Environmental Soil Samples Research Articles

Pathogenic and phylogenetic features of 2 multiresistant Pseudomonas aeruginosa strains originated from remediated sites.

To evaluate the possible occupational hazard of environmental strains of opportunistic Pseudomonas aeruginosa on hydrocarbon contaminated sites during remediation, 2 multidrug-resistant isolates originating from environmental (soil and groundwater) samples were examined. Antibiotic resistance profiles of the examined 2 strains were determined by Etest® against 20 different agents. Virulence investigations included the hemolytic activity test, the detection of virulence-related gene sequences such as exoA, exoU, exoS, exoY, exoT and the determination of intraperitoneal LD50 (the lethal dose, 50%) values in a mouse model. The hydrocarbon-degrading ability was evaluated in a gravimetric experiment, in vitro. The phylogenetic relationship of the isolates was investigated with a multilocus sequence typing scheme. Multidrug resistant environmental strains of P. aeruginosa are strongly related to isolates that have proven effects on the infection of patients who suffer from cystic fibrosis, have a notable hemolytic activity, carry important virulence markers (exoS or exoU, respectively) and retain their hydrocarbon degradation ability (87.4% and 62.8% hydrocarbon degradation rate, respectively). Pseudomonas aeruginosa presumably raise considerable concerns for human health in the environment, already well known among nosocomial isolates, and the application of environmental strains of this species for environmental purposes is questionable.

Measurement of radon gas concentration in water and soil samples in AL-Najaf governorate by using nuclear track detector (CR-39)

The radon gas concentration in environmental samples soil and water of selected regions in Al-Najaf governorate was measured by using alpha-emitters registrations which are emitted form radon gas in (CR-39) nuclear track detector. The first part is concerned with the determination of radon gas concentration in soil samples, results of measurements indicate that the highest average radon concentration in soil samples was found in (Al-Moalmen) region which was (100.0±7.0 Bq/m3), while the lowest average radon concentration was found in (Al-Askary) region which was (38.5±4.7 Bq/m3), with an average value of (64.23±14.9 Bq/m3) ,the results show that the radon gas concentrations in soil is below the allowed limit from (ICRP) agency which is (200 Bq/m3), while the radon exhalation rate (RER) ranged from (35.23-91.52 µBq/m2h), and average value which was (58.77±13.6 µBq/m2h). The second part is concerned with the determination of radon gas concentration in samples of tap water obtained from networks in dwellings in Al-Najaf governorate, the results indicate that the highest average radon concentration in water samples was found in (Meassan) region which was (0.59±0.08 Bq/L), while the lowest average radon concentration was found in (Al-Jamhorah) region which was (0.16±0.04 Bq/L), with an average value of (0.36±0.1 Bq/L), the present results show that the radon gas concentrations in tap water is below the allowed limit from (ICRP) agency which is (0.5994 Bq/L), while the radon exhalation rate (RER) ranged from (2.15-0.58 ?Sv/y), and average value which was (1.28±0.31 ?Sv/y).

Measurement of radon gas concentration in water and soil samples in AL-Najaf governorate by using nuclear track detector (CR-39)

The radon gas concentration in environmental samples soil and water of selected regions in Al-Najaf governorate was measured by using alpha-emitters registrations which are emitted form radon gas in (CR-39) nuclear track detector. The first part is concerned with the determination of radon gas concentration in soil samples, results of measurements indicate that the highest average radon concentration in soil samples was found in (Al-Moalmen) region which was (100.0±7.0 Bq/m3), while the lowest average radon concentration was found in (Al-Askary) region which was (38.5±4.7 Bq/m3), with an average value of (64.23±14.9 Bq/m3) ,the results show that the radon gas concentrations in soil is below the allowed limit from (ICRP) agency which is (200 Bq/m3), while the radon exhalation rate (RER) ranged from (35.23-91.52 µBq/m2h), and average value which was (58.77±13.6 µBq/m2h). The second part is concerned with the determination of radon gas concentration in samples of tap water obtained from networks in dwellings in Al-Najaf governorate, the results indicate that the highest average radon concentration in water samples was found in (Meassan) region which was (0.59±0.08 Bq/L), while the lowest average radon concentration was found in (Al-Jamhorah) region which was (0.16±0.04 Bq/L), with an average value of (0.36±0.1 Bq/L), the present results show that the radon gas concentrations in tap water is below the allowed limit from (ICRP) agency which is (0.5994 Bq/L), while the radon exhalation rate (RER) ranged from (2.15-0.58 ?Sv/y), and average value which was (1.28±0.31 ?Sv/y).

