Strain YL Research Articles

Kinetic model of a newly-isolated Lysinibacillus sp. strain YL and elastic properties of its biogenic CaCO3 towards biocement application.

Biocement, calcifying bacteria-incorporated cement, offers an environmentally-friendly way to increase the cement lifespan. This work aimed to investigate the potential use of Lysinibacillus sp. strain YL towards biocement application in both theoretical and experimental ways. Strain YL was grown using calcium acetate (Ca(C2 H3 O2 )2 ), calcium chloride (CaCl2 ) and calcium nitrate (Ca(NO3 )2 ). Maximum bacterial growth of ~0.09 hr-1 and the highest amount of CaCO3 precipitation of ~8.0 g/L were obtained when using Ca(C2 H3 O2 )2 . The SEM and XRD results confirmed that biogenic CaCO3 were calcites. The bulk, Young's and shear moduli of biogenic CaCO3 calculated via the VRH approximation were ~1.5-2.3 times larger than those of ordinary Portland cement. The Poisson's ratio was 0.382 and negative in some directions, suggesting its ductility and auxetic behaviors. The new model was developed to explain the growth kinetic of strain YL in the presence of Ca(C2 H3 O2 )2 , whose concentration was optimized for biocement experiments. Strain YL could increase the compressive strength of cement up to ~50% higher than that of the uninoculated cement. Strain YL is a promising candidate for biocement applications. This work represents the trials of experiments and models allowing quantitatively comparison with large-scale production in the future.

Nitrogen removal and aggregation characteristics of Pseudomonas aeruginosa YL and its application capacity for ammonium-rich wastewater treatment

Pseudomonas aeruginosa YL, which was isolated and purified from activated sludge, performed a high-efficiency simultaneous nitrification and denitrification ability through the efficient utilization of sole and mixed N-sources. Kinetics analysis carried out by Gompertz model (R2 > 0.99) explicated the optimal condition of N-degradation, and its denitrification pathway was proposed as a sequential heterotrophic nitrification-aerobic denitrification process. Moreover, strain YL had higher flocculating ability, relative hydrophobicity and lower negative charges when NH4+-N used as N-source, which fully proved the stronger aggregation ability of the isolate during heterotrophic nitrification process. The formation mechanism of cell aggregates was explained by discussing the variations of extracellular polymeric substances (EPS) components, and exhibited an obviously relevance of EPS and bioflocculation. Furthermore, the great nutrients removal, stable existence of functional strain and the excellent flocculation-sedimentation performance in a sequencing batch reactor, further confirmed the good potential of strain YL for treating ammonium-rich wastewater.

Insight Into Function and Subcellular Localization of Plasmopara viticola Putative RxLR Effectors.

Grapevine downy mildew, caused by oomycete fungus Plasmopara viticola, is one of the most devastating diseases of grapes across the major production regions of the world. Although many putative effector molecules have been identified from this pathogen, the functions of the majority of these are still unknown. In this study, we analyzed the potential function of 26 P. viticola effectors from the highly virulent strain YL. Using transient expression in leaf cells of the tobacco Nicotiana benthamiana, we found that the majority of the effectors could suppress cell death triggered by BAX and INF1, while seven could induce cell death. The subcellular localization of effectors in N. benthamiana was consistent with their localization in cells of Vitis vinifera. Those effectors that localized to the nucleus (17/26) showed a variety of subnuclear localization. Ten of the effectors localized predominantly to the nucleolus, whereas the remaining seven localized to nucleoplasm. Interestingly, five of the effectors were strongly related in sequence and showed identical subcellular localization, but had different functions in N. benthamiana leaves and expression patterns in grapevine in response to P. viticola. This study highlights the potential functional diversity of P. viticola effectors.

Denitrification Process and N2O Production Characteristics of Heterotrophic Nitrifying Bacterium Pseudomonas aeruginosa YL

