Metabacillus dongyingensis sp. nov. Is Represented by the Plant Growth-Promoting Bacterium BY2G20 Isolated from Saline-Alkaline Soil and Enhances the Growth of Zea mays L. under Salt Stress

Klebsiella sp. confers enhanced tolerance to salinity and plant growth promotion in oat seedlings (Avena sativa)

Salt stress is one of the major abiotic constraints that inflicts impaired growth and reduces production potential in crop plants. Under salt stress conditions, numerous plant growth processes are affected, i.e., hormonal and nutritional imbalance, ion toxicity, physiological disorders, and susceptibility to insect and pest attack. The growing menace of salinity is predicted to intensify both in its extent and severity, posing a stern challenge for developing a resilient food production system in coming years. Various agro-biotechnological interventions are being employed to improve salt stress tolerance in plants. However, the complexity associated with plant salinity tolerance has only allowed marginal progress for breeders and genetic engineers. Use of soil microbial resources to promote plant growth by alleviating the exposed stress factor has gained much needed attention in recent times. The application of plant growth promoting rhizobacteria (PGPR) and arbuscular mycorrhizal fungi (AMF) based bioinoculant strategy is perceived to enhance plant growth under salt stress. Microbial inoculation evoked plant stress tolerance response and improved plant growth, which is mainly triggered by modulating nutritional and hormonal balance, producing plant growth regulators, solubilizing nutrients, and inducing disease resistance. In this chapter, we describe causes of soil salinization and discuss potential impacts of salinity stress on plants. In addition, we also discussed the action mechanisms of plant growth promotion and/or regulation exhibited by PGPR and AMF, and highlighted their intrinsic traits that can be up scaled to increase their usefulness as a value-added product for stress agriculture.

Understanding the primary mechanisms for plant promotion under salt stress with plant growth promoting rhizobacteria (PGPR) inoculation of different salt-tolerant plant groups would be conducive to using PGPR efficiently. We conducted a meta-analysis to evaluate plant growth promotion and uncover its underlying mechanisms in salt-sensitive plants (SSP) and salt-tolerant plants (STP) with PGPR inoculation under salt stress. PGPR inoculation decreased proline, sodium ion (Na+) and malondialdehyde but increased plant biomass, nutrient acquisition (nitrogen, phosphorus, potassium ion (K+), calcium ion (Ca2+), and magnesium ion (Mg2+)), ion homeostasis (K+/Na+ ratio, Ca2+/Na+ ratio, and Mg2+/Na+ ratio), osmolytes accumulation (soluble sugar and soluble protein), antioxidants (superoxide dismutase), and photosynthesis (chlorophyll, carotenoid, and photosynthetic rate) in both SSP and STP. The effect size of total biomass positively correlated with the effect sizes of nutrient acquisition and the homeostasis of K+/Na+, and negatively correlated with the effect size of malondialdehyde in both SSP and STP. The effect size of total biomass also positively correlated with the effect sizes of carotenoid and the homeostasis in Ca2+/Na+ and Mg2+/Na+ and negatively correlated with the effect size of Na+ in SSP, but it only negatively correlated with the effect size of Ca2+ in STP. Our results suggest that the plant growth improvement depends on the nutrient acquisition enhancement in both SSP and STP, while ion homeostasis plays an important role and carotenoid may promote plant growth through protecting photosynthesis, reducing oxidative damage and promoting nutrient acquisition only in SSP after PGPR inoculation under salt stress.

