Heterologous expression of phosphoenolpyruvate carboxylase enhances the phosphate solubilizing ability of fluorescent pseudomonads by altering the glucose catabolism to improve biomass yield

Genomic insight of phosphate solubilization and plant growth promotion of two taxonomically distinct winter crops by Enterobacter sp. DRP3

AIMS

Study of rhizospheric microbiome-mediated plant growth promotional attributes currently highlighted as a key tool for the development of suitable bio-inoculants for sustainable agriculture purposes. In this context, we have conducted a detailed study regarding the characterization of phosphate solubilizing potential by plant growth-promoting bacteria that have been isolated from the rhizosphere of a pteridophyte Dicranopteris sp., growing on the lateritic belt of West Bengal.

METHODS AND RESULTS

We have isolated three potent bacterial strains, namely DRP1, DRP2, and DRP3 from the rhizoids-region of Dicranopteris sp. Among the isolated strains, DRP3 is found to have the highest phosphate solubilizing potentiality and is able to produce 655.89 and 627.58 µg ml-1 soluble phosphate by solubilizing tricalcium phosphate (TCP) and Jordan rock phosphate, respectively. This strain is also able to solubilize Purulia rock phosphate moderately (133.51 µg ml-1). Whole-genome sequencing and further analysis of the studied strain revealed the presence of pyrroloquinoline quinone (PQQ)-dependent glucose dehydrogenase gdh gene along with several others that were well known for their role in phosphate solubilization. Further downstream, quantitative reverse transcriptase PCR-based expression study revealed 1.59-fold upregulation of PQQ-dependent gdh gene during the solubilization of TCP. Root colonization potential of the studied strain on two taxonomically distinct winter crops viz. Cicer arietinum and Triticum aestivum has been checked by using scanning electron microscopy. Other biochemical analyses for plant growth promotion traits including indole acetic acid production (132.02 µg ml-1), potassium solubilization (3 mg l-1), biofilm formation, and exopolymeric substances productions (1.88-2.03 µg ml-1) also has been performed.

CONCLUSION

This study highlighted the active involvement of PQQ-dependent gdh gene during phosphate solubilization from any Enterobacter group. Moreover, our study explored different roadmaps for sustainable farming methods and the preservation of food security without endangering soil health in the future.

Roles of phosphate-solubilizing bacteria in mediating soil legacy phosphorus availability

Phosphorus (P), an essential macronutrient for all life on Earth, has been shown to be a vital limiting nutrient element for plant growth and yield. P deficiency is a common phenomenon in terrestrial ecosystems across the world. Chemical phosphate fertilizer has traditionally been employed to solve the problem of P deficiency in agricultural production, but its application has been limited by the non-renewability of raw materials and the adverse influence on the ecological health of the environment. Therefore, it is imperative to develop efficient, economical, environmentally friendly and highly stable alternative strategies to meet the plant P demand. Phosphate-solubilizing bacteria (PSB) are able to improve plant productivity by increasing P nutrition. Pathways to fully and effectively use PSB to mobilize unavailable forms of soil P for plants has become a hot research topic in the fields of plant nutrition and ecology. Here, the biogeochemical P cycling in soil systems are summarized, how to make full use of soil legacy P via PSB to alleviate the global P resource shortage are reviewed. We highlight the advances in multi-omics technologies that are helpful for exploring the dynamics of nutrient turnover and the genetic potential of PSB-centered microbial communities. Furthermore, the multiple roles of PSB inoculants in sustainable agricultural practices are analyzed. Finally, we project that new ideas and techniques will be continuously infused into fundamental and applied research to achieve a more integrated understanding of the interactive mechanisms of PSB and rhizosphere microbiota/plant to maximize the efficacy of PSB as P activators.

Stress preadaptation and overexpression of rpoS and hfq genes increase stress resistance of Pseudomonas fluorescens ATCC13525

Pseudomonas fluorescens ATCC13525 is an important growth-promoting rhizobacteria (PGPR) and plant disease biocontrol bacterium. However, due to poor stress resistance, it is prone to be inactivated by preparation, drying and storage. In this study, we investigated the effects of different stress preadaptation methods (2.0∼3.0 wt% NaCl, 0.01∼0.20 wt% H₂O₂, and 35∼44 °C) and two stress adaptation genes (rpoS, and hfq) on the stress resistance of P. fluorescens ATCC13525 (PF-WT). After stress preadaptation with low stress of 3.0 wt% NaCl, 0.05 wt% H₂O₂, and 41 °C for 30 min, the tolerance of PF-WT toward high lethal stress environments (20.0 wt% NaCl, 1.00 wt% H₂O₂, and 47 °C) were significantly improved. Moreover, knockout of rpoS and hfq genes resulted in slower culture growth than PF-WT under the sublethal stress culture conditions (5.0 wt% NaCl, 0.08 wt% H₂O₂, and 35 °C), whereas rpoS and hfq overexpressed strains (PF-pBBR2-rpoS and PF-pBBR2-hfq) obviously grew better than the control strain PF-pBBR2. Further, we prepared biocontrol agents (BACs) of different strains after different stress preadaptation treatments. Compared to PF-WT without stress preadaptation, preadaptation by 0.05 wt% H₂O₂ for 30 min resulted in 5.65 times higher survival rate, while treatment with 3.0 wt% NaCl for 30 min of PF-pBBR2-rpoS led to 5.60 times higher survival rate. This finding provides the simple and effective protection methods for P. fluorescens ATCC13525 BACs preparation by stress preadaptation and overexpression of stress adaptation genes.