Rapid MPN-Qpcr Screening for Pathogens in Air, Soil, Water, and Agricultural Produce

A sensitive, high-throughput, and cost-effective method for screening bacterial pathogens in the environment was developed. A variety of environmental samples, including aerosols, soil of various types (sand, sand/clay mix, and clay), wastewater, and vegetable surface (modeled by tomato), were concomitantly spiked with Salmonella enterica and/or Pseudomonas aeruginosa to determine recovery rates and limits of detection. The various matrices were first enriched with a general pre-enrichment broth in a dilution series and then enumerated by most probable number (MPN) estimation using quantitative PCR for rapid screening of amplicon presence. Soil and aerosols were then tested in non-spiked environmental samples, as these matrices are prone to large experimental variation. Limit of detection in the various soil types was 1–3 colony-forming units (CFU) g−1; on vegetable surface, 5 CFU per tomato; in treated wastewater, 5 CFU L−1; and in aerosols, >300 CFU mL−1. Our method accurately identified S. enterica in non-spiked environmental soil samples within a day, while traditional methods took 4 to 5 days and required sorting through biochemically and morphologically similar species. Likewise, our method successfully identified P. aeruginosa in non-spiked aerosols generated by a domestic wastewater treatment system. The obtained results suggest that the developed method presents a broad approach for the rapid, efficient, and reliable detection of relatively low densities of pathogenic organisms in challenging environmental samples.

Simultaneous spectrophotometric determination of phosphate and silicate in different water and soil samples using chemometrics approach

Continuous wavelet transform together with zero-crossing technique was applied to the overlapping visible spectra, as a very simple and accurate method, for the simultaneous determination of phosphate and silicate without any prior separation steps. Daubechies-4, Symlet 8, and Meyer continuous wavelet transforms for signal treatments were found to be suitable. The calibration graphs for estimation of complexes were obtained by measuring the wavelet coefficients at zero-crossing points for silicomolybdenum blue and phosphomolybdenum blue. The constructed calibration functions were tested by analyzing the composition of the different binary mixtures. The experimental data were also analyzed using partial least squares and first-order derivative spectrophotometric method. The proposed method was validated by simultaneous determination of phosphate and silicate in different environmental waters and soil samples. The results of proposed method have been compared with those predicted by partial least squares and standard methods.

Efficiency corrections in determining the 137Cs inventory of environmental soil samples by using relative measurement method and GEANT4 simulations

The determination of 137Cs inventory is widely used to estimate the soil erosion or deposition rate. The generally used method to determine the activity of volumetric samples is the relative measurement method, which employs a calibration standard sample with accurately known activity. This method has great advantages in accuracy and operation only when there is a small difference in elemental composition, sample density and geometry between measuring samples and the calibration standard. Otherwise it needs additional efficiency corrections in the calculating process. The Monte Carlo simulations can handle these correction problems easily with lower financial cost and higher accuracy. This work presents a detailed description to the simulation and calibration procedure for a conventionally used commercial P-type coaxial HPGe detector with cylindrical sample geometry. The effects of sample elemental composition, density and geometry were discussed in detail and calculated in terms of efficiency correction factors. The effect of sample placement was also analyzed, the results indicate that the radioactive nuclides and sample density are not absolutely uniform distributed along the axial direction. At last, a unified binary quadratic functional relationship of efficiency correction factors as a function of sample density and height was obtained by the least square fitting method. This function covers the sample density and height range of 0.8–1.8 g/cm3 and 3.0–7.25 cm, respectively. The efficiency correction factors calculated by the fitted function are in good agreement with those obtained by the GEANT4 simulations with the determination coefficient value greater than 0.9999. The results obtained in this paper make the above-mentioned relative measurements more accurate and efficient in the routine radioactive analysis of environmental cylindrical soil samples.

