Optimization of nutrient components for enhanced phenazine-1-carboxylic acid production by gacA-inactivated Pseudomonas sp. M18G using response surface method

Development of chemically defined media for Lactococcus lactis subsp. lactis YF11 to eliminate the influence of hyperosmotic stress

Chemically defined media (CDM) can eliminate or lessen the interference that occurs in complex culture media (CCM) caused by the undefined substrate pools, and various CDM have been designed and employed for investigating microbial physiology and multiomics. Herein, using the measured amount of total amino acids in CCM and combined with the in vivo and in vitro amino acid content of Lactococcus lactis subsp. lactis YF11, new enriched CDM were designed and then optimized using a statistical design-of-experiment method coupling with fed-batch fermentation to eliminate or lessen the influence of hyperosmotic pressure. Cell volume was introduced as a target index to assess the performance of CDM, and average osmotic pressure (AOP) was employed to describe the osmotic pressure of CDM. The AOP was significantly decreased from 610 mOsm/kg·H2O in the initial CDM (I-CDM) to 360 mOsm/kg·H2O in fed-batch CDM (F-CDM), and the cell volume was increased from 0.142 ± 0.004 μm3 in I-CDM to 0.198 ± 0.008 μm3 in F-CDM, which was close to 0.206 ± 0.005 μm3 found in CCM, indicating that the strategy of designing and improving CDM followed by a statistical design-of-experiment coupling with fed-batch cultivation presented a promising pathway for extensive utilization of CDM.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03788-5.

Induced resistance to rice sheath blight (Rhizoctonia solani Kühn) by β-amino-butyric acid conjugate of phenazine-1-carboxylic acid

Rice sheath blight caused by Rhizoctonia solani Kühn is a major fungal disease that plagues commercially grown rice. Occurring mainly in leaf sheaths and leaves, the disease leads to great losses in food production. β-amino-butyric acid (BABA) has been demonstrated to activate an induced resistance response and is a potent inducer of broad-spectrum disease resistance in different plant species. In this study, β-amino-butyric acid conjugate of phenazine-1-carboxylic acid (PCA) with prominent induced resistance to rice sheath blight was tested. The in vitro fungicidal activity, as well as in vivo efficacy, systemicity, induced resistance and defense enzyme activity of BABA conjugate of PCA against R. solani in rice seedlings was systematically evaluated. The results indicated that in vitro fungicidal activity of PCA-β-aminobutyric acid (4e) against R. solani was lower than that of PCA, but in vivo curative ability of 4e was the highest among all tested compounds. The systemicity tests in rice seedlings revealed that PCA did not possess phloem mobility, while 4e exhibited moderate phloem mobility but much lower thanα-amino-butyric acid conjugate of PCA (4d). In addition, Compound 4e showed the highest induced activity against rice sheath blight. The observed effects of defense enzymes help to explain this high level of induced activity. The current research results indicate that in rice seedlings, BABA conjugate of PCA induce observable resistance to rice sheath blight and exhibit moderate phloem mobility, which could be used as an induced resistance fungicide against rice sheath blight in commercial rice production. The BABA conjugate of PCA might provide a useful example of induced resistance to R. solani.

Recent Developments in the Biological Activities, Bioproduction, and Applications of Pseudomonas spp. Phenazines

Phenazines are a large group of heterocyclic nitrogen-containing compounds with demonstrated insecticidal, antimicrobial, antiparasitic, and anticancer activities. These natural compounds are synthesized by several microorganisms originating from diverse habitats, including marine and terrestrial sources. The most well-studied producers belong to the Pseudomonas genus, which has been extensively investigated over the years for its ability to synthesize phenazines. This review is focused on the research performed on pseudomonads' phenazines in recent years. Their biosynthetic pathways, mechanism of regulation, production processes, bioactivities, and applications are revised in this manuscript.

