Egyptian Soil Samples Research Articles

Diverse thermophilic Bacillus species with multiple biotechnological activities are associated within the Egyptian soil and compost samples.

Thermophilic strains of Bacillus can express enzymes of higher thermal stability, which allows carrying out industrial fermentations under higher temperatures. This lowers the contamination potential, accelerates mixing rates and facilitates the recovery of fermentation end products. The present study was thus designed to isolate and characterize thermophilic Bacillus cultures from soil and compost samples. Forty-two thermophilic Bacillus isolates could be identified employing morphological, physiological and the 16S rRNA gene sequencing analyses. The isolates showed a high degree of biological diversity involving 13 Bacillus species and 1 subspecies but were dominated by Bacillus licheniformis. Phylogenetic analysis of B. licheniformis isolates based on the DNA sequencing of gyrA and rpoB genes presented them in two main genetic groups. Isolates of five thermophilic species including B. licheniformis, Bacillus altitudinis, Bacillus paralicheniformis, Bacillus subtilis and Bacillus thermoamylovorans showed multiple activities to degrade all of cellulose, hemicellulose and lignin. Those multifunctional thermophilic Bacillus isolates can be harnessed in the degradation of plant wastes for the production of biofuels and compost.

Indole Derivatives Obtained from Egyptian Enterobacter sp. Soil Isolates Exhibit Antivirulence Activities against Uropathogenic Proteus mirabilis.

Proteus mirabilis is a frequent cause of catheter associated urinary tract infections (CAUTIs). Several virulence factors contribute to its pathogenesis, but swarming motility, biofilm formation, and urease activity are considered the hallmarks. The increased prevalence in antibiotic resistance among uropathogens is alarming and requires searching for new treatment alternatives. With this in mind, our study aims to investigate antivirulence activity of indole derivatives against multidrug resistant P. mirabilis isolates. Ethyl acetate (EtOAc) extracts from Enterobacter sp. (rhizobacterium), isolated from Egyptian soil samples were tested for their ability to antagonize the virulence capacity and biofilm activity of P. mirabilis uropathogens. Extracts of two Enterobacter sp. isolates (coded Zch127 and Cbg70) showed the highest antivirulence activities against P. mirabilis. The two promising rhizobacteria Zch127 and Cbg70 were isolated from soil surrounding: Cucurbita pepo (Zucchini) and Brassica oleracea var. capitata L. (Cabbage), respectively. Sub-minimum inhibitory concentrations (Sub-MICs) of the two extracts showed potent antibiofilm activity with significant biofilm reduction of ten P. mirabilis clinical isolates (p-value < 0.05) in a dose-dependent manner. Interestingly, the Zch127 extract showed anti-urease, anti-swarming and anti-swimming activity against the tested strains. Indole derivatives identified represented key components of indole pyruvate, indole acetamide pathways; involved in the synthesis of indole acetic acid. Additional compounds for indole acetonitrile pathway were detected in the Zch127 extract which showed higher antivirulence activity. Accordingly, the findings of the current study model the feasibility of using these extracts as promising antivirulence agent against the P. mirabilis uropathogens and as potential therapy for treatment of urinary tract infections (UTIs).

Biosynthesis and Bio-sensing Applications of Silver and Gold Metal Nanoparticles

Biogenic nanoparticles have gained major interest because of their eco-friendly approach, as non-toxic chemicals are involved in the biosynthesis, and the preparation process carried out at ambient pressure and temperature. In the present study, two fungal strains (MM1and MM2) showed the ability to biosynthesize silver and gold nanoparticles, respectively, were isolated from local Egyptian soil samples. These two fungi were identified by the molecular technique 18srRNA as Aspergillus terreus isolate MM1-EGY and Aspergillus flavus isolate MM2-EGY. The biosynthesized silver nanoparticles by Aspergillus terreus isolate MM1-EGY exhibited UV absorbance around 420 nm and particle size range of 15-35 nm as measured by transmission electron microscopy (TEM). On the other hand, gold nanoparticles biosynthesized by Aspergillus flavus isolate MM2-EGY showed maximum UV/Vis absorbance around 550 nm and size range of 20-50 nm. The XRD of both AgNPs and AuNPS was constructed. The green synthesized gold nanoparticles were tested for sensitive and selective simultaneous voltammetric determination of neurotransmitter metabolite, vanillylmandelic acid (VMA) and homovanillic acids (HVA), while silver nanoparticles were applied for the fabrication of disposable screen-printed Ag/AgCl planner reference electrode.

