Repression of mineral phosphate solubilizing phenotype in the presence of weak organic acids in plant growth promoting fluorescent pseudomonads

Prospects of phosphate solubilizing microorganisms in sustainable agriculture

Phosphorus (P), an essential macronutrient for various plant processes, is generally a limiting soil component for crop growth and yields. Organic and inorganic types of P are copious in soils, but their phyto-availability is limited as it is present largely in insoluble forms. Although phosphate fertilizers are applied in P-deficit soils, their undue use negatively impacts soil quality and the environment. Moreover, many P fertilizers are lost because of adsorption and fixation mechanisms, further reducing fertilizer efficiencies. The application of phosphate-solubilizing microorganisms (PSMs) is an environmentally friendly, low-budget, and biologically efficient method for sustainable agriculture without causing environmental hazards. These beneficial microorganisms are widely distributed in the rhizosphere and can hydrolyze inorganic and organic insoluble P substances to soluble P forms which are directly assimilated by plants. The present review summarizes and discusses our existing understanding related to various forms and sources of P in soils, the importance and P utilization by plants and microbes,, the diversification of PSMs along with mixed consortia of diverse PSMs including endophytic PSMs, the mechanism of P solubilization, and lastly constraints being faced in terms of production and adoption of PSMs on large scale have also been discussed.

Pseudomonas taetrolens ULE-PH5 and Pseudomonas sp. ULE-PH6 Isolated from the Hop Rhizosphere Increase Phosphate Assimilation by the Plant

Most of the phosphorus incorporated into agricultural soils through the use of fertilizers precipitates in the form of insoluble salts that are incapable of being used by plants. This insoluble phosphorus present in large quantities in soil forms the well-known "phosphorus legacy". The solubilization of this "phosphorus legacy" has become a goal of great agronomic importance, and the use of phosphate-solubilizing bacteria would be a useful tool for this purpose. In this work, we have isolated and characterized phosphate-solubilizing bacteria from the rhizosphere of hop plants. Two particular strains, Pseudomonas taetrolens ULE-PH5 and Pseudomonas sp. ULE-PH6, were selected as plant growth-promoting rhizobacteria due to their high phosphate solubilization capability in both plate and liquid culture assays and other interesting traits, including auxin and siderophore production, phytate degradation, and acidic and alkaline phosphatase production. These strains were able to significantly increase phosphate uptake and accumulation of phosphorus in the aerial part (stems, petioles, and leaves) of hop plants, as determined by greenhouse trials. These strains are promising candidates to produce biofertilizers specifically to increase phosphate adsorption by hop plants.

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.

Sporadic Pb accumulation by plants: Influence of soil biogeochemistry, microbial community and physiological mechanisms

Recent results revealed that considerable Pb accumulation in plants is possible under specific soil conditions that make Pb phytoavailable. In this review, the sources and transformations of Pb in soils, the interaction of Pb with bacteria and specifically the microbiota in the soil, factors and mechanisms of Pb uptake, translocation and accumulation in plants and Pb toxicity in living organisms are comprehensively elaborated. Specific adsorption and post-adsorption transformations of Pb in soil are the main mechanisms affecting the mobility, bioavailability, and toxicity of Pb. The adsorption ability of Pb largely depends on the composition and properties of soils and environmental conditions. Microbial impact on Pb mobility in soil and bioavailability as well as bacterial resistance to Pb are considered. Specific mechanisms conferring Pb-resistance, including Pb-efflux, siderophores, and EPS, have been identified. Pathways of Pb entry into plants as well as mechanisms of in planta Pb transport are poorly understood. Available evidence suggests the involvement of Ca transporters, organic acids and the phytochelatin pathway in Pb transport, mobility and detoxification, respectively.

Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri

Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse order to that of enterobacteria, and this process is controlled by RNA-binding translational repressors and regulatory ncRNA antagonists. However, their roles in microbe-plant interactions and the underlying mechanisms remain uncertain. Here we show that root-associated diazotrophic Pseudomonas stutzeri A1501 preferentially catabolizes succinate, followed by the less favorable substrate citrate, and ultimately glucose. Furthermore, the Hfq/Crc/CrcZY regulatory system orchestrates this preference and contributes to optimal nitrogenase activity and efficient root colonization. Hfq has a central role in this regulatory network through different mechanisms of action, including repressing the translation of substrate-specific catabolic genes, activating the nitrogenase gene nifH posttranscriptionally, and exerting a positive effect on the transcription of an exopolysaccharide gene cluster. Our results illustrate an Hfq-mediated mechanism linking carbon metabolism to nitrogen fixation and root colonization, which may confer rhizobacteria competitive advantages in rhizosphere environments.