β-cyclodextrin functionalized meso-/macroporous magnetic titanium dioxide adsorbent as extraction material combined with gas chromatography-mass spectrometry for the detection of chlorobenzenes in soil samples

A high-performance and selective adsorbent was developed for simultaneous extraction of 6 chlorobenzenes residues in soil samples by using magnetic solid phase extraction (MSPE) combined with automated SPE followed by gas chromatography-mass spectrometry (GC-MS). The adsorbent was synthesized by grafting carboxymethyl-β-cyclodextrin (CM-β-CD) on the surface of porous core–shell magnetic Fe3O4@flower like TiO2 microspheres (Fe3O4@fTiO2-CMCD), used as a carrier. The main factors (adsorbent amount, adsorption time, elution solvent, elution volume, and elution flow rate) affecting the extraction efficiency were investigated in detail. The adsorbent exhibited high loading capacity (25.6mgg−1 for 1,3-dichlorobenzene). This maybe due to meso-/macroporous TiO2 having high specific surface area; as a carrier of the β-cyclodextrin film, it could obviously increase the number of recognition sites. The newly developed adsorbent also showed good selectivity towards chlorobenzenes based on host–guest interactions between β-cyclodextrin (on adsorbent's surface) and targets, which can minimize complex matrix interference in soil samples. The proposed method was successfully applied for the analysis of environmental soil samples with recovery ranging from 87.3 to 104.3%. All target compounds showed good linearities with correlation coefficients (r) higher than 0.996. The limits of quantitation for the 6 CBs were 0.03–0.09μgkg−1. These findings confirmed meso-/macroporous structure Fe3O4@fTiO2-CMCD as a highly effective extraction material for use in trace CB analyses in complex soil samples.

Accelerated solvent extraction combined with dispersive liquid-liquid microextraction before gas chromatography with mass spectrometry for the sensitive determination of phenols in soil samples.

A method combining accelerated solvent extraction with dispersive liquid-liquid microextraction was developed for the first time as a sample pretreatment for the rapid analysis of phenols (including phenol, m-cresol, 2,4-dichlorophenol, and 2,4,6-trichlorophenol) in soil samples. In the accelerated solvent extraction procedure, water was used as an extraction solvent, and phenols were extracted from soil samples into water. The dispersive liquid-liquid microextraction technique was then performed on the obtained aqueous solution. Important accelerated solvent extraction and dispersive liquid-liquid microextraction parameters were investigated and optimized. Under optimized conditions, the new method provided wide linearity (6.1-3080 ng/g), low limits of detection (0.06-1.83 ng/g), and excellent reproducibility (<10%) for phenols. Four real soil samples were analyzed by the proposed method to assess its applicability. Experimental results showed that the soil samples were free of our target compounds, and average recoveries were in the range of 87.9-110%. These findings indicate that accelerated solvent extraction with dispersive liquid-liquid microextraction as a sample pretreatment procedure coupled with gas chromatography and mass spectrometry is an excellent method for the rapid analysis of trace levels of phenols in environmental soil samples.

Optimization of cylindrical sample geometry in determining the radioactive activity of environmental soil samples by using a Broad Energy Germanium detector

This paper describes the optimization of the geometric parameters of cylindrical geometry to maximize the detection efficiency for given sample volumes with a BEGe detector. A Monte Carlo model was developed and the detector efficiencies were studied for different sample geometries. The optimal sample dimensions that maximize the detection efficiencies have been determined by changing the sample dimensions through consecutive studies. The results show that the maximal detection efficiency depends on the appropriate selection of sample dimensions for a given sample volume. For the cylindrical geometry, the maximal detection efficiency can be obtained with the average sample radius/sample height value of about 1.75 (1.61 ∼ 1.91) for the corresponding given sample volume ranging from 150 to 400 cm3. Further studies show that the optimal sample height for a fixed cylindrical radius strongly depends on the measuring photon energy, and simply increasing the sample height does not generate higher full-energy peak net count rate. At last, optimal sample dimensions for the cylindrical geometry are recommended for a given detector specification with different sample volumes and photon energies.

