Egyptian Soil Research Articles

Studying the Ability of some Bacteria Isolated from Egyptian Soils to Fix Nitrogen and Solubilize Phosphate, In Vitro

Nitrogen and phosphorous are critical determinants for plant growth and productivity. Some soil bacteria can provide them in available forms to plants. These bacteria can be used as nitrogen fixers biofertilizers. In the current study, eighteen isolates of Azotobacter spp. were separated. The efficacy concentrations of the N2-fixation were examined using acetylene reduction technique, the isolates reduced acetylene at rates of 31.01 to 861.01 nmoles C2H4/ml/day. The highest lively isolate was No. AZ 14; recognized as Azotobacter beijerinckii. 8 phosphate-solubilizing bacteria (PSB) were insulated. These 8 P-solubilizing bacteria were analyzed for the tendency to solubilize P from tri-calcium phosphate in liquid Pikovskaya’s medium. The uppermost amount of free phosphorus in vigorously developing culture was 0.3652g g/100 ml after 28 days of cultivation and 0.1515g/100 ml after 7 days of cultivation on tri-calcium phosphate, correspondingly by isolate PSB 5 which was recognized as Bacillus paramycoides. Both nitrogen fixing bacteria and P-solubilizing bacteria isolates were genetically identified according to www. ncbi.nlm.nih.gov/blast data bank. The two isolates were defined according to standard morphological and biochemical tests as well as molecular tests.

Promotion of growth, yield and fiber quality attributes of Egyptian cotton by bacillus strains in combination with mineral fertilizers

Implementation of proper management practices using biological approaches is important to maintain soil quality and cotton yield in sandy desert soils of Egypt. This experiment was conducted at the Agriculture Experimental farm, Kafer El-Sheikh governorate, Cotton Research Institute of Egypt during 2016–2017 seasons to study the effect of inoculation with bacterial strains of Bacillus circulance (BC) and Bacillus megatherium (BM) and their co-inoculation in combinations with 50% and 100% of recommended dose fertilization (RDF) on growth, yield, and fiber properties of Egyptian cotton Giza-94. Results showed that all important morphological attributes of cotton such as plant growth, number of fruit sympodial branches, number of bolls per plant, boll weight, lint cotton yield and fiber properties significantly increased with the increase rate of RDF, and inoculation of cotton seeds with the bacterial strains exerted additive effects. The highest increase of cotton yield was observed at the combined use of bacterial strains BC + BM with 50% RDF followed by BC + BM with 100% RDF treatment which attributed on the cotton yield increase by 33% and 15% compared to the respective control. The application of Bacillus strains as a biofertilizer could be an alternative option to reduce considerable amounts of chemical fertilizers input by enhancing nutrient use efficiency (NUE) and, thereby, improves cotton productivity.

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.

Complete Genome Sequence of Enterococcus faecium QU50, a Thermophilic Lactic Acid Bacterium Capable of Metabolizing Xylose.

Herein, we report the complete genome sequence of Enterococcus faecium QU50, isolated from Egyptian soil and exhibiting intermediate susceptibility to vancomycin. The genome contains a 2,535,796-bp circular chromosome and two plasmids of 196,595 bp and 17,267 bp. IS1062-like sequences were not found.

In silico genomic mining reveals unexplored bioactive potential of rare actinobacteria isolated from Egyptian soil

