1. Introduction

Extensive nutrient mining and risky application of synthetic agrochemicals, including various chemical fertilizers and growth regulators, are considered the triggering factors for the deleterious fate of global arable soils in conventional farming [1]. Therefore, sustainable nutrient cycling and soil health management become challenging through conventional farming practices. To address these critical complications, soil-inhabiting rhizobacteria with beneficial features for plant growth were regarded as the potential alternatives for synthetic fertilizers [2]. Beneficial rhizobacteria should be considered as a sustainable option instead of conventional practices due to multifunctional benefits in terms of cost, environmental impact, and soil fertility [3]. However, the sustainable application of these potential and beneficial rhizobacteria was considered as the hammer and nails of green agricultural microbiology.

Rhizobacteria are bacteria from diverse genera which are living in the rhizosphere of plants. Among the rhizobacterial bulk, several genera of bacteria have been proven for plant growth promotion are termed as ‘beneficial rhizobacteria’ ^[4][5][4,5]. There are various modes of action for plant growth promotion through the adoption of beneficial rhizobacteria [6]. The growth promotion should be rendered by direct mechanisms, such as nutrient cycling and solubilization, production of phytohormones, and modulation of bioactive materials ^{[5][6][7][8][9][10][11]}[5,6,7,8,9,10,11]. In addition, several indirect mechanisms, such as biocontrol activities, induction of stress mitigating genes, production of secondary metabolites, and volatile organic compounds via beneficial rhizobacteria, were reported during root colonization ^[8][11][12][8,11,12]. Several potential genera, such as Bacillus, Pseudomonas, Enterobacter, Lysobacter, Serratia , and Burkholderia , have exhibited excellent growth promotion and plant defense features towards sustainable agriculture through genetic advancement of soil-inhabiting beneficial rhizobacteria ^{[7][8][9][10]}[7,8,9,10]. However, Bacilli are considered as the key drivers for the enhancement of plant growth through biostimulation and biocontrol mechanisms ^[10][11][10,11]. As a result, beneficial rhizobacteria present innate potential for plant nutrition maintenance.

In general, a plant can modulate its physiological strategies to tolerate various climate change-oriented abiotic stress conditions, such as drought, salinity, heat stress, and metal toxicity ^[5][6][11][5,6,11]. However, osmoregulation, proline accumulation, total soluble solid and osmotic adjustment, antioxidant activities, regulation of stress-responsive gene (SOD, GR, CAT, POD, etc.), and inducing heat shock proteins were considered as predominating mechanisms of plants to ameliorate the stressful conditions ^[6][7][6,7]. Thus, there is an urgent need to introduce an environment-friendly approach for sustainable agriculture to feed the growing population worldwide [13]. Beneficial rhizobacteria may enhance crop productivity and improve plant growth by handling the stressful conditions of plants, such as plant diseases, pest attacks, and various biotic and abiotic stresses in a sustainable manner ^[13][14][13,14]. Increasing evidence of earlier research revealed that beneficial rhizobacteria could enhance soil fertility, nutrient bioavailability, and plant growth and development while maintaining the surrounding environment in an ecofriendly manner ^[15][16][15,16].

Rhizobacteria enhance a plant’s tolerance to various stresses, such as pest infestation, drought, salinity, hot and cold stresses, and improve the yield of crops under changing climatic conditions ^[17][18][17,18]. Despite the multifunctional benefits of rhizobacteria for sustainable plant nutrient management, there are still several challenges that exist as a barrier to the commercial application of these rhizobacteria in real field conditions ^[13][19][20][13,19,20]. Thus, soil microbiological research has extended to the elucidation of the mechanisms for the prevailing constraints of the commercialization of beneficial rhizobacteria [14]. In light of the current research demand for beneficial rhizobacteria and their long-term application in soil and plant health, currthent researchs goal of this review is to focus on current beneficial rhizobacteria research trends, existing research uncertainties, and practical challenges for commercial and field applications. The specific goals of this review were to (i) explore the multivariate features of beneficial rhizobacteria for mitigating climate change-related stress conditions; (ii) accelerate the understanding of the underlying mechanisms of beneficial rhizobacteria-mediated stress mitigations; and (iii) unlock the potentialities of biotechnological advancement (including OMICS-derived bacteriological engineering). Furthermore, the commercial and long-term usage of beneficial rhizobacteria for sustainable agriculture is emphasized.

2. Rhizosphere as a Crucial Hotbed for Plant-Beneficial Rhizobacteria Interaction

The rhizosphere is the ‘playhouse’ near the soil and root zone where soil, plants, and microorganisms are interlinked for the development of a platform for soil–plant–microbe interactions ^[20][21][20,21]. The most important stakeholders in the rhizosphere can merge their interactive physics, chemistry, and biology for making the rhizosphere a home for microscopic soil drivers, such as bacteria, fungi, and archaea [12]. The term ‘Rhizosphere’ was introduced by eminent scientist Hiltner in 1904. According to him, the soil zone near the root is the rhizosphere, which is distinctly divided into ecto-rhizosphere, rhizoplane, and endo-rhizosphere regions [22].

