Soil microorganisms perform a variety of functions, some of which are extremely helpful to the maintenance of ecological sustainability. Bacteria thriving in the plant rhizosphere drive plant development through a variety of ways, which are referred to as PGPRs (plant growth-promoting rhizobacteria). Despite the fact that there are many different types of PGPRs, their significance and applications in sustainable agriculture are still debated and limited. The performance of PGPRs vary, which might be related to a variety of environmental conditions that impact their development and proliferation in plants. PGPR is a nonpathogenic, friendly bacterium that stimulates plant development by altering hormone concentrations and nutritional needs, as well as mitigating stress-related damage. PGPRs colonize root hairs and lateral roots in plants, where they may exhibit their beneficial characteristics. Rhizobacteria that promote plant development have the ability to control root system architecture (RSA), as well as the vegetative growth and physiology of the entire plant. The generation of hormones like Indole acetic acid (IAA) by PGPR has long been linked to RSA effects. This book chapter reviews the effects of PGPRs on the growth, the physiological, biochemical, and molecular characteristics of plant roots as well as the mechanisms involved.
Agriculture is vital to a country’s economic well-being. Many biotic and abiotic stressors are plaguing the industry, which has resulted in massive plant productivity losses throughout the world. Nutrient shortage, heavy metal pollution, high temperature, diseases, plant invasions, pests, salt, and soil erosion are all stress factors. The absence of reliable and consistent traits has generally hampered crop breeding for abiotic stress resistance. Multiple genes operate collectively to promote stress tolerance. Furthermore, the use of agrochemicals to combat biotic stressors and nutritional shortages hastens environmental pollution and has a detrimental impact on the biogeochemical cycle system, and poses a health risk to humans. The potential consequences of the aforementioned stresses are substantial, implying the need for solid, cost-effective, and ecologically acceptable ways to reduce the negative impacts of these challenges on plants. As a result, interest in ecologically friendly and organic agriculture techniques has surged . Bio-fertilization, revitalizing root growth, rhizoremediation, disease resistance, and other methods of microbial revival employing plant growth stimulants have been used.
Plants, unlike animals, cannot employ avoidance and escape as stress-relieving techniques; as a result, their evolution has been distinguished by the development of extremely advantageous relationships with their more mobile partners, microorganisms. Interactions between plants and microbiomes including soil bacteria are in high demand all around the world. Microorganisms are considerably more prevalent in the rhizosphere, or soil/root contact than they are in bulk soil. This is due to the fact that roots release a large portion of their photo-assimilates, serving the primary food source for the rhizobacteria. In exchange, they are able to have a positive impact on plant development and play an important part in plant adaptation to the environment [2, 3].
Soil microorganisms perform a variety of functions, some of which are extremely helpful to the maintenance of ecological sustainability. Bacteria thriving in the plant rhizosphere drive plant development through a variety of ways, which are referred to as PGPR . The rhizosphere is the confined zone of soil directly around the roots  whereas rhizobacteria refer to a group of rhizosphere bacteria capable of inhabiting the root environment . PGPR is a nonpathogenic, friendly bacterium that stimulates plant development by altering hormone concentrations and nutritional needs, as well as mitigating stress-related damage [7, 8].
Plant growth could be boosted by PGPRs in both direct and/or indirect ways. The direct ways are 1) secreting growth regulators such as cytokinins, auxin, and gibberellins, 2) decreasing the levels of ethylene in plants, 3) solubilizing inorganic phosphate, 4) mineralising organic phosphate, 5) Non- Symbiotic nitrogen fixation, 6) forming organic matter, which comprises amino acids, 7) synthesizing enzymes and 8) activating disease-resistance pathways . Indirectly, PGPRs may serve as biocontrol agents by controlling plant disease-causing organisms. They also help to relieve the effects of cold, drought, metal toxicity, and excessive salinity. The drought resistance and water usage efficiency of plants grown in arid and semi-arid climates might be increased by PGPR inoculation, which promotes plant abiotic stress tolerance with an osmotic component. Plant’s biochemical changes resulting in improved tolerance to abiotic stress have been suggested as PGPR induced root growth, nutrient uptake efficiency, and systemic tolerance. They can also fix asymbiotic nitrogen, help with mineral phosphate and other nutrient solubilization; manage plant disease caused by other bacteria and fungi, and produce antibiotics, enzymes, and siderophores, among other functions. Certain PGPR may infer particular growth-promoting properties like abiotic stress tolerance, and phytopathogen and insect biological control . The stimulation of disease tolerance of the inoculated plant, N2 fixation, phosphorus solubilization, and/or phytohormone synthesis are all possible explanations for PGPR’s growth-promoting effects on plants . Phytohormones (a.k.a. plant growth regulators) that influence the development of plants. Plant growth regulators are another name for them. Auxins, gibberellins, ethylene, cytokinins, and abscisic acid are the five principal categories of phytohormones known by botanists. Indole acetic acid is a phytohormone that affects plant growth in a variety of ways, including organogenesis, tropic responses, cell division, and cell differentiation.
