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Here, phytoremediation studies of toxic metal and organic compounds using plants augmented with plant growth-promoting bacteria, published in the past few years, were summarized and reviewed. These studies complemented and extended the many earlier studies in this area of research. The studies summarized here employed a wide range of non-agricultural plants including various grasses indigenous to regions of the world. The plant growth-promoting bacteria used a range of different known mechanisms to promote plant growth in the presence of metallic and/or organic toxicants and thereby improve the phytoremediation ability of most plants. Both rhizosphere and endophyte PGPB strains have been found to be effective within various phytoremediation schemes. Consortia consisting of several PGPB were often more effective than individual PGPB in assisting phytoremediation in the presence of metallic and/or organic environmental contaminants.
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Three Cd2+ resistant bacterium's minimal inhibition concentrations were assessed and their percentages of Cd2+ accumulation were determined by measurements using an atomic absorption spectrophotometer (AAS). The results revealed that two isolates Bacillus paramycoides (PM51) and Bacillus tequilensis (PM52), identified by 16S rDNA gene sequencing, showed a higher percentage of Cd2+ accumulation i.e., 83.78% and 81.79%, respectively. Moreover, both novel strains can tolerate Cd2+ levels up to 2000 mg/L isolated from district Chakwal. Amplification of the czcD, nifH, and acdS genes was also performed. Batch bio-sorption studies revealed that at pH 7.0, 1 g/L of biomass, and an initial 150 mg/L Cd2+ concentration were the ideal bio-sorption conditions for Bacillus paramycoides (PM51) and Bacillus tequilensis (PM52). The experimental data were fit to Langmuir isotherm measurements and Freundlich isotherm model R2 values of 0.999 for each of these strains. Bio sorption processes showed pseudo-second-order kinetics. The intra-diffusion model showed Xi values for Bacillus paramycoides (PM51) and Bacillus tequilensis (PM52) of 2.26 and 2.23, respectively. Different surface ligands, was investigated through Fourier-transformation infrared spectroscopy (FTIR). The scanning electron microscope SEM images revealed that after Cd2+ adsorption, the cells of both strains became thick, adherent, and deformed. Additionally, both enhanced Linum usitatissimum plant seed germination under varied concentrations of Cd2+ (0 mg/L, 250 mg/L,350 mg/L, and 500 mg/L). Current findings suggest that the selected strains can be used as a sustainable part of bioremediation techniques.
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Bacillus , Cadmio , Bacillus/metabolismo , Bacillus/genética , Cadmio/metabolismo , Plantones/metabolismo , Plantones/efectos de los fármacos , Plantones/microbiología , Biodegradación Ambiental , AdsorciónRESUMEN
Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.
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The growth of crop plants, particularly spinach (Spinacia oleracea L.), can be significantly impeded by salinity and drought. However, pre-treating spinach plants with traditional biofertilizers like Jeevamrit and Beejamrit (JB) substantially reverses the salinity and drought-induced inhibitory effects. Hence, this study aims to elucidate the underlying mechanisms that govern the efficacy of traditional fertilizers. The present work employed comprehensive biochemical, physiological, and molecular approaches to investigate the processes by which JB alleviates abiotic stress. The JB treatment effectively boosts spinach growth by increasing nutrient uptake and antioxidant enzyme activity, which mitigates the detrimental effects of drought and salinity-induced stress. Under salt and drought stress conditions, the application of JB resulted in an impressive rise in germination percentages of 80 and 60%, respectively. In addition, the application of JB treatment resulted in a 50% decrease in electrolyte leakage and a 75% rise in the relative water content of the spinach plants. Furthermore, the significant reduction in proline and glycine betaine levels in plants treated with JB provides additional evidence of the treatment's ability to prevent cell death caused by environmental stressors. Following JB treatment, the spinach plants exhibited substantially higher total chlorophyll content was also observed. Additionally, using 16S rRNA sequencing, we discovered and characterized five plant-beneficial bacteria from the JB bio-inoculants. These bacterial isolates comprise a number of traits that contribute to growth augmentation in plants. These evidences suggest that the presence of the aforesaid microorganisms (along with additional ones) is accountable for the JB-mediated stimulation of plant growth and development.
