Surface-mediated chromate-resistant mechanism of Enterobacter cloacae bacteria investigated by atomic force microscopy

Power Laws Describe Bacterial Viscoelasticity

Bacterial cells survive in a wide range of different environments and actively tune their mechanical properties for purposes of growth, movement, division, and nutrition. In Gram-negative bacteria, the cell envelope with its outer membrane and peptidoglycan are the main determinants of mechanical properties and are common targets for the use of antibiotics. The study of bacterial mechanical properties has shown promise in elucidating a structure-function relationship in bacteria, connecting, shape, mechanics, and biochemistry. In this work, we study frequency and time-dependent viscoelastic properties of E. coli cells by atomic force microscopy (AFM). We perform force cycles, oscillatory microrheology, stress relaxation, and creep experiments, and use power law rheology models to fit the experimental results. All data sets could be fitted with the models and provided power law exponents of 0.01 to 0.1 while showing moduli in the range of a few MPa. We provide evidence for the interchangeability of the properties derived from these four different measurement approaches.

Proteomics and bioinformatics analysis reveal potential roles of cadmium-binding proteins in cadmium tolerance and accumulation of Enterobacter cloacae

Background

Enterobacter cloacae (EC) is a Gram-negative bacterium that has been utilized extensively in biotechnological and environmental science applications, possibly because of its high capability for adapting itself and surviving in hazardous conditions. A search for the EC from agricultural and industrial areas that possesses high capability to tolerate and/or accumulate cadmium ions has been conducted in this study. Plausible mechanisms of cellular adaptations in the presence of toxic cadmium have also been proposed.

Methods

Nine strains of EC were isolated and subsequently identified by biochemical characterization and MALDI-Biotyper. Minimum inhibitory concentrations (MICs) against cadmium, zinc and copper ions were determined by agar dilution method. Growth tolerance against cadmium ions was spectrophotometrically monitored at 600 nm. Cadmium accumulation at both cellular and protein levels was investigated using atomic absorption spectrophotometer. Proteomics analysis by 2D-DIGE in conjunction with protein identification by QTOF-LC-MS/MS was used to study differentially expressed proteins between the tolerant and intolerant strains as consequences of cadmium exposure. Expression of such proteins was confirmed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Bioinformatics tools were applied to propose the functional roles of cadmium-binding protein and its association in cadmium tolerance mechanisms.

Results

The cadmium-tolerant strain (EC01) and intolerant strain (EC07) with the MICs of 1.6 and 0.4 mM, respectively, were isolated. The whole cell lysate of EC01 exhibited approximately two-fold higher in cadmium binding capability than those of the EC07 and ATCC 13047, possibly by the expression of Cd-binding proteins. Our proteomics analysis revealed the higher expression of DUF326-like domain (a high cysteine-rich protein) of up to 220 fold in the EC01 than that of the EC07. Confirmation of the transcription level of this gene by qRT-PCR revealed a 14-fold induction in the EC01. Regulation of the DUF326-like domain in EC01 was more pronounced to mediate rapid cadmium accumulation (in 6 h) and tolerance than the other resistance mechanisms found in the ATCC 13047 and the EC07 strains. The only one major responsive protein against toxic cadmium found in these three strains belonged to an antioxidative enzyme, namely catalase. The unique proteins found in the ATCC 13047 and EC07 were identified as two groups: (i) ATP synthase subunit alpha, putative hydrolase and superoxide dismutase and (ii) OmpX, protein YciF, OmpC porin, DNA protection during starvation protein, and TrpR binding protein WrbA, respectively.

Conclusion

All these findings gain insights not only into the molecular mechanisms of cadmium tolerance in EC but also open up a high feasibility to apply the newly discovered DUF326-like domain as cadmium biosorbents for environmental remediation in the future.

Cr(VI) reduction by an extracellular polymeric substance (EPS) produced from a strain of Pseudochrobactrum saccharolyticum

A better understanding of the Cr(VI) reduction position and mechanisms by a Cr(VI)-reducing strain is important for the bioremediation of Cr pollution in the environment. In the present study, we were interested in figuring out the role of extracellular polymeric substances (EPS) as the main area for Cr(VI) reduction in the newly reported strain of Pseudochrobactrum saccharolyticum LY10. We investigated the subcellular distribution and reduction capability of each cellular component as the main area of Cr(VI) reduction by scanning electron microscopy and soft X-ray spectromicroscopy. The results suggested that most of Cr was presented in the supernatants as Cr(III) after reduction. In the cells, Cr was mostly distributed in the EPS and cell wall, while the EPS had the maximum Cr(VI) reduction rate (81.5%) as compared with the cell wall (30.1%). Soft X-ray spectromicroscopy analysis indicated that Cr accumulated more in the EPS. Therefore, the results suggested that the EPS were the main area for Cr(VI) reduction in the bacteria of P. saccharolyticum LY10.