A comprehensive synthesis unveils the mysteries of phosphate-solubilizing microbes

Phosphate-solubilizing microbes (PSMs) drive the biogeochemical cycling of phosphorus (P) and hold promise for sustainable agriculture. However, their global distribution, overall diversity and application potential remain unknown. Here, we present the first synthesis of their biogeography, diversity and utility, employing data from 399 papers published between 1981 and 2017, the results of a nationwide field survey in China consisting of 367 soil samples, and a genetic analysis of 12986 genome-sequenced prokaryotic strains. We show that at continental to global scales, the population density of PSMs in environmental samples is correlated with total P rather than pH. Remarkably, positive relationships exist between the population density of soil PSMs and available P, nitrate-nitrogen and dissolved organic carbon in soil, reflecting functional couplings between PSMs and microbes driving biogeochemical cycles of nitrogen and carbon. More than 2704 strains affiliated with at least nine archaeal, 88 fungal and 336 bacterial species were reported as PSMs. Only 2.59% of these strains have been tested for their efficiencies in improving crop growth or yield under field conditions, providing evidence that PSMs are more likely to exert positive effects on wheat growing in alkaline P-deficient soils. Our systematic genetic analysis reveals five promising PSM genera deserving much more attention.

Inorganic Phosphate Solubilization by Rhizosphere Bacterium Paenibacillus sonchi: Gene Expression and Physiological Functions

Due to the importance of phosphorus (P) in agriculture, crop inoculation with phosphate-solubilizing bacteria is a relevant subject of study. Paenibacillus sonchi genomovar Riograndensis SBR5 is a promising candidate for crop inoculation, as it can fix nitrogen and excrete ammonium at a remarkably high rate. However, its trait of phosphate solubilization (PS) has not yet been studied in detail. Here, differential gene expression and functional analyses were performed to characterize PS in this bacterium. SBR5 was cultivated with two distinct P sources: NaH2PO4 as soluble phosphate source (SPi) and hydroxyapatite as insoluble phosphate source (IPi). Total RNA of SBR5 cultivated in those two conditions was isolated and sequenced, and bacterial growth and product formation were monitored. In the IPi medium, the expression of 68 genes was upregulated, whereas 100 genes were downregulated. Among those, genes involved in carbon metabolism, including those coding for subunits of 2-oxoglutarate dehydrogenase, were identified. Quantitation of organic acids showed that the production of tricarboxylic acid cycle-derived organic acids was reduced in IPi condition, whereas acetate and gluconate were overproduced. Increased concentrations of proline, trehalose, and glycine betaine revealed active osmoprotection during growth in IPi. The cultivation with hydroxyapatite also caused the reduction in the motility of SBR5 cells as a response to Pi depletion at the beginning of its growth. SBR5 was able to solubilize hydroxyapatite, which suggests that this organism is a promising phosphate-solubilizing bacterium. Our findings are the initial step in the elucidation of the PS process in P. sonchi SBR5 and will be a valuable groundwork for further studies of this organism as a plant growth-promoting rhizobacterium.

Biodegradation of carbendazim by a potent novel Chryseobacterium sp. JAS14 and plant growth promoting Aeromonas caviae JAS15 with subsequent toxicity analysis

In the present study, carbendazim (MBC) degrading bacterial strains were isolated and identified as Chryseobacterium sp. JAS14 and Aeromonas caviae JAS15. Both the strains completely degraded 200 mg l^-1 of MBC in the aqueous medium and soil within 4-9 days of incubation. In an aqueous medium, the degradation process was characterized by a rate constant of 53.16 day^-1 and 42.60 day^-1, following zero order model and DT₅₀ was 1.8 days and 2.34 days for Chryseobacterium sp. JAS14 and A. caviae JAS15, respectively. A Chryseobacterium sp. JAS14 and A. caviae JAS15 inoculated into the soil without the addition of nutrients showed the degradation rate constant of 27.30 day^-1 and 23.87 day^-1, and DT₅₀ was 3.66 days and 4.18 days, respectively. The metabolites during MBC biodegradation by Chryseobacterium sp. JAS14 and A. caviae JAS15 were identified as 2-aminobenzimidazole, 2-hydroxybenzimidazole, 1, 2 diaminobenzene and catechol. To our knowledge, this is the first study of the detailed biodegradation pathway of MBC by Chryseobacterium sp. JAS14 was proposed. Phytotoxicity and cytogenotoxicity assays showed that the toxicity of the MBC reduced after biodegradation by Chryseobacterium sp. JAS14 and A. caviae JAS15. In addition, A. caviae JAS15 possess important plant growth promoting traits under normal and MBC stress condition. These results suggest the Chryseobacterium sp. JAS14 and A. caviae JAS15 could be used as a bioresource for the reclamation of MBC contaminated soil.