The use of experimental design for optimisation of QuEChERS extraction of commonly used pesticides in Egyptian soil and drainage water and their determination by GC/MS

ABSTRACT In this study, a Quick, Easy, Cheap, Effective, Rugged and Safe method (QuEChERS) method was optimised to extract 30 pesticides which are the most used in Egypt in soil and drainage water. Optimisation was performed by Experimental Design expert 7.1 to get better recoveries. The procedure combined with a developed GC-MS for determination of these pesticides. Total analysis time was 36 min with 1 ml injection volume. The limit of quantification (LOQ) was ranged between 4.59 ng/ml, and 15.91 ng/ml for all pesticides. Most standard deviations were in the range between 0.41 and 1.41 indicating satisfactory accuracy. The validated method was applied to Egyptian soil and drainage water samples brought from different places in Damietta city. Dimethoate, β-Endosulfan, DDD, Malathion, Vinclozolin, DDT, Endrin, Cyprodinil, Primiphos ethyl, Tetradifon, Parathion ethyl and Diazinon were detected and quantified. So risk assessment on human health should be considered especially for those pesticides.

Radium content and radon exhalation rates in Egyptian soil samples using active and passive techniques

In this study, we look at radium content in soil samples collected from different locations in Egypt which have been measured using active gamma ray spectrometry with high-purity germanium (HPGe) detector and the passive sealed cup technique with LR-115 nuclear track detectors. Furthermore, the radon exhalation rates (mass and area) were measured using passive technique with LR-115 detectors. This investigation was undertaken to evaluate the possible health risks posed by the elements in question. Radium content values were found to vary from 20.83 to 47.57 Bq/kg with an average value of 32.46 ± 7.75 Bq/kg and 17.30 to 42.70 Bq/kg with an average 29.15 ± 6.75 Bq/kg using HPGe and LR-115 detectors, respectively. Area (surface) exhalation rate values were found to vary from 2.88 × 10-6 to 8.53 × 10-6 Bq/m2/h with an average value of 5.75 × 10-6 Bq /m2/h. Mass exhalation rate values were found to vary from 42.9 × 10-9 to 128 × 10-9 Bq/kg/h with an average value of 78.7 × 10-9 Bq/kg/h. All the results obtained in this particular study were found to be less than their corresponding world limits. Overall, the present results have revealed that radium content and both area and mass exhalation rates in the studied area do not pose a risk to human health. The results were compared nationally and with various other countries.

A68 Characterization and comparative genomic analysis of two Bacillus megaterium lytic bacteriophages

Next-generation sequencing technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Many Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. Here, we describe biological characteristics and whole-genome sequences and their annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), isolated from Egyptian soil samples and representing two different groups according to their host range and amplified fragment length polymorphism profiles. Both phages have been displaying different thermal inactivation points (82 and 78 °C) and pH tolerance range (5–9.2 and 5–8.4 pH) while having the same longevity in vitro (192 h). Electron microscopy observation has proved that both phages belonged to the Myoviridiae family. Furthermore, growth analyses indicated that phages BM5 and BM10 have a shorter latent period (20 and 25 min) and smaller burst size (103 and 117 PFU) than is typical for Bacillus phages. The genome sizes of phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with a modular organization. Bioinformatic analyses of BM5 and BM10 genomes enabled assignments of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of BM5 and BM10 genome structures with other B. megaterium bacteriophages revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7) within L cluster and display different lifestyles (lysogenic and lytic). Sequenced phages encode proteins associated with Bacillus pathogenesis. BM5 does not contain any tRNA sequences, while BM10 genome codes for 17 tRNAs.

