Identification of a phosphorus-solubilizing Tsukamurella tyrosinosolvens strain and its effect on the bacterial diversity of the rhizosphere soil of peanuts growth-promoting

Metagenomic Analysis to Assess the Impact of Plant Growth-Promoting Rhizobacteria on Peanut (Arachis hypogaea L.) Crop Production and Soil Enzymes and Microbial Diversity

Peanut production could be increased through plant growth-promoting rhizobacteria (PGPR). In this regard, the present field research aimed at elucidating the impact of PGPR on peanut yield, soil enzyme activity, microbial diversity, and structure. Three PGPR strains (Bacillus velezensis, RI3; Bacillus velezensis, SC6; Pseudomonas psychrophila, P10) were evaluated, along with Bradyrhizobium japonicum (BJ), taken as a control. PGPR increased seed yield by 8%, improving the radiation use efficiency (4-14%). PGPR modified soil enzymes (fluorescein diacetate activity by 17% and dehydrogenase activity by 28%) and microbial abundance (12%). However, PGPR did not significantly alter microbial diversity; nonetheless, it modified the relative abundance of key phyla (Actinobacteria > Proteobacteria > Firmicutes) and genera (Bacillus > Arthrobacter > Pseudomonas). PGPRs modified the relative abundance of genes associated with N-fixation and nitrification while increasing genes related to N-assimilation and N-availability. PGPR improved agronomic traits without altering rhizosphere diversity.

The seed endophytic microbe Microbacterium testaceum M15 enhances the cold tolerance and growth of rice (Oryza sativa L.)

The potential of seed endophytic microbes to enhance plant growth and resilience is well recognized, yet their role in alleviating cold stress in rice remains underexplored due to the complexity of these microbial communities. In this study, we investigated the diversity of seed endophytic microbes in two rice varieties, the cold-sensitive CB9 and the cold-tolerant JG117. Our results revealed significant differences in the abundance of Microbacteriaceae, with JG117 exhibiting a higher abundance under both cold stress and room temperature conditions compared to CB9. Further analysis led to the identification of a specific cold-tolerant microbe, Microbacterium testaceum M15, in JG117 seeds. M15-inoculated CB9 plants showed enhanced growth and cold tolerance, with a germination rate increase from 40 % to 56.67 % at 14℃ and a survival rate under cold stress (4℃) doubling from 22.67 % to 66.67 %. Additionally, M15 significantly boosted chlorophyll content by over 30 %, increased total protein by 16.31 %, reduced malondialdehyde (MDA) levels by 37.76 %, and increased catalase activity by 26.15 %. Overall, our study highlights the potential of beneficial endophytic microbes like M. testaceum M15 in improving cold tolerance in rice, which could have implications for sustainable agricultural practices and increased crop productivity in cold-prone regions.

Transcriptional alterations of peanut root during interaction with growth-promoting Tsukamurella tyrosinosolvens strain P9

The plant growth-promoting rhizobacterium Tsukamurella tyrosinosolvens P9 can improve peanut growth. In this study, a co-culture system of strain P9 and peanut was established to analyze the transcriptome of peanut roots interacting with P9 for 24 and 72 h. During the early stage of co-culturing, genes related to mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction, ethylene synthesis, and cell wall pectin degradation were induced, and the up-regulation of phenylpropanoid derivative, flavonoid, and isoflavone synthesis enhanced the defense response of peanut. The enhanced expression of genes associated with photosynthesis and carbon fixation, circadian rhythm regulation, indoleacetic acid (IAA) synthesis, and cytokinin decomposition promoted root growth and development. At the late stage of co-culturing, ethylene synthesis was reduced, whereas Ca2+ signal transduction, isoquinoline alkaloid synthesis, and ascorbate and aldarate metabolism were up-regulated, thereby maintaining root ROS homeostasis. Sugar decomposition and oxidative phosphorylation and nitrogen and fatty acid metabolism were induced, and peanut growth was significantly promoted. Finally, the gene expression of seedlings inoculated with strain P9 exhibited temporal differences. The results of our study, which explored transcriptional alterations of peanut root during interacting with P9, provide a basis for elucidating the growth-promoting mechanism of this bacterial strain in peanut.

Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects

Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.

Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.

Isolation and identification of antagonistic Bacillus amyloliquefaciens HSE-12 and its effects on peanut growth and rhizosphere microbial community

The HSE-12 strain isolated from peanut rhizosphere soil was identified as Bacillus amyloliquefaciens by observation of phenotypic characteristics, physiological and biochemical tests, 16S rDNA and gyrB gene sequencing. In vitro experiments showed that the strain possessed biocontrol activity against a variety of pathogens including Sclerotium rolfsii. The strain has the ability to produce hydrolytic enzymes, as well as volatile organic compounds with antagonistic and probiotic effects such as ethyleneglycol and 2,3-butanediol. In addition, HSE-12 showed potassium solubilizing (10.54 ± 0.19 mg/L), phosphorus solubilization (168.34 ± 8.06 mg/L) and nitrogen fixation (17.35 ± 2.34 mg/g) abilities, and was able to secrete siderophores [(Ar-A)/Ar × 100%: 56%] which promoted plant growth. After inoculating peanut with HSE-12, the available phosphorus content in rhizosphere soil increased by 27%, urease activity increased by 43%, catalase activity increased by 70% and sucrase activity increased by 50% (p < 0.05). The dry weight, fresh weight and the height of the first pair of lateral branches of peanuts increased by 24.7, 41.9, and 36.4%, respectively, compared with uninoculated peanuts. In addition, compared with the blank control, it increased the diversity and richness of peanut rhizosphere bacteria and changed the community structure of bacteria and fungi. The relative abundance of beneficial microorganisms such as Sphingomonas, Arthrobacter, RB41, and Micromonospora in rhizosphere soil was increased, while the relative abundance of pathogenic microorganisms such as Aspergillus, Neocosmospora, and Rhizoctonia was decreased.

Isolation and Identification of a Phosphate-Solubilizing Pantoea dispersa with a Saline-Alkali Tolerance and Analysis of Its Growth-Promoting Effects on Silage Maize Under Saline-Alkali Field Conditions

Phosphate-solubilizing bacteria (PSB) are microorganisms that can dissolve insoluble phosphorus (P) to accessible forms. This study aimed to screen saline-alkali-tolerant PSB and analyze its growth promoting properties, and evaluate its effects on the growth, quality, soil nutrient balance, and enzyme activities of silage maize in the field. We isolated six phosphate-solubilizing strains from rhizosphere soil of silage maize planted in saline-alkali land, and FC-1 with the best P-solubilizing effect was used for further study. The morphological, physiological and biochemical analysis, and 16S rDNA and housekeeping gene atpD sequencing were performed for identification. FC-1 was identified as Pantoea dispersa and had high P solubility. The phosphate solubility of FC-1 using four P sources ranged from 160.79 to 270.22 mg l-1. FC-1 produced indole-3-acetic acid (IAA) and decreased the pH of the growth media by secreting organic acids, including citric acid, malic acid, succinic acid, and acetic acid. The results of a field experiment indicated that FC-1 treatment increased the height, stem diameter, fresh weight, dry weight, starch content, crude protein content, and total P content of silage maize by 9.8, 9.2, 12.6, 11.7, 12.6, 18.3, and 17.4%, respectively. The nitrogen, potassium, phosphorus, and organic matter contents in the rhizosphere soil of silage maize increased by 29.8, 17.1, 17.9, and 25.3%, respectively; urease, catalase, sucrase, and alkaline phosphatase levels also increased by 24.7, 26.7, 24.0, and 19.5%, respectively. FC-1 promoted the growth of silage maize by improving nutrient metabolism and enzyme activities in saline-alkali soil and may be an effective alternative to fertilizers.