Isolation and Characterization of Phosphorus Solubilizing Bacteria With Multiple Phosphorus Sources Utilizing Capability and Their Potential for Lead Immobilization in Soil

Phosphorus solubilizing bacteria (PSB) can promote the level of plant-absorbable phosphorus (P) in agro-ecosystems. However, little attention has been paid to PSB harboring abilities in utilizing multiple phosphorus sources and their potentials for heavy metal immobilization. In this study, we applied the strategy of stepwise acclimation by using Ca₃(PO₄)₂, phytate, FePO₄, and AlPO₄ as sole P source. We gained 18 PSB possessing abilities of multiple P sources utilization, and these bacteria belonged to eight genera (Acinetobacter, Pseudomonas, Massilia, Bacillus, Arthrobacter, Stenotrophomonas, Ochrobactrum, and Cupriavidus), and clustered to two apparent parts: Gram-positive bacteria and Gram-negative bacteria. The isolate of Acinetobacter pittii gp-1 presented good performance for utilizing Ca₃(PO₄)₂, FePO₄, AlPO₄, and phytate, with corresponding P solubilizing levels were 250.77, 46.10, 81.99, and 7.91 mg/L PO₄^3–-P, respectively. The PSB A. pittii gp-1 exhibited good performance for solubilizing tricalcium phosphate in soil incubation experiments, with the highest values of water soluble P and available P were 0.80 and 1.64 mg/L, respectively. Additionally, the addition of A. pittii gp-1 could promote the immobilization of lead (Pb), and the highest Pb immobilization efficiency reached 23%. Simultaneously, we found the increases in abundances of both alkaline phosphatase gene (phoD) and β-propeller phytase gene (bpp) in strain gp-1 added soils. Besides, we observed the expression up-regulation of both pyrroloquinoline quinone gene (pqq) and polyphosphate kinases gene (ppk), with the highest relative expression levels of 18.18 and 5.23, respectively. We also found the polyphosphate particles using granule staining. To our knowledge, our findings first suggest that the solubilizing of tricalcium phosphate by phosphorus solubilizing bacterium belonging to Acinetobacter is coupled with the synthesis of polyphosphate. Taken together, A. pittii gp-1 could be a good candidate in improving soil fertility and quality.

Modulation of PQQ-dependent glucose dehydrogenase (mGDH and sGDH) activity by succinate in phosphate solubilizing plant growth promoting Acinetobacter sp. SK2

Prospective plant growth promoting rhizobacteria isolated from the rhizosphere of Vigna radiata was identified as Acinetobacter sp. SK2 that solubilized 682 μg ml^-1 of tricalcium phosphate (TCP) and 86 μg ml^-1 of rock phosphate (RP) with concomitant decrease in pH up to 4 due to the production of gluconate. The biochemical basis of the P solubilization suggested that the gluconate production was mediated by mGDH and sGDH enzymes. Our results illustrate the role of succinate in repression of P solubilization via suppression of mGDH and sGDH activity which correlated with repression of expression of respective genes, gdhA and gdhB. SK2 also produced IAA (117 μg ml^-1), siderophore (87% units), HCN, ammonia and solubilized minerals of Zn and K. Our findings imply that it is important to understand the cause of failure of several phosphate solubilizing bacteria in field conditions where catabolite repression may control the expression of several genes and pathways including that of mineral phosphate solubilization. Furthermore, Acinetobacter sp. SK2 bearing two glucose dehydrogenase (gdhA and gdhB) genes was recognized as promising strain for P biofortification and enhanced plant growth promotion.

Glucose and arabinose dependent mineral phosphate solubilization and its succinate-mediated catabolite repression in Rhizobium sp. RM and RS

Rhizobium sp. RM and RS are Vigna radiata root nodule isolates with the ability to solubilize tricalcium phosphate and rock phosphate under 50 mM Tris-Cl buffering conditions. Rhizobium sp. RM and RS were unique as they could produce two different organic acids, gluconic acid and oxalic acid using glucose and arabinose, respectively, which are two of the most prominent sugars present in the rhizospheric soil. However, P solubilization in these isolates was repressed in the presence of succinate resembling the phenomenon of catabolite repression. RM and RS produced 24 mM and 20 mM gluconic acid in presence of glucose which was repressed to 10 mM and 8 mM, respectively, in glucose + succinate conditions. Similarly, RM and RS produced 28 mM and 23 mM oxalic acid in arabinose containing media which was repressed to 9 mM and 8 mM, respectively, in the presence of arabinose + succinate. Results of enzyme activities indicated 66% repression of quinoprotein glucose dehydrogenase in glucose + succinate compared to glucose grown cells and 84% repression of glyoxylate oxidase in arabinose + succinate compared to arabinose grown cells. This is perhaps the first report on mechanism of P solubilization in rhizobia through utilization of two different sugars, glucose and arabinose and its repression by succinate. Succinate-mediated catabolite repression of arabinose is the unique aspect of this study.