Characterization and comparative genomic analysis of virulent and temperate Bacillus megaterium bacteriophages.

Next-Generation Sequencing (NGS) technologies provide unique possibilities for the comprehensive assessment of the environmental diversity of bacteriophages. Several Bacillus bacteriophages have been isolated, but very few Bacillus megaterium bacteriophages have been characterized. In this study, we describe the biological characteristics, whole genome sequences, and annotations for two new isolates of the B. megaterium bacteriophages (BM5 and BM10), which were isolated from Egyptian soil samples. Growth analyses indicated that the phages BM5 and BM10 have a shorter latent period (25 and 30 min, respectively) and a smaller burst size (103 and 117 PFU, respectively), in comparison to what is typical for Bacillus phages. The genome sizes of the phages BM5 and BM10 were 165,031 bp and 165,213 bp, respectively, with modular organization. Bioinformatic analyses of these genomes enabled the assignment of putative functions to 97 and 65 putative ORFs, respectively. Comparative analysis of the BM5 and BM10 genome structures, in conjunction with other B. megaterium bacteriophages, revealed relatively high levels of sequence and organizational identity. Both genomic comparisons and phylogenetic analyses support the conclusion that the sequenced phages (BM5 and BM10) belong to different sub-clusters (L5 and L7, respectively), within the L-cluster, and display different lifestyles (lysogenic and lytic, respectively). Moreover, sequenced phages encode proteins associated with Bacillus pathogenesis. In addition, BM5 does not contain any tRNA sequences, whereas BM10 genome codes for 17 tRNAs.

Determination of glyphosate residues in Egyptian soil samples

A sensitive linker-assisted enzyme-linked immunosorbent assay (L'ELISA) was developed for the analysis of glyphosate in Egyptian soil samples. Polyclonal glyphosate antibodies were produced from rabbits immunized with glyphosate protein conjugate. The conjugate was prepared by activating the carboxylic groups of proteins; thyroglobulin or bovine serum albumin with 1-ethyl-3- (3-diaminopropyl) carbodiimide hydrochloride and N-hydroxysulfosuccinimide followed by directly coupled to the amino group of glyphosate. The L'ELISA used succinic anhydride to derivatize glyphosate, which mimics the epitopic attachment of glyphosate to thyroglobulin. L'ELISA recognized the derivatized glyphosate with a limit of detection (LOD) of 0.8 ng g−1 and sensitivity (IC50 value) of 0.018 μg g−1. The recovery values of the spiked soil samples with different concentrations of glyphosate were in the range of 87.4–97.2%. Good correlation was achieved between L'ELISA and conventional high-pressure liquid chromatography (HPLC) with fluorescence detection. This study demonstrated the utility and convenience of the sensitive, simple, practical and cost-effective L'ELISA method for glyphosate analysis in soil samples. Also, it is ideal for rapid screening of a large number of environmental samples.

Diversity of Bacillus thuringiensis isolates from Egyptian soils as shown by molecular characterization.

Different techniques were adopted for molecular characterization of several indigenous strains of Bacillus thuringiensis (Bt) previously isolated from Egyptian soil samples. These isolates show different toxicity levels against neonate larvae of both insect species; Spodoptera littoralis (Biosduval); and Helicoverpa armigera (Hübner). The parasporal crystals among the most potent isolates contained polypeptides of about 127 and 130 kDa. PCR screening for genes encoding different Cry genes was performed. The Cry 1 gene is the most abundant in these isolates (83.33%) among tested Cry-type genes, followed by Cry 1 gene subfamilies (Cry 1B and Cry 1C) with percentage of 38.88% and 77.77%, respectively. The tested isolates showed the presence of Cry 2A(a,b) gene, but not all of these isolates were positive for Cry 2 gene (55.55%). Only 27.77% and 16.66% of the tested isolates harbor Cry 4 and Cry 3 genes, respectively. All strains were negative in PCR assays for the Vip 3Aa1 gene. Moreover, DNA fingerprinting using RAPD-PCR was performed to detect the genetic similarities and dissimilarities among the different isolates and standard strains. Assessment of Bt diversity based on the combined analysis of their protein and RAPD-PCR banding patterns was performed. This study demonstrates that Bt strains isolated from Egyptian soil samples can be distinguished and identified on the basis of the distribution of Cry-type genes and RAPD fingerprints.