Despite the fact that there are many different types of PGPR, their significance and applications in sustainable agriculture are still debated and limited. The performance of PGPR varies, which might be related to a variety of environmental conditions that impact their development and proliferation in plants ( Figure 1 ) . Due to these effects, the use of PGPRs in agriculture has begun to be studied. In this work, we used the currently widely used databases and tools including Web of Science, Science Direct, Google Scholar etc., and key words such as roots, PGPR, growth, development, root structure, chemical characteristics, genes etc.
2. PGPR’s effect on the architecture and structure of root systems
The plant’s aboveground development is heavily reliant on its underground root structure. The root system of most terrestrial plants develops to scrutinize soil and reach nutrients. Root comprises the root tip, differentiation and elongation zones, root meristem, and emerging lateral roots . Each of these regions has a unique significance. According to gene expression research, root hairs are specialized epidermal cells that are crucial for nutrient uptake . The functional specialization of roots is also reflected in plant-microbe interactions. The root tip, for example, is the most essential area for initiating the rhizobial colonization, which leads to the development of a nodule in the Fabaceae family . PGPR colonizes roots in plants where they can exert their beneficial properties . RSA encompasses spatial arrangement of primary and lateral roots, as well as the number and length of different root types. It can be affected by a variety of abiotic and biotic variables, including PGPR strains. The potential of PGPR to interfere with the plant hormones modifies root system architecture ( Figure 2 ).
PGPR engages in some activities in the soil to keep it active in crop production and sustainability . PGPR colonize roots systems competitively, regulate root development, surface area and enhance plant growth through and a variety of mechanisms, including phosphate solubilization , nitrogen fixation , production of siderophores , 1-amino-cyclopropane-1-carboxylate (ACC) deaminase and hydrogen cyanide .
Ironically, some microorganisms, such as PGPR, may trigger the synthesis of phytohormones in plants. Phytohormones are organic compounds that stimulate, hinder, or change plant growth at low concentrations . Gibberellins, cytokinins, abscisic acid, ethylene, brassinosteroids, and auxins are examples of phytohormones that cause the root cell to proliferate by overproducing lateral roots and root hairs . Plant growth regulators may be given exogenously to plants or plant tissues as extracted hormones or synthetic counterparts. Phytohormones are classified according to where they act. This is critical for nutrient absorption regulation based on soil type and climatic conditions. The most prevalent effects are a slowdown in primary root development rate and an increased lateral roots and root hairs. The synthesis of growth metabolites by PGPRs may play a role in conferring resilience to water stress in host root colonization, leading to increased strategic crop output. By root repair, beneficial rhizobacteria may adapt to specific environmental circumstances and gain stress resistance.
Auxin, cytokinin, ethylene, and to a lesser extent gibberellin and abscisic acid (ABA) interactions with PGPR might induce variations in the root system . Auxin-cytokinin balance is a fundamental regulator of plant organogenesis and influences root characteristics . PGPR can alter the auxin to cytokinin ratio because they may produce a variety of phytohormones as well as secondary metabolites that might disrupt hormonal pathways. Several PGPRs generate phytohormones and secondary metabolites that interfere with auxin pathway in plants. PGPR can generate IAA, which promotes primary root elongation ( Figure 2 ) [25, 26]. IAA is often produced by PGPR via various routes, which can be present in various quantities in root exudates depending on the plant genotype. Indirect activation of the plant auxin pathway by PGPR can also promote plant growth. Several PGPR strains, such as
Cytokinin production has been shown by PGPR like
PGPR has been shown in several studies to be capable of producing ABA or gibberellic acid, as well as controlling the levels of these hormones in plants . ABA, for example, plays an important role in drought stress. Elevated ABA levels under water stress induce stomata to close, reducing water loss . ABA, on the other hand, has a variety of functions during lateral root growth . In Arabidopsis,
3. The structural properties of the root by PGPR
PGPRs can alter the chemical composition and, as a result, the structural characteristics of root cell walls ( Figure 2 ) . The biocontrol agent
Lower lignin concentration, on the other hand, may aid cell elongation and hence total root growth.