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Indole-3-acetic acid (IAA), a fundamental phytohormone categorized under auxins, not only influences plant growth and development but also plays a critical role in plant-microbe interactions. This study reviews the role of IAA in bacteria-plant communication, with a focus on its biosynthesis, regulation, and the subsequent effects on host plants. Bacteria synthesize IAA through multiple pathways, which include the indole-3-acetamide (IAM), indole-3-pyruvic acid (IPyA), and several other routes, whose full mechanisms remain to be fully elucidated. The production of bacterial IAA affects root architecture, nutrient uptake, and resistance to various abiotic stresses such as drought, salinity, and heavy metal toxicity, enhancing plant resilience and thus offering promising routes to sustainable agriculture. Bacterial IAA synthesis is regulated through complex gene networks responsive to environmental cues, impacting plant hormonal balances and symbiotic relationships. Pathogenic bacteria have adapted mechanisms to manipulate the host's IAA dynamics, influencing disease outcomes. On the other hand, beneficial bacteria utilize IAA to promote plant growth and mitigate abiotic stresses, thereby enhancing nutrient use efficiency and reducing dependency on chemical fertilizers. Advancements in analytical methods, such as liquid chromatography-tandem mass spectrometry, have improved the quantification of bacterial IAA, enabling accurate measurement and analysis. Future research focusing on molecular interactions between IAA-producing bacteria and host plants could facilitate the development of biotechnological applications that integrate beneficial bacteria to improve crop performance, which is essential for addressing the challenges posed by climate change and ensuring global food security. This integration of bacterial IAA producers into agricultural practice promises to revolutionize crop management strategies by enhancing growth, fostering resilience, and reducing environmental impact.
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Resiliencia Psicológica , Ácidos Indolacéticos/metabolismo , Reguladores del Crecimiento de las Plantas/metabolismo , Bacterias/genética , Bacterias/metabolismo , Plantas/microbiología , AgriculturaRESUMEN
In the rhizosphere, plants and microbes communicate chemically, especially under environmental stress. Over millions of years, plants and their microbiome have coevolved, sharing various chemicals, including signaling molecules. This mutual exchange impacts bacterial communication and influences plant metabolism. Inter-kingdom signal crosstalk affects bacterial colonization and plant fitness. Beneficial microbes and their metabolomes offer eco-friendly ways to enhance plant resilience and agriculture. Plant metabolites are pivotal in this dynamic interaction between host plants and their interacting beneficial microbes. Understanding these associations is key to engineering a robust microbiome for stress mitigation and improved plant growth. This review explores mechanisms behind plant-microbe interactions, the role of beneficial microbes and metabolomics, and the practical applications for addressing climate change's impact on agriculture. Integrating beneficial microbes' activities and metabolomics' application to study metabolome-driven interaction between host plants and their corresponding beneficial microbes holds promise for enhancing crop resilience and productivity.
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Microbiota , Resiliencia Psicológica , Productos Agrícolas/metabolismo , Productos Agrícolas/microbiología , Bacterias/metabolismo , MetabolómicaRESUMEN
Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.
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Bacillus , Bacillus/fisiología , Suelo , Raíces de Plantas/microbiología , Bacterias/genética , AntioxidantesRESUMEN
Here, a brief summary of the biosynthesis of 1-aminocyclopropane-1-carboxylate (ACC) and ethylene in plants, as well as overviews of how ACC and ethylene act as signaling molecules in plants, is presented. Next, how the bacterial enzyme ACC deaminase cleaves plant-produced ACC and thereby decreases or prevents the ethylene or ACC modulation of plant gene expression is considered. A detailed model of ACC deaminase functioning, including the role of indoleacetic acid (IAA), is presented. Given that ACC is a signaling molecule under some circumstances, this suggests that ACC, which appears to have evolved prior to ethylene, may have been a major signaling molecule in primitive plants prior to the evolution of ethylene and ethylene signaling. Due to their involvement in stimulating ethylene production, the role of D-amino acids in plants is then considered. The enzyme D-cysteine desulfhydrase, which is structurally very similar to ACC deaminase, is briefly discussed and the possibility that ACC deaminase arose as a variant of D-cysteine desulfhydrase is suggested.
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Numerous biotic and abiotic stress in some geographical regions predisposed their agricultural matrix to challenges threatening plant productivity, health, and quality. In curbing these threats, different customary agrarian principles have been created through research and development, ranging from chemical inputs and genetic modification of crops to the recently trending smart agricultural technology. But the peculiarities associated with these methods have made agriculturists rely on plant rhizospheric microbiome services, particularly bacteria. Several bacterial resources like Proteobacteria, Firmicutes, Acidobacteria, and Actinomycetes (Streptomycetes) are prominent as bioinoculants or the application of their by-products in alleviating biotic/abiotic stress have been extensively studied, with a dearth in the application of rare Actinomycetes metabolites. Rare Actinomycetes are known for their colossal genome, containing well-preserved genes coding for prolific secondary metabolites with many agroactive functionalities that can revolutionize the agricultural industry. Therefore, the imperativeness of this review to express the occurrence and distributions of rare Actinomycetes diversity, plant and soil-associated habitats, successional track in the rhizosphere under diverse stress, and their agroactive metabolite characteristics and functionalities that can remediate the challenges associated with agricultural productivity.
