Plant Growth-Promoting Rhizobacteria as a Green Alternative for Sustainable Agriculture

Abstract

Environmental stress is a major challenge for sustainable food production as it reduces yield by generating reactive oxygen species (ROS) which pose a threat to cell organelles and biomolecules such as proteins, DNA, enzymes, and others, leading to apoptosis. Plant growth-promoting rhizobacteria (PGPR) offers an eco-friendly and green alternative to synthetic agrochemicals and conventional agricultural practices in accomplishing sustainable agriculture by boosting growth and stress tolerance in plants. PGPR inhabit the rhizosphere of soil and exhibit positive interaction with plant roots. These organisms render multifaceted benefits to plants by several mechanisms such as the release of phytohormones, nitrogen fixation, solubilization of mineral phosphates, siderophore production for iron sequestration, protection against various pathogens, and stress. PGPR has the potential to curb the adverse effects of various stresses such as salinity, drought, heavy metals, floods, and other stresses on plants by inducing the production of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. Genetically engineered PGPR strains play significant roles to alleviate the abiotic stress to improve crop productivity. Thus, the present review will focus on the impact of PGPR on stress resistance, plant growth promotion, and induction of antioxidant systems in plants.

Highlights

• PGPR offer an eco-friendly and green alternative to synthetic agrochemicals and conventional agricultural practices.
• PGPR accomplish sustainable agriculture by boosting growth and stress tolerance in plants.
• PGPR inhabit in the rhizosphere of soil and exhibit positive interaction with plant roots.
• PGPR have the potential to curb the adverse effects of various stresses.

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 Bacillus, Pseudomonas, Azospirillum, Azotobacter, Klebsiella, Enterobacter, Alcaligenes, Arthrobacter, Burkholderia, 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. Agrobacterium, Serratia, Azospirillum, Bacillus, Erwinia, Micrococcus, 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, Mesorhizobium, Rhizobium, 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. Mechanism of Action

Plant growth-promoting rhizobacteria augment plant growth due to the presence of peculiar traits [41]. PGPR promote plant growth either directly or indirectly by preventing phytopathogens, synthesis phytostimulators, and sequestration of nutrients such as nitrogen, phosphorous, and iron [42,43] (Figure 1).

Table 1. Various PGPR action mechanisms augmenting plant growth.

PGPR Mechanism	Microorganism	References
Nitrogen fixation	Bacillus, Rhizobium, Azotobacter, Azospirillum, Frankia, Gluconacetobacter, Burkholderia, Azorhizobium, Beijerinckia, Cyanobacteria	[21,38,44,45]
Phosphate solubilzation	Arthrobacter, Burkholderia, Enterobacter, Microbacterium Pseudomonas, Bacillus, Erwinia, Rhizobium, Mesorhizobium, Flavobacterium, Rhodococcus, Serratia	[46,47]
Siderophore production	Pseudomonas, Bacillus, Rhizobium, Azotobactor, Enterobacter, Serratia	[48]
Phytohormone production	Rhizobium, Bradyrhizobium, Mesorhizobium, Bacillus, Pantoea, Arthrobacter Pseudomonas, Enterobacter, Burkholderia, Agrobacterium, Xanthomonas, Azospirillum,	[49,50]
Antibiotic production	Bacillus species, Pseudomonas species, Burkholderia, Brevibacterium, Streptomyces	[51,52]
Volatile metabolite production	Pseudomonas, Bacillus, Burkholderia, Agrobacterium, Paenibacillus polymyxa, Xanthomonas	[53]
Lytic enzyme production	Bacillus, Pseudomonas species	[54]
Induced systemic resistance	Pseudomonas, Bacillus, Serratia, Azospirillum, Trichoderma	[55]
Stress tolerance	Pseudomonas, Bacillus, Pantoea, Burkholderia, Rhizobium	[36,56]
Biocontrol agents	Pseudomonas, Bacillus, Trichoderma	[57,58]

summarizes various PGPR mechanisms and the organisms reported as PGPR for augmenting plant growth and biocontrol.

2.1. Direct Plant Growth Promotion

PGPR increase plant growth directly by aiding in the procurement of nutrients such as nitrogen, phosphate, and iron from the soil, and by the production of phytohormones such as auxins, cytokinins, and ethylene [42,59].

2.1.1. Biological Nitrogen Fixation

Nitrogen is a vital nutrient for enhancing plant growth. It is an essential component of nucleic acids, proteins, and enzymes. However, nitrogen dominates the atmosphere in a gaseous form, and it is inaccessible to plants and animals. For the assimilation of nitrogen by plants, atmospheric nitrogen needs to be converted to ammonia. This conversion is assisted by nitrogen-fixing microorganisms which contain an enzymatic complex called nitrogenase, and the process is called biological nitrogen fixation [60,61]. Nitrogen-fixing microorganisms are abundant in the rhizosphere area of soil. Biological nitrogen fixation can be either symbiotic or non-symbiotic. The symbiotic association is a mutualistic association between microbe and plant in which both organisms benefit [62]. Rhizobium, Bradyrhizobium, Sinorhizobium, and Mesorhizobium form a symbiotic association with leguminous plants, while Frankia associates with non-leguminous trees and shrubs [44]. Cyanobacteria (Nostoc, Anabaena), Azospirillum, Azotobacter, Burkholderia, Enterobacter, Gluconacetobacter, and Pseudomonas form a non-symbiotic association which may be either free-living or endophytic [21,63,64]. Thus, inoculation of nitrogen-fixing microorganism with seeds, seedlings, or soil stimulates plant growth, enhances the quality of the soil, and sustains the level of nitrogen in the soil [65].