Stress-Resistance and Growth-Promoting Characteristics and Effects on Vegetable Seed Germination of Streptomyces sp. Strains Isolated from Wetland Plant Rhizospheres

Wetlands are the most biologically diverse ecosystems on Earth. The isolation of Streptomyces strains from wetlands is helpful to study their diversity and functions in such habitats. In this study, six strains of Streptomyces were isolated from the rhizosphere soil of three plant species in the Huaxi Wetland at Guiyang and were identified as Streptomyces galilaeus, S. avidinii, S. albogriseolus, S. albidoflavus, S. spororaveus, and S. cellulosae, respectively. The six strains all solubilized phosphate, fixed nitrogen, and produced ACC deaminase and siderophores, and four strains also secreted indole-3-acetic acid. The six strains had the ability to resist to certain degrees of salinity, drought, and acidic/alkaline pH stress. In addition, the S. avidinii WL3 and S. cellulosae WL9 strains significantly promoted seed germination of mung bean, pepper, and cucumber, especially the WL3 strain. A pot experiment further showed that WL3 significantly promoted the growth of cucumber seedlings. Thus, strains of six species of Streptomyces with multiple plant growth-promoting characteristics were isolated from the wetland. These results lay a foundation for their potential use as microbial agents for seed-coating treatments.

Effects of different fertilization methods on Lolium multiflorum Lam. growth and bacterial community in waste slag

Waste slag has low nutrient content, so it has insufficient nutrient cycling and transformation in the soil ecosystem. There are few studies on the application of oligotrophic phosphate-solubilizing bacteria and phosphate (P) fertilizer to improve the properties of waste slags. In this study, three oligotrophic bacterial strains with P solubilizing activity, namely, Bacillus subtilis 2C (7.23 μg/mL), Bacillus subtilis 6C (4.07 μg/mL), and Bacillus safensis 2N (5.05 μg/mL), were isolated from waste slags. In the pot experiment, compared with no application of P fertilizer, inoculation of Bacillus subtilis 2C with a 50% recommended dose of P fertilizer significantly increased the available phosphorus (AP), total phosphorus (TP), and total nitrogen (TN) in slag by 33.16%, 76.70%, and 233.33%, respectively. The N, P uptake and fresh weight of Lolium multiflorum Lam. were significantly improved by 114.15%, 139.02%, and 100%, respectively. The analysis of the bacterial community showed that the application of P fertilizer decreased the diversity and richness of the bacterial community, and with the addition of phosphorus fertilizer and Bacillus subtilis 2C, the bacterial community in the slag developed towards eutrophication. Redundancy analysis (RDA) showed that the TP content in the slag was significantly correlated with the bacterial community (P = 0.001, < 0.01), followed by the TN content. This study on different P fertilizer application methods can provide some basic ideas for improving the performance of waste slag.

Phosphate-Solubilizing Capacity of Paecilomyces lilacinus PSF7 and Optimization Using Response Surface Methodology

Phosphorus-solubilizing microorganisms release organic acids that can chelate mineral ions or reduce the pH to solubilize insoluble phosphates for use by plants; it is important to study potential phosphorus-solubilizing microorganisms for use in agriculture. In this study, PSF7 was isolated from the soil of the Wengfu Phosphorus Tailings Dump in Fuquan City, Guizhou Province, China. PSF7 was identified as Paecilomyces lilacinus, based on morphological characterization and ITS sequencing analysis. The relationship between the phosphorus-solubilizing capacity and pH variation of PSF7 under liquid fermentation was studied. The results showed that there was a significant negative correlation (-0.784) between the soluble phosphorus content of PSF7 and the pH value. When PSF7 was placed under low phosphorus stress, eight organic acids were determined from fermentation broth using HPLC, of which tartaric acid and formic acid were the main organic acids. Different optimization parameters of medium components were analyzed using response surface methodology. The optimized medium components were 23.50 g/L sucrose, 1.64 g/L ammonium sulfate and soybean residue, 1.07 g/L inorganic salts, and 9.16 g/L tricalcium phosphate, with a predicted soluble phosphorus content of 123.89 mg/L. Under the optimum medium composition, the actual phosphorus-solubilizing content of PSF7 reached 122.17 mg/L. Moreover, scanning electron microscopy analysis of the sample was carried out to characterize the phosphate-solubilizing efficiency of PSF7 on mineral phosphate. The results provide useful information for the future application of PSF7 as a biological fertilizer.