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Actinobacteria , Actinobacteria/genética , Actinomyces , Bacterias/genética , Rizosfera , Agricultura , Suelo , Microbiología del SueloRESUMEN
The development of recombinant DNA technology during the past thirty years has enabled scientists to isolate, characterize, and manipulate a myriad of different animal, bacterial, and plant genes. This has, in turn, led to the commercialization of hundreds of useful products that have significantly improved human health and well-being. Commercially, these products have been mostly produced in bacterial, fungal, or animal cells grown in culture. More recently, scientists have begun to develop a wide range of transgenic plants that produce numerous useful compounds. The perceived advantage of producing foreign compounds in plants is that compared to other methods of producing these compounds, plants seemingly provide a much less expensive means of production. A few plant-produced compounds are already commercially available; however, many more are in the production pipeline.
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Cytokinin is a major phytohormone that has been used in agriculture as a plant-growth stimulating compound since its initial discovery in the 1960s. Isopentenyl transferase (IPT) is a rate-limiting enzyme for cytokinin biosynthesis, which is produced by plants as well as bacteria including both plant pathogenic species and plant growth-promoting bacteria (PGPB). It has been hypothesized that there may be differences in IPT function between plant pathogens and PGPB. However, a comprehensive comparison of IPT genes between plant pathogenic and PGPB species has not been performed. Here, we performed a global comparison of IPT genes across bacteria, analyzing their DNA sequences, codon usage, phyletic distribution, promoter structure and genomic context. We found that adenylate type IPT genes are highly specific to plant-associated bacteria and subdivide into two major clades: clade A, largely composed of proteobacterial plant pathogens; and clade B, largely composed of actinomycete PGPB species. Besides these phylogenetic differences, we identified several genomic features that suggest differences in IPT regulation between pathogens and PGPB. Pathogen-associated IPTs tended to occur in predicted virulence loci, whereas PGPB-associated IPTs tended to co-occur with other genes involved in cytokinin metabolism and degradation. Pathogen-associated IPTs also showed elevated gene copy numbers, significant deviation in codon usage patterns, and extended promoters, suggesting differences in regulation and activity levels. Our results are consistent with the hypothesis that differences in IPT regulation and activity exist between plant pathogens and PGPB, which determine their effect on plant host phenotypes through the control of cytokinin levels.
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Phytohormones are regulators of plant growth and development, which under different types of stress can play a fundamental role in a plant's adaptation and survival. Some of these phytohormones such as cytokinin, gibberellin, salicylic acid, auxin, and ethylene are also produced by plant growth-promoting bacteria (PGPB). In addition, numerous volatile organic compounds are released by PGPB and, like bacterial phytohormones, modulate plant physiology and genetics. In the present work we review the basic functions of these bacterial phytohormones during their interaction with different plant species. Moreover, we discuss the most recent advances of the beneficial effects on plant growth of the phytohormones produced by PGPB. Finally, we review some aspects of the cross-link between phytohormone production and other plant growth promotion (PGP) mechanisms. This work highlights the most recent advances in the essential functions performed by bacterial phytohormones and their potential application in agricultural production.
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Microalgae are important members of the soil and plant microbiomes, playing key roles in the maintenance of soil and plant health as well as in the promotion of plant growth. However, not much is understood regarding the potential of different microalgae strains in augmenting plant growth, or the mechanisms involved in such activities. In this work, the functional and genomic characterization of strain NFX-FRZ, a eukaryotic microalga belonging to the Micractinium genus that was isolated from the rhizosphere of a plant growing in a natural environment in Portugal, is presented and analyzed. The results obtained demonstrate that strain NFX-FRZ (i) belongs to a novel species, termed Micractinium rhizosphaerae sp. nov.; (ii) can effectively bind to tomato plant tissues and promote its growth; (iii) can synthesize a wide range of plant growth-promoting compounds, including phytohormones such as indole-3-acetic acid, salicylic acid, jasmonic acid and abscisic acid; and (iv) contains multiple genes involved in phytohormone biosynthesis and signaling. This study provides new insights regarding the relevance of eukaryotic microalgae as plant growth-promoting agents and helps to build a foundation for future studies regarding the origin and evolution of phytohormone biosynthesis and signaling, as well as other plant colonization and plant growth-promoting mechanisms in soil/plant-associated Micractinium.