2.1.2. Phosphate Solubilization

Phosphorus is another vital macro-nutrient required by plants for optimum growth. It is an inevitable nutrient as it plays a major role in the metabolic processes, signal transduction, biosynthesis of macromolecules, and photosynthesis [66]. More than 90% of available phosphorus is insoluble, immobilized, or precipitated, thus it is challenging for plants to absorb it. Plants are capable of utilizing phosphate as monobasic or dibasic ions. Phosphate solubilizing bacteria shows its abundance in the rhizosphere soil [67]. These phosphate solubilizing bacteria are capable of solubilizing and mineralizing phosphate [68], synthesize certain low molecular weight organic acids, such as gluconic acid and citric acid, and possess phosphatase enzyme which can solubilize inorganic phosphorus to monobasic or dibasic ions [69]. PGPR belonging to the genera Arthrobacter, Bacillus, Beijerinckia, Burkholderia, Enterobacter, Microbacterium Pseudomonas, Erwinia, Rhizobium, Mesorhizobium, Flavobacterium, Rhodococcus, and Serratia are phosphate solubilizers [47]. However, the most potent phosphate solubilizers belong to the genera of Bacillus, Enterobacter, Erwinia, and Pseudomonas [46]. Apart from catering soluble phosphorus to the plants, it also boosts plant growth by invigorating the adeptness to fix nitrogen by nitrogen-fixing microorganisms [70].

2.1.3. Siderophore Production

Iron (Fe) is another crucial nutrient required by plants. It generally exists as Fe³⁺ and Fe²⁺ forms, insoluble hydroxides and oxyhydroxides in an aerobic environment due to which it is not available for assimilation by plants [71]. Rhizospheric bacteria secrete siderophores which are low molecular weight iron chelators having an affinity for complex iron. PGPR strains such as Pseudomonas, Bacillus, Rhizobium, Azotobactor, Enterobacter, and Serratia are reported to produce siderophores [48]. These PGPR strains are water-soluble, can be extracellular or intracellular, can solubilize iron from minerals or organic compounds under iron-limiting conditions, and can form stable complexes with heavy metals as well as with radioactive particles [72]. This ability indirectly aids the host plant to ease stress imposed by heavy metals in soil [42,73,74]. Assimilation of iron by plants from siderophores utilizes different mechanisms such as chelating and releasing iron, direct uptake of siderophores-iron complexes, or by a ligand exchange reaction [75].

Microbial siderophores play a dual role by helping in iron sequestration [76] followed by the abatement of stress imposed on plants by heavy metals [74]. Siderophores produced by Pseudomonads are known for their high affinity to ferric ions [77]. Siderophore production by biocontrol pseudomonads has been reported to inhibit phytopathogens such as Fusarium, Pythium, and Aspergillus species [78,79]. Pyoverdine, a siderophore produced by pseudomonads, was reported to control potato wilt disease caused by Fusarium oxysporum [80]. It also suppressed the phytopathogens Fusarium moniliforme, Fusarium graminearum, and Macrophomina phaseolina in peanuts and maize [81].

2.1.4. Phytohormone Production

Phytohormones are the most vital growth regulators, as they trigger plant metabolism and stimulate plant defense mechanisms [65]. Phytohormones such as auxins, cytokinins, gibberellins, and ethylene can be induced by certain PGPR which play an important role in root revitalization [82,83]. Bacteria belonging to the genera Rhizobium, Bradyrhizobium, Mesorhizobium, Bacillus, Pantoea, Arthrobacter Pseudomonas, Enterobacter, and Burkholderia produce various types of phytohormones [49]. The majority of microorganisms isolated from the rhizosphere possessed the ability to synthesize and release auxins [73].

Auxins play a crucial role in plant cell division and differentiation, germination, phototropism, geotropism, biosynthesis of metabolites, and resistance to stress [41]. Tryptophan amino acid in root exudates of the plant acts as a precursor for the biosynthesis of auxin in bacteria [84]. It has been reported that bacteria produce auxins as a secondary metabolite to detoxify tryptophan. There are reports stated that auxin biosynthesis is independent of tryptophan [85]. Bacteria may exhibit multiple pathways for auxin biosynthesis [86] and also function as signaling molecules to communicate and coordinate the activities of bacteria [87]. Cytokinins play a decisive role in cell division, seed germination, delaying senescence, and plant resistance to biotic and abiotic stress [88,89]. Cytokinin production was observed in PGPR strains Bacillus, Pseudomonas sp., Agrobacterium, Xanthomonas, Arthrobacter, and Azospirillum [50,90].