Prevention of Surface-Associated Calcium Phosphate by the Pseudomonas syringae Two-Component System CvsSR

CvsSR is a Ca²⁺-induced two-component system (TCS) in the plant pathogen Pseudomonas syringae pv. tomato DC3000. Here, we discovered that CvsSR is induced by Fe³⁺, Zn²⁺, and Cd²⁺ However, only supplementation of Ca²⁺ to medium resulted in rugose, opaque colonies in ΔcvsS and ΔcvsR strains. This phenotype corresponded to formation of calcium phosphate precipitation on the surface of ΔcvsS and ΔcvsR colonies. CvsSR regulated swarming motility in P. syringae pv. tomato in a Ca²⁺-dependent manner, but swarming behavior was not influenced by Fe³⁺, Zn²⁺, or Cd²⁺ We hypothesized that reduced swarming displayed by ΔcvsS and ΔcvsR strains was due to precipitation of calcium phosphate on the surface of ΔcvsS and ΔcvsR cells grown on agar medium supplemented with Ca²⁺ By reducing the initial pH or adding glucose to the medium, calcium precipitation was inhibited, and swarming was restored to ΔcvsS and ΔcvsR strains, suggesting that calcium precipitation influences swarming ability. Constitutive expression of a CvsSR-regulated carbonic anhydrase and a CvsSR-regulated putative sulfate major facilitator superfamily transporter in ΔcvsS and ΔcvsR strains inhibited formation of calcium precipitates and restored the ability of ΔcvsS and ΔcvsR bacteria to swarm. Lastly, we found that glucose inhibited Ca²⁺-based induction of CvsSR. Hence, CvsSR is a key regulator that controls calcium precipitation on the surface of bacterial cells.IMPORTANCE Bacteria are capable of precipitating and dissolving minerals. We previously reported the characterization of the two-component system CvsSR in the plant-pathogenic bacterium Pseudomonas syringae CvsSR responds to the presence of calcium and is important for causing disease. Here, we show that CvsSR controls the ability of the bacterium to prevent calcium phosphate precipitation on the surface of cells. We also identified a carbonic anhydrase and transporter that modulate formation of surface-associated calcium precipitates. Furthermore, our results demonstrate that the ability of the bacterium to swarm is controlled by the formation and dissolution of calcium precipitates on the surface of cells. Our study describes new mechanisms for microbially induced mineralization and provides insights into the role of mineral deposits on bacterial physiology. The discoveries may lead to new technological and environmental applications.

Effect of succinate on phosphate solubilization in nitrogen fixing bacteria harbouring chick pea and their effect on plant growth

Diverse nitrogen fixing bacteria harbouring chick pea rhizosphere and root nodules were tested for multiple plant growth promoting traits like tricalcium phosphate (TCP) and rock phosphate (RP) solubilization, production of ammonia, indole 3-acetic acid, chitinase, phytase and alkaline phosphatase. Isolates belonged to diverse genus like Enterobacter, Acinetobacter, Erwinia, Pseudomonas, Rhizobium, Sinorhizobium, Ensifer, Klebsiella, etc. Most isolates solubilized TCP and RP along with the lowering of media pH, indicating acidification to be the chief mechanism behind this solubilization. However, lowering of media pH and P release decreased by 32-100% when media was supplemented with succinate, a major component of plant root exudates indicating succinate mediated repression of P solubilization. Maximum TCP and RP solubilization with P release of 850μg/mL and 2088μg/mL was obtained with lowering of media pH up to 2.8 and 3.3 for isolate E43 and PSB1 respectively. This pH drop changed to 4.4 and 4.8 with 80% and 87% decrease in P solubilization in the presence of succinate. Maximum 246μg/mL indole 3-acetic acid production in Lh3, 44.8U/mL chitinase activity in MB3, 11.3U/mL phytase activity in I91 and 9.4U/mL alkaline phosphatase activity in SM1 were also obtained. Most isolates showed multiple PGP traits which resulted in significant plant growth promotion of chick pea plants. Present study shows repression of P solubilization by succinate for various bacterial groups which might be one of the reasons why phosphate solubilizing bacteria which perform well in vitro often fail in vivo. Studying this repression mechanism might be critical in understanding the in vivo efficacy.