Understanding the role of clay minerals in the chromium(VI) bioremoval by Pseudomonas aeruginosa CCTCC AB93066 under growth condition: microscopic, spectroscopic and kinetic analysis

Laboratory batch experiments were conducted to investigate the role of clay minerals, e.g., kaolinite and vermiculite, in microbial Cr(VI) reduction by Pseudomonas aeruginosa under growth condition in glucose-amended mediums as a method for treating Cr(VI)-contaminated subsurface environment such as soil. Our results indicated that glucose could acted as an essential electron donor, and clay minerals significantly enhanced microbial Cr(VI) reduction rates by improving the consumption rate of glucose and stimulating the growth and propagation of P. aeruginosa. Cr(VI) bioreduction by both free cells and clay minerals-amended cells followed the pseudo-first-order kinetic model, with the latter one fitting better. The mass balance analyses and X-ray photoelectron spectroscopy analysis found that Cr(VI) was reduced to Cr(III) and the adsorption of total chromium on clay minerals-bacteria complex was small, implying that Cr(VI) bioremoval was not mainly due to the adsorption of Cr(VI) onto cells or clay minerals or clay minerals-cells complex but mainly due to the Cr(VI) reduction capacity of P. aeruginosa under the experimental conditions studied (e.g., pH 7). Atomic force microscopy revealed that the addition of clay minerals (e.g. vermiculite) decreased the surface roughness of Cr(VI)-laden cells and changed the cell morphology and dimension. Fourier transform infrared spectroscopy revealed that organic matters such as aliphatic species and/or proteins played an important role in the combination of cells and clay minerals. Scanning electron microscopy confirmed the attachment of cells on the surface of clay minerals, indicating that clay minerals could provide a microenvironment to protect cells from Cr(VI) toxicity and serve as growth-supporting materials. These findings manifested the underlying influence of clay minerals on microbial reduction of Cr(VI) and gave an understanding of the interaction between pollutants, the environment and the biota.

Hydrothermal growth of large-size UO2 nanoparticles mediated by biomass and environmental implications

We reveal the hydrothermal conversion rule for amorphous U(vi) to large-size UO₂.

Toxicity detection of sodium nitrite, borax and aluminum potassium sulfate using electrochemical method

Based on the inhibition effect on the respiratory chain activity of microorganisms by toxicants, an electrochemical method has been developed to measure the current variation of a mediator in the presence of microorganisms contacted with a toxicant. Microelectrode arrays were adopted in this study, which can accelerate the mass transfer rate of an analyte to the electrode and also increase the total current signal, resulting in an improvement in detection sensitivity. We selected Escherichia coli as the testee and the standard glucose-glutamic acid as an exogenous material. Under oxygen restriction, the experiments in the presence of toxicant were performed at optimum conditions (solution pH 7.0, 37 degrees C and reaction for 3 hr). The resulting solution was then separated from the suspended microorganisms and was measured by an electrochemical method, using ferricyanide as a mediator. The current signal obtained represents the reoxidation of ferrocyanide, which was transformed to inhibiting efficiency, IC50, as a quantitative measure of toxicity. The IC50 values measured were 410, 570 and 830 mg/L for sodium nitrite, borax and aluminum potassium sulfate, respectively. The results show that the toxicity sequence for these three food additives is consistent with the value reported by other methods. Furthermore, the order of damage degree to the microorganism was also observed to be: sodium nitrite > borax > aluminum potassium sulfate > blank, according to the atomic force microscopy images of E. coli after being incubated for 3 hr with the toxic compound in buffer solutions. The electrochemical method is expected to be a sensitive and simple alternative to toxicity screening for chemical food additives.

Escherichia coli NemA is an efficient chromate reductase that can be biologically immobilized to provide a cell free system for remediation of hexavalent chromium

Hexavalent chromium is a serious and widespread environmental pollutant. Although many bacteria have been identified that can transform highly water-soluble and toxic Cr(VI) to insoluble and relatively non-toxic Cr(III), bacterial bioremediation of Cr(VI) pollution is limited by a number of issues, in particular chromium toxicity to the remediating cells. To address this we sought to develop an immobilized enzymatic system for Cr(VI) remediation. To identify novel Cr(VI) reductase enzymes we first screened cell extracts from an Escherichia coli library of soluble oxidoreductases derived from a range of bacteria, but found that a number of these enzymes can reduce Cr(VI) indirectly, via redox intermediates present in the crude extracts. Instead, activity assays for 15 candidate enzymes purified as His6-tagged proteins identified E. coli NemA as a highly efficient Cr(VI) reductase (k_cat/K_M  = 1.1×10⁵ M⁻¹s⁻¹ with NADH as cofactor). Fusion of nemA to the polyhydroxyalkanoate synthase gene phaC from Ralstonia eutropha enabled high-level biosynthesis of functionalized polyhydroxyalkanoate granules displaying stable and active NemA on their surface. When these granules were combined with either Bacillus subtilis glucose dehydrogenase or Candida boidinii formate dehydrogenase as a cofactor regenerating partner, high levels of chromate transformation were observed with only low initial concentrations of expensive NADH cofactor being required, the overall reaction being powered by consumption of the cheap sacrificial substrates glucose or formic acid, respectively. This system therefore offers promise as an economic solution for ex situ Cr(VI) remediation.