Modelling the effects of particle size pretreatment method on biogas yield of groundnut shells

Optimising biogas yields from anaerobic digestion of organic wastes is significant to maximum energy recovery in the biodigestion process and has become an important topic of interest. Substrate particle size is an important process parameter in biogas production, and it precedes other pretreatments methods for the majority of the lignocellulose materials. Optimisation of biogas yield using Response Surface Methodology (RSM) was done, and temperature, hydraulic retention time and particle size were considered variables to develop the predictive models. Pretreatment of groundnut shells was investigated using particle size reduction of mechanical pretreatment methods. After pretreatment, 30 samples were digested in a batch digester at mesophilic temperature. The experimental results showed that the temperature, hydraulic retention time and particle size had significant effects of interaction (p < 0.05). The optimum experimental and predicted yields are: 44.70 and 42.92 (l_NkgoDM) organic dry matter biogas yield, 20.80 and 19.09 (l_N/kgFM) fresh mass biogas yield, 24.00 and 22.68 (l_NCH₄oDM) organic dry methane yield and 12.30 and 15.59 (l_NCH₄FM) fresh mass methane yield, respectively. The R² recorded for the four yield components were 0.6268, 0.5875, 0.6109 and 0.5547. These values seem to be lower and a sign of the average fit of the model. Biogas production from groundnut shells was significantly improved with statistical optimisation and the pretreatment method.

Implications of carbon catabolite repression for plant-microbe interactions

Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.

A Potential High-Risk Clone of Pseudomonas aeruginosa ST463

Pseudomonas aeruginosa is one of the most common opportunistic pathogens, which causes severe nosocomial infections because of its well-known multidrug-resistance and hypervirulence. It is critical to curate routinely the epidemic P. aeruginosa clones encountered in the clinic. The aim of the present study was to investigate the connection between virulence factors and antimicrobial resistance profiles in epidemic clones. Herein, we found that ST463 (O4), ST1212 (O11), and ST244 (O5) were prevalent in 30 isolates derived from non-cystic fibrosis patients, based on multilocus sequence type (MLST) and serotype analysis. All isolates were multidrug-resistant (MDR) and each was resistance to at least three classes of antibiotics in antimicrobial susceptibility tests, which was consistent with the presence of the abundant resistance genes, such as bla OXA-50, bla PAO, aph(3'), catB7, fosA, crpP, and bla KPC-2. Notably, all bla KPC-2 genes were located between ISKpn6-like and ISKpn8-like mobile genetic elements. In addition, classical exotoxins encoded by exoU, exoS, and pldA were present in 43.44% (13/40), 83.33% (25/30), and 70% (21/30) of the isolates, respectively. The expression of phz operons encoding the typical toxin, pyocyanin, was observed in 60% of isolates (18/30) and was quantified using triple quadrupole liquid chromatograph mass (LC/MS) assays. Interestingly, compared with other MLST types, all ST463 isolates harbored exoU, exoS and pldA, and produced pyocyanin ranging from 0.2 to 3.2 μg/mL. Finally, we evaluated the potential toxicity of these isolates using hemolysis tests and Galleria mellonella larvae infection models. The results showed that ST463 isolates were more virulent than other isolates. In conclusion, pyocyanin-producing ST463 P. aeruginosa, carrying diverse virulence genes, is a potential high-risk clone.

Overexpression of oxyR Increases Phenazine-1-Carboxylic Acid Biosynthesis via Small RNA phrS in the Rhizobacterium Strain Pseudomonas PA1201

Phenazine-1-carboxylic acid (PCA) is the primary active component in the newly registered, commercial biopesticide Shenqinmycin and is produced during fermentation by the engineered rhizobacterium strain Pseudomonas PA1201. Both phz1 and phz2 gene clusters contribute to PCA biosynthesis. In this study, we evaluated the role of OxyR in the regulation of PCA biosynthesis in PA1201. We first showed a functional link between oxyR expression and PCA biosynthesis. Deletion of oxyR and overexpression of oxyR both increase PCA biosynthesis. The molecular mechanisms underlying OxyR regulation of PCA production were investigated using several approaches. OxyR acts divergently in phz1 and phz2. Overexpression of oxyR activated the expression of phz1 and phz1-dependent PCA production. However, overexpression of oxyR had little effect on phz2-dependent PCA biosynthesis, while deletion of oxyR promoted phz2-dependent PCA production and exerted a negative effect on phz2 expression. Further, OxyR directly bound to the phz2 promoter region. In addition, the regulation of PCA biosynthesis by OxyR was associated with quorum sensing (QS) systems. Overexpression of OxyR positively regulated pqs QS system. Finally, transcriptomic analysis and subsequent genetic analysis revealed the small RNA phrS plays a key role in OxyR-dependent PCA accumulation. Specifically, OxyR directly binds to the phrS promoter region to positively regulate phrS expression wherein PhrS regulates the PCA positive regulator MvfR in order to control PCA biosynthesis.