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Increasing demand for safe food by an ever-growing human population emphasizes the urgency for increasing crop yields and reducing the losses caused by abiotic and biotic stresses; a partial solution to this problem is to develop a better understanding of plant-microbe interactions. Plant roots continuously release a wide range of compounds including organic acids in root exudates. These root exudates stimulate growth of specific microbial communities in the rhizosphere, which affect complex biological and physico-chemical interactions occurring between plant roots and the surrounding soil environment. In addition, organic acids are also released by different microbes and during decomposition of organic matter and plant residues in the soil. Interestingly, the available organic acids in the rhizosphere play crucial roles in various physio-chemical processes including the chemoattraction of microbes (both beneficial and pathogenic), mineralization and solubilization of complex minerals (P, K and Zn), biocontrol of phytopathogens, induction of systemic resistance, biogas formation, mitigation of abiotic stresses and, detoxification of metals and residual pesticides. Thus, organic acids play a significant role in the sustainable management of the soil ecosystem and in environmental sustainability. This review discusses the role of organic acids in the stimulation or enrichment of specific root-associated microbial communities and their effect on plant-microbe interactions at the root surface. In addition, the potential for root microbiome modification to enhance nutrient cycling and nutrient acquisition, and in amelioration of environmental stresses for increasing food production is discussed.
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Microbiota , Suelo , Humanos , Suelo/química , Microbiología del Suelo , Raíces de Plantas , Plantas , Microbiota/fisiologíaRESUMEN
Some genotypes of date palms (Phoenix dactylifera L.) are salt-tolerant; however, salinity significantly affects others. This study aimed to determine the root epiphytic bacterial contributions to the salt tolerance mechanism in the date palm and to verify if the salt-tolerant "Umsila" and the salt-susceptible "Zabad" cultivars have different bacterial communities. Therefore, the epiphytic bacterial community structures were investigated in both cultivars when grown under control and salinity conditions. The proximal soils of the roots were collected, the DNA was extracted, and a culture-independent approach using Illumina® MiSeq™ sequence analysis was carried out to identify the changes in the bacterial community structures in the soil samples due to the changes in salinity and the genotypes of the plants based on 16S rRNA gene sequencing. While salt tolerance response differences were evident between the two cultivars, the 16S rRNA gene sequencing results revealed 771 operational taxonomic units (OTUs), including 62 that were differentially accumulated in response to salinity. The ordination analysis showed significant (p = 0.001) changes among the communities in response to salinity in both cultivars. However, the results showed that the two cultivars had distinct bacterial communities when grown under controlled conditions, whereas they had a more similar bacterial community structure when grown under salinity conditions. The plant genotype does not affect the epiphyte bacterial community structure under salinity, probably because salinity affects the plant-microbe interaction similarly in both cultivars. Also, the identified rhizospheric bacteria are not directly associated with the root's physiological processes in response to salinity.
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Bacterial pathogenesis-associated characteristics such as biofilm formation, synthesis of hydrolyzing enzymes, and toxins are regulated by Acyl Homoserine Lactones (AHLs), small peptides and diffusing signal factors (DSF). Lelliottia amnigena is gram negative bacteria and its pathogenicity is regulated by the luxR and luxI class of quorum sensing. The signaling molecules and their concentrations are essential for the virulence of the pathogenic bacterium. To suppresses the pathogenicity; the concentration of signalling molecules must be controlled or degraded. The lactonase have the ability to hydrolyze lactones of different chain length. The present study deals with a newer approach to control the pathogenesis of Lelliottia amnigena through isolation and characterization of Aiia lactonase from Bacillus cereus RC1. Aiia lactonase specific primers were used to amplify the gene, and the sequence thus obtained was submitted to the Genbank database under accession # OK643884.1. The gene was cloned in pBE-S shuttle vector and transformed in the recombinant host. The expressed and purified protein had a molecular weight of 28.00 KDa and exhibited its optimum activity at 37â by inhibiting the violacein pigment of the monitor strain Chromobacterium violaceum MTCC 2656. The proteinaceous nature of the purified molecule was confirmed by incubating it in the presence of proteinase K for 1 h. The activity of the pathogenesis-related protein, polygalacturonase was drastically reduced in the presence of the purified Aiia protein. The purified protein also showed a zone of inhibition when plated together with Lelliottia amnigena RCE (MZ712952.1). Searches of the Conserved Domain Database suggested that this protein belonged to the Metallo-beta-lactamase superfamily and is closely related to Aiia from B. thuringiensis serovar kurstaki. Modeling of the protein structure was done using I-TASSER; a C-score of 0.55 suggested that the model was of good quality. To be used commercially, this recombinant protein needs to be purified at an industrial scale; it can then be used to repress the growth of soft rot causing bacteria in horticultural crops during their storage period.