Organic Acid Profiles of Phosphate Solubilizing Bacterial Strains in the Presence of Different Insoluble Phosphatic Sources Under In vitro Buffered Conditions

The production of weak organic acids by microorganisms has been attributed as the prime reason for the solubilization of insoluble phosphates under both in vitro and soil conditions. Literature seems to be heavily biased towards gluconic acid production by microbes and its subsequent release into the environment as the key factor responsible for phosphate solubilization. This has found credibility since gluconic acid being a product of the Kreb’s cycle is often detected in large quantities in the culture media, when assayed under in vitro conditions. In the present work, the organic acid profiles of four elite phosphate solubilising isolates were determined in the presence of different insoluble sources of phosphates, under in vitro buffered culture conditions by HPLC (High-Performance Liquid Chromatography). While most previous studies did not use a buffered culture media for elucidating the organic acid profile of phosphate solubilizing bacterial isolates, we used a buffered media for estimation of the organic acid profiles. The results revealed that apart from gluconic acid, malic acid is produced in significant levels by phosphate solubilizing bacterial isolates, and there seems to be a differential pattern of production of these two organic acids by the isolates in the presence of different insoluble phosphate sources.

Engineering rhizobacteria for sustainable agriculture

Exploitation of plant growth promoting (PGP) rhizobacteria (PGPR) as crop inoculants could propel sustainable intensification of agriculture to feed our rapidly growing population. However, field performance of PGPR is typically inconsistent due to suboptimal rhizosphere colonisation and persistence in foreign soils, promiscuous host-specificity, and in some cases, the existence of undesirable genetic regulation that has evolved to repress PGP traits. While the genetics underlying these problems remain largely unresolved, molecular mechanisms of PGP have been elucidated in rigorous detail. Engineering and subsequent transfer of PGP traits into selected efficacious rhizobacterial isolates or entire bacterial rhizosphere communities now offers a powerful strategy to generate improved PGPR that are tailored for agricultural use. Through harnessing of synthetic plant-to-bacteria signalling, attempts are currently underway to establish exclusive coupling of plant-bacteria interactions in the field, which will be crucial to optimise efficacy and establish biocontainment of engineered PGPR. This review explores the many ecological and biotechnical facets of this research.

Effects of tetracycline on growth, oxidative stress response, and metabolite pattern of ryegrass

Tetracycline is an antibiotic that frequently contaminates the environment. In this study, the growth and metabolites of ryegrass seedlings treated with tetracycline (0, 1, 10 or 100 mg/L) for 5 days were investigated. The results showed that the growth of ryegrass and the concentrations of carotenoid and chlorophyll decreased as the tetracycline concentration increased. Tetracycline increased the production of reactive oxygen species (ROS) and cell permeability and triggered mitochondrial membrane potential loss in the roots of ryegrass. The metabolic profiles of ryegrass differed between the control and tetracycline-treated groups. The contents of glucose, shikimic acid, aconitic acid, serine, lactose, phenylalanine, mannitol, galactose, gluconic acid, asparagine, and glucopyranose were positively correlated with root length and had high variable importance projection values. These compounds may have crucial functions in root extension. Tetracycline also affected aminoacyl-tRNA biosynthesis, nitrogen metabolism, and alanine, aspartate and glutamate metabolism in the roots. Tetracycline may affect root extension by regulating the synthesis/degradation of these metabolites or the activity of their biosynthetic pathways. These results provide an insight into the stress response of ryegrass to tetracycline.

