This strain was not only used as a biostimulator but also served as a bio-control agent against Fusarium through the increased production of phytoalexin. Another group used lettuce, tomato, and soybean plants, to which B. subtilis was applied for plant growth, and this PGP species affected the shoot growth of the plants under salt stress conditions . Bisht et al. studied the alleviation of nutrient defficiency-induced stress in chickpea through the use of Paenibacillus lentimorbus, and a study conducted by Kuzmicheva et al. analyzed the soybean varieties Nice-Mecha, Bara, and Svapa in the presence and absence of Pseudomonas oryzihabitans. However, root rot epidemics have become a continual threat to crop production in commercial greenhouses that use soilless cultivation systems. Airborne dust, irrigation water, farm tools, and transplants are some of the main sources of pathogen contamination in such systems . The use of PGPRs to suppress plant diseases is a newly emerging and valuable option in soilless cropping systems . Nevertheless, the rapid identiffication and utilization of these potential bacteria with classical microbiology methods is challenging , drainage planter pot as many PGPRs are overlooked because many relevant genes are not expressed in the absence of natural chemical triggers .

The advancement of next-generation sequencing methods has enabled researchers to further investigate and understand microorganisms around the globe from different perspectives . Genome mining, which involves the analysis of the whole-genome sequence data of a PGPR to identify the genes encoding beneficial bacterial enzymes and metabolites, has revolutionized the identification and use of potential beneficial microbes . Several studies have adopted a genome mining strategy to identify PGPR strains with novel antimicrobial gene clusters that have immense biocontrol potential and plant growth stimulatory effects. Furthermore, the reliable differentiation of potentially human pathogenic PGPR strains from nonpathogenic strains has been a challenge in bacterial diagnostics . However, genome sequencing coupled with machine learning approaches, such as PaPrBaG  and DeePaC , has been reported to reliably discriminate potentially pathogenic strains from nonpathogenic strains. The modern advances in sequencing technology have not only enabled more accurate classification of bacteria according to their genomes but also allowed for deeper taxonomic identification of complex microbiomes, which represent the combined genetic material of all microorganisms occupying an environment . Such advanced techniques have also enabled us to track the spatiotemporal dynamics of PGPRs using strain-specific primers designed from whole genome sequence data . Few studies have reported on qPCR-based methods successfully used to monitor the population dynamics of inoculants in nonsterile soil and plant roots, wherein complex microbial communities reside, let alone under soilless conditions. Furthermore, Jo et al. simultaneously monitored the population of a bioinoculant and the surrounding microbiota over time.

Advanced molecular biology tools have been used to describe the structure and diversity of the entire microbial community in various environments and can help to investigate the functional roles of such communities. Korenblum et al. stated that the microbial communities associated with roots provide specifc functions to their hosts to help regulate plant growth, health, and productivity. Dong et al. also reported on the positive impact of natural microfora in controlling diseases of tomato seedlings in a soilless cultivation system. They found that Pseudomonas, which had been reported to improve plant growth and induce stress resistance in tomato and red pepper plants, was one of the most predominant genera in the nutrient solution. Furthermore, some benefcial PGP fungi, such as Trichoderma virens and Trichoderma harzianum, were detected. Sheridan et al. analyzed PGP microorganisms in the plant root zone microbiome in hydroponic cultivation systems for diferent crops through the use of amplicon sequencing targeting 16S rRNA genes. In their study, four diferent crops were inoculated with a number of strains, including Pseudomonas spp., Bacillus spp., Enterobacter spp., Streptomyces spp., Gliocladium spp., and Trichoderma spp. The authors concluded that the application of PGPRs to the plant root zone could change the microbial community even when only a small portion of the inoculated microbes colonized the root zone. Mamphogoro et al. used a similar technique to analyze the microbial communities associated with the sweet pepper Capsicum annum to identify potential biocontrol agents against pathogens. They found that the majority of the genera present in the communities consisted of Acinetobacter, Agrobacterium, and Burkholderia, which are known fungal antagonists.

Similarly, Ye et al. found that Corallococcus sp. strain EGB controlled cucumber Fusarium wilt in a hydroponic system by migrating to the plant root and regulating the microbial community. In a different study, Hultberg et al. investigated the influence of the root microbiome in the presence of inoculated Pythium ultimum at three different stages of tomato plant growth; they reported that P. ultimum changed the composition of the microbial communities in the plant rhizoplane, wherein Bacteroidetes was the dominant phylum in the presence of P. ultimum, and Proteobacteria was more abundant in the control. Another advancement in the biotechnological application of PGPRs is the use of transcriptomics. Understanding a transcriptome is essential for inferring the functional features of a genome and obtaining information on the molecular makeup of cells and tissues . Leeet al. made use of such an approach to gain insight into the responses of lettuce following treatment with the beneficial microbe Pseudomonas chlororaphis. This treatment led to the increased expression of genes involved in the response to pathogens and external stress. Moreover, the authors showed that the nodulin family, which is known to regulate phosphorylation and signaling and stimulate transport activity and resistance to osmotic and environmental stress, was expressed. Bharti et al. used a similar approach to identify the stress-responsive genes of wheat through inoculation with the PGP Dietzia natronolimnaea STR1. Their study confirmed the involvement of the ABA signaling cascade, as TaABARE and TaOPR1 were upregulated in PGPR-inoculated plants, which led to the induction of TaMYB and TaWRKY expression followed by the stimulation of the expression of a plethora of stress-related genes. Their results also showed enhanced expression of TaST, a salt stress-induced gene associated with the promotion of salinity tolerance in PGPR-inoculated plants. A group led by Gómez-Godínez used metatranscriptomics to study nitrogen fxation in maize plantlets inoculated with a group of PGPRs , which showed the expression of Azospirillum nif genes in the presence of the PGPRs. Another work by Yi et al. involved comparative transcriptomics of Bacillus mycoides strains in potatoes and provided insights into the transcriptomic profles and survival strategies of plant-associated endophytes and soil isolates of this species. Despite the plethora of studies performed to date, there remains a huge knowledge gap that needs to be addressed to commercialize PGPRs for sustainable soilless agriculture. Hence, the development of proper strategies and additional research and trials are required.In agricultural production systems, amending the soil with chemical fertilizers is considered indispensable for achieving optimum yield. However, it is well known that the constant and excessive use of chemical fertilizers disrupts the ecology of soil, affects the microbial population in the rhizosphere, pollutes groundwater and has harmful effects on human health . Therefore, the application of PGPRs in agricultural production has become popular because it significantly reduces the use of chemical fertilizers and pesticides. The use of PGPRs instead of harmful chemicals in modern agriculture is considered to be an excellent eco-friendly biotechnological approach . PGPR application increases the germination rate, development of roots, yield, leaf area, chlorophyll ratio, nitrogen ratio, protein ratio, hydraulic activity, thirst tolerance, and root and stem weight, delays the aging of leaves and provides resistance to some diseases. In the field, PGPRs may not provide expected results due to unexpected conditions.