PGPR produces enzymes such ACC-deaminase, 1,3-glucanase, and chitinase, which are involved in the lysis of cell walls and pathogen neutralization . Because most fungal cell wall components are made up of 1,4-N-acetylglucoseamine and chitin, bacteria that produce 1,3-glucanase and chitinase regulate their development.
4. PGPR’s systemic effects on the physiology and functioning of the whole plant
PGPR may alter the physiology and function of tissues far from colonized areas in plants. PGPR can improve plant root nutrient availability and absorption. Some PGPR, on the other hand, causes particular systemic reactions, most of which are triggered by unknown signaling pathways. PGPR has been shown to affect gene expression and metabolite accumulationin plants which have been demonstrated by studies of plant transcriptome and metabolomic. These findings show that PGPR has a broad impact on plant physiology and function, and they highlight ways to better understand PGPR’s systemic impact.
4.1 PGPR’s effect on plant nutrition
Plant nutrition may be affected by PGPR through impacts on nutrient absorption and/or plant development . Nutrient absorption can be improved as a result of the enhanced root growth induced by PGPR. To promote both higher nutrient uptake and plant growth, PGPR is involved in pathways that coordinate plant development and nutrition ( Figure 2 ). Rhizobacteria that promote plant development can enhance nutrient supplies in the rhizosphere and/or activate root ion transport mechanisms. One of the most important effects of PGPR on plant nutrition is phosphate solubilization. Soils typically contain a lot of phosphorus, which builds up over time as a result of fertilizer treatments, but only a tiny quantity of it is available to plants. Plants may absorb mono and dibasic phosphate on their own; organic and insoluble phosphate must be mineralized or solubilized by microbes . Pseudomonas, Bacillus, and Rhizobium may dissolve phosphate in insoluble forms .
Miller et al.  identified that various linked bacteria have the ability to fix N2 and so supply nitrogen to the plant. For some plants, particularly sugar cane, evidence of PGPR engagement in the plant N budget has been documented . Also, non-fixing rhizobacteria can promote plant growth, indicating that external fertilizer application may not be necessary to increase plant growth and yield.
Only a few research on the influence of PGPR on nutrient absorption have been reported so far though. NO3 and K uptake have been shown to increase after canola was inoculated with
4.2 PGPR’s effect on plant transcriptome
Effects of PGPR applications on gene expression in plants has been described. Inoculation of Arabidopsis leaves with
4.3 PGPR’s effect on plant metabolome
Researches have looked at the metabolomic changes caused by PGPR by examining the metabolite content in plants under non-stressed and stressed circumstances ( Figure 2 ). PGPR has been found in certain studies to cause modifications in the activity of root enzymes, which play role in the synthesis of metabolites . The level of carbon compounds released from roots was increased by up to one-third in several Azospirillum strains . Furthermore, microbially produced chemicals such as phenazines and DAPG have the potential to increase total net amino acid outflow in plant species .
5. PGPR population ecology and impact on root system performance
PGPR’s methods of action have been studied extensively utilizing only one strain and one host plant. However, PGPRs do not function in the rhizosphere as individuals. A diverse range of PGPR populations are interacting with the same host plant, and they may have antagonistic or synergistic effects. Different taxonomic groupings of plant growth-promoting rhizobacteria strains exist, and these groups may coexist in a particular soil . PGPR strains from different taxonomic groups might coexist in soil and colonize the same rhizosphere. This potential has been recorded several times, particularly when determining the taxonomic identity of bacterial isolates chosen for their beneficial influence on plant growth . It appears that this option is the rule rather than the exception. A functional group is made up of PGPR populations that perform the same function (for example, ISR, nitrogen fixation, plant growth promotion, and so on). When particular genes are documented, functional group methods can be used. The coexistence of genetically contrasting PGPR strains has two effects when examining the PGPR-plant connection in fields. If the PGPR populations have synergistic effects, the PGPR function may be higher than only one kind of strain. The higher the function leads to increased nutrient availability to the plant. Others, such as the generation of auxinic signals, will require fine-tuning of the functional group’s performance to prevent production levels that are too small or too big . Regulatory effects should also be considered to bridge the gap between the PGPR function and its actual execution . Some interactions between various PGPR strains in the same rhizosphere are crucial. Interactions between different PGPR functional groups can be competitive and inhibitory  and positive signaling . These interactions have the ability to influence PGPR effectiveness by modulating spatial colonization patterns on roots .