Gibberellins are significant regulators of fruit ripening, seed germination, and viable seeds [91,92]. PGPR strains such as Bacillus spp. Enterococcus faecium, Pseudomonas sp., and Promicromonospora were reported to stimulate the synthesis of gibberellins [50]. Ethylene acts as a plant growth hormone and plays a major role in fruit ripening, leaf senescence, gravitropism in roots, and response to biotic and abiotic stresses [21,93,94]. Bacterial genera are rarely reported to produce ethylene, but possess an enzyme capable of alleviating the negative effect of ethylene on plants. PGPR strains such as Azospirillum, Rhizobium, Agrobacterium, Achromobacter, Burkholderia, Ralstonia, Pseudomonas, and Enterobacter possess ACC (1-aminocyclopropane-1-carboxylate) deaminase enzyme which helps the plants to mitigate the effect of stress [95,96]. PGPR aids in the expression of genes encoding ethylene synthesis enzymes ACC-synthase and ACC-oxidase [97,98].

2.2. Indirect Mechanisms

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 [40].

2.2.1. Non-Volatile Biocidals (Antibiotics and Fungicidals)

PGPR produces low molecular weight compounds possessing antimicrobial activity even at low concentrations [99]. Due to these compounds PGPR are the first choice among biological control agents for sustainable agriculture. PGPR produce non-volatile compounds such as phenazines, phloroglucinols, pyoluteorin, pyrrolnitrin, and cyclic lipopeptides (CPLs) to suppress plant pathogens [90]. PGPR belonging to the genera of Bacillus, Pseudomonas, and Streptomyces have been reportedly exploited for the management of plant diseases in many economically important crop plants [100,101,102].

Phloroglucinols is a broad-spectrum antibiotic produced by many strains of bacteria that induce systemic resistance in plants by aiding as a peculiar elicitor of phytoalexins [103]. Fluorescent pseudomonads strains producing 2,4-diacetylphloroglucinol (DAPG) are associated with plant root protection against soil-borne phytopathogens [104]. It is reported to inhibit fungal pathogens such as Fusarium, Pythium, Rhizoctonia, and Alternaria, causing diseases such as damping off, root rot, and wilting diseases [105,106,107]. Phenazines are heterocyclic nitrogenous compounds produced by bacterial genera Pseudomonas, Burkholderia, Brevibacterium, and Streptomyces [108,109]. They are known for their competency to control plant pathogenic fungi and nematodes [52,107]. Fluorescent pseudomonads such as Pseudomonas fluorescens, Pseudomonas chlororaphis, and Pseudomonas aeruginosa are reported to produce phenazine derivative phenazine-1-carboxylic acid effective against various fungal and bacterial pathogens such as Gaeumannomyces graminis, Pythium sp., Polyporus sp., Rhizoctonia solani, Actinomyces viscosus, Bacillus subtilis, and Erwinia amylovora [57].

Fluorescent and non-fluorescent strains of Pseudomonas species were reported to produce broad-spectrum antifungal metabolite pyrrolnitrin with excellent fungicidal activity against plant pathogenic fungi such as Rhizoctonia solani, Fusarium graminearum, and Phytophthora capsici [110,111,112]. Pseudomonas and Bacillus sp. are reported to produce diverse cyclic lipopeptides that possess plant resistance induction by stimulating and strengthening plant defense mechanisms, facilitation of root colonization, and antimicrobial potential [113,114]. Based on the length and composition of the fatty acid tail, along with the number, nature, and configuration of the amino acids in the peptide moiety, cyclic lipopeptides (CLPs) of Pseudomonas sp. have been classified into four major groups, namely viscosin, amphisin, tolaasin, and syringomycin [115]. Members of the Bacillus species were reported to produce three types of cyclic lipopeptides namely iturin, surfactin, and plipastatin-fengycin based on their amino acid sequence and fatty acid branching [116]. These cyclic lipopeptides have been reported cidal to may phytopathogens such as Pseudomonas syringae, Xanthomonas axonopodis, Sclerotinia sclerotium, Botrytis cinerea, Colletotrichum gloeosporioides, Aspergillus species, Fusarium moniliforme, and Alternaria alternata [114]. Therefore, the production of non-volatile compounds by PGPR provides antagonistic agents against numerous phytopathogens [117].

2.2.2. Volatiles Biocidal

Bacteria produce numerous secondary metabolites of a volatile nature such as fatty acid derivatives, aromatic, nitrogen, and sulphur-containing compounds as a result of various fermentation pathways [118,119,120]. These volatiles are capable of diffusing through the soil pores so that roots can efficiently absorb them. Bacterial volatiles are diverse in their chemical structures ranging from aliphatic (dimethyl disulfide), aromatic (indole), ketones, alkanes, or alkenes (1-undecene), and terpenes (e.g., geosmin) [121,122]. Bacterial volatiles have been isolated from species of Pseudomonas, Bacillus, Burkholderia, Agrobacterium, Paenibacillus polymyxa, and Xanthomonas [123]. Each bacterial strain produces a peculiar combination of volatiles that play an imperative role in the interaction of bacteria with other organisms. The volatiles produced by PGPR are reported to trigger signaling pathways of auxin, gibberellins, cytokinins, salicylic acid, and brassinosteroids [124,125,126,127]. Thus, in plants, PGPR enhance growth, seed germination, and biomass production, induce flowering, improve fruit and seed formation, and act as virulence-modulating factors, which helps in mitigating biotic and abiotic stress [53,125,128].