Rapid fusion method for the determination of Pu, Np, and Am in large soil samples

A new rapid sodium hydroxide fusion method for the preparation of 10–20 g soil samples has been developed by the Savannah River National Laboratory. The method enables lower detection limits for plutonium, neptunium, and americium in environmental soil samples. The method also significantly reduces sample processing time and acid fume generation compared to traditional soil digestion techniques using hydrofluoric acid. Ten gram soil aliquots can be ashed and fused using the new method in 1–2 h, completely dissolving samples, including refractory particles. Pu, Np and Am are separated using stacked 2 mL cartridges of TEVA and DGA resin and measured using alpha spectrometry. Total sample preparation time, including chromatographic separations and alpha spectrometry source preparation, is less than 8 h.

Concurrent determination of 237Np and Pu isotopes using ICP-MS: analysis of NIST environmental matrix standard reference materials 4357, 1646a, and 2702

An optimized method was developed to analyze environmental soil and sediment samples for 237Np, 239Pu, and 240Pu by ICP-MS using a 242Pu isotope dilution standard. The high yield, short time frame required for analysis, and the commercial availability of the 242Pu tracer are significant advantages of the method. Control experiments designed to assess method uncertainty, including variation in inter-element fractionation that occurs during the purification protocol, suggest that the overall precision for measurements of 237Np is typically on the order of ±5%. Measurements of the 237Np concentration in a Peruvian Soil blank (NIST SRM 4355) spiked with a known concentration of 237Np tracer confirmed the accuracy of the method, agreeing well with the expected value. The method has been used to determine neptunium and plutonium concentrations in several environmental matrix standard reference materials available from NIST: SRM 4357 (Radioactivity Standard), SRM 1646a (Estuarine Sediment) and SRM 2702 (Inorganics in Marine Sediment).

NMR metabolomics for soil analysis provide complementary, orthogonal data to MIR and traditional soil chemistry approaches--a land use study.

The present study was designed to analyse soils by different methodologies to determine the range of traits that could be investigated for the study of environmental soil samples. Proton nuclear magnetic resonance spectroscopy ((1) H NMR) was employed for metametabolomic analysis of soils from agricultural systems (managed) or from soils in a native state (remnant). The metabolomic methodologies employed (grinding and extraction with sonication) are capable of breaking up cell walls and so enabled characterisation of both extracellular and intracellular components of soil. Diffuse mid-infrared spectroscopy (MIR) data was obtained for the same sample sets, and in addition, elemental composition was determined by conventional laboratory chemical testing methods. Also investigated was the antibiotic activity of the soil extracts. Resilient or suppressive soils are valued in the agricultural setting as they convey disease resistance (against bacterial and fungal pathogens) to crop plants. In order to test if any such biological activity could be detected in the soils, the extracts were tested against the bacteria Bacillus subtilis. Several extracts showed strong growth inhibition against the bacteria with the most active clustered together in principle component analysis (PCA) of the metabolomic data. The study showed that the NMR metabolomic approach corresponds more accurately to land use and biochemical properties potentially associated with suppression, while MIR data correlated well to inorganic chemical analysis. Thus, the study demonstrates the utility in combining these spectroscopic methods for soil analysis.

Comparative Study of Glyphosate and AMPA Determination in Environmental Samples by Two Green Methods

Glyphosate, N-phosphonomethyl-glycine (GLY), is a systemic post-emergence herbicide that controls weeds with great efficiency whose low cost is reflected in its wide application. In the environment, the presence of aminomethylphosphonic acid (AMPA), its main degradation product, is indicative of the application of GLY to the land. The aim of this study was to develop two analytical methods for the determination of GLY by HPLC-UV and GLY and AMPA by GC-MS, in water, soil and sediment samples. The proposed HPLC-UV method proved to be an efficient way of determining GLY in environmental samples of water, soil and sediment, eliminating the step of extraction and clean-up. On the other hand, the GC-MS method can be used to determine both GLY and AMPA simultaneously. The limits of detection (LOD) and quantitation (LOQ) for GLY by the HPLC method were 9.93 and 30.1 μg·L﹣1 for water samples, and 0.040 and 0.120 mg·kg﹣1 for soil and sediment samples, respectively. By the GC-MS method, the LOD and LOQ for GLY were 0.67 and 2.02 μg·L﹣1 for water samples, and 0.0027 and 0.0081 mg·kg﹣1 for soil and sediment samples, respectively. For AMPA, these limits were 0.15 and 0.45 μg·L﹣1 for water samples and 0.0006 and 0.0018 mg·kg﹣1 for soil and sediment samples, respectively. The recoveries ranged from 70% to 120% for water, soil and sediment samples.