Unfavorable environmental conditions, such as pH changes in the soil, high temperatures, low rainfall and humidity, plant pot with drainage and nutrient defficiencies, result in reduced microorganism colonization . Because conditions are more controlled in soilless agriculture practices, successful microorganism colonization increases. The presence of PGPRs increases plant resistance to stress, and they can be easily applied at any stage of the plant life cycle. Soilless agricultural practices and the application of PGPRs are likely to positively increase plant resistance to abiotic and biotic stress. PGPR application has positive effects on plant physiology and morphology to eliminate the harmful effects of stress, such as affecting plant water content, abnormal changes in hormone concentrations, and osmolytes . Soilless agriculture is expected to become even more successful in combination with effective PGPR application. To date, some studies have provided clues to its success. PGPRs have been shown to increase lentil growth and development under field and controlled environmental conditions . Studies analyzing the effects of PGPR application on tomatoes and cucumbers grown in a soilless agriculture system under greenhouse conditions have shown that PGPR application contributed positively to yield in both species . Baset Mia et al. examined the effects of PGPR application on banana plantlets produced in nitrogen free hydroponic culture. They reported that the Sp7 and UPMB10 strains increased banana seedling growth compared with that under control conditions and could be used as biofertilizers. Another study confirmed that Azospirillum spp. and Azotobacter spp. enhance the growth of strawberry in hydroponic culture . Furthermore, it was reported that Paenibacillus polymyxa increases watermelon growth in hydroponic culture . In contrast with soil culture, aquaculture practices offer the ability to control and reuse benefcial microorganisms and manage nutrient availability. In fact, the naturally occurring microbial consortia of the hydroponics are a result of the presence of roots, and dormant endophytic microbes living in the seed can initiate growth simultaneously with the plant. Therefore, all hydroponic systems have a microfora in the rhizosphere under normal conditions. However, largely because it is dependent on the chemical compounds released from the plant roots, there might be differences between the systems due to physicochemical differences in the water content and the environment surrounding the roots. For instance, hydroponic suspend roots in nutrient solution, and therefore, the compounds released from them are subject to relatively large dilution effects. On the other hand, solid cultures equipped with drip emitters are less disruptive as they do not create the same constant mass flow. The rhizosphere effect reaches further in hydroponics, yet the concentration of root exudates decreases much faster than in solid culture . While many publications focus on the PGPRs involved in the nitrogen cycle, others highlight the potential effects of PGPRs against plant pathogens in soilless culture . Indeed, limited attention has been paid to the possible natural plant protection capacity of aquaponic microbiota. However, the potential of this protective action can be envisaged with regard to different elements already known to be involved in hydroponics or re-circulated aquaculture . The suppression capacity demonstrated by the soilless medium is discussed by Postma et al. and Vallance et al. . While some authors have comprehensively described plant pathogens, such as Phytophthora cryptogea, Pythium spp., P. aphanidermatum and Fusarium oxysporum, which are suppressed by the natural microbiota, they have not clearly identified the microorganisms responsible for this suppressive action . Suppressiveness in hydroponics can be interpreted as the pathogens not persisting or establishing, which also leads to little or no damage. The suppressive action of an environment can be related to the abiotic milieu. On the other hand, in most situations, suppressiveness is considered to be related directly or indirectly to microorganism activity or metabolites . Microbial inclusion in the suppressive effect in soilless agriculture is generally verified via the initial destruction of the microbiota of the soilless substrate by sterilization. Then, the beneficial microorganisms are reinoculated. In contrast to that in traditional culture, in which water recirculation does not occur, the suppressive activity in soilless culture can be explained by water recirculation, which allows for the enhanced development and dispersal of beneficial microorganisms . As a result, the combination of PGPRs and soilless agriculture is considered to be necessary for success in sustainable agriculture.Growing human populations have led to accelerating rates of natural resource use and land conversion, particularly for urbanization and agriculture . Human-altered landscapes are often associated with declining natural habitat, non-native species, fragmentation, and transformations in habitat structure, inputs, climate, and connectivity. These changes collectively have resulted in shifts in both spatial distributions and species interactions across many taxa including birds, mammals, reptiles, amphibians, invertebrates, and plants. However, many of these studies are either static snapshots of the measured community, or lumped across time, which may miss some of the dynamics of how communities respond to anthropogenic change.