BackgroundAntibiotic resistance occurs rapidly and naturally. However, the misuse of antibiotics is accelerating the process. And therefore, exploring new antibiotics has been a great demand in order to save people’s life. Actinobacteria have been the major source of antibiotics. In this study, we focused on rare types of actinobacteria which are hard to isolate from the environment by traditional methods. Fifty rare actinobacteria were isolated from Egyptian soils, and they were screened against some bacterial pathogens (Staphylococcus aureus ATCC 6538, Pseudomonas aeruginosa ATCC 10145, Klebsiella pneumonia CCM 4415, Streptococcus mutans ATCC 25175, Escherichia coli O157:H7 ATCC 51659, and Salmonella enterica ATCC 25566). Illumina whole genome sequencing was performed for potent isolates. The whole genomes of selected rare actinobacteria were investigated via bioinformatics analysis using neighbor-joining phylogenetic analysis and Antibiotics and Secondary Metabolite Analysis SHell.ResultsIsolates Rc5 and Ru87 showed the highest inhibition activity against selected Gram-positive and Gram-negative pathogens. Neighbor-joining phylogenetic analysis confirmed that isolate Rc5 belonged to Micromonospora oryzae and Micromonospora harpali with 73% bootstrap value while isolate Ru87 was grouped with Streptomyces gingianensis and Streptomyces morales with 89% bootstrap value. Bioinformatics analysis using antiSMASH 3.0 predicted 33 and 19 secondary metabolite gene clusters in Micromonospora sp. Rc5 and Streptomyces sp. Ru87, respectively. Gene annotation predicted the presence of valuable biosynthetic gene clusters in both strains such as polyketides, non-ribosomal peptides, terpenes, siderophores, bacteriocin, lasso peptide, ectoine, and lantipeptide.ConclusionWe concluded that exploring cryptic and novel biosynthetic gene clusters via Illumina whole genome sequencing and bioinformatics analysis is a useful method. We confirmed that Egyptian soil is very rich in high potential biosynthetic of rare actinobacteria. Further genetic engineering manipulation of biosynthetic pathways would eventually lead to producing novel bioactive molecules.

Modeling of Fertilizer Transport for Various Fertigation Scenarios under Drip Irrigation

Frequent application of nitrogen fertilizers through irrigation is likely to increase the concentration of nitrate in groundwater. In this study, the HYDRUS-2D/3D model was used to simulate fertilizer movement through the soil under surface (DI) and subsurface drip irrigation (SDI) with 10 and 20 cm emitter depths for tomato growing in three different typical and representative Egyptian soil types, namely sand, loamy sand, and sandy loam. Ammonium, nitrate, phosphorus, and potassium fertilizers were considered during simulation. Laboratory experiments were conducted to estimate the soils’ adsorption behavior. The impact of soil hydraulic properties and fertigation strategies on fertilizer distribution and use efficiency were investigated. Results showed that for DI, the percentage of nitrogen accumulated below the zone of maximum root density was 33%, 28%, and 24% for sand, loamy sand, and sandy loam soil, respectively. For SDI with 10 and 20 cm emitter depths, it was 34%, 29%, and 26%, and 44%, 37%, and 35%, respectively. Results showed that shallow emitter depth produced maximum nitrogen use efficiency varying from 27 to 37%, regardless of fertigation strategy. Therefore, subsurface drip irrigation with a shallow emitter depth is recommended for medium-textured soils. Moreover, the study showed that to reduce potential fertilizer leaching, fertilizers should be added at the beginning of irrigation events for SDI and at the end of irrigation events for DI. As nitrate uptake rate and leaching are affected by soil’s adsorption, it is important to determine the adsorption coefficient for nitrate before planting, as it will help to precisely assign application rates. This will lead to improve nutrient uptake and minimize potential leaching.

Adsorption and thermodynamic parameters of chlorantraniliprole and dinotefuran on clay loam soil with difference in particle size and pH

The behavior of chlorantraniliprole (CAP) and dinotefuran (DNF) insecticides was investigated in clay loam soil, a common type of the Egyptian soil. Effect of temperature, pH and particle size of the soil on the adsorption process was studied. Adsorption isotherm by bulk soil and its constituents; humic acid (HA), clay, silt and sand fractions was measured using batch equilibration technique. The results showed that the adsorption of the insecticides tested was significantly affected by the temperature and was a spontaneous interfacial process in the soil. Freundlich model accurately predicted the adsorption behavior of both insecticides. The interaction between soil and insecticides was endothermic and the highest adsorption for CAP and DNF was obtained at pH 9. However, the effect of pH on the adsorption of DNF was lower than that of CAP. Sorption of CAP and DNF on HA fraction was significantly greater than on clay fraction and bulk soil. In addition, the adsorption was significantly increased with particle size decrease. It could be inferred that the adsorption of CAP and DNF on clay loam soil was physical in nature and greatly influenced by the soil components, pH and temperature.