Soil salinity is one of the major abiotic stresses known to drastically reduce agricultural productivity. Prolonged salinity stress in glycophytic plants may cause oxidative damage to the cells, thereby causing cell death. Although salt-tolerant crops can be produced by genetic engineering by introducing novel transgenes or by altering the expression levels of the existing genes, substantial enhancement of crop productivity is questionable, and the introduction of genetically modified transgenic plants into the ecosystem is not well received. Breeding for environmental stress tolerance in plants is also challenging, time consuming and cost intensive. Alternative to the above mentioned, the identification and usage of beneficial rhizobacteria are efficient, cost-effective approaches that have been successfully employed in various crops to improve their growth, yield and tolerance to salt stress. These beneficial plant growth-promoting rhizobacteria are naturally occurring soil bacteria that rapidly colonize plant roots and benefit plants by various mechanisms. These bacteria are able to survive in high-salt concentrations of the soil due to their inherent capability to accumulate some of the important compatible osmolytes required for maintaining intracellular osmotic homeostasis or possess the transporters that help them survive under high-salt conditions among other adaptive mechanisms. These soil bacteria grow luxuriously under high-salt conditions and possess plant growth-promoting and protecting traits that are responsible for facilitating plant growth and survival under high-salt conditions in the soil. In this chapter, we summarize the salinity stress responses in plants in terms of physiological, biochemical and molecular mechanisms followed by the plant growth-promoting rhizobacteria-mediated stress amelioration phenomenon. We describe the role of ‘omics’ approaches in generating comprehensive information essential for better understanding of plant growth promotion by plant growth-promoting rhizobacteria.

Soil salinity adversely affects crop growth and development, leading to reduced soil fertility and agricultural productivity. The indigenous salt-tolerant plant growth-promoting rhizobacteria (PGPR), as a sustainable microbial resource, do not only promote growth and alleviate salt stress, but also improve the soil microecology of crops. The strain H5 isolated from saline-alkali soil in Bachu of Xinjiang was studied through whole-genome analysis, functional annotation, and plant growth-promoting, salt-tolerant trait gene analysis. Phylogenetic tree analysis and 16S rDNA sequencing confirmed its classification within the genus Halomonas. Functional annotation revealed that the H5 genome harbored multiple functional gene clusters associated with plant growth promotion and salt tolerance, which were critically involved in key biological processes such as bacterial survival, nutrient acquisition, environmental adaptation, and plant growth promotion. The pot experiment under moderate salt stress demonstrated that seed inoculation with Halomonas sp. H5 not only significantly improved the agronomic traits of tomato seedlings, but also increased plant antioxidant enzyme activities under salt stress. Additionally, soil analysis revealed H5 treatment significantly decreased the total salt (9.33%) and electrical conductivity (8.09%), while significantly improving organic matter content (11.19%) and total nitrogen content (10.81%), respectively (p < 0.05). Inoculation of strain H5 induced taxonomic and functional shifts in the rhizosphere microbial community, increasing the relative abundance of microorganisms associated with plant growth-promoting and carbon and nitrogen cycles, and reduced the relative abundance of the genera Alternaria (15.14%) and Fusarium (9.76%), which are closely related to tomato diseases (p < 0.05). Overall, this strain exhibits significant potential in alleviating abiotic stress, enhancing growth, improving disease resistance, and optimizing soil microecological conditions in tomato plants. These results provide a valuable microbial resource for saline soil remediation and utilization.