Coenzyme Q biosynthesis in the biopesticide Shenqinmycin-producing Pseudomonas aeruginosa strain M18

Coenzyme Q (ubiquinone) is a redox-active isoprenylated benzoquinone commonly found in living organisms. The biosynthetic pathway for this lipid has been extensively studied in Escherichia coli and Saccharomyces cerevisiae; however, little is known in Pseudomonas aeruginosa. In this study, we observed that CoQ9 is the predominant coenzyme Q synthesized by the Shenqinmycin-producing strain M18. BLASTP and domain organization analyses identified 15 putative genes for CoQ biosynthesis in M18. The roles of 5 of these genes were genetically and biochemically investigated. PAM18_4662 encodes a nonaprenyl diphosphate synthase (Nds) and determines the number of isoprenoid units of CoQ9 in M18. PAM18_0636 (coq7PA) and PAM18_5179 (ubiJPA) are essential for aerobic growth and CoQ9 biosynthesis. Deletion of ubiJPA, ubiBPA and ubiKPA led to reduced CoQ biosynthesis and an accumulation of the CoQ9 biosynthetic intermediate 3-nonaprenylphenol (NPP). Moreover, we also provide evidence that the truncated UbiJPA interacts with UbiBPA and UbiKPA to affect CoQ9 biosynthesis by forming a regulatory complex. The genetic diversity of coenzyme Q biosynthesis may provide targets for the future design of specific drugs to prevent P. aeruginosa-related infections.

Synthesis and antifungal evaluation of PCA amide analogues

To improve the physical and chemical properties of phenazine-1-carboxylic acid (PCA) and find higher antifungal compounds, a series of PCA amide analogues were designed and synthesized and their structures were confirmed by ¹H NMR, HRMS, and X-ray. Most compounds showed some antifungal activities in vitro. Particularly, compound 3d exhibited inhibition effect against Pyriculariaoryzac Cavgra with EC₅₀ value of 28.7 μM and compound 3q exhibited effect against Rhizoctonia solani with EC₅₀ value of 24.5 μM, more potently active than that of the positive control PCA with its EC₅₀ values of 37.3 μM (Pyriculariaoryzac Cavgra) and 33.2 μM (Rhizoctonia solani), respectively.

Taxonomic characterization and antimicrobial compound production from Streptomyces chumphonensis BDK01 isolated from marine sediment

Streptomyces sp. isolated from marine sediment collected from Palk Strait, Bay of Bengal was investigated for its antagonistic potential. The isolate exhibited antimicrobial activity against selected bacterial strains of clinical importance such as Staphylococcus aureus MTCC 3160, Bacillus pumilus NCIM 2327, S. aureus (methicillin resistant), Escherichia coli MTCC 1698, E. coli (ESBL), Shigella flexneri MTCC 1457, Proteus vulgaris and Enterobacter cloacae. Phenotypic and molecular characterization ascertained the isolate BDK01 as Streptomyces chumphonensis. Media optimization with one variable-at-a-time strategy was attempted to identify the ideal concentrations of starch (5-15 g/l), casein (0.01-0.05 g/l), NaCl 1.0-3.0 g/l, pH (4.0-9.0 g/l), temperature (25-45 °C) and inoculum level (0.5-5 ml) towards achieving maximum antimicrobial compound production. Statistical optimization of production media was carried by establishing an 11 variables 17 run experiment through PB model which evinced starch, calcium carbonate, pH and inoculum concentration that highly influenced bioactive compound production. Spectral data of active ethyl acetate extract revealed the presence of various bioactive compounds such as Salicyl alcohol, N-phenyl benzamide. 6-Octadecenoic acid, (Z), 1,3,5-Cycloheptatriene. Antiproliferation activity of active fraction against MCF-7 Cell line exhibited IC50 value of 9.5 µg/ml. Overall, it is observed that the marine actinomycete S. chumphonensis BDK01 could be employable as promising strain for novel antimicrobial and cytotoxic metabolites.

Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments

Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.

Engineering Pseudomonas for phenazine biosynthesis, regulation, and biotechnological applications: a review

Pseudomonas strains are increasingly attracting considerable attention as a valuable bacterial host both for basic and applied research. It has been considered as a promising candidate to produce a variety of bioactive secondary metabolites, particularly phenazines. Apart from the biotechnological perspective, these aromatic compounds have the notable potential to inhibit plant-pathogenic fungi and thus are useful in controlling plant diseases. Nevertheless, phenazines production is quite low by the wild-type strains that necessitated its yield improvement for large-scale agricultural applications. Metabolic engineering approaches with the advent of plentiful information provided by systems-level genomic and transcriptomic analyses enabled the development of new biological agents functioning as potential cell factories for producing the desired level of value-added bioproducts. This study presents an up-to-date overview of recombinant Pseudomonas strains as the preferred choice of host organisms for the biosynthesis of natural phenazines. The biosynthetic pathway and regulatory mechanism involved in the phenazine biosynthesis are comprehensively discussed. Finally, a summary of biological functionalities and biotechnological applications of the phenazines is also provided.

Enhanced candicidal compound production by a new soil isolate Penicillium verruculosum MKH7 under submerged fermentation

BACKGROUND

Microorganisms are a rich source of structurally diverse secondary metabolites that exert a major impact on the control of infectious diseases and other medical conditions. The biosynthesis of these metabolites can be improved by manipulating the nutritional or environmental factors. This work evaluates the effects of fermentation parameters on the production of a lactone compound effective against Candida albicans by Penicillium verruculosum MKH7 under submerged fermentation. Design-Expert version8.0 software was used for construction of the experimental design and statistical analysis of the experimental data.

RESULTS

The important factors influencing antibiotic production selected in accordance with the Plackett-Burman design were found to be initial pH, temperature, peptone, MgSO4.7H2O. Orthogonal central composite design and response surface methodology were adopted to further investigate the mutual interaction between the variables and identify the optimum values that catalyse maximum metabolite production. The determination coefficient (R2) of the fitted second order model was 0.9852. The validation experiments using optimized conditions of initial pH 7.4, temperature 27 °C, peptone 9.2 g/l and MgSO4.7H2O 0.39 g/l resulted in a significant increase (almost 7 fold from 30 to 205.5 mg/l) in the metabolite production which was in agreement with the prediction (211.24 mg/l). Stability of the compound was also assessed on the basis of its response to physical and chemical stresses.

CONCLUSIONS

So far as our knowledge goes, till date there are no reports available on the production of antibiotics by Penicillium verruculosum through media optimization using RSM. Optimization not only led to a 7 fold increase in metabolite yield but the same was achieved at much lesser time (8-10 days compared to the earlier 12-15 days). The enhanced yield of the antibiotic strongly suggests that the fungus P. verruculosum MKH7 can be efficiently used for antibiotic production on a large scale.

Improved yield of α-L-arabinofuranosidase by newly isolated Aspergillus niger ADH-11 and synergistic effect of crude enzyme on saccharification of maize stover

Background

In the view of depleting resources and ever-increasing price of crude oil, there is an urge for the development of alternative sources to solve the issue of fuel in the coming years. Lignocellulosic biomass is considered to be the most potential alternative resources for fossil fuel. Bioconversion of cellulosic and hemicellulosic components into fermentable sugars is the key step in producing fuel ethanol from lignocellulose. The enzymatic hydrolysis of lignocellulosic biomass needs a highly balanced composition of cellulases and hemicellulases. Commercial enzymes are usually poor in accessory hemicellulolytic enzymes like α-L-arabinofuranosidase. The addition of such accessory enzymes in combination with cellulase or hemicellulase plays a vital role in improving the total yield of fuel ethanol by enhancing the saccharification yield.