The role of gluconate production by Pseudomonas spp. in the mineralization and bioavailability of calcium-phytate to Nicotiana tabacum

Organic phosphorus (P) is abundant in most soils but is largely unavailable to plants. Pseudomonas spp. can improve the availability of P to plants through the production of phytases and organic anions. Gluconate is a major component of Pseudomonas organic anion production and may therefore play an important role in the mineralization of insoluble organic P forms such as calcium-phytate (CaIHP). Organic anion and phytase production was characterized in 2 Pseudomonas spp. soil isolates (CCAR59, Ha200) and an isogenic mutant of strain Ha200, which lacked a functional glucose dehydrogenase (Gcd) gene (strain Ha200 gcd::Tn5B8). Wild-type and mutant strains of Pseudomonas spp. were evaluated for their ability to solubilize and hydrolyze CaIHP and to promote the growth and assimilation of P by tobacco plants. Gluconate, 2-keto-gluconate, pyruvate, ascorbate, acetate, and formate were detected in Pseudomonas spp. supernatants. Wild-type pseudomonads containing a functional gcd could produce gluconate and mineralize CaIHP, whereas the isogenic mutant could not. Inoculation with Pseudomonas improved the bioavailability of CaIHP to tobacco plants, but there was no difference in plant growth response due to Gcd function. Gcd function is required for the mineralization of CaIHP in vitro; however, further studies will be needed to quantify the relative contribution of specific organic anions such as gluconate to plant growth promotion by soil pseudomonads.

2-ketogluconic acid secretion by incorporation of Pseudomonas putida KT 2440 gluconate dehydrogenase (gad) operon in Enterobacter asburiae PSI3 improves mineral phosphate solubilization

Enterobacter asburiae PSI3 is known to efficiently solubilize rock phosphate by secretion of approximately 50 mM gluconic acid in Tris-buffered medium in the presence of 75 mM glucose and in a mixture of seven aldosugars each at 15 mM concentration, mimicking alkaline vertisol soils. Efficacy of this bacterium in the rhizosphere requires P release in the presence of low amount of sugars. To achieve this, E. asburiae PSI3 has been manipulated to express gluconate dehydrogenase (gad) operon of Pseudomonas putida KT 2440 to produce 2-ketogluconic acid. E. asburiae PSI3 harboring gad operon had 438 U of GAD activity, secreted 11.63 mM 2-ketogluconic and 21.65 mM gluconic acids in Tris-rock phosphate-buffered medium containing 45 mM glucose. E. asburiae PSI3 gad transformant solubilized 0.84 mM P from rock phosphate in TRP-buffered liquid medium. In the presence of a mixture of seven sugars each at 12 mM, the transformant brought about a drop in pH to 4.1 and released 0.53 mM P.

Repression of oxalic acid-mediated mineral phosphate solubilization in rhizospheric isolates of Klebsiella pneumoniae by succinate

Two strains of Klebsiella (SM6 and SM11) were isolated from rhizospheric soil that solubilized mineral phosphate by secretion of oxalic acid from glucose. Activities of enzymes for periplasmic glucose oxidation (glucose dehydrogenase) and glyoxylate shunt (isocitrate lyase and glyoxylate oxidase) responsible for oxalic acid production were estimated. In presence of succinate, phosphate solubilization was completely inhibited, and the enzymes glucose dehydrogenase and glyoxylate oxidase were repressed. Significant activity of isocitrate lyase, the key enzyme for carbon flux through glyoxylate shunt and oxalic acid production during growth on glucose suggested that it could be inducible in nature, and its inhibition by succinate appeared to be similar to catabolite repression.

Changes in labile phosphorus forms during maturation of vermicompost enriched with phosphorus-solubilizing and diazotrophic bacteria

The aim of this study was to assess the effect of N(2)-fixing and P-solubilizing bacteria during maturation of vermicompost on phosphorus availability. A bacterial suspension containing Burkholderia silvatlantica, Burkholderia spp. and Herbaspirillum seropedicae was applied at the initial stage of vermicomposting. At the end of the incubation time (120days), the nitrogen content had increased by18% compared to uninoculated vermicompost. Water-soluble P was 106% higher in inoculated vermicompost while resin-extractable P increased during the initial vermicomposting stage and was 21% higher at 60days, but was the same in inoculated and uninoculated mature compost. The activity of acid phosphatase was 43% higher in inoculated than uninoculated vermicompost. These data suggest that the introduction of the mixed culture had beneficial effects on vermicompost maturation.