Molecular mechanism of Tsukamurella tyrosinosolvens strain P9 in response to root exudates of peanut

Tsukamurella tyrosinosolvens strain P9 is a rare actinomycete with plant growth-promoting properties and can improve the growth of peanut. We analyzed the differentially expressed genes (DEGs) of P9 under the influence of peanut root exudates from RNA-sequencing data and analyzed the effects of root exudates and their organic acid and amino acid components on the growth and growth-promoting effects of this strain to explore the molecular mechanism of the P9 response. The results showed that peanut root exudates promoted the growth and growth-promoting activity of P9. Transcriptome analysis revealed 126 DEGs in P9, comprising 81 up-regulated and 45 down-regulated genes. The DEGs were significantly enriched in 17 KEGG metabolic pathways, including arginine biosynthesis, butyric acid metabolism, fatty acid degradation, and tryptophan metabolism. Peanut root exudates induced up-regulation of nutrient transport, carbohydrate metabolism and energy production, siderophore and IAA biosynthesis, adhesion, and biofilm formation, and down-regulation of arginine biosynthesis and the urea cycle in P9. Organic acids and amino acids are the major components of peanut root exudates. Glycine, proline, and alanine promoted the growth and IAA secretion of P9. Proline, alanine (40 mM), and oxalic acid significantly enhanced siderophore biosynthesis, whereas citric acid, oxalic acid, and malic acid significantly promoted biofilm formation of P9. This study clarifies the response of T. tyrosinosolvens P9 to peanut root exudates at the molecular level, examining the molecular basis of the relationship between P9 and peanut, and provides a theoretical foundation for improved exertion of the growth-promoting properties of P9.

Maize-soybean intercropping facilitates chemical and microbial transformations of phosphorus fractions in a calcareous soil

Intercropping often substantially increases phosphorus (P) availability to plants compared with monocropping, which could be an effective strategy for soil legacy P recovery and agricultural production. However, the biogeochemical interactions among plants, microbes, and soil that mobilize P remain largely unknown in intercropping systems. Pot experiments with maize-soybean intercropping in a calcareous soil were conducted to investigate the potential chemical and biological transformation mechanisms of inorganic P (Pi) and organic P (Po) using sequential extraction and Illumina MiSeq sequencing. Compared to monocropping of each crop, maize-soybean intercropping significantly enhanced total P uptake of the two crops by mobilizing Ca2-Pi [extracted by bicarbonate (NaHCO3)], Al-Pi/Po [extracted by ammonium fluoride (NH4F)] and Fe-Pi [extracted by sodium hydroxide and sodium carbonate (NaOH-Na2CO3)] fractions. Furthermore, there were significant increases in the organic carbon content and alkaline phosphomonoesterase (ALP) and phosphodiesterase (PDE) activities as well as the abundances of Microvirga, Lysobacter, Microlunatus and Sphingomonas under maize-soybean intercropping relative to monocropping. In contrast, compared to monocroppping, no significant change in the soil pH was observed under maize-soybean intercropping. Therefore, the enhanced P uptake of the maize-soybean intercropping probably resulted from a synergistic effect of rhizosphere organic carbon deposit, increased activities of ALP and PDE, together with the bacteria (Microvirga, Lysobacter, Microlunatus and Sphingomonas) which showed correlation with soil P forms, while the generally recognized rhizosphere acidification was excluded in this investigated calcareous soil. Moreover, the selected bacterial genera exhibited a closer network in the rhizosphere of soybean compared to maize, suggesting enhanced interactions among bacteria in the soybean rhizosphere. These results provide theoretical bases for the recovery of soil legacy P by maize-soybean intercropping.