Extraction and determination of sulfonylurea herbicides in water and soil samples by using ultrasound-assisted surfactant-enhanced emulsification microextraction and analysis by high-performance liquid chromatography

An ultrasound-assisted surfactant-enhanced emulsification microextraction (UASEME) with low-density extraction solvents was developed for the extraction of sulfonylurea herbicides from water and soil samples prior to high-performance liquid chromatography coupled with ultraviolet detection (HPLC–UV). In this technique, a surfactant was used as emulsifier which could enhance the dispersion of water-immiscible extraction solvent into aqueous phase and was favorable for the mass-transfer of the analytes from aqueous phase to organic phase. The target analytes were extracted into an extraction phase (Aliquat-336 in1-octanol) and dispersed in an aqueous solution. After extraction and phase separation, the organic solvent on top of the solution was withdrawn into a syringe and 20µL of it was injected into a HPLC instrument for analysis. Influential factors in extraction were investigated and optimized. Under optimum experimental conditions, calibration curve was linear in the concentration range from 1 to 100µg/L, with coefficients of estimation (R2 values) varying from 0.9928 to 0.9952, and satisfactory repeatabilities (4.7<RSDs%<6.1) were attained. High preconcentration factors were achieved ranging from 103 to 153. Applicability of the method to the extraction of sulfonylurea herbicides from different types of complicated matrices, such as water and soil samples, was studied. The obtained results indicated that the proposed method is efficient, fast and inexpensive for extraction and determination of sulfonylurea herbicides in environmental aqueous and soil samples.

A palladium imprinted polymer for highly selective and sensitive electrochemical determination of ultra-trace of palladium ions

We report on the design of a palladium(II)-selective electrode based on the use of palladium(II) imprinted polymer nanoparticles (IP-NPs), and its application for the anodic stripping deferential pulse voltammetry determination of palladium ions. The IP-NPs were obtained by precipitation polymerization of 4-vinylpyridine (the functional monomer), ethylene glycol dimethacrylate (the cross-linker), 2,2'-azobisisobutyronitrile (the initiator), eriochrome cyanine R (the palladium-binding ligand), and palladium ions (the template ion) in methanol solution. After polymerization, the Pd2+ in the polymer nanoparticles were leached out with dilute hydrochloric acid to create cavities for hosting Pd2+. The new sensor showed high selectivity for palladium ions in the presence of common potential interferences according to the specific recognition nature of the synthesized imprinted material. A carbon paste electrode was modified with the IP-NPs, and differential pulse stripping voltammetry was applied as the detection technique after open-circuit sorption of Pd2+ ions and its reduction to the metallic form. An explicit difference in the response was observed between the electrodes modified with IP-NPs and electrodes modified with non-IP-NPs. The modified electrode responses to Pd2+ was linear in the 0.01 nmol dm−3 to 1.0 nmol dm−3 (with sensitivity of 92.25nA/nmol dm−3) and in the 1.0 nmol dm−3 to 1.0μmol dm−3 (with sensitivity of 16.12μA/μmol dm−3) concentration ranges. The limit of detection (LOD) of the sensor was 3.0pmol dm−3 (at S/N=3). The sensor was successfully applied to the trace determination of Pd2+ in spiked environmental water and soil samples.

Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering.

DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, DNA labeling, mutagenesis, and other experiments. Thermostable DNA polymerases are especially useful and became quite valuable after the development of PCR technology. A DNA polymerase from Thermus aquaticus (Taq polymerase) is the most famous DNA polymerase as a PCR enzyme, and has been widely used all over the world. In this study, the gene fragments of the family A DNA polymerases were amplified by PCR from the DNAs from microorganisms within environmental soil samples, using a primer set for the two conserved regions. The corresponding region of the pol gene for Taq polymerase was substituted with the amplified gene fragments, and various chimeric DNA polymerases were prepared. Based on the properties of these chimeric enzymes and their sequences, two residues, E742 and A743, in Taq polymerase were found to be critical for its elongation ability. Taq polymerases with mutations at 742 and 743 actually showed higher DNA affinity and faster primer extension ability. These factors also affected the PCR performance of the DNA polymerase, and improved PCR results were observed with the mutant Taq polymerase.