Results

The newly isolated fungal strain Aspergillus niger ADH-11 produced a maximum of 22.14 U/g of α-L-arabinofuranosidase under solid-state fermentation using wheat bran as the substrate and modified Mandels-Weber medium at 30°C after 180 h of incubation. The optimization of various fermentation parameters was performed by response surface methodology employing Plackett-Burman design followed by Box-Behnken design. The yield of α-L-arabinofuranosidase was enhanced by 2.34-fold after executing statistical optimization of various fermentative parameters. Crude α-L-arabinofuranosidase was found to be highly stable for 3 h at its optimum temperature (55°C) and pH (4.0). The assessment of the crude enzyme extract in saccharification of alkali-treated maize stover revealed that the supplementation of crude α-L-arabinofuranosidase to commercial cellulase and crude xylanase mixture increased the saccharification yield up to 730 mg/g of maize stover.

Conclusions

The newly isolated A. niger ADH-11 was found to be a potential producer of α-L-arabinofuranosidase. The crude enzyme was active at low pH and high temperature which makes it suitable for various industrial applications such as enzymatic saccharification of lignocellulosic biomass. The supplementation of α-L-arabinofuranosidase enzyme to commercial cellulases and hemicellulases improves the bioconversion of lignocellulosic biomass to a greater extent.

Optimization of antifungal production by an alkaliphilic and halotolerant actinomycete, Streptomyces sp. SY-BS5, using response surface methodology

OBJECTIVE

Optimization of medium components and physicochemical parameters for antifungal production by an alkaliphilic and salt-tolerant actinomycete designated Streptomyces sp. SY-BS5; isolated from an arid region in south of Algeria.

MATERIALS AND METHODS

The strain showed broad-spectrum activity against pathogenic and toxinogenic fungi. Identification of the actinomycete strain was realized on the basis of 16S rRNA gene sequencing. Antifungal production was optimized following one-factor-at-a-time (OFAT) and response surface methodology (RSM) approaches. The most suitable medium for growth and antifungal production was found using one-factor-at-a-time methodology. The individual and interaction effects of three nutritional variables, carbon source (glucose), nitrogen source (yeast extract) and sodium chloride (NaCl) were optimized by Box-Behnken design. Finally, culture conditions for the antifungal production, pH and temperature were studied and determined.

RESULTS

Analysis of the 16S rRNA gene sequence (1454 nucleotides) assigned this strain to Streptomyces genus with 99% similarity with Streptomyces cyaneofuscatus JCM4364(T), the most closely related. The results of the optimization study show that concentrations 3.476g/L of glucose, 3.876g/L of yeast extract and 41.140g/L of NaCl are responsible for the enhancement of antifungal production by Streptomyces sp. SY-BS5. The preferable culture conditions for antifungal production were pH 10, temperature 30°C for 09 days.

CONCLUSION

This study proved that RSM is usual and powerful tool for the optimization of antifungal production from actinomycetes.

Regulation of gene expression in Pseudomonas aeruginosa M18 by phenazine-1-carboxylic acid

Phenazine-1-carboxylic acid (PCA), an environmentally compatible redox-active metabolite produced by Pseudomonas sp., has been found to effectively protect against various phytopathogens. The objective of this study was to discover whether PCA can also act as a signaling molecule that regulates gene expression in Pseudomonas aeruginosa M18. We constructed a series of PCA-producing mutant strains (high PCA, M18MSU1; low PCA, M18MS; and no PCA, M18MSP1P2) and analyzed their gene expression by using a custom microarray DNA chip. We found that the expression of PCA in both M18MSU1 and M18MS altered the expression of a total of 545 different genes; however, the higher level of PCA in M18MSU1 altered more genes (489) than did the lower level of PCA in M18MS (129). Of particular note, 73 of these genes were commonly regulated between the two mutants, indicating their importance in the downstream function of PCA. PCA molecules upregulated genes that function primarily in energy production, cell motility, secretion, and defense mechanisms and downregulated genes involved in transcription, translation, cell division, and gene expression in the prophage. We found that PCA worked to alter the expression of an efflux pump gene mexH through a SoxR-mediated mechanism; we further hypothesized that other pathways should also be affected by this interaction. Taken together, our results provide the first evidence of PCA-derived molecular responses at the transcriptional level. They also help to elucidate the future of genetically engineered P. aeruginosa strains for the production of PCA used in a number of applications.