6. PGPR’s effects on regulated phyto and microbial beneficial protein interactions
PGPR efficacy is connected to the mutual gene regulation between PGPR and plants during colonization. This regulation has positive effects on growth, nutrient absorption, and metabolite upregulation, as well as on proteins and biological processes, and gene expression [88, 89, 90]. PGPR produces a number of phytobeneficial and desirable features, including increased phytohormone production and resistance to biotic and abiotic stress . Increases in gene expression and particular protein families, which interfere with hormone production, cellular breakdown, and signaling pathway modulation, are linked to the positive effect. The capacity of sulfatase to cycle ambient sulfur via degradation or cellular remodeling might explain the rise in element compositions after PGPR inoculation. Because of a rise in the Carbohydrate Kinases protein family the rise in biomass in plants is linked to the increased sugars and carbohydrates shown in their study .
Heat Shock Protein 70 (Hsp70) is a family of conserved proteins that are found in the cytoplasm and in the chloroplasts. Hsp70 is involved in protein synthesis, stress protection, and protein translocation help. The preservation of cellular homeostasis and protection from various forms of stress. Phytobeneficial characteristics were modulated by reciprocal protein activation via microbe–plant interactions during and after colonization by PGPR. Furthermore, bacterial gene regulators linked to bacterial signaling, DNA binding transcriptional regulators, and cell proliferation were induced by plant root exudates . Climate change has a significant impact on the efficiency of PGPR, yet unfavorable growing circumstances in the field are to be expected as part of the routine operation of agriculture . Multiple mechanisms, such as phosphate solubilization, dinitrogen fixation, ACC deaminase, and antifungal activity, IAA and siderophore biosynthesis, and others, are responsible for plant growth promotion and increased yield . Following PGPR treatments, significant increases in yields of several agricultural plants have been seen in both natural agro-ecological niches and controlled soil conditions. Because there is a global aversion to eating foods made from genetically engineered plants, PGPR might be useful for encouraging plant development. The widespread use of PGPR might reduce the world’s reliance on agricultural pesticides. Furthermore, it is a technology that farmers in both rich and poor nations may easily obtain .
7. PGPR as a growth enhancer
Plant development is aided by PGPR through both direct and indirect processes, which include improving plant physiology and resistance to diverse phytopathogens via a variety of modes and activities . These include nutrition fixation, biotic and abiotic stress neutralization, and disease prevention through the production of volatile organic compounds and enzymes. However, depending on the kind of host plant ( Figure 3 ), the manner of action of different kinds of PGPR differs . Plant genotypes, developmental phases, defense systems, and other members of the microbial community are among the biotic and abiotic elements that impact them .
Auxin may be produced by a wide range of bacterial species (Indole acetic acid).
Plants have developed a variety of biotic relationships with microbial communities in the soil, ranging from commensalism to mutualism. Plant-PGPR collaboration plays a key part in this continuum of interactions, boosting the development and health of a wide range of plants. Recent research has aided in understanding important characteristics of plant-PGPR interactions, such as mechanisms of action and ecology, although substantial information gaps remain. Rhizobacteria that promote plant development have the ability to control RSA, as well as the growth and physiology of plant. The generation of IAA by PGPR has long been linked to RSA effects. Remarkably, bacterial regulation of auxin distribution and IAA signal pathways has also been discovered, independent of IAA synthesis by PGPR. Plant hormones control the expression of genes involved in the production of other hormones or hormonal pathway components. As a result, it explains why PGPR has such pleiotropic effects on plants.
Understanding how PGPR influences the plant hormonal balance and signaling pathways is one of the key ongoing scientific problems ahead. PGPR populations from different soils can work together to exhibit plant-beneficial characteristics. As previously stated, plant-rhizo-microbiome interactions are complicated and vary depending on plant genotypes and soil-inhabiting populations. The taxonomic and functional diversity of next-generation sequencing methods have begun to emerge. They’ve started to provide fresh information on the ecology of PGPR groupings. Metatranscriptomics and metaproteomics are likely to advance dramatically in the near future, allowing for greater knowledge of the ecological behavior of PGPR in the rhizosphere.