Enhanced production of thermostable lipase from Bacillus cereus ASSCRC-P1 in waste frying oil based medium using statistical experimental design

This study aim to isolate, identify and optimize lipase producing strains using frying oil waste. Nine strains were isolated from an Egyptian soil samples. Among the isolates, a potent bacterial candidate ASSCRC-P1 was found to be the most potent lipase producer strain at 60 °C. Genotypic identification of ASSCRC-P1 showed 94% similarity with Bacillus sp. strains. Phylogenetic tree confirmed that ASSCRC-P1 was nearly similar to Bacillus cereus. Therefore, it was given the name Bacillus cereus ASSCRC-P1 and its 16S rRNA nucleotide has been deposited in the GenBank Data Library under the accession number: KJ531440. A sequential optimization strategy, based on statistical experimental designs, was employed to enhance the lipase production by this strain. A 2-level Plackett–Burman design was applied to differentiate between the bioprocess parameters that significantly influence lipase production followed by Box-Behnken design to optimize the amounts of variables which have the highest positive significant effect on lipase production. Overall more than 2.15-fold improvement in lipase production was achieved due to optimization compared to that obtained using the basal medium.

Calculation of gamma-ray mass attenuation coefficients of some Egyptian soil samples using Monte Carlo methods

Monte Carlo simulations, FLUKA and Geant4, were performed to study mass attenuation for various types of soil at 59.5, 356.5, 661.6, 1173.2 and 1332.5 keV photon energies. Appreciable variations are noted for all parameters by changing the photon energy and the chemical composition of the sample. The simulations parameters were compared with experimental data and the XCOM program. The simulations show that the calculated mass attenuation coefficient values were closer to experimental values better than those obtained theoretically using the XCOM database for the same soil samples. The results indicate that Geant4 and FLUKA can be applied to estimate mass attenuation for various biological materials at different energies. The Monte Carlo method may be employed to make additional calculations on the photon attenuation characteristics of different soil samples collected from other places.

Empirical Models Estimating Carbon Dioxide Accumulation in Two Petroleum Hydrocarbon–Contaminated Soils

ABSTRACT Bioremediation is a popular method in degrading diesel fuel contaminants from soil. Bioremediation can be enhanced by estimating the effect of important environmental parameters on microbial activity. Respirometry was used to develop empirical models describing the effects of temperature, moisture, nitrogen, and phosphorus concentration on microbial activity in a diesel-contaminated soil from Wyoming. Carbon dioxide (CO2) data were analyzed using a base equation where its coefficient values were functions of each parameter. Two physiologically different groups of microorganisms were identified from the results under different operating temperatures. The empirical correlations were combined into one model and this model was tested against a hydrocarbon-contaminated soil collected from a site in Egypt with similar history of contamination. The predicted CO2 evolution agreed well with the actual data obtained from the Egyptian soil samples, showing a sound predicting power of the empirical model for petroleum hydrocarbon biodegradation. Overall, the empirical correlations developed from the respirometric data provide a method to describe microbial activity in diesel-contaminated soils.

Affinity purification of a siderophore that exhibits an antagonistic effect against soft rot bacterium

Bacterial colonies were isolated from different Egyptian soil samples. From these isolates, one bacterial species was found to produce siderophore. Using classical and biochemical identification methods, the siderophore producing isolate was identified as Pseudomonas fluorescens. Based on the affinity of siderophores for metal ions, an affinity chromatography system was designed for the purification of the siderophore in one step. It was possible to isolate 25 mg siderophore per liter of culture media. The purified siderophore was found to exist in two forms of approximately 30 and 90 kD. They are believed to be polymers of several siderophore molecules. Both forms were found to be active against the pathogen Erwinia carotovora var. carotovora, the causal bacteria of soft rot disease on potato tubers. The advantage of this method over other purification methods is that it uses metal ion so it can be applied for the purification of the known types of siderophores. Moreover, the purification is based on affinity chromatography, so the siderophore purity state permits several biotechnological applications without further treatments.