Actinobacteria-Plant Interactions in Alleviating Abiotic Stress

Abiotic stressors, such as drought, flooding, extreme temperature, soil salinity, and metal toxicity, are the most important factors limiting crop productivity. Plants use their innate biological systems to overcome these abiotic stresses caused by environmental and edaphic conditions. Microorganisms that live in and around plant systems have incredible metabolic abilities in mitigating abiotic stress. Recent advances in multi-omics methods, such as metagenomics, genomics, transcriptomics, and proteomics, have helped to understand how plants interact with microbes and their environment. These methods aid in the construction of various metabolic models of microbes and plants, resulting in a better knowledge of all metabolic exchanges engaged during interactions. Actinobacteria are ubiquitous and are excellent candidates for plant growth promotion because of their prevalence in soil, the rhizosphere, their capacity to colonize plant roots and surfaces, and their ability to produce various secondary metabolites. Mechanisms by which actinobacteria overcome abiotic stress include the production of osmolytes, plant hormones, and enzymes, maintaining osmotic balance, and enhancing nutrient availability. With these characteristics, actinobacteria members are the most promising candidates as microbial inoculants. This review focuses on actinobacterial diversity in various plant regions as well as the impact of abiotic stress on plant-associated actinobacterial diversity and actinobacteria-mediated stress mitigation processes. The study discusses the role of multi-omics techniques in expanding plant-actinobacteria interactions, which aid plants in overcoming abiotic stresses and aims to encourage further investigations into what may be considered a relatively unexplored area of research.

Nitrogen removal from low C/N wastewater in a novel Sharon&DSR (denitrifying sulfide removal) reactor

Denitrification reactions commonly remove nitrate and other reactive nitrogen (Nr) from wastewater. The C/N ratio indicates the sufficiency of organic carbons to drive heterotrophic denitrification; a low C/N ratio frequently leads to poor denitrification performance in wastewater treatment. This study proposed and tested a novel Sharon&DSR (denitrifying sulfide removal) process, with nitrite generated by the Sharon reactions and sulfide from sulfur-reducing reactions for promoting the following nitrite-based denitrification and denitrifying sulfide removal (DSR) process. The present reactor can remove nitrate at an efficiency of 97.7 %-93.5 % at an influent C/N ratio of 0.646-0.737 over a 96-d continuous-flow test. The microbial community study reveals the functional strains corresponding to individual groups of critical reactions. The stoichiometry analysis reveals the potential to apply the nitrite-based DSR process for Nr removal from ultra-low C/N (<0.64) wastewaters, experimentally demonstrated in the present study with a C/N ratio of 0.16-0.39.

Obligate aerobic, gram-positive, weak acid-fast, nonmotile bacilli, Tsukamurella tyrosinosolvens: Minireview of a rare opportunistic pathogen