Geochemical characteristics of agricultural soils, Assiut governorate, Egypt

BackgroundThe geochemical investigation of agricultural soil is a great demand because of its help in the characterization of soil and its suitability for cultivation. The urbanization, cultivation, and industrial activities at Assiut Governorate have adversely impacted the chemical composition of soil, especially its content of heavy metals. The study area includes El-Madabgh sewage station and many big industries; cement, fertilizers, and pharmaceutical.ResultsThe Nile Valley soils are very comparable in composition and composed mainly of SiO2, Al2O3, Fe2O3, CaO, MgO, and TiO2 which represent about 88% of its chemical composition. The chemical composition gave an indication about the mineralogical assemblage of soil; quartz, clay minerals, and calcite. The results pointed to the mixed source (geogenic and anthropogenic) of Fe, Co, Cu, Ni, Zn, Zr, and Cr and the anthropogenic source of As, Pb, and Cd (especially phosphatic fertilizers) in the studied soil.ConclusionThe studied soil chemistry affected mainly by the agricultural practices (application of fertilizers, pesticides, manure, and wastewater irrigation), industrial inputs, and atmospheric deposition. Generally, the Egyptian soil needs more geochemical studies to monitor its quality and enhance of its productivity.

English

The main objective of this work was to study the effect of sulphur application and irrigation water quality on some soil properties of the calcareous, alluvial and sandy soils. A lysimeter experiment was conducted and filled with calcareous, alluvial and sandy soils to evaluate the impact of using elemental sulfur on the yields and mineral uptake of wheat plant. The experiment was cultivated with wheat plant (Triticum Vulgare L.), and irrigated by saline water (diluted sea water recording EC values of 2000, 3000 and 4000 mgl-1). The rate of sulfur applications were 0, 476 and 952 kg Sha-1. The results showed that increasing salinity to 4000 mgl-1 gradually and significantly decreased the fresh and dry weights of wheat were as follow: Sandy > alluvial > calcareous soils, and the reductions in the grain yield under the same condition were 27, 15 and 23% relative to the control for calcareous, alluvial and sandy soils, respectively. Salinity levels also significantly reduced the total uptake of NPK of all crops cultivated in different soils under study. Under sulfur application, the fresh and dry weights of wheat significantly increased relative to the control treatment. Under high salinity level 4000 ppm and high rate of sulfur (952 kg Sha-1), the increment in the crop under study and cultivated in calcareous, alluvial and sandy soils were 74, 60 and 46% for wheat grain yield, relative to the control, respectively. Also, sulfur applications significantly increased total uptake of NPK of wheat crop cultivated in different soils, especially calcareous soil. The chemical composition of soils under study after cropping showed that each of electrical conductivity (EC), sodium adsorption ratio (SAR) and soil pH increased with increasing salinity levels in the irrigation water, while, sulfur application decreased each of EC and pH and reduced SAR. Key words: Water quality, elemental sulfur, Egyptian soils, wheat.

Mineralogical and petrographical studies of agricultural soil, Assiut Governorate, Egypt

BackgroundThe lack of information about the Egyptian soil needs more attention, especially mineralogical, petrographical studies, and quality data. Thus, the aim of this study was to evaluate the physicochemical parameters of north Assiut agricultural soil; pH, moisture%, CaCO3%, organic matter (OM%), and mineralogical contents of the studied soil.ResultsThe studied soil is characterized by alkaline nature, low organic matter, and high CaCO3%. Mineralogically, the studied agricultural soil samples consist mainly of quartz, plagioclase, and minor calcite (as non-clay minerals), as well as montmorillonite, vermiculite, and illite in decreasing abundance order as clay minerals. The plagioclase consists of two minerals; calcined albite and anorthite.ConclusionThe clay minerals in the studied soils may be derived from the old alluvial plain (Plio-Pleistocene sediments) by successive Nile floods and reworking. The recorded clay minerals in the studied soils are montmorillonite, vermiculite, and illite in decreasing order of abundance. They have the ability to retain the irrigation water and adsorb more exchangeable cations in aqueous media which can feed the plants.