Production of Gluconic Acid by Some Local Fungi

Forty-one fungal species belonging to 15 fungal genera isolated from Egyptian soil and sugar cane waste samples were tested for their capacity of producing acidity and gluconic acid. For the tests, the fungi were grown on glucose substrate and culture filtrates were examined using paper chromatography analysis. Most of the tested fungi have a relative wide potentiality for total acid production in their filtrates. Nearly 51% of them showed their ability of producing gluconic acid. Aspergillus niger was distinguishable from other species by its capacity to produce substantial amounts of glueonie acid when it was cultivated on a selective medium. The optimized cultural conditions for glueonie acid yields were using submerged culture at 30°C at initial pH 6.0 for 7 days of incubation. Among the various concentrations of substrate used, glucose (14%, w/v) was found to be the most suitable carbon source for maximal glueonie acid during fermentation. Maximum values of fungal biomass (10.02 g/l) and glueonie acid (58.46 g/l) were obtained when the fungus was grown with 1% peptone as sole nitrogen source. Influence of the concentration of some inorganic salts as well as the rate of aeration on the glueonie acid and biomass production is also described.

Further Studies on Free-living Nitrogen-Fixing Microorganisms, Other than Azotobacter, Isolated from Egyptian Soils and Waters

Summary Re-examination of the twenty organisms previously isolated by Abd-El-Malek et al. (1979), using the acetylene reduction test, showed that only one isolate, identified as Bacillus sp., had the ability for reducing acetylene. Screening several hundred fresh isolates from Egyptian soil and water samples for N2-fixing ability revealed that 115 organisms were capable of repeated growth on N-deficient medium, showing nitrogen gains by the Kjeldahl analysis. Only five isolates were able to reduce acetylene under aerobic conditions. Addition of 0.01 % Difco yeast extract was essential for growth stimulation and increasing the amount of nitrogen gains by these isolates. Amounts of nitrogen fixed ranged from 4.8 to 10.5 ppm and from 9.6 to 26.7 ppm in the N-deficient medium and the N-poor medium, respectively. On the basis of morphological, cultural, and biochemical characteristics, the N2-fixing cultures were identified as two strains of Bacillus (S15/b and S77/g), two strains of Pseudomonas (S44/b and W70/n), one strain of Klebsiella (S145/m), and one strain of Micrococcus (S171/h).

Characterization of a red pigment‐antibiotic produced by Streptomyces sp. strain NRC‐C7

The streptomycete strain NRC-C 7 isolated from some Egyptian soil samples, produces a red-coloured pH indicator antibiotic active against gram positive bacteria. The producing organism belongs to the grey series of the genus Streptomyces and has grey coloured aerial mycelium with violet pigmented substrate mycelium, the violet pigment does not diffuse into the agar medium. Glucose sodium nitrate medium proved the most suitable medium for the production of this antibiotic. The pigment was extracted from the broth and purified. The solubility, Rf values, minimal inhibiting concentrations, optical rotation, UV, and IR spectra were studied. Melting point 180, elemental analysis: carbon 51.71%, hydrogen 6.25%, and oxygen 42.04%.

Biological and Chemical Determination of Available Phosphorus in Soil

A study for correlating some biological and chemical methods to determine available phosphorus as affected by some soil properties was carried out, using 30 Egyptian soil samples. The Aspergillus method appeared to be superior in the quantities of phosphorus extracted from soil, followed by the Olsen and then the Egner method. This microbiological method showed a negative highly significant correlation with CaCO3 in soil, and a positive significant one with the Egner method, but was not significantly correlated with either clay content, organic matter percent, soil pH or the Olsen method.