Because of the massive discharge of nitrogenous wastewater, the eutrophication of a water body is becoming increasingly serious, and how to effectively remove nitrogen from this wastewater remains an urgent problem to be solved. In this study, due to disadvantages in the traditional biological nitrogen removal process, such as complex and long procedures, high energy consumption, weak impact resistance, and N2O release, the nitrogen removal theory by heterotrophic nitrification was further analyzed by discussing the physiological-biochemical, heterotrophic nitrification-aerobic denitrification, and N2O production characteristics of a high-efficiency heterotrophic nitrifying bacteria Pseudomonas aeruginosa YL. Results show that the strain YL had an eminent heterotrophic nitrification and aerobic denitrification ability, and NH4+-N, NO2--N, and NO3--N with concentration of 100 mg·L-1 could be completely removed during the 24-hour incubation period. There was almost no intermediate product in the process of heterotrophic nitrification, however when NO3--N was used as nitrogen source, the accumulation of NO2--N reached 25.55 mg·L-1. Meanwhile, the successful expression of denitrification genes napA, nirK, and nosZ further confirmed the aerobic denitrification ability of strain YL. Gaseous nitrogen products accounted for about 30%-40% of removed TN in the heterotrophic nitrification-aerobic denitrification process by strain YL, and N2 was the main denitrification product. When NH4+-N, NO2--N, and NO3--N were used as the sole nitrogen source, N2 production amounted to 3.46, 3.49, and 3.36 mg, respectively. In contrast, only small amounts of N2O were produced in the denitrification process by strain YL, and the total amount was 6.63 μg when NH4+-N was the nitrogen source, which was much lower than in the cases of NO2--N and NO3--N as the sole nitrogen source. In addition, high C/N, low pH, high temperature, high NH4+-N, and high NO2--N conditions could result in more N2O generation. Nevertheless, most environmental factors had little effect on N2O production of strain YL, and the maximum N2O production was significantly lower than that of short-cut nitrification system and autotrophic nitrification system. These results demonstrated that strain YL exhibited excellent abilities of nitrogen removal, N2O emission control, and tolerance to environmental conditions, and could be an effective candidate for treating wastewater without secondary air pollution.

Optimization and Partial Characterization Studies of Alkaline Protease from Aeromonas Hydrophila Strain YL 17 Isolated from Honey Sample

Optimization and Partial Characterization Studies of Alkaline Protease from Aeromonas Hydrophila Strain YL 17 Isolated from Honey Sample

In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1

Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues, Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1. Methodology and results: The enzyme was built using a homology modeling technique; the structure of crystallized LDEX YL from Pseudomonas sp. strain YL as a template. Model validation was performed using PROCHECK to generate the Ramachandran plot. The results showed 80.4% of its residues were located in the most favoured regions suggested that the model is acceptable. Molecular dynamics simulation of the model protein was performed in water for 10 nanoseconds in which Na+ was added to neutralize the negative charge and achieved energy minimization. The energy value and RMSD fluctuation of Ca backbone of the model were computed and confirmed the stability of the model protein. Conclusion, significance and impact of study: In silico or computationally based function prediction is important to complement with future empirical approaches. L-haloacid dehalogenase (DehL), previously isolated from Rhizobium sp. RC1 was known to degrade halogenated environmental pollutants. However, its structure and functions are still unknown. This structural information of DehL provides insights for future work in the rational design of stereospecific haloalkanoic acid dehalogenases.

Nitrogen removal by Providencia rettgeri strain YL with heterotrophic nitrification and aerobic denitrification

ABSTRACTProvidencia rettgeri strain YL shows the capability of nitrogen removal under sole aerobic conditions. By using isotope ratio mass spectrometry, 15N-labelled N2O and N2 were detected in aerobic batch cultures containing , or . Strain YL converted , and to produce more N2O than N2 in the presence of . An 15N isotope tracing experiment confirmed that the nitrogen removal pathway of strain YL was heterotrophic nitrification-aerobic denitrification. The optimal treatment conditions for nitrogen removal were pH of 8, C/N ratio of 12, temperature of 25°C and shaking speed of 105 rpm. A continuous aerobic bioreactor inoculated with strain YL was developed. With an influent concentration of 90–200 mg/L, the removal efficiency ranged from 80% to 97% and the total nitrogen removal efficiency ranged from 72% to 95%. The nitrogen balance in the continuous bioreactor revealed that approximately 35–52% of influent was denitrified aerobically to form gaseous nitrogen. These findings show that the P. rettgeri strain YL has potential application in wastewater treatment for nitrogen removal under sole aerobic conditions.