The relationship of rhizospheric bacteria and plant roots is transient and depended on the exchange of nutrients and carbon sources among the interactive organisms. ‘Root exudates’ are the driving force for the enhanced interaction of rhizobacteria and plant roots in the rhizosphere zone [23]. The nutrient compounds, such as carbohydrates, organic acids, and hormones present in root exudates may act as the signaling chemicals to colonize in the rhizospheric root for the soil-inhabiting microbes including beneficial rhizobacteria ^[8][19][22][8,19,22]. Thus, a mutual exchange of root exudates and plant nutrients derived from beneficial bacteria turn the rhizosphere into a hotbed for diverse genera of beneficial rhizobacteria [23] ( Figure 1 ). However, the beneficial and positive interaction of plant roots and associated rhizobacteria primarily should be governed by the modulation of root exudates, compounds such as carbohydrates, and the flow of root exudates irrespective of plant species ^[24][25][24,25]. Therefore, the proliferation of the root systems is not considered as a triggering factor for plant–microbe interactions if the complex interactions and composition of root exudates are relatively poor. This kind of positive interaction of beneficial rhizobacteria and plant roots is a blessing for green and sustainable agriculture [19].

Figure 1. Plant-microbes interactions in the rhizosphere (a hotbed for interlinked microbes and plant root zone) mediated by system signaling, exudates secretion, and colonization potentiality are directly and indirectly improve plant growth and stress tolerance.

Although the rhizosphere is a niche for several bioactive molecules, volatile organic compounds, sugars, and organic acids, the engineering of the rhizosphere can alter the chemical feature of the rhizosphere in a positive direction [26]. The complex and biochemical and metabolic processes between plants and associated rhizobacteria are mainly facilitated by carbon deposition and their utilizations [27]. The microbial signal can vary based on the plant types, soil properties, and root exudates during the interaction of plant-microbe in the region of the rhizosphere [28]. A recent study noticed a positive correlation between the abundance of rhizospheric bacteria and fungi with soil organic matter (SOC) and conducive pH conditions [29]. Additionally, the vegetation patterns of the soil rhizosphere may also trigger the microbial ecology of the rhizosphere. Similarly, soil organic amendment is reported as the key driver for the dramatic shift of the rhizobacterial community [30]. The interaction of the N-cycler bacterial community with the nematode is evident for the sustainable improvement of nutrient cycling. Thus, a multivariate interaction to explore the plant–microbe relationship has occurred in the rhizospheric region mediated by various factors. Plant– microbe interactions in the rhizosphere simultaneously may enhance the growth of plants [31] and alleviate the plant biotic and abiotic stress conditions ^[8][17][18][8,17,18]. Therefore, the rhizosphere works as a playground for the interlinked microbes including beneficial rhizobacteria [31].

3. Application of PGPR for Sustainable Soil Health and Native Microbial Diversity

The soil health and productivity of the soil are mostly controlled by the abundance and interaction of the native soil microbial community ^{[32][33][34][35][36]}[174,175,176,177,178]. Soil-inhabiting beneficial rhizobacteria (i.e., PGPR) are the most influential and environmentally sustainable biological drivers to enhance soil quality and fertility ^{[37][38][39][40][41][42][43]}[179,180,181,182,183,184,185]. Beneficial rhizobacteria may help in fixing atmospheric nitrogen, biogeochemical cycling of minor plant nutrients, solubilization of soil-bound nutrients, production of plant growth promoting hormone, and modulation of polysaccharides. These polysaccharides are helpful during soil structure formation and thus maintaining the sustainable biodiversity of soil biota and improved crop production ^[44][186]. Potential PGPR may regulate nutrient cycling through various mechanisms as an in-situ green alternative to synthetic fertilization ^[45][46][187,188]. In addition, PGPR improves soil health through decomposing crop residues, synthesizing and mineralizing soil organic matter ^[47][189]. Soil organic matter and root signaling for the secretion of exudates at the rhizosphere region act as the key factors for the positive interaction of the rhizospheric microbiome with the plant to improve soil quality ^[25][29][25,29]. Thus, PGPR are considered the best natural alternatives to chemical fertilizers to maintain sustainable soil health.