The PGPR volatiles dimethyl hexadecylamine and indole boost the length of primary and lateral roots and root hair density which indirectly increases root volume and surface area [129]. The PGPR volatiles 2,3-butanediol and its precursor acetoin were reported to induce plant growth and systemic resistance in plants [130]. Paenibacillus strain produces 2,5-bis(1-methylethyl)-pyrazine capable of inhibiting plant pathogens such as Rhizoctonia solani and Fusarium culmorum [131]. Bacillus megaterium XTBG34 secretes the metabolite 2-pentylfuran capable of invigorating the growth of Arabidopsis thaliana [132], while Pseudomonas fluorescens SS101 produces 13-tetradecadien-1-ol, 2-butanone and 2-methyl-n-1-tridecene capable of promoting the growth of Nicotiana tabacum [133]. Among PGPR species, Bacillus spp. are considered to be the most efficient producer of biocidal volatiles [134].

2.2.3. Hydrolytic Enzymes

PGPR produces hydrolytic enzymes such as chitinase, proteinase, cellulase, and glucanases, which directly suppress the growth of plant pathogens by damaging the structural integrity of their cell walls [135]. Hydrolytic enzymes degrade components in the cell wall of fungi and oomycetes [136]. PGPR strains of Bacillus and Pseudomonas are reported to produce hydrolytic enzymes that suppress the growth and development of filamentous fungi in vitro and in vivo conditions. Bacterial enzymes ravage oospores, affect spore germination, and germ-tube elongation of phytopathogenic fungi [137]. Thus, hydrolytic enzyme-producing bacteria are reportedly used as biocontrol agents to combat phytopathogenic fungi [54,138,139,140,141].

2.2.4. Induced Systemic Resistance

Boosting the physical defense mechanism of the plant without altering the genome of the plant is known as induced or acquired resistance. Colonization of PGPR strains near the plant roots is reported to elicit an induced systemic resistance response in plants effective against a broad spectrum of phytopathogens, and at the same time they stimulate plant growth [142,143]. PGPR strains such as Pseudomonas, Bacillus, Serratia, Azospirillum, and Trichoderma have been reported to induce systemic resistance. Ethylene and jasmonic acid signaling pathway are also reported to trigger induced systemic resistance in plants [55,144].

2.2.5. Stress Tolerance

Plants are exposed to a variety of environmental stress which hampers their growth and productivity [145]. PGPR strains are reported to induce stress tolerance in plants through a variety of mechanisms [34,146,147,148]. PGPR genera such as Pseudomonas, Bacillus, Pantoea, Burkholderia, and Rhizobium enhance the tolerance of plants against drought, salinity, heat stress, and chilling injury [36,56,149]. PGPR strains induce systemic tolerance in plants against abiotic stresses by direct as well as indirect mechanisms [146]. PGPR enhance stress tolerance by modulating osmotic balance, ion homeostasis, phytohormone signaling, boosting the activity of antioxidant enzymes such as superoxide dismutase (SOD), and peroxidase (POD) [150,151,152].

2.2.6. Osmoprotectants

PGPR associated with plants helps in alleviating osmotic stress by producing compatible solutes (osmolytes), such as proline, trehalose, polyamines, and betaines, which aid in maintaining osmotic balance and protect plants from cellular oxidative damage [152,153]. PGPR have protein-stabilizing properties that aid in the precise folding of polypeptides under in vitro and in vivo denaturing conditions [154]. These bacterial osmolytes mimic the plant osmolytes and help in enhancing plant growth [155]. PGPR strains produce exopolysaccharides which, when released into the rhizosphere, enhance the soil structure and water transport and form a rhizosheath around the roots that protect the plant from desiccation, and phytopathogens [156,157]. PGPR is reported to augment abiotic stress tolerance in crops by boosting the production of cellular metabolites either by up-regulating or down-regulating genes [158]. Halophilic Bacillus subtilis subsp. inaquosorum and Marinobacter lipolyticus SM19 produce exopolysaccharides to withstand the detrimental effect of salt and drought stress in wheat [159].

Accumulation of osmolytes such as trehalose, proline, glycine-betaine, and polyamines has been reported in plants in response to many abiotic stresses [160,161]. Amino acids and organic acids are accountable for maintaining water potential from soil to plants while the osmotic potential is adjusted by soluble sugar [160]. PGPR strains such as Azospirillum brasilense, Rhizobium etli, Corynebacterium glutamicum, and Pseudomonas stutzeri produce non-reducing disaccharide trehalose that plays multiple roles such as a signaling molecule, reserve carbohydrate, and an osmoprotectant that stabilizes enzymes and membranes [146]. Exogenous trehalose application was reported to increase the defense response of proteins and tolerance to salt and drought stress in rice plants [162]. Trehalose accumulation was reported in root nodules of Medicago truncatula and Phaseolus vulgaris under drought and salinity stress [163]. Inoculation of maize plants with genetically modified Azospirillum brasilense for trehalose biosynthesis was reported to aid in drought tolerance [164].