Soil salinity is one of the main factors limiting agricultural development worldwide and has an adverse effect on plant growth and yield. To date, plant growth-promoting rhizobacteria (PGPR) are considered to be one of the most promising eco-friendly strategies for improving saline soils. The bacterium Bacillus megaterium ZS-3 is an excellent PGPR strain that induces growth promotion as well as biotic stress resistance and tolerance to abiotic stress in a broad range of host plants. In this study, the potential mechanisms of protection against salinity stress by B. megaterium ZS-3 in Arabidopsis thaliana were explored. Regulation by ZS-3 improved growth in A. thaliana under severe saline conditions. The results showed that ZS-3 treatment significantly increased the biomass, chlorophyll content and carotenoid content of A. thaliana. Compared to the control, the leaf area and total fresh weight of plants inoculated with ZS-3 increased by 245% and 271%, respectively; the chlorophyll a, chlorophyll b, and carotenoid contents increased by 335%, 146%, and 372%, respectively, under salt stress. Physiological and biochemical tests showed that ZS-3 regulated the content of osmotic substances in plants under salt stress. Compared to the control, the soluble sugar content of the ZS-3-treated group was significantly increased by 288%, while the proline content was significantly reduced by 41.43%. Quantification of Na+ and K+ contents showed that ZS-3 treatment significantly reduced Na+ accumulation and increased the K+/Na+ ratio in plants. ZS-3 also isolated Na+ in vesicles by upregulating NHX1 and AVP1 expression while limiting Na+ uptake by downregulating HKT1, which protected against Na+ toxicity. Higher levels of peroxidase and catalase activity and reduced glutathione were detected in plants inoculated with ZS-3 compared to those in uninoculated plants. In addition, it was revealed that ZS-3 activates salicylic acid (NPR1 and PR1) and jasmonic acid/ethylene (AOS, LOX2, PDF1.2, and ERF1) signaling pathways to induce systemic tolerance, thereby inducing salt tolerance in plants. In conclusion, the results of this study indicate that ZS-3 has the potential to act as an environmentally friendly salt tolerance inducer that can promote plant growth in salt-stressed environments.

The objective of this paper was to study the effects of two strains of isolated plant growth-promoting rhizobacteria (PGPR) on physiological and biochemical changes of wheat leaves under salinity conditions. The sterilized seeds were soaked in distilled water (control) and Nutrient Broth liquid medium of Enterobacter cloacae and Bacillus cereus (inoculated treatment) for 2 hours. After 10 days of growth, seedlings were selected for salinity stress treatments (0, 100, and 200 mM NaCl). After 10 days of starting salinity treatments, plants were harvested. Results showed that wheat plant growth, chlorophyll content and catalase activity were reduced under salinity condition; however PGPRs pre-treatments improved them under stress condition. Salinity significantly increased phenolic, carotenoids, proline and sugars content and peroxidase activity. Moreover, inoculation of seeds by PGPRs increased them under salinity. Lipid peroxidation increased but ascorbate peroxidase activity decreased as a response of saline stress and PGPRs pretreatment of seeds reduced them. Salinity increased sodium content, and PGPRs pretreatments decreased sodium absorption under salt stress. Moreover, in this study, Enterobacter cloacae inoculation of seeds increased wheat plants magnesium and potassium content in control condition as well as under salt stress. Data of experiment showed that the priming with PGPRs which tested in the present study especially E. cloacae can promote plant growth and salt tolerance.

Salinity adversely affects plant growth and development. Halotolerant plant-growth-promoting rhizobacteria (PGPR) alleviate salt stress and help plants to maintain better growth. In the present study, six PGPR strains were analyzed for their involvement in salt-stress tolerance in Arachis hypogaea. Different growth parameters, electrolyte leakage, water content, biochemical properties, and ion content were analyzed in the PGPR-inoculated plants under 100 mM NaCl. Three bacterial strains, namely, Brachybacteriumsaurashtrense (JG-06), Brevibacteriumcasei (JG-08), and Haererohalobacter (JG-11), showed the best growth of A. hypogaea seedlings under salt stress. Plant length, shoot length, root length, shoot dry weight, root dry weight, and total biomass were significantly higher in inoculated plants compared to uninoculated plants. The PGPR-inoculated plants were quite healthy and hydrated, whereas the uninoculated plant leaves were desiccated in the presence of 100 mM NaCl. The percentage water content (PWC) in the shoots and roots was also significantly higher in inoculated plants compared to uninoculated plants. Proline content and soluble sugars were significantly low, whereas amino acids were higher than in uninoculated plants. The MDA content was higher in uninoculated plants than in inoculated plants at 100 mM NaCl. The inoculated plants also had a higher K+/Na+ ratio and higher Ca2+, phosphorus, and nitrogen content. The auxin concentration was higher in both shoot and root explants in the inoculated plants. Therefore, it could be predicted that all these parameters cumulatively improve plant growth under saline conditions in the presence of PGPR. This study shows that PGPR play an important role in inducing salinity tolerance in plants and can be used to grow salt-sensitive crops in saline areas.