Optimization of headspace solid phase microextraction based on nano-structured ZnO combined with gas chromatography–mass spectrometry for preconcentration and determination of ultra-traces of chlorobenzenes in environmental samples

In this study, a simple, novel and efficient preconcentration method for the determination of some chlorobenzenes (monochlorobenzene (MCB), three isomeric forms of dichlorobenzene (diCB), 1,3,5-trichlorobenzene (triCB) and hexachlorobenze (hexaCB)) has been developed using a headspace solid phase microextraction (HS-SPME) based on nano-structured ZnO combined with capillary gas chromatography–mass spectrometry (GC–MS). ZnO nanorods have been grown on fused silica fibers using a hydrothermal process. The diameter of ZnO nanorods was in the range of 50–80nm. The effect of different variables on the extraction efficiency was studied simultaneously using an experimental design. The variables of interest in the HS-SPME were stirring rate, desorption time and temperature, ionic strength, extraction time and temperature. For this purpose, a multivariate strategy was applied based on an experimental design using a Plackett–Burman design for screening and a Box–Behnken design for optimizing of the significant factors. The detection limit and relative standard deviation (RSD) (n=5) for the target analytes were in the range of 0.01–0.1ngL−1 and 4.3–7.6%, respectively. The developed technique was found to be successfully applicable to preconcentration and determination of the target analytes in environmental water and soil samples.

Radioactive particles in soil, plant, and dust samples after the Fukushima nuclear accident

Environmental samples of soil, plant and air dust collected after the Fukushima Daiichi Nuclear Power Plant accident were analyzed by autoradiograph, and significant amounts of radioactive particles containing higher cesium-134 (134Cs) and cesium-137 (137Cs) were found. Most of the radioactive soil particles were clay sized. The main part of the radioactivity and radioactive particles of air dust was detected from the 1.1–2.0μm fraction of an Andersen sampler filter. A considerable part of the radioactive particles on the air dust filter were not water soluble. Radioactive particles attached to outdoor plant leaves persisted for nearly 1 year. Thus, soil, leaf and air dust similarly contained sparingly water-soluble, micron-sized radioactive particles each with comparable ranges of elevated radio-Cs. A sheet dilution method was proposed and used to select and purify these radioactive particles. Using selected radioactive particles, the relation between area × gray value on autoradiograph and radioactivity was estimated. Radioactivity per particle was up to a few Bq and the geometrical average radioactivity of detected particles was around 0.1 Bq per particle or less. The configuration, chemical composition, origin and formation mechanisms of the radioactive particles require clarification.

Comparison of DNA Extraction and Purification Methods from Different Soils for Metagenomic Sequencing

There is an increased interest in the extraction of nucleic acids from various environmental samples, since only a minority of naturally occurring microbes can be cultured using standard techniques. Nucleic acids extraction and purification from soils are extremely challenging due to the low biomass, high organic contents and high variability of soil types. This has been regarded as one of the major difficulties that hamper the development of soil microbial ecology study. No commercial nucleic acids kits currently available are capable of preparing the DNAs without modifications. The cost can be very high for DNA extraction from extreme environmental soil samples, such as soils that have extreme high or low pHs. In this work, we developed and optimized soil DNA extraction and purification methods on different soils and compared the impact of three different DNA extraction protocols on DNA yield and purity. For the three different types of soil we used, direct extraction obtained the highest DNA recover rate, but required more cleanup steps. MoBio PowerSoil® DNA Isolation Kit yields less but do not require as many downstream cleaning steps. Both of the two methods obtained a more abundant microbial community than Meta-G-NomeTM DNA Isolation Kit.

The environmental biological signature: NGS profiling for forensic comparison of soils

The identification of the source of a specific soil sample is a crucial step in forensic investigations. Rapid advances in next generation sequencing (NGS) technology and the strong reduction of the cost of sequencing have recently opened new perspectives. In the present work a metabarcoding approach has been successfully applied to forensic and environmental soil samples, allowing the accurate and sensitive analysis of microflora (mfDNA), plants, metazoa, and protozoa DNA. The identification of the biological component by DNA metabarcoding is a strong element for the discrimination of samples geologically very similar but coming for distinct environments.