Optimization of BY-2 cell suspension culture medium for the production of a human antibody using a combination of fractional factorial designs and the response surface method

We have developed a strategy for the optimization of plant cell suspension culture media using a combination of fractional factorial designs (FFDs) and response surface methodology (RSM). This sequential approach was applied to transformed tobacco BY-2 cells secreting a human antibody (M12) into the culture medium, in an effort to maximize yields. We found that the nutrients KNO₃, NH₄NO₃ and CaCl₂ and the hormones 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BAP) had the most significant impact on antibody accumulation. The factorial screening revealed strong interactions within the nutrients group (KNO₃, NH₄NO₃ and CaCl₂) and also individually between 2,4-D and three other components (KNO₃, NH₄NO₃ and BAP). The RSM design resulted in a fivefold increase in the antibody concentration after 5 days and a twofold reduction in the packed cell volume (PCV). Longer cultivation in the optimized medium led to the further accumulation of antibody M12 in the culture medium (up to 107 μg/mL, day 10). Because the packed cell volume was reduced in the optimized medium, this enhanced the overall yield by 20-fold (day 7) and 31-fold (day 10) compared to the conventional MS medium.

Extractive fermentation for enhanced production of thailandepsin A from Burkholderia thailandensis E264 using polyaromatic adsorbent resin Diaion HP-20

Thailandepsin A is natural product of Burkholderia thailandensis E264 with potent histone deacetylase inhibitory activities and promising anticancer activities. The titer of thailandepsin A is very low (less than 10 mg/l) from limited empirical fermentation. To facilitate preclinical evaluations and potentially clinical development of thailandepsin A, systematic optimization and extractive fermentation of thailandepsin A from B. thailandensis E264 culture in flasks were investigated in this pilot study. The main fermentation parameters—28°C, pH 7.0, inoculum ratio 1% (v/v), incubation duration 60 h, medium volume 26%, shaking speed 170 rpm, and chloroform as extracting solvent—were determined by single factor experiments. Polyaromatic adsorbent resin Diaion HP-20, when added at a concentration of 4% (w/v), was most effective to reduce feedback inhibition of thailandepsin A and to significantly increase the titer of target product. Central composite design was used to further optimize the fermentation medium for B. thailandensis E264. The optimized medium contains glucose 17.89 g/l, tryptone 34.98 g/l, potassium phosphate 24.84 g/l, and sodium citrate 0.01 g/l, which resulted in a large increase of the titer of thailandepsin A to 236.7 mg/l. Finally kinetic models based on the modified logistic and Luedeking–Piret equations were developed, delivering a good description of temporal variations of biomass, product, and substrate in the fermentation process, which could be used as references for developing large-scale fermentation.

Regulatory feedback loop of two phz gene clusters through 5'-untranslated regions in Pseudomonas sp. M18

Background

Phenazines are important compounds produced by pseudomonads and other bacteria. Two phz gene clusters called phzA1-G1 and phzA2-G2, respectively, were found in the genome of Pseudomonas sp. M18, an effective biocontrol agent, which is highly homologous to the opportunistic human pathogen P. aeruginosa PAO1, however little is known about the correlation between the expressions of two phz gene clusters.

Methodology/Principal Findings

Two chromosomal insertion inactivated mutants for the two gene clusters were constructed respectively and the correlation between the expressions of two phz gene clusters was investigated in strain M18. Phenazine-1-carboxylic acid (PCA) molecules produced from phzA2-G2 gene cluster are able to auto-regulate expression itself and activate the expression of phzA1-G1 gene cluster in a circulated amplification pattern. However, the post-transcriptional expression of phzA1-G1 transcript was blocked principally through 5′-untranslated region (UTR). In contrast, the phzA2-G2 gene cluster was transcribed to a lesser extent and translated efficiently and was negatively regulated by the GacA signal transduction pathway, mainly at a post-transcriptional level.