Increase in soil salinity is a serious concern as it adversely impacts the growth, development and yield of agricultural crops. The disruption in the ionic composition thereby affecting the fertility of the soil is observed in salt-affected soils warranting the development of technologies for improved crop growth under salinity conditions. Whilst generation of transgenic plants harbouring genes important for imparting tolerance to salinity stress conditions is considered a feasible biotechnological approach, the usage of transgenic crops for human consumption is not well received. Further, breeding approaches for generation of salt tolerant varieties is time consuming. In this context, the usage of halotolerant Plant Growth Promoting Rhizobacteria (PGPR) for improvement of salinity tolerance in crop plants is considered as an eco-friendly and cost-effective approach. This approach will also maintain the soil microbial diversity thereby protecting it from salinity-induced degradation. Few PGPR such as Pseudomonas and Bacillus species although have been effectively used for imparting plant growth promotion under control conditions, isolation of halotolerant PGPR, their effective utilization and optimization for agronomical application in salt-affected soils are key factors for improvement of salinity tolerance in crop plants. Further, whilst many of the isolated halotolerant PGPR show plant-growth promoting traits under laboratory conditions, their efficiency is questionable under field conditions. In the current chapter, the methodologies employed for inoculation of isolated halotolerant PGPR either singly or as a consortium to agricultural crops and the changes observed in the plants towards improvement in salinity tolerance will be discussed. The efficient delivery methods with carriers like nanoparticles, biopolymers and organic carriers along with preparation of formulations, the route of administration for improvement of salinity tolerance in crop plants and their survival in saline soil will be elaborately discussed.

Agriculture production was effectively decreased by abiotic and biotic stresses, which affect the plant growth by ion toxicity, hormonal and nutritional imbalance, and physiological and metabolic changes. Plant growth-promoting rhizobacteria (PGPR) are the root-colonizing non-pathogenic bacterium, which helps in plant growth promotion and alleviation of the stress-induced changes to result in the maintenance of agricultural productivity. Plants inoculated with the PGPR provide resistance to various abiotic stresses such as salt, drought, and heavy metal toxicity. Some PGPR strains protect both the biotic and abiotic stresses. In addition, several PGPR contribute to multiple abiotic stress tolerance in plants. PGPR produce phytohormones, siderophores, organic acids, and stress-induced metabolites such as osmotic solutes, prolines, and antioxidant enzymes and up- and downregulates the expression of various stress-responsive genes that provide resistance to the plants under stressful conditions. The use of PGPR is a simple and effective alternative approach to genetic engineering and breeding methods for crop improvement, since breeding and genetic engineering are time-consuming, expensive, and laborious procedures. In this chapter, we described the potential role of PGPR in the abiotic stress tolerance in plants. Moreover, the mechanism of PGPR in drought, salt, and heavy metal stress alleviation was described briefly.