Microbial reduction of chromate in the presence of nitrate by three nitrate respiring organisms

A major challenge for the bioremediation of toxic metals is the co-occurrence of nitrate, as it can inhibit metal transformation. Geobacter metallireducens, Desulfovibrio desulfuricans, and Sulfurospirillum barnesii are three soil bacteria that can reduce chromate [Cr(VI)] and nitrate, and may be beneficial for developing bioremediation strategies. All three organisms respire through dissimilatory nitrate reduction to ammonia (DNRA), employing different nitrate reductases but similar nitrite reductase (Nrf). G. metallireducens reduces nitrate to nitrite via the membrane bound nitrate reductase (Nar), while S. barnesii and D. desulfuricans strain 27774 have slightly different forms of periplasmic nitrate reductase (Nap). We investigated the effect of DNRA growth in the presence of Cr(VI) in these three organisms and the ability of each to reduce Cr(VI) to Cr(III), and found that each organisms responded differently. Growth of G. metallireducens on nitrate was completely inhibited by Cr(VI). Cultures of D. desulfuricans on nitrate media was initially delayed (48 h) in the presence of Cr(VI), but ultimately reached comparable cell yields to the non-treated control. This prolonged lag phase accompanied the transformation of Cr(VI) to Cr(III). Viable G. metallireducens cells could reduce Cr(VI), whereas Cr(VI) reduction by D. desulfuricans during growth, was mediated by a filterable and heat stable extracellular metabolite. S. barnesii growth on nitrate was not affected by Cr(VI), and Cr(VI) was reduced to Cr(III). However, Cr(VI) reduction activity in S. barnesii, was detected in both the cell free spent medium and cells, indicating both extracellular and cell associated mechanisms. Taken together, these results have demonstrated that Cr(VI) affects DNRA in the three organisms differently, and that each have a unique mechanism for Cr(VI) reduction.

Cr(VI) uptake mechanism of Bacillus cereus

In this study, we investigated the Cr(VI) uptake mechanism in an indigenous Cr(VI)-tolerant bacterial strain -Bacillus cereus through batch and microscopic experiments. We found that both the cells and the supernatant collected from B. cereus cultivation could reduce Cr(VI). The valence state analysis revealed the complete transformation from Cr(VI) into Cr(III) by living B. cereus. Further X-ray absorption fine structure and Fourier transform infrared analyses showed that the reduced Cr(III) was coordinated with carboxyl and amido functional groups from either the cells or supernatant. Scanning electron microscopy and atomic force microscopy observation showed that noticeable Cr(III) precipitates were accumulated on bacterial surfaces. However, Cr(III) could also be detected in bacterial inner portions by using transmission electron microscopy thin section analysis coupled with energy dispersive X-ray spectroscopy. Through quantitative analysis of chromium distribution, we determined the binding ratio of Cr(III) in supernatant, cell debris and cytoplasm as 22%, 54% and 24%, respectively. Finally, we further discussed the role of bacterium-origin soluble organic molecules to the remediation of Cr(VI) pollutants.

Identification and characterization of the chromium (VI) responding protein from a newly isolated Ochrobactrum anthropi CTS-325

A Gram-negative, chromium(VI) tolerant and reductive strain CTS-325, isolated from a Chinese chromate plant, was identified as Ochrobactrum anthropi based on its biochemical properties and 16S rDNA sequence analysis. It was able to tolerate up to 10 mmol/L Cr(VI) and completely reduce 1 mmol/L Cr(VI) to Cr(III) within 48 h. When the strain CTS-325 was induced with Cr(VI), a protein increased significantly in the whole cell proteins. Liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis revealed that this protein was a superoxide dismutase (SOD) homology. The measured superoxide dismutase activity was 2694 U/mg after three steps of purification. The SOD catalyzes the dismutation of the superoxide anion (O2*-) into hydrogen peroxide and molecular oxygen. This protein is considered to be one of the most important anti-oxidative enzymes for O. anthropi as it allows the bacterium to survive high oxygen stress environments, such as the environment produced during the reduction process of Cr(VI).