Conclusions/Significance

A single molecule, PCA, produced in different quantities by the two phz gene clusters acted as the functional mediator and the two phz gene clusters developed a specific regulatory mechanism which acts through 5′-UTR to transfer a single, but complex bacterial signaling event in Pseudomonas sp. strain M18.

The optimization of biohydrogen production by bacteria using residual glycerol from biodiesel synthesis

In this research the production of hydrogen by Klebsiella pneumoniae BLb01 using residual glycerol discharged from a biodiesel fuel production plant was investigated. Klebsiella pneumoniae BLb01 was isolated from a bacteria-rich sludge of an upflow anaerobic sludge blanket reactor (UASB) of a soybean processing plant. A Plackett-Burman design (P-B) and Response Surface Methodology (RSM) were employed to determine the optimal condition for enhanced hydrogen production. The maximal hydrogen production, which was 45.0 mol % and with 98% of glycerol degradation, was achieved with the optimized medium with the following composition: 30 g L(-1) glycerol; 3 g L(-1) yeast ex tract 3 g L(-1) K(2)HPO(4); 1 g L(-1) KH(2)PO(4); temperature 39°C and pH 9.0. These results show the ability of this new strain of effectively converting residual glycerol into value-added energy products.

Biodecolorization of Acid Red GR by a newly isolated Dyella ginsengisoli LA-4 using response surface methodology

Decolorization of Acid Red GR by a newly isolated biphenyl-degrading bacterium, Dyella ginsengisoli LA-4 was presented in this paper. The optimal decolorization conditions were determined by response surface methodology (RSM) based on the rotatable central composite design. The results indicated that strain LA-4 possessed the highest decolorizing activity under anaerobic conditions with inoculation amount 6.49%, pH 7.06 and temperature 29 degrees C. Some ions such as Cu(2+), Zn(2+) could inhibit the decolorization, whereas 1 mmol/L of Mg(2+), Ca(2+), Co(2+), Fe(3+), Ni(2+) and Mn(2+) had no effects on the process. It was demonstrated that anthraquinone as a redox mediator could significantly accelerate the reduction process of azo dyes.

Optimization of phenazine-1-carboxylic acid production by a gacA/qscR-inactivated Pseudomonas sp. M18GQ harboring pME6032Phz using response surface methodology

Phenazine-1-carboxylic acid (PCA) production was enhanced in Pseudomonas sp. M18 wild strain and its mutants carrying recombinant pME6032Phz for phz gene cluster overexpression, among which Pseudomonas sp. strain M18GQ/pME6032Phz, a gacA and qscR double gene chromosomally inactivated mutant harboring pME6032Phz, showed the highest PCA yield. The conditions for fermentation and isopropyl-beta-D-1-thiogalactopyranoside (IPTG) induction were optimized for strain M18GQ/pME6032Phz in shake flask experiments. A one-factor-at-a-time approach, followed by a fractional factorial design identified soybean meal, corn steep liquor, and ethanol as statistically significant factors. Optimal concentrations and mutual interactions of the factors were then determined by the method of steepest ascent and by response surface methodology based on the center composite design. The predicted PCA production was 6,335.2 mg/l after 60 h fermentation in the optimal medium of 65.02 g soybean meal, 15.36 g corn steep liquor, 12 g glucose, 21.70 ml ethanol, and 1 g MgSO(4) per liter in the flask fermentations, with induction of 1.0 mmol/l IPTG 24 h after inoculation. In an experimental validation under these conditions, the maximum PCA production was 6,365.0 mg/l. This represents a approximately 60% increase over production by strain M18GQ in optimal conditions. The negative effect of plasmid pME6032 on the expression of chromosomally located phz gene cluster was found in Pseudomonas sp. M18GQ, and the possible reason was discussed in the text.