Tsukamurella species are obligate aerobic, gram-positive, weak acid-fast, nonmotile bacilli. They are found in various environments, such as soil, water, sludge, and petroleum reservoir wastewater, and belong to the order Actinomycetales. In 2016, there was a reclassification of species within the genus Tsukamurella, merging the species Tsukamurella tyrosinosolvens (T. tyrosinosolvens) and Tsukamurella carboxydivorans. Tsukamurella species are clinically considered to be a rare opportunistic pathogen, because most reported cases have been related to bacteremia and intravascular prosthetic devices and immunosuppression. To date, it has been isolated only from human specimens, and has always been associated with clinical disease; human infections are very rare. Reported infections have included pneumonia, brain abscesses, catheter-related bloodstream infections, ocular infections, bacteremia, and sepsis presenting with septic pulmonary emboli in patients who are immunocompromised. To date, there is no commercially available test for identification. On the other hand, sequence-based identification, including matrix-assisted laser desorption ionization time-of-flight mass spectrometry, is an alternative method for identifying clinical isolates that are either slow growers or difficult to identify through biochemical profiling. The golden standards for diagnosis and optimal management still remain to be determined. However, newer molecular biological techniques can provide accurate identification, and contribute to the appropriate selection of definitive therapy for infections caused by this organism. Combinations of several antimicrobial agents have been proposed for treatment, though the length of treatment for infections has yet to be determined, and should be individualized according to clinical response. Immunocompromised patients often experience severe cases due to infection, and life-threatening T. tyrosinosolvens events associated with dissemination and/or failure of source control have occurred. Favorable prognoses can be achieved through earlier identification of the cause of infection, as well as successful management, including appropriate antibiotic therapy together with source control. Further analyses of similar cases are required to establish the most adequate diagnostic methods and treatment regimens for infections.

Streptomyces can be an excellent plant growth manager

Streptomyces, the most abundant and arguably the most important genus of actinomycetes, is an important source of biologically active compounds such as antibiotics, and extracellular hydrolytic enzymes. Since Streptomyces can have a beneficial symbiotic relationship with plants they can contribute to nutrition, health and fitness of the latter. This review article summarizes recent research contributions on the ability of Streptomyces to promote plant growth and improve plant tolerance to biotic and abiotic stress responses, as well as on the consequences, on plant health, of the enrichment of rhizospheric soils in Streptomyces species. This review summarizes the most recent reports of the contribution of Streptomyces to plant growth, health and fitness and suggests future research directions to promote the use of these bacteria for the development of a cleaner agriculture.

The Impact of the Inoculation of Phosphate-Solubilizing Bacteria Pantoea agglomerans on Phosphorus Availability and Bacterial Community Dynamics of a Semi-Arid Soil

The bacterial genus Pantoea has been widely evaluated as promising bacteria to increase phosphorus (P) availability in soil. The aim of this study was to characterize the phosphate solubilizing (PS) activity of a Pantoea agglomerans strain and to evaluate the impact of its application in a semi-arid soil on phosphate availability and structure of the bacterial communities as a whole. An incubation experiment under close-to-natural soil environmental conditions was conducted for 15 days at 30 °C. High-throughput sequencing of the bacterial 16S rRNA gene was used to characterize and to compare the bacterial community structure of P. agglomerans-inoculated soil with non-inoculated control. Furthermore, a qPCR-based method was developed for detection and quantification of the functional genes related to the expression of mineral phosphate solubilization (MPS) phenotype in P. agglomerans. The results showed that in vitro solubilization of Ca3(PO4)2 by P. agglomerans strain was very efficient (980 mg/L), and it was associated with a drop in pH due to the secretion of gluconic acid; these changes were concomitant with the detection of gdh and pqqC genes. Moreover, P. agglomerans inoculum application significantly increased the content of available P in semi-arid soil by 69%. Metagenomic analyses showed that P. agglomerans treatment modified the overall edaphic bacterial community, significantly impacting its structure and composition. In particular, during P. agglomerans inoculation the relative abundance of bacteria belonging to Firmicutes (mainly Bacilli class) significantly increased, whereas the abundance of Actinobacteria together with Acidobacteria and Chloroflexi phyla decreased. Furthermore, genera known for their phosphate solubilizing activity, such as Aneurinibacillus, Lysinibacillus, Enterococcus, and Pontibacter, were exclusively detected in P. agglomerans-treated soil. Pearson's correlation analysis revealed that changes in soil bacterial community composition were closely affected by soil characteristics, such as pH and available P. This study explores the effect of the inoculation of P. agglomerans on the bacterial community structure of a semi-arid soil. The effectiveness in improving the phosphate availability and modification in soil bacterial community suggested that P. agglomerans represent a promising environmental-friendly biofertilizer in arid and semi-arid ecosystems.