Amino acid proline act as an osmoregulatory solute in plants under stressed conditions [165]. Higher accumulation of proline in plants indicates increased tolerance of the plant towards stress. Inoculation of PGPR strains has been found effective to enhance proline content in plants under stress. An increase in proline content was reported in salt-stressed rice seedlings inoculated with PGPR Bacillus species [166,167]. Lycopersicon esculentum treated with Bacillus polymyxa reported an enhanced level of proline to survive drought stress [168]. A PGPR strain Pseudomonas fluorescens MSP-393 was reported to synthesize osmolytes such as alanine, glycine, glutamic acid, serine, and threonine as a result of salt tolerance [153].

2.2.7. Ion Homeostasis

Regulation of ionic gradient is essential for the proper functioning of biological processes. The high concentration of inorganic ions such as Na⁺, K⁺, Ca²⁺, Mg²⁺, and Cl⁻ in the soil makes soil saline and generates osmotic and ionic stress in plants. Osmotic stress is generated when salt concentrations are higher outside roots, leading to a reduction in water uptake while ionic stress is generated due to the accumulation of Na⁺ above a threshold in leaves [169,170]. Thus, the maintenance of ion homeostasis is essential for the development and growth of plants under salt stress [171].

Sodium chloride (NaCl) contributes a major share in imparting soil salinity. Elevated levels of Na⁺ and Cl⁻ contend with the absorption of mineral ions such as K⁺ and Ca²⁺, thereby altering intracellular ionic balance and other processes such as activation of enzymes and induction of protein conformations associated with these mineral ions [172,173]. Negative impacts of salt stress can be mitigated by increasing the level of K⁺ and Ca²⁺ [174]. To minimize salt stress, plants adopt a mechanism that helps in the efflux of Na⁺ and influx of K⁺ [175]. Thus, the study of transport and compartmentalization of Na⁺ is very essential to understand salinity tolerance in plants.

Plants utilize multiple sodium transporters to maintain sodium homeostasis. Na⁺/H⁺ antiporter plays an important role in salinity stress tolerance in plants by transporting Na⁺ into the vacuole when it enters the cytoplasm [176]. Protons pump V-ATPase (H⁺-ATPase) present in vacuolar membranes aid in secondary transport, solute homeostasis, and vesicle diffusion in plants [177]. The high-affinity potassium transporters (HKTs) are another class of Na⁺ transporters that salvage Na⁺ from the xylem stream and contain them in the roots, thus shielding the aerial tissues from salt injury [178,179]. HKT transporters are reported to retain stability between sodium and potassium ions under salinity stress to diminish sodium ion toxicity [180]. A salt overly sensitive (SOS) pathway produces proteins that regulate Na⁺ efflux from a cell by encoding the plasma membrane Na⁺/H⁺ exchanger [181].

PGPR helps in maintaining ion homeostasis by a variety of mechanisms such as the formation of rhizosheaths around roots which not only alter root structure but also help in trapping cations, regulating the expression of ion transporters, enhanced macro and micronutrient exchange to mitigate the deleterious impact of a high influx of Na⁺ and Cl⁻ ions [152]. PGPR boosts the activity of high-affinity potassium transporters which helps alleviate the levels of Na⁺. Inoculation of a novel PGPR Kocuria rhizophila Y1on salt stressed maize showed improved Na⁺ exclusion [182]. Arbuscular mycorrhizal fungi Glomus intraradices selectively uptake K⁺, Mg²⁺, and Ca²⁺ leaving Na⁺ uptake to alleviate salinity stress in the host plant [183]. Puccinellia tenuiflora ahalophytic grass when inoculated with Bacillus subtilis GB03 exhibited a reduced accumulation of Na⁺ [184]. A halotolerant plant growth-promoting rhizobacterium Bacillus sp. SR-2-1/1 augmented salt tolerance of maize plants and exhibited positive expression of plant ion homeostasis genes NHX1, SOS1, H⁺-PPase, and HKT1 [185]. Another halo tolerant plant growth-promoting rhizobacteria (PGPR) Sphingobacterium BHU-AV3 improved salt tolerance in tomato by expressing salt stress proteins such as enolase, ATP synthase, thiamine biosynthesis protein, elongation factor 1 alpha (EF1-alpha), and catalase [186].

2.2.8. Antioxidant Enzymes

Plants being exposed to multiple stress leads to the production of ROS, such as superoxide anion radicals, hydrogen peroxide, hydroxyl radicals, and singlet oxygen, which react with biomolecules such as proteins, lipids, and nucleic acids, and lead to oxidative damage to cell components, thereby hindering their normal functions [187,188,189]. To surmount the negative impact of these reactive oxygen species, plants develop antioxidant defense systems that restrict the accumulation of reactive oxygen species and mitigate the oxidative damage due to stressed environments [190]. Antioxidant defense systems in plants can be enzymatic or nonenzymatic.

Enzymes such as SOD, POD, catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR), and non-enzymatic components such as tocopherol, flavonoids, phenols, glutathione, and ascorbic acid are associated in scavenging ROS molecules [191,192]. PGPR inoculation has been reported to reduce oxidative damage to plants caused by multiple abiotic stresses such as drought, salinity, water, and heavy metals by activating antioxidant defense systems in plants [56,188,193]. PGPR induced an enhanced expression of antioxidant enzymes such as superoxide dismutase, peroxidase, catalase, and polyphenol oxidase [194,195,196].