However, potential PGPR strains isolated from the rhizosphere can influence the diversity of the indigenous rhizosphere microbiome by modifying the quality and quantity of root exudates, producing antibiotics and siderophores, and maintaining a cooperative relationship with closely associated microorganisms ^[48][49][50][102,103,190]. Besides, the addition of exogenous PGPR is regarded as a potential competitor to native microbial activities and diversities ^{[34][51][52][53][54][55][56][57]}[176,191,192,193,194,195,196,197]. Therefore, the potential change of the microbial population affected by the PGPR is a key concern of soil microbial ecology, while PGPR are now widely used to improve crop production ^[58][198]. Kokalis-Burelle et al. (2006) reported the inoculation of Capsicum annuum with two PGPR strains B. subtilis GBO3 and B. amyloliquefaciens IN937a did not adversely affect the native beneficial bacterial population, whereas, increased fungal population without causing any root diseases ^[59][199]. Similarly, the inoculation of pepper seedlings with a beneficial bacteria ( B. amyloliquefaciens ) increased the native bacterial and fungal biomass in the rhizosphere of soil ^[60][200]. In contrast, none of the halo-tolerant PGPR inoculations disturb the soil microbial population in maize ^[61][140], cucumber ^[62][201], and peanut ^[58][198]. However, the bacterial community in the rhizosphere mostly differed due to the soil type and crop growth stage ^[63][202]. A recent study reported the mutual relationship between the soil microbial diversity and dynamic soil function, which may be manifested by various interactions of plant–microbes for enhancement of overall soil quality ^[64][203]. Therefore, further research should be designed on different soil types and crop growth stages to explore the effect of PGPR strains on native microbial diversity.

4. Advanced Biotechnological Tools for Improving Beneficial Rhizobacteria

The key challenges to the commercial application of beneficial rhizobacteria are the lack of suitable formulations during storage, varied performance in real field applications, and loss of potency over time ^[65][213]. These research drawbacks can be managed by enhancing the genetic makeup of beneficial rhizobacteria through various advanced genetic tools, such as genomics, metabolomics, and proteomics (see Figure 24 ). Among the smart biotechnological tools, next-generation sequencing (NGS) is a fairly popular attempt to screen out the target beneficial gene or gene cluster ^[66][214]. Comparative screening of the stress mitigating gene pool (i.e., hyperosmotic stress-tolerant gene) was carried out for the proteobacteria through various biotechnological approaches by Kohler and coworkers ^[66][214]. Similarly, a partial genome sequencing of P. polymyxa was performed to select the potential gene of beneficial rhizobacteria for sustainable agriculture ^[67][215].

Figure 2. Advancement of biotechnological approaches for a sustainable enhancement of beneficial rhizobacteria.

However, an encouraging study revealed the comparative genomic feature amongst the four species of Pseudomonas for identifying similarities and dissimilarities of plant growth promoting and plant stress alleviating gene clusters ^[68][108]. Based on study findings, the effect of Clusters of Orthologous Groups (COGs) among the studied pseudomonads exhibited common characteristic features, such as metabolism for bioactive molecules, root colonization at the rhizospheric regions, and tolerance for salinity and toxic metals. The gene analysis through advanced genomics technique among the studied PGPR and associated proteobacteria have identified the beneficial gene sequence for the plant growth promotion ^[69][216]. Additionally, several detailed genomics studies reported that the gene contributed to plant growth promotion and enhancement of plant nutrition for B. amyloliquefaciens and two Streptomyces species through whole-genome sequencing ^[70][217]. Thus, advanced genomics study of beneficial rhizobacteria may expose the potential gene/gene cluster contributing to the plant growth promotion toward green and sustainable soil microbiology.

In addition, the detailed proteomics study of PGPR ( P. fluorescens ) reported the expression of the whole protein responsible for the salt stress tolerance for upregulation of the gene and further salinity tolerance mechanism ^[71][218]. Proteomics study refers to a detailed study among the multi-omics approaches for the genetic characterization of potential rhizobacteria for plant growth promotion ^[71][72][218,219]. The study of proteomics should be coupled with transcriptomics to elucidate the complex mechanisms for plant growth promotion through the secondary metabolism of beneficial rhizospheric microbes ^[73][220]. However, the biggest limitation of proteomics and transcriptomics is the cross-checking of the potentiality of screened whole protein or transcriptomics, potentiality due to lack of available protein and transcriptional databases ^[74][221]. The metagenomics study for interpreting the genetic potentiality of the studied beneficial rhizobacteria from the environmental samples has a promising future in the advanced biotechnological screening of plant growth promoting rhizobacteria ^[75][76][222,223]. Furthermore, the innovative and interlinked studies regarding the genetic advancement of beneficial rhizobacteria can be useful for the overall development of sustainability and screening of perfect rhizobacteria for plant growth enhancement ^[77][211]. Although the application of smart biotechnological tools towards the enhancement of beneficial rhizobacteria is established, several controversial issues concerning the biosafety of PGPR studies with advanced biotechnological and microbial approaches reported ^{[78][79][35][36][80]}[39,55,177,178,224]. Therefore, extensive and appropriate care should be taken to maintain biosafety during the molecular and biotechnological studies with potential rhizobacteria to avoid any cross-contamination and further pathogenesis. The improvement of beneficial rhizobacteria through multi-omics approaches will unveil the hidden genetic mystery towards sustainable plant growth promotion.