A meeting on the molecular basis of ionic homeostasis and salt tolerance in plants took place in Madrid, Spain, October 22–24, 2001. This meeting was organized by Eduardo Blumwald (Davis, CA) and Alonso Rodriguez‐Navarro (Madrid, Spain) at the Centre for International Meetings on Biology (‘Instituto Juan March de Estudios e Investigaciones’). ![][1] Ionic homeostasis is a fundamental cellular phenomenon. All living cells maintain an intracellular ionic composition compatible with their constituent molecules, and this requires the regulation of multiple membrane transporters and signal transduction pathways. Other biophysical parameters such as turgor and electrical potential are also part of this essential regulation. How ionic homeostasis is achieved, however, is not completely understood. Although most transporters have already been identified, their physiological function is only starting to be demonstrated and the receptors and most components of the regulatory pathways that effect ionic homeostasis remain unknown. In the case of plants, this problem is related to mineral nutrition and salinity tolerance, both of which have great relevance for agriculture. In fact, as demonstrated by this meeting, salinity stress has been one of the keys to opening the black box of ionic homeostasis in general. Another has been the novel molecular genetics of the plant Arabidopsis thaliana . Of course, other approaches have also contributed to our present understanding of ion homeostasis in plants and were represented at the meeting. For further details, see Blumwald (2000), Hasegawa et al . (2000), Bohnert et al . (2001), Serrano and Rodriguez‐Navarro (2001) and Zhu (2001). ### Some physiology of salt tolerance Salt stress is an important threat to the future of agriculture in many productive areas of the planet. In countries such as Australia and Pakistan, salinity is already a national concern, as it was in the past in ancient Mesopotamia. Areas of California and the Mediterranean region are also threatened. … [1]: /embed/graphic-1.gif

ABSTRACTThe accumulation of autotoxins in soil causes continuous cropping obstacle stress in crops, and the bioremediation of autotoxins by microorganisms is an efficient process. In this study, strain ZH07 was isolated from the peanut rhizosphere and was found to be utilizing multiple autotoxins as its carbon sources. Based on its genomic characteristics and a phylogenetic analysis, ZH07 represents a member of Klebsiella variicola subsp. variicola. A comparative genomic analysis exhibited evolutionary dynamics exhibited by mobile genetic elements (MGEs), strain-specific genes, potential horizontal genes, and evolutionary constraints driven by purifying selection, which facilitated its genomic adaptation to rhizosphere soil. Genome mining revealed the potential genomic properties associated with plant growth promotion, such as nitrogen fixation, indole acetic acid synthesis, phosphonate solubilization and assimilation, siderophore production, and secondary metabolite synthesis. Moreover, abundant genes putatively responsible for the biodegradation of aromatic xenobiotics, including benzoic acid, cinnamic acid, vanillic acid, protocatechuic acid, phenylacetic acid, and p-hydroxybenzoic acid were also observed in the ZH07 genome. Compared to autotoxin stress alone, the combination of ZH07 application promoted peanut germination and seedling growth. Our analysis revealed the genetic adaptation of ZH07 to the rhizosphere environment and the potential genetic basis and effectiveness of the isolate to serve as a plant growth stimulator.IMPORTANCE Continuous cropping obstacles reduce the production and quality of agricultural products, and the application of rhizosphere beneficial microbes is an important strategy. Strain ZH07 showed autotoxin-degrading and plant growth-promoting capacities. The objectives of this study were to characterize its genomic evolution and the potential genetic basis of the autotoxin degradation and plant growth promotion. ZH07 represents a member of Klebsiella variicola subsp. variicola, based on genomic and phylogenetic analyses. Its genomic components have undergone different degrees of purifying selection, and the disparity in the evolutionary rate may be associated with its niche adaptation. A systematic analysis of the ZH07 genome identified the potential genetic basis that contributes to plant growth promotion and to aromatic xenobiotic biodegradation. This study demonstrates that plant growth-promoting rhizobacteria (PGPR) play important roles in autotoxin biodegradation and can be used as biofertilizers to enhance the growth of peanuts in response to continuous cropping obstacle stress.