Modulation in light utilization by a microalga Asteracys sp. under mixotrophic growth regimes

This study is the first to explore the influence of incident light intensity on the photosynthetic responses under mixotrophic growth of microalga Asteracys sp. When grown mixotrophically, there was an enhanced regulation of non-photochemical quenching (NPQ) of the excited state of chlorophyll (Chl) a within the cells in response to white cool fluorescent high light (HL; 600 µmol photons m^-2 s^-1). Simultaneous measurement of reactive oxygen species (ROS) production as malondialdehyde (MDA) and ascorbate peroxidase (APX), an ROS scavenger, showed improved management of stress within mixotrophic cells under HL. Despite the observed decrease in quantum yield of photosynthesis measured through the Chl a fluorescence transient, no reduction in biomass accumulation was observed under HL for mixotrophy. However, biomass loss owing to photoinhibition was observed in cells grown phototrophically under the same irradiance. The measurements of dark recovery of NPQ suggested that "state transitions" may be partly responsible for regulating overall photosynthesis in Asteracys sp. The partitioning of photochemical and non-photochemical processes to sustain HL stress was analysed. Collectively, this study proposes that mixotrophy using glucose leads to a change in the photosynthetic abilities of Asteracys sp. while enhancing the adaptability of the alga to high irradiances.

Effect of Phosphate-Solubilizing Bacteria on the Mobility of Insoluble Cadmium and Metabolic Analysis

Phosphate-solubilizing bacteria (PSB) can promote plant growth by dissolving insoluble phosphate. Therefore, PSB may have the potential to improve the mobility of heavy metals in soils and enhance phytoextraction. This study isolated a few PSB strains that could dissolve CdCO₃ and solid Cd in soil. Two typical PSB, namely, high- and low-Cd-mobilizing PSB (Pseudomonas fluorescens gim-3 and Bacillus cereus qh-35, respectively), were selected to analyze the metabolic profiles, metabolic pathways, and mechanisms of mobilization of insoluble Cd. A total of 34 metabolites secreted by the two PSB strains were identified. Gluconic acid was the main contributor to Cd dissolution (42.4%) in high-Cd-mobilizing PSB. By contrast, gluconic acid was not secreted in low-Cd-mobilizing PSB. Metabolic pathway analysis showed that gluconic acid was produced by the peripheral direct oxidation pathway. Hence, PSB with peripheral direct oxidation pathway were likely to have high-Cd-mobilizing capacity.

Draft Genome Sequence of Phosphate-Solubilizing Bacterium Paraburkholderia tropica Strain P-31 Isolated from Pomegranate (Punica granatum) Rhizosphere

We report the 8.9 Mb draft genome sequence of phosphate-solubilizing bacterium Paraburkholderia tropica strain P-31, isolated from pomegranate (Punica granatum) rhizosphere. The draft genome sequence of Paraburkholderia tropica strain P-31 consists of 8,881,246 bp with a G+C content of 64.7%, 8,039 protein-coding genes, and 49 RNAs.

HemX is required for production of 2-ketogluconate, the predominant organic anion required for inorganic phosphate solubilization by Burkholderia sp. Ha185

The bacterium Burkholderia sp. Ha185 readily solubilizes inorganic phosphate by releasing the low molecular weight organic anion, 2-ketogluconate. Using random transposon mutagenesis and in silico analysis, a mutation that caused almost complete abolition of phosphate solubilization was located within hemX, which is part of the hem operon. Burkholderia sp. Ha185 HemX is a multidomain protein, predicted to encode a bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase, which has not previously been implicated in phosphate solubilization. Complementation of hemX restored the ability of the mutant to solubilize phosphate in both plate and liquid cultures. Based on a combination of organic-anion profiling, quantitative polymerase chain reaction and in silico analyses, hemX was confirmed to be solely responsible for hydroxyapatite solubilization in Burkholderia sp. Ha185. It is proposed that the biosynthesis of a yet to be determined redox cofactor by HemX is the main pathway for generating 2-ketogluconate via a haem-dependent gluconate 2-dehydrogenase in Burkholderia sp. Ha185.

Artificial citrate operon confers mineral phosphate solubilization ability to diverse fluorescent pseudomonads

Citric acid is a strong acid with good cation chelating ability and can be very efficient in solubilizing mineral phosphates. Only a few phosphate solubilizing bacteria and fungi are known to secrete citric acids. In this work, we incorporated artificial citrate operon containing NADH insensitive citrate synthase (gltA1) and citrate transporter (citC) genes into the genome of six-plant growth promoting P. fluorescens strains viz., PfO-1, Pf5, CHAO1, P109, ATCC13525 and Fp315 using MiniTn7 transposon gene delivery system. Comprehensive biochemical characterization of the genomic integrants and their comparison with plasmid transformants of the same operon in M9 minimal medium reveals the highest amount of ∼7.6±0.41 mM citric and 29.95±2.8 mM gluconic acid secretion along with ∼43.2±3.24 mM intracellular citrate without affecting the growth of these P. fluorescens strains. All genomic integrants showed enhanced citric and gluconic acid secretion on Tris-Cl rock phosphate (TRP) buffered medium, which was sufficient to release 200–1000 µM Pi in TRP medium. This study demonstrates that MPS ability could be achieved in natural fluorescent pseudomonads by incorporation of artificial citrate operon not only as plasmid but also by genomic integration.