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Acil-Butirolactonas , Bacillus cereus , Acil-Butirolactonas/metabolismo , Bacillus cereus/genética , Bacillus cereus/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Hidrolasas de Éster Carboxílico/genética , Hidrolasas de Éster Carboxílico/metabolismo , Clonación Molecular , Endopeptidasa K , Enterobacteriaceae , Poligalacturonasa , Percepción de Quorum/genética , Proteínas Recombinantes/genética , Transactivadores/genética , beta-LactamasasRESUMEN
There is an increasing interest in the use of beneficial microorganisms as alternatives to chemically synthesized or plant-derived molecules to produce therapeutic agents. Bacterial endophytes are plant-associated microorganisms that can colonize different parts of living plants without causing any diseases. Diverse endophytic bacteria possess the ability to synthesize a wide range of secondary metabolites with unique chemical structures that have been exploited for their anti-microbial, antiviral, anti-cancer, and anti-inflammatory properties. Additionally, production of these bioactive compounds can also benefit the host plant as they may play a significant role in a plant's interaction with the environment for adaptation and defense. As a result of their significant impact as curative compounds or as precursors to produce new drugs, the biotechnological possibilities of secondary metabolites derived from endophytic bacteria are immense.
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Improvements to the world's food supply chain are needed to ensure sufficient food is produced to meet increasing population demands. Growing food in soilless hydroponic systems constitutes a promising strategy, as this method utilizes significantly less water than conventional agriculture, can be situated in urban areas, and can be stacked vertically to increase yields per acre. However, further research is needed to optimize crop yields in these systems. One method to increase hydroponic plant yields involves adding plant growth-promoting bacteria (PGPB) into these systems. PGPB are organisms that can significantly increase crop yields via a wide range of mechanisms, including stress reduction, increases in nutrient uptake, plant hormone modulation, and biocontrol. The aim of this review is to provide critical information for researchers on the current state of the use of PGPB in hydroponics so that meaningful advances can be made. An overview of the history and types of hydroponic systems is provided, followed by an overview of known PGPB mechanisms. Finally, examples of PGPB research that has been conducted in hydroponic systems are described. Amalgamating the current state of knowledge should ensure that future experiments can be designed to effectively transition results from the lab to the farm/producer, and the consumer.
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Many different experimental approaches have been applied to elaborate and study the beneficial interactions between soil bacteria and plants. Some of these methods focus on changes to the plant and others are directed towards assessing the physiology and biochemistry of the beneficial plant growth-promoting bacteria (PGPB). Here, we provide an overview of some of the current techniques that have been employed to study the interaction of plants with PGPB. These techniques include the study of plant microbiomes; the use of DNA genome sequencing to understand the genes encoded by PGPB; the use of transcriptomics, proteomics, and metabolomics to study PGPB and plant gene expression; genome editing of PGPB; encapsulation of PGPB inoculants prior to their use to treat plants; imaging of plants and PGPB; PGPB nitrogenase assays; and the use of specialized growth chambers for growing and monitoring bacterially treated plants.
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Crop plants are affected by a series of inhibitory environmental and biotic factors that decrease their growth and production. To counteract these adverse effects, plants work together with the microorganisms that inhabit their rhizosphere, which is part of the soil influenced by root exudates. The rhizosphere is a microecosystem where a series of complex interactions takes place between the resident microorganisms (rhizobiome) and plant roots. Therefore, this study analyzes the dynamics of plant-rhizobiome communication, the role of exudates (diffusible and volatile) as a factor in stimulating a diverse rhizobiome, and the differences between rhizobiomes of domesticated crops and wild plants. The study also analyzes different strategies to decipher the rhizobiome through both classical cultivation techniques and the so-called "omics" sciences. In addition, the rhizosphere engineering concept and the two general strategies to manipulate the rhizobiome, i.e., top down and bottom up engineering have been revisited. In addition, recent studies on the effects on the indigenous rhizobiome of inoculating plants with foreign strains, the impact on the endobiome, and the collateral effects on plant crops are discussed. Finally, understanding of the complex rhizosphere interactions and the biological repercussions of rhizobiome engineering as essential steps for improving plant growth and health is proposed, including under adverse conditions.