanediol synthesis, and N2 fixation [69]Pseudomonas putida and Novosphingobium sp. reduce salt-stress in citrus plants by reducing the level of salicylic acid (SA) and abscisic acid (ABA), the efficiency of photosystem II (Fv/Fm), the accumulation of root chloride and proline, and increasing IAA accumulation under salt stress [70]Enterobacter sp. UPMR18, a ST-PGPR strain, produces ACC deaminase to improve crop productivity by upregulating ROS pathway genes and enhancing antioxidative enzymes such as APX, SOD, and CAT [71]. The effect of salt stress on plant development is represented in Figure 2.

3. PGPR Impact on Plant Gene Expression

PGPR promotes plant growth promotion by recruiting a variety of direct as well as indirect mechanisms. The most beneficial growth mechanism of PGPR is biological nitrogen fixation, and molecular studies on nitrogen-fixing PGPR isolates revealed the presence of many nif genes coding for nitrogenase enzyme. Apart from nif genes, another gene, fixABCX, was also reported in nitrogen-fixing Rhizobium species and other diazotrophs that coded for a membrane complex, aiding in electron transfer to nitrogenase enzyme [72].
Apart from nitrogen fixation, PGPR isolates are well known for their phosphate solubilization. PGPR solubilizes mineral phosphates by producing gluconic acid catalyzed by the membrane-bound enzyme glucose dehydrogenase and its enzymatic cofactor pyrroloquinoline quinine (PQQ) encoded by pqq operon with six core genes, namely pqqApqqBpqqCpqqDpqqE, and pqqF [73]. Phosphate-solubilization genes, such as gabYphoCacpAnapD, and napE genes, and the pqq gene family, were isolated from Pseudomonas cepaciaMorganella morganiiFrancisella tularensis, and Burkholderia cepacia [74]. Siderphore production by PGPR is another important characteristic that helps promote plant growth by solubilizing and transporting iron by the formation of soluble Fe3+. Siderophores production by PGPR is reported to be due to the up-regulation of sid gene [75]. PGPR alters gene expression in plants by upregulating and downregulating phytohormone genes, metabolism-related genes, stress-response genes, and defense-related genes. Exudates secreted from plants act as signaling molecules and affect the gene expression of microbionts. The root colonization of a halotolerant Rhizobacteria MBE02 on Arachis hypogaea L. (peanut) was reported to reprogram the expression of hormonal signaling genes, which resulted in the overall growth promotion of the peanut. RNA-sequencing analysis revealed the differential expression of 1260 genes in which 979 genes were up-regulated, while 281 were down-regulated by MBE02 treatment. Most of the differentially regulated activated genes were associated with induced systemic resistance (ISR), and hormonal homeostasis in peanut [76]. PGPR were reported to induce changes in the gene expression of nitrate and ammonium uptake genes in Arabidopsis thaliana [77].
Inoculation of Bacillus amyloliquefaciens SN13 on rice (Oryza sativa) inoculation led to extensive alterations in rice root transcriptome under stress. It induced considerable changes in the expression of a variety of genes involved in photosynthesis, hormone- and stress-response, cell walls, and lipid metabolism under salt stress [78]. PGPR strain Bacillus subtilis JS was reported to up-regulate genes involved in metabolic and cellular processes such as the photosynthetic pathway and photosynthate transport, while it down-regulated the antioxidant enzyme encoding genes such as glutathione S-transferase and methionine-R-sulfoxide reductase [79]. Kerff et al. [80] reported a protein EXLX1 produced by B. subtilis having a structure similar to plant β-expansin which binds to plant cell walls to promote their extension. B. subtilis colonization around A. thaliana plants downregulated the genes related to defense mechanisms in root as well as cell wall related genes [81][82]B. subtilis RR4 is reported to suppress various defense-related genes during colonization to roots of rice plantlets to boost plant immunity [83]. Understanding the molecular mechanisms boosting plant growth by PGPR isolates is still evolving and further studies are necessary to verify how PGPR regulate phytobeneficial traits by gene regulation between bacteria and plants during plant colonization.

4. Impact of Environmental Changes on Growth and Development of Microorganism

Climatic and soil condition alters the relative abundance and function of soil communities due to differences in their physiology, temperature sensitivity, and growth rates [84][85]. Increments of 5 °C in a temperate forest altered the relative abundances of soil bacteria and increased the relation in between the community of bacterial and fungus ratio [86]. Specific microbial groups can regulate ecosystem functions such as N2 fixation, nitrification, denitrification, and methanogenesis [87]. Relative changes in the abundance of microorganisms regulate specific processes and show direct impact on the rate of that process. Some processes, such as nitrogen mineralization, are more firmly correlated with abiotic factors, such as moisture and temperature, than the composition of a diverse microbial community [88]. Warming directly alters soil respiration rates of a microbial community due to temperature sensitivity [89]. Clearly, the direct effects of temperature on microbial physiology are mediated by microbial adaptations, their evolution, and specific interactions with the time. Changes in temperature and drought are often united with changes in moisture of soil [90]. Less than 30% reduction in water holding capacity in soil can alter the microbial community, which may shift from one member to another microbial community which remains constant. Microbes continually respond to changes in resources to form complex interaction networks [91][92][93]. Rising temperatures increase carbon allocation symbiotic to parasitic association [94][95] and exacerbate the interaction, negatively or positively, between the plant and their associated community. However, climate conditions, such as soil pH, temperature, and fertility, influence PGPR efficiency and alter the production of biomass, food, and materials from cultivated plants.

5. Conclusion

Among the biological materials used for sustainable agricultural production, PGPR-based bioformulations have sparked immense attention because they provide wide-ranging beneficiary impact on plants using direct and indirect mechanisms they may offer new hope in sustainable agriculture by improving soil fertility, crop productivity, nutrient cycling, and disease tolerance. PGPR also establishes the mutualistic interactions of plant and nutrient absorption such as nitrogen fixation, potassium and phosphorous solubilization, stress tolerance against biotic and abiotic factors, regulation of development and physiology of plants.


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