Humic acid acts as a natural antidote of graphene by regulating nanomaterial translocation and metabolic fluxes in vivo

Graphene-related research has intensified rapidly in a wide range of disciplines, but few studies have examined ecosystem risks, particularly phytotoxicity. This study revealed that graphene significantly inhibits the number of wheat roots and the biosynthesis of chlorophyll, and altered the morphology of shoots. Humic acid (HA), a ubiquitous form of natural organic matter, significantly (P < 0.05) relieved this phytotoxicity and recovered the sharp morphology of shoot tips. Both graphene and graphene-HA were transferred from wheat roots to shoots and were found in the cytoplasms and chloroplasts. HA increased the disordered structure and surface negative charges, and reduced the aggregation of graphene. HA enhanced the storage of graphene in vacuoles, potentially indicating an effective detoxification path. The content of cadaverine, alkane, glyconic acid, and aconitic acid was up-regulated by graphene, greatly contributing to the observed phytotoxicity. Conversely, inositol, phenylalanine, phthalic acid, and octadecanoic acid were up-regulated by graphene-HA. The metabolic pathway analysis revealed that the direction of metabolic fluxes governed nanotoxicity. This work presents the innovative concept that HA acts as a natural antidote of graphene by regulating its translocation and metabolic fluxes in vivo. This knowledge is critical for avoiding the overestimation of nanomaterial risks and can be used to control nanomaterial contamination.

Role of central metabolism in the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens

Bacterial osmoadaptation involves the cytoplasmic accumulation of compatible solutes to counteract extracellular osmolarity. The halophilic and highly halotolerant bacterium Chromohalobacter salexigens is able to grow up to 3 m NaCl in a minimal medium due to the de novo synthesis of ectoines. This is an osmoregulated pathway that burdens central metabolic routes by quantitatively drawing off TCA cycle intermediaries. Consequently, metabolism in C. salexigens has adapted to support this biosynthetic route. Metabolism of C. salexigens is more efficient at high salinity than at low salinity, as reflected by lower glucose consumption, lower metabolite overflow, and higher biomass yield. At low salinity, by-products (mainly gluconate, pyruvate, and acetate) accumulate extracellularly. Using [1-(13)C]-, [2-(13)C]-, [6-(13)C]-, and [U-(13)C6]glucose as carbon sources, we were able to determine the main central metabolic pathways involved in ectoines biosynthesis from glucose. C. salexigens uses the Entner-Doudoroff pathway rather than the standard glycolytic pathway for glucose catabolism, and anaplerotic activity is high to replenish the TCA cycle with the intermediaries withdrawn for ectoines biosynthesis. Metabolic flux ratios at low and high salinity were similar, revealing a certain metabolic rigidity, probably due to its specialization to support high biosynthetic fluxes and partially explaining why metabolic yields are so highly affected by salinity. This work represents an important contribution to the elucidation of specific metabolic adaptations in compatible solute-accumulating halophilic bacteria.

The metabolic reprogramming evoked by nitrosative stress triggers the anaerobic utilization of citrate in Pseudomonas fluorescens

Nitrosative stress is an ongoing challenge that most organisms have to contend with. When nitric oxide (NO) that may be generated either exogenously or endogenously encounters reactive oxygen species (ROS), it produces a set of toxic moieties referred to as reactive nitrogen species (RNS). As these RNS can severely damage essential biomolecules, numerous organisms have evolved elaborate detoxification strategies to nullify RNS. However, the contribution of cellular metabolism in fending off nitrosative stress is poorly understood. Using a variety of functional proteomic and metabolomic analyses, we have identified how the soil microbe Pseudomonas fluorescens reprogrammed its metabolic networks to survive in an environment enriched by sodium nitroprusside (SNP), a generator of nitrosative stress. To combat the RNS-induced ineffective aconitase (ACN) and tricarboxylic acid (TCA) cycle, the microbe invoked the participation of citrate lyase (CL), phosphoenolpyruvate carboxylase (PEPC) and pyruvate phosphate dikinase (PPDK) to convert citrate, the sole source of carbon into pyruvate and ATP. These enzymes were not evident in the control conditions. This metabolic shift was coupled to the concomitant increase in the activities of such classical RNS detoxifiers as nitrate reductase (NR), nitrite reductase (NIR) and S-nitrosoglutathione reductase (GSNOR). Hence, metabolism may hold the clues to the survival of organisms subjected to nitrosative stress and may provide therapeutic cues against RNS-resistant microbes.