PGPR inoculation improves the antioxidant status of plants. Inoculation of Pseudomonas lini, Serratia plymuthica, and the combination of both bacteria significantly decreased the detrimental effects of oxidative damage by increasing production of antioxidant enzymes such as SOD and POD in Ziziphus jujube [112]. Root inoculation of two PGPR strains, Pseudomonas fluorescens WCS417r and Bacillus amyloliquefaciens GB03, on Mentha piperita grown under drought stress reported increased peroxidase and superoxide dismutase enzyme activities [197]. Bacillus licheniformis (FMCH001) inoculation on plants reported an increased activity of catalase enzymes in roots, which neutralizes the deleterious effect of ROS by hydrolyzing hydrogen peroxide to water and oxygen [198]. Tomato plants inoculated with the salt-tolerant PGPR strain Sphingobacterium BHU-AV3 induced salt tolerance and antioxidant enzymes such as POD, SOD, and polyphenol oxidase (PPO) in the plant [186].

3. PGPR as a Sink for ACC Deaminase Enzyme

Plants growing under stressful conditions produce increased levels of 1-aminocyclopropane-1-carboxylic acid (ACC) which immediately act as a precursor for ethylene biosynthesis [199,200]. However, ethylene is a phytohormone involved in regulating various physiological processes of plants, its increased concentration imposes senescence leading to a reduction in plant growth [201] (Figure 2). PGPR helps to control plant ethylene homeostasis by expressing the genes for enzyme ACC deaminase that cleave ethylene precursor ACC to ammonia and α-ketobutyrate, thereby alleviating the level of ethylene in plants [96,202]. ACC deaminase enzyme has been reported in rhizobacteria belonging to the genera Achromobacter, Acidovorax, Alcaligenes, Enterobacter, Klebsiella, Methylobacterium, Pseudomonas, Rhizobium, and Variovorax [203].

Biosynthesis of indole acetic acid by PGPR trigger the plant cell elongation which induces the transcription of a key enzyme for ethylene biosynthesis, i.e., ACC synthase enzyme which catalyzes the conversion of S-adenosyl methionine to ACC which is further converted into ethylene by the enzyme ACC oxidase [205,206]. Plants, when exposed to stress, induce the enzyme ACC synthase, which catalyzes the synthesis of ACC, which exudes from roots to the soil. The increased concentration of ACC induces the bacterial ACC deaminase enzyme, which catabolizes. The use of PGPR with ACC deaminase activity for improving plant growth and stress tolerance is a promising biotechnological approach for sustainable agriculture. ACC deaminase-producing PGPR bacteria Aneurinibacillus aneurinilyticus and Paenibacillus sp., from rhizospheric soil of garlic promoted plant growth by alleviating the negative effects of salinity stress on Phaseolus vulgaris L. [200]. Inoculation of ACC deaminase producing Variovorax paradoxus RAA3 and a consortium of Pseudomonas sp. Enhanced the growth, nutrient content, and antioxidant properties of Triticum aestivum L. under rainfed and drought conditions [207]. ACC deaminase-producing rhizobacteria have been reported to enhance plant growth by mitigating the detrimental effect of salt stress [117,208].

4. PGPR and Disease Suppression

Plant pathogens significantly impact plant growth and limit productivity in many crop plants. The use of PGPR strains are gaining interest as potential biocontrol agents for suppressing plant pathogens and induce disease resistance in plants. PGPR root colonizers, such as Pseudomonas and Bacillus strains, are reported to elicit plant defenses [77,209]. These organisms produce metabolites having antimicrobial activity and secrete extracellular cell wall lysing enzymes which inhibit plant pathogens, compete for nutrients, aid in promoting plant growth, and induce host systemic resistance [51,189,210].

PGPR activate the expression of dormant defense mechanisms in plants on exposure to phytopathogens by triggering the synthesis of signaling molecules such as salicylic acid, jasmonic acid, and ethylene [211,212]. PGPR also produce phytopathogen growth-inhibiting substances such as pyrrolnitrin and pyoluteorin, 2,4-DAPG [142]. These PGPR combine diverse mechanisms of microbial antagonism and plant growth promotion to suppress phytopathogens to augment plant growth [213,214]. PGPR strains have been reported to suppress a range of fungal pathogens of the plant such as Rhizoctonia, Fusarium, Pythium, Alternaria, Ralstonia, Phytophthora, and Botrytis [215,216]. PGPR strains Bacillus sp. and Pseudomonas sp. are the most effective to control various plant diseases through various mechanisms [134,217]. These strains are reported for the production of metabolites such as hydrogen cyanide, lytic enzymes, antibiotics such as 2,4-DAPG, acyl-homoserine lactone, siderophores (pyochelin and pyoverdines), biosurfactants such as glycolipids, phospholipids, fatty acids, lipopeptides, and lipoproteins which play a major role in phytopathogen inhibition [79,218,219].