Temperature-dependent expression of phzM and its regulatory genes lasI and ptsP in rhizosphere isolate Pseudomonas sp. strain M18

Pseudomonas sp. strain M18, an effective biological control agent isolated from the melon rhizosphere, has a genetic background similar to that of the opportunistic human pathogen Pseudomonas aeruginosa PAO1. However, the predominant phenazine produced by strain M18 is phenazine-1-carboxylic acid (PCA) rather than pyocyanin (PYO); the quantitative ratio of PCA to PYO is 105 to 1 at 28 degrees C in strain M18, while the ratio is 1 to 2 at 37 degrees C in strain PAO1. We first provided evidence that the differential production of the two phenazines in strains M18 and PAO1 is related to the temperature-dependent and strain-specific expression patterns of phzM, a gene involved in the conversion of PCA to PYO. Transcriptional levels of phzM were measured by quantitative real-time PCR, and the activities of both transcriptional and translational phzM'-'lacZ fusions were determined in strains M18 and PAO1, respectively. Using lasI::Gm and ptsP::Gm inactivation M18 mutants, we further show that expression of the phzM gene is positively regulated by the quorum-sensing protein LasI and negatively regulated by the phosphoenolpyruvate phosphotransferase protein PtsP. Surprisingly, the lasI and ptsP regulatory genes were also expressed in a temperature-dependent and strain-specific manner. The differential production of the phenazines PCA and PYO by strains M18 and PAO1 may be a consequence of selective pressure imposed on P. aeruginosa PAO1 and its relative M18 in the two different niches over a long evolutionary process.

Investigation of extractive microbial transformation in nonionic surfactant micelle aqueous solution using response surface methodology

Extractive microbial transformation of L-phenylacetylcarbinol (L-PAC) in nonionic surfactant Triton X-100 micelle aqueous solution was investigated by response surface methodology. Based on the Box-Behnken design, a mathematical model was developed for the predication of mutual interactions between benzaldehyde, Triton X-100, and glucose on L-PAC production. It indicated that the negative or positive effect of nonionic surfactant strongly depended on the substrate concentration. The model predicted that the optimal concentration of benzaldehyde, Triton X-100, and glucose was 1.2 ml, 15 g, and 2.76 g per 100 ml, respectively. Under the optimal condition, the maximum L-PAC production was 27.6 mM, which was verified by a time course of extractive microbial transformation. A discrete fed-batch process for verification of cell activity was also presented.

Optimization of culture conditions for hydrogen production by Ethanoligenens harbinense B49 using response surface methodology

The design of an optimum and cost-efficient medium for high-level production of hydrogen by Ethanoligenens harbinense B49 was attempted by using response surface methodology (RSM). Based on the Plackett-Burman design, Fe(2+) and Mg(2+) were selected as the most critical nutrient salts. Subsequently, the optimum combination of the selected factors and the sole carbon source glucose were investigated by the Box-Behnken design. Results showed that the maximum hydrogen yield of 2.21 mol/mol glucose was predicted when the concentrations of glucose, Fe(2+) and Mg(2+) were 14.57 g/L, 177.28 mg/L and 691.98 mg/L, respectively. The results were further verified by triplicate experiments. The batch reactors were operated under an optimized condition of the respective glucose, Fe(2+) and Mg(2+) concentration of 14.5 g/L, 180 mg/L and 690 mg/L, the initial pH of 6.0 and experimental temperature of 35+/-1(o)C. Without further pH adjustment, the maximum hydrogen yield of 2.20 mol/mol glucose was obtained based on the optimized medium with further verified the practicability of this optimum strategy.

Exploring antagonistic metabolites of established biocontrol agent of marine origin

Biocontrol ability of Pseudomonas aeruginosa ID 4365, a biocontrol agent of groundnut phytopathogens from marine origin, was previously attributed to the production of pyoverdin type of siderophores. However, pyoverdin-rich supernatants of this organism showed better antifungal activity compared to equivalent amount of purified pyoverdin indicating presence of undetected metabolite(s) in pyoverdin rich supernatants. On the basis of observation that antagonistic activity was iron-dependent and iron-independent, an attempt was made to detect the presence of additional metabolites. In addition to pyoverdin, strain produced additional siderophores, viz. pyochelin and salicylic acid. Two broad spectrum antifungal compounds, viz. pyocyanin and phenazine-1-carboxylic acid, were detected, characterized, and activity against phytopathogens was demonstrated. Iron- and phosphate-dependent co-production of siderophores and phenazines was confirmed. Strain showed additional features like production of hydrogen cyanide, indol-3-acetic acid, and phosphate solubilization.