Among the biotic stresses, plant pathogens can reduce yield crop which affected potential loss to crop productivity. Plant growth-promoting rhizobacteria (PGPR) can help plants to be resistant against biotic stress via direct antagonism to pathogens or by induction of systemic resistance to pathogens. The presence of high levels of nutrients exuded from various roots of most plants can support bacterial growth and metabolism as well as maintain health of the plant in the growth process. PGPR promote plant growth due to their abilities in phytohormone production, nitrogen fixation, and phosphorus solubilization; produce several substances which are related to pathogen control, i.e., exhibiting competition with plant pathogens, synthesis of antibiotics, antifungal metabolites and defense enzymes, and secretion of iron-chelating siderophores; and trigger induced systemic resistance (ISR) via methyl jasmonate and methyl salicylate in plants. The ISR resembles pathogen-induced systemic acquired resistance (SAR) through the salicylic acid-dependent SAR pathway under conditions where the inducing bacteria and the challenging pathogen remain spatially separated. The use of PGPR combinations of different mechanisms of action, i.e., induced resistance and antagonistic PGPR, might be useful in formulating inoculants leading to a more efficient use for biological control strategies to improve crop productivity. Many PGPR have been isolated from the tissues of many plants, and various species of bacteria, i.e., Azotobacter, Azospirillum, Alcaligenes, Arthrobacter, Bacillus, Burkholderia, Enterobacter, Klebsiella, Pseudomonas, and Serratia, have been reported to control several diseases and enhance plant growth. PGPR belonging to the genera Pseudomonas and Bacillus are also well known for their antagonistic effects and their ability to trigger ISR. An increasingly successful study to reduce disease severity is the use of bacteria, namely, Bacillus subtilis, P. fluorescens, Serratia, and the fungus Trichoderma. Tea and rice plants are cultivated in Indonesia predominantly in Java and Sumatra islands. Major constraints of cultivation include low fertility of soils, poor input management, low germination, and high susceptibility to the diseases. The strategies employed by PGPR provide promising approaches to alter agricultural crops and plantation practices toward sustainable environmental development. Research has been conducted to know the effect of PGPR on tea plant growth that can work optimally as a biological fertilizer and plant-induced resistance to suppress blister blight (Exobasidium vexans Massee), a major disease in tea plantation that can decrease yield loss up to 50%. Individual PGPR strains for in vitro broad-spectrum pathogen suppression and production of several physiological/biochemical activities related to plant growth promotion have been screened. Numerous bacterial isolates have been found to function both as biofertilizers and biological control agents, namely, Chryseobacterium sp. AzII-1, Acinetobacter sp., Alcaligenes sp. E5, Bacillus E65, and Burkholderia E76. Study about synergism among bacteria has been carried out in the laboratory test using four combinations, i.e., (a) Chryseobacterium sp. AzII-1 + Acinetobacter sp., (b) Chryseobacterium sp. AzII-1 + Alcaligenes sp. E5, (c) Chryseobacterium sp. AzII-1 + Bacillus E65, and (d) Chryseobacterium sp. AzII-1 + Burkholderia E76. All bacterial combinations had a synergistic effect. It was shown that the bacterial population was not significantly different with the average of the total bacterial population (4.62 × 108 CFU/ml). The effect of bacterial combinations to blister blight and plant growth under a tea nursery trial revealed that combination of Chryseobacterium sp. AzII-1 75% + Alcaligenes sp. E5 25% could increase the growth of tea plant and suppress the intensity of blister blight up to 1.27%. The disease intensity of blister blight decreased in all treatments under field trial, while the Acinetobacter sp. treatment in tea shoots was 17.26% higher than the control. PGPR have also been isolated from cultivated rice. Serratia SKM, Burkholderia E76, and Bacillus E65 have the potential for controlling rice diseases and induce plant growth promotion. Under in vitro antagonistic assay, it was shown that these isolates could suppress effectively the growth of rice pathogens Xanthomonas oryzae pv. oryzae, the causal agent of bacterial blight (BB). Kaolin formulation of these three isolates was evaluated as a foliar application on rice. PGPR application under experimental plots resulted in enhancement of rice growth and yield, with the yield increment on cv. Sintanur being 12.8 percent higher compared with control (cv. Ciherang). Based on PGPR application technology which is demonstrated in farmers’ plots, the severity of BB disease was reduced to 76.8 percent compared with the untreated plot. The farmers were convinced with the beneficial effects of PGPR on both plant growth and yield and reduction of BB disease incidence. PGPR technologies have the potential to reduce agrochemical application. They can also be exploited as low in input and environmentally friendly for sustainable plant management. PGPR is highly diverse, and in this review, we focus on PGPR in plant growth promotion, as well as understanding the role of PGPR in crop protection.