5. PGPR and Quorum Quenching System

One communication strategy employed by bacteria is the use of specific signaling molecules called N-acyl homoserine lactones (AHLs), which act as self-inducers to sense environmental changes and bacterial population density [220]. It regulates the expression of multiple genes, many of which have been associated with virulence factors or biofilm formation in various plant pathogens [100,221,222]. The disruption of quorum sensing (QS) can thus be used as a strategy to combat phytopathogens in agriculture [223] (Figure 3). Quorum quenching (QQ) is a strategy that enzymatically degrades AHL signals which further interrupts QS [224]. Many Gram-positive and Gram-negative bacteria such as Bacillus, Agrobacterium, Rhodococcus, Streptomyces, Arthrobacter, Pseudomonas, and Klebsiella have been reported to possess QQ strategy [225]. Many species of the genus Bacillus possess quorum quenching enzyme AHL-lactonase (AiiA) that hydrolyze the lactone ring and amide linkage in AHLs, thereby blocking the QS systems and mitigating the phytopathogenesis [226,227].

The QQ enzyme-based disruption of QS systems is an innovative strategy to silence the pathogenicity genes [223] and can be used as a versatile technique to substitute traditional antibiotic treatments. Many rhizobacteria have been reported to utilize AHLs as signaling molecules to intercede functional activities such as eliciting systemic resistance in host and production of antifungal metabolites for their survival or the establishment of beneficial interactions with the plant [139,228,229]. While quorum quenching bacteria and their enzymes have been thoroughly investigated by researchers, the practical applicability of this strategy remains limited due to the high substrate specificity of these enzymes. This strategy thus presents a challenge in developing approaches that target a broad range of signaling molecules.

6. 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 [230]. According to Nemecek and Gaillard [231], 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 [232,233]. 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 [234,235] (Figure 4).

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 [236,237,238,239]. Reclamation of such saline soils for agricultural activities is time consuming and not cost effective [240,241]. 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 [242] but these processes possess fewer efficacies in hypersaline soils [243]. Salt tolerant PGPR (ST-PGPR) have been reported to ameliorate salt stress in the plant by direct and indirect mechanisms [36,244,245]. PGPRs produce phytohormones such as cytokinins, auxins, and gibberellins [246], antioxidative enzyme ACC deaminase [117,245], exopolysaccharides [247,248], and osmolytes [249,250] (Figure 5). Pseudomonas, Enterobacter, Bacillus, Klebsiella, Streptomyces, Agrobacterium, and Ochromobacter are reported to improve the productivity of crops under salt stress [251,252]. Rajput et al. [253] 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 [254]. 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 [255]. Its genome deciphering revealed the presence of several genes which enabled it to function in drought, hypersaline, polyaromatic hydrocarbons (PAHs), and heavy metal contamination.

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 [256]. 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 [257]. 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 [258]. 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 [259]. The effect of salt stress on plant development is represented in Figure 5.

7. 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 [260].

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 pqqA, pqqB, pqqC, pqqD, pqqE, and pqqF [261]. Phosphate-solubilization genes, such as gabY, phoC, acpA, napD, and napE genes, and the pqq gene family, were isolated from Pseudomonas cepacia, Morganella morganii, Francisella tularensis, and Burkholderia cepacia [262]. 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 [263]. 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 [69]. PGPR were reported to induce changes in the gene expression of nitrate and ammonium uptake genes in Arabidopsis thaliana [264].

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 [265]. 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 [266]. Kerff et al. [267] 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 [268,269]. B. subtilis RR4 is reported to suppress various defense-related genes during colonization to roots of rice plantlets to boost plant immunity [270]. 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.

8. Triggers for PGPR Colonization

The efficiency of PGPR as inoculants for crop plants is influenced by multiple factors. Soil health and exudates secreted by plant roots play a major role in bacterial colonization. Root exudates initiate the rhizospheric relation between plants and microbes through the secretion of a variety of compounds [268,271]. The chemical composition of root exudates is under the genetic control of the host plant [272]. These molecules can act as signaling molecules, chemotaxis agents to establish symbiotic or non-symbiotic relationships with microbes, and function in defense against pathogens [273]. Secretion of flavonoids by plants is reported to trigger the expression of rhizobial genes (nod, nol, and noe) which are essential for nodulation and efficient nitrogen fixation [274]. Various secondary metabolites such as triterpenes, glucosinolates, cinnamic, coumaric, ferulic, syringic, and vanillic acids are also reported to elicit defense mechanisms [273,275]. Root exudates can cause variations in the microbial community structure and diversity in the rhizosphere [276,277]. Thus, the secretion of the root exudates leads to chemical changes in the composition, properties, and nutrients in the rhizosphere [278]. It can therefore be concluded that root exudates define the association between the plant and rhizosphere microbial communities.

9. Molecular Mechanisms of PGPR

Genomes of plants contain a large number of genes which showed specific expression against heavy metal abiotic stress [279,280,281]. As essential nutrients and heavy metals share some similarity; PGPR can transfer to root via nutrient transport pathway with the help of genes and membrane transporter proteins. A large number of genes play key roles in metal transport and their accumulation. The transporter gene families such as ZRT- and IRT-like protein (ZIP), heavy metal ATPase (HMA), cation diffusion facilitator (CDF), natural resistance-associated macrophage protein (NRAMP), cation proton exchanger (CAX), ABC transporter, calcium cation exchangers (CCX), and low-affinity cation transporters (LCT) are involved in transportation of heavy metal and their accumulation [282,283].