A marked enhancement in production of amylase by Bacillus amyloliquefaciens in flask fermentation using statistical methods

A total of 126 bacterial strains were isolated from soil samples. Among them, 11 isolates were found positive for amylase production. Strain YL produced the largest zone of clearance on plate assay. The isolate YL was identified as Bacillus sp. based on morphological and physiochemical characterization. According to 16S rRNA gene sequencing data, the closest phylogenetic neighbor of strain YL was Bacillus amyloliquefaciens (99.54%). After that, an optimization of culture conditions was carried out for the improvement of α-amylase production. Response surface methodology (RSM) was applied to evaluate the effect of medium components including wheat bran, cottonseed extract, yeast extract, starch, NaCl and CaCl2. Three variables (wheat bran, cottonseed extract, and starch), which were identified to significantly affect amylase production by Plackett-Burman design were further optimized using response surface methodology of Box-Behnken design (BBD). The optimal concentrations estimated for each variable related to the maximum of amylase activity (86 kU/mL) were 10.80 g/L wheat bran, 9.90 g/L cottonseed extract, 0.5 g/L starch, 2.0 g/L yeast extract, 5.00 g/L NaCl and 2.00 g/L CaCl2. The fermentation using optimized culture medium allowed a significant increase in amylase production (by 3-fold). The improvement in the α-amylase production after optimization process can be considered adequate for large-scale applications.

2-Haloacrylate Hydratase, a New Class of Flavoenzyme That Catalyzes the Addition of Water to the Substrate for Dehalogenation

Enzymes catalyzing the conversion of organohalogen compounds are useful in the chemical industry and environmental technology. Here we report the occurrence of a new reduced flavin adenine dinucleotide (FAD) (FADH(2))-dependent enzyme that catalyzes the removal of a halogen atom from an unsaturated aliphatic organohalogen compound by the addition of a water molecule to the substrate. A soil bacterium, Pseudomonas sp. strain YL, inducibly produced a protein named Caa67(YL) when the cells were grown on 2-chloroacrylate (2-CAA). The caa67(YL) gene encoded a protein of 547 amino acid residues (M(r) of 59,301), which shared weak but significant sequence similarity with various flavoenzymes and contained a nucleotide-binding motif. We found that 2-CAA is converted into pyruvate when the reaction was carried out with purified Caa67(YL) in the presence of FAD and a reducing agent [NAD(P)H or sodium dithionite] under anaerobic conditions. The reducing agent was not stoichiometrically consumed during this reaction, suggesting that FADH(2) is conserved by regeneration in the catalytic cycle. When the reaction was carried out in the presence of H(2)(18)O, [(18)O]pyruvate was produced. These results indicate that Caa67(YL) catalyzes the hydration of 2-CAA to form 2-chloro-2-hydroxypropionate, which is chemically unstable and probably spontaneously dechlorinated to form pyruvate. 2-Bromoacrylate, but not other 2-CAA analogs such as acrylate and methacrylate, served as the substrate of Caa67(YL). Thus, we named this new enzyme 2-haloacrylate hydratase. The enzyme is very unusual in that it requires the reduced form of FAD for hydration, which involves no net change in the redox state of the coenzyme or substrate.

Heterotrophic nitrogen removal by Providencia rettgeri strain YL

Providencia rettgeri strain YL was found to be efficient in heterotrophic nitrogen removal under aerobic conditions. Maximum removal of NH(4) (+)-N occurred under the conditions of pH 7 and supplemented with glucose as the carbon source. Inorganic ions such as Mg(2+), Mn(2+), and Zn(2+) largely influenced the growth and nitrogen removal efficiency. A quantitative detection of nitrogen gas by gas chromatography was conducted to evaluate the nitrogen removal by strain YL. From the nitrogen balance during heterotrophic growth with 180 mg/l of NH(4) (+)-N, 44.5% of NH(4) (+)-N was in the form of N(2) and 49.7% was found in biomass, with only a trace amount of either nitrite or nitrate. The utilization of nitrite and nitrate during the ammonium removal process demonstrated that the nitrogen removal pathway by strain YL was heterotrophic nitrification-aerobic denitrification. A further enzyme assay of nitrate reductase and nitrite reductase activity under the aerobic condition confirmed this nitrogen removal pathway.

Expression of recombinant envelope protein of Japanese encephalitis virus YL strain in Escherichia coli possesses hemagglutination activity.

The nucleotide sequence of glycoprotein E of YL vaccine strain was cloned, sequenced and expressed in E. coli. Phylogenetic analysis of envelope (E) amino acid sequences of 18 JEVs in GenBank showed that the vaccine strain YL closer to the virulent strain HVI which is a Taiwanese isolate. We found only two amino acid mutations (K-138 and G-389) of E protein might lead viral attenuation in YL. In this study, we used pRSET vector system to construct three recombinant plasmids (pRSET/F1R1, pRSET/F2R2 and pRSET/F1R2), which encoded and expressed different or overlapping amino acid region of E protein. The antigenicity and hemagglutination activity of these recombinant proteins were examined by western blotting and hemagglutination test, respectively. Our results demonstrated that the recombinant protein of pRSET/F1R2 possesses predominant antigenicity and hemagglutination activity.