Plant growth-promoting rhizobacteria (PGPR) are known for growth promotion and mitigating environmental stresses. Here, we examined the propitiousness of three indigenous salt-tolerant PGPR, i.e., Bacillus subtilis (NBRI 28B), B. subtilis (NBRI 33N), and B. safensis (NBRI 12M) for plant growth promotion and salt stress amelioration in Zea mays. Results of the in vitro plant growth-promoting attribute revealed NBRI 12M demonstrated the highest values at 1M salt (NaCl) concentration. Furthermore, the greenhouse experiment using three Bacillus strains confirmed plant growth-promoting and salt stress-ameliorating ability, through colonizing successfully and mitigating the adverse effects of ethylene by modulating 1-aminocyclopropane-1-carboxylic acid (ACC) accumulation, ACC-oxidase (ACO), and ACC-synthase (ACS) activities under salt stress. Bacillus sp. inoculation has also induced plant response for defense enzymes, chlorophyll, proline and soluble sugar under salt stress. Among three Bacillus strains, NBRI 12M not only demonstrated higher values for plant growth-promoting (PGP) attributes but also the same was observed in the greenhouse experiment. Thus, the outcomes of this comparative study represent for the first time that salt-tolerant Bacillus strains exhibiting multiple PGP attributes under salt stress along with high rhizosphere competence can alleviate salt stress by reducing the stress ethylene level in the host plant.

Globally, due to widespread dispersion, intraspecific diversity, and crucial ecological components of halophilic ecosystems, halophilic bacteria is considered one of the key models for ecological, adaptative, and biotechnological applications research in saline environments. With this aim, the present study was to enlighten the plant growth-promoting features and investigate the systematic genome of a halophilic bacteria, Virgibacillus halodenitrificans ASH15, through single-molecule real-time (SMRT) sequencing technology. Results showed that strain ASH15 could survive in high salinity up to 25% (w/v) NaCl concentration and express plant growth-promoting traits such as nitrogen fixation, plant growth hormones, and hydrolytic enzymes, which sustain salt stress. The results of pot experiment revealed that strain ASH15 significantly enhanced sugarcane plant growth (root shoot length and weight) under salt stress conditions. Moreover, the sequencing analysis of the strain ASH15 genome exhibited that this strain contained a circular chromosome of 3,832,903 bp with an average G+C content of 37.54%: 3721 predicted protein-coding sequences (CDSs), 24 rRNA genes, and 62 tRNA genes. Genome analysis revealed that the genes related to the synthesis and transport of compatible solutes (glycine, betaine, ectoine, hydroxyectoine, and glutamate) confirm salt stress as well as heavy metal resistance. Furthermore, functional annotation showed that the strain ASH15 encodes genes for root colonization, biofilm formation, phytohormone IAA production, nitrogen fixation, phosphate metabolism, and siderophore production, which are beneficial for plant growth promotion. Strain ASH15 also has a gene resistance to antibiotics and pathogens. In addition, analysis also revealed that the genome strain ASH15 has insertion sequences and CRISPRs, which suggest its ability to acquire new genes through horizontal gene transfer and acquire immunity to the attack of viruses. This work provides knowledge of the mechanism through which V. halodenitrificans ASH15 tolerates salt stress. Deep genome analysis, identified MVA pathway involved in biosynthesis of isoprenoids, more precisely “Squalene.” Squalene has various applications, such as an antioxidant, anti-cancer agent, anti-aging agent, hemopreventive agent, anti-bacterial agent, adjuvant for vaccines and drug carriers, and detoxifier. Our findings indicated that strain ASH15 has enormous potential in industries such as in agriculture, pharmaceuticals, cosmetics, and food.