The expressions of several metal transporter genes are greatly significantly influenced by PGPR inoculations. Bacillus amyloliquefaciens strain was able to change the expression of FIT1, IRT1, and FRO2 genes, for the accumulation of Fe and Cd in Arabidopsis tissues [284]. Pseudomonas fluorescens Sasm05 strain enhance the growth and metal accumulation in Sedum alfredii tissues by expressing SaHMAs, SaNRAMPs, and SaZIPs genes families [285]. A bacterial strain, SaMR12, up-regulates the expression of large number of metal transporter gene in S. alfredii plant [286]. As per Ghassemi and Mostajeran [287], Azospirillum brasilense enhances the Cd tolerance in T. aestivum with the help of Tatm20 gene. Jebara et al. [288] reported PCS and F-box as the main genes for Cd tolerance in Sulla coronaria.

The inoculation of PGPR plays a key role in genes expression related to growth and metabolic processes to systematize the physiological growth (surface area, biomass, lateral root number, thickness, bushiness, and lateral root formation) of plants and their biochemical expressions (SOD, CAT, APX, DHAR, and GR genes) against environmental stress [289]. Auxin metabolism genes OsIAA1, OsIAA4, OsIAA11, and OsIAA13 expression enhanced after inoculation of Bacillus altitudinis strain [290]. PGPR incoculation up-regulates mRNA expression of antioxidant genes (SOD, POD, and PPO) in Lycopersicon esculentum under metal stress [291]. Multiple literature reviews have demonstrated that PGPR strains can differentially affect genes involved in growth and metabolism of plants. The advancements in sequencing technologies and differential gene expression analysis will further improve our potential to analyze alterations in plant gene expression in response to diverse signals and stresses.

10. Genetically Engineered PGPR Strains

Genetically modified bacteria and plant interactions have been studied for various abiotic stresses [292]. Genetically engineered PGPR can be responsible for biotic-abiotic stress regulation, metal uptake transport, chelation, degradative enzymes regulation, homeostasis, and risk mitigation [293]. Genetically engineered PGPR isolates should possess several important criteria such as (i) stability with high expression, (ii) tolerance, and (iii) survival capacity in plant rhizosphere [294].

Genetically engineered Pseudomonas putita 06909 have been used as a bioinoculant to reduce the phytotoxicity effect of Cd [295]. Qiu et al. [296] reported that genetically engineered PGPR strain Enterobacter sp. CBSB1 with bi-functional glutathione synthase gene (gcsgs) improve the heavy metal tolerance in Brassica juncea. MerP and MerT proteins and metallothionein were studied in Rhodopseudomonas palustris for expression against heavy metal [297]. PGPR strains were engineered to protect host plants, to improve seed germination, and to enhance biotic and abiotic stresses [298]. Transgenic plants transformed with IMT1 gene encode myo-inositol-O-methyltransferase enzyme for the biosynthesis of D-ononitol to tolerate abiotic stress.

11. 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 [299,300]. 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 [301]. Specific microbial groups can regulate ecosystem functions such as N₂ fixation, nitrification, denitrification, and methanogenesis [302]. 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 [303]. Warming directly alters soil respiration rates of a microbial community due to temperature sensitivity [304]. 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 [305]. 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 [306,307,308]. Rising temperatures increase carbon allocation symbiotic to parasitic association [309,310] 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.

12. Future Perspectives and Conclusions

The demand of food production is increasing as the human population is growing under climate change and a limited base of farmland. These challenges have been addressed so far with molecular techniques and chemical application (using fertilizers and pesticides). The growth of organic food production has boosted in recent years owing to an increased awareness amongst people about the side effects of chemically grown food products. The emerging pandemic has boosted the demand for consuming organic and healthy food free from chemical fertilizers and pesticide residues. A sustainable alternative to replace chemical fertilizers and pesticides is the use of bio-derived materials. Among the biological materials used for sustainable agricultural production, PGPR-based bioformulations have sparked immense attention as 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, and regulation of development and physiology of plants. Despite the enormous advantages offered by PGPR to the host plant, their full-fledged use for agricultural purposes poses several challenges. Many PGPR formulations fail when they are moved from lab conditions to field trials. Multidisciplinary research is necessary to unravel the rhizospheric chemistry and to identify potent rhizospheric microbes and microbial communities for efficient formulations. Microbiome engineering and rhizosphere engineering using multi-omics techniques such as metabolomics, metagenomics, transcriptomics, and metatranscriptomics hold the potential to identify and manipulate microbial diversity and characterize potent strains based on their persistence in the field. ST-PGPR could serve as an effective and significant measure to alleviate salinity to improve production of global food. The utilization and commercialization of beneficial phytomicrobiome members are now widely being considered to a great extent. Enhancement of saline soils productivity will help to achieve food security, as will enhancing the quality and content of soil organic matter in nutritionally poor agro-systems. It will also help to combat climate change and reduce the carbon footprint.