ISOLATION AND MOLECULAR IDENTIFICATION OF INDIGENOUS BACTERIAL ISOLATES ABLE TO DEGRADE ORGANOPHOSPHATES

The wide and indiscriminate use of pesticides for pest control in agriculture has inflicted serious harm and problems to humans as well as to the biodiversity. Microbial degradation of pesticides in contaminated soils has been considered advantageous to decontaminate areas that have been polluted by pesticides. Chlorpyrifos and diazinon were the most persistent residues in Egyptian soils. Four bacterial isolates were isolated from organophosphorus insecticides contaminated soils and genetically identified based on DNA sequence of 16s rDNA gene, Cronobacter muytjensii GH10, Achromobacter xylosoxidans GH9OP, Pseudomonas aeruginosa GH2NO8 and Pseudomonas putida GH4SNO/P were able to degrade 92.59%, 97.75%, 91.82%, and 90.78% of diazinon (600mg/l) as compared with 16.99% in control and 93.43%, 78.51%, 93.18% and 95.36% of chlorpyrifos (480mg/l) as compared with 4.28%, in control, respectively after 20 days of incubation.

The Soil Management Practices and Land Use Periods in Relation to Soil Health of Some Sandy Calcareous Soils in Egypt

The Soil Management Practices and Land Use Periods in Relation to Soil Health of Some Sandy Calcareous Soils in Egypt

Potential biosurfactant production by a promising Chaetomium madrascence AUMC 9376 isolated from Egyptian soil

Chaetomium madrascence AUMC 9376 isolated from the soil of Cairo governorate is the most promising isolate that produce biosurfactant using apple pomace as agro industrial substrates. The highest biosurfactant yield was obtained at 7 days incubation, 30oC and pH 8. Moreover, it was revealed that corn steep liquor and Tween 20 are the most suitable sources for optimal biosuractant production. The extracted biosurfactant was fractionated using HPLC resulting in 5 fractions. The purified biosurfactant has a critical micelle concentration of 120 mg/ml. The stability studies revealed that biosurfactanthas a wide range of temperature, pH, and salinity concentration. Additionally, these purified biosurfactant has a strong antimicrobial activity against E. coli, Agrobacterium tumefaciens, Pseudomonas aeruginosa, Staphylococcus aureus, Aspergillus flavus and Candida albicans. Moreover, they possess a good antioxidant activity by DPPH scavenging activity at 1.5 mg/ml.

Atrazine mineralization by Stenotrophomonas maltophilia and Agrobacterium tumefaciens Egyptian soil isolates

Atrazine mineralization by Stenotrophomonas maltophilia and Agrobacterium tumefaciens Egyptian soil isolates

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.

Architecture of the Great Pyramid of Giza Concept and Construction

Egyptian culture of the old kingdom was locally and regionally simple and efficient; belief was in the sky and humanism was regulated by Ma’at as the key concept in Egyptian mentality. IUNU was the capital of the black land KEMET where ”IUNU UNIVERSITY” is located. Physics were well studied; was already known; the right angle triangle of members 3, 4, and 5 with the 53o angle was in use. Supremacy was integrated on earth by multiple interpretations in architecture. The great pyramid of Giza was and still the best magnificent structure ever built on earth without having contemporary science’s final word been said. Massive lime stone blocks are now arranged there in a huge massive number of about two and half million pieces; their weight could reach 6.5 million tons. Conceptually there was a strong belief that symbolism connects hot spots on the Egyptian soil as it represented the known world, as well as the main stars were connected in multiple constellations on the dome of the observed sky. Pyramids of Giza plateau, Saqqara plateau, and Abusir plateau were all examples of that concept. Other pyramids of Iunu era were also related to the same concept. Structurally the Giza axis coincided on the Giza plateau. Giza plateau was a part of the Moqattam plateau during the Eocene formation. Pyramids on the worked out surface of the plateau were built with the local lime stone. Pyramids’ blocks were extracted, shaped and transported to its definite place within the precinct of the plateau. Chiseled pieces of stone - as waste from shaping blocks - were thrown out on the northern edge of the plateau. Constructional perception of what and why the Khufu pyramid took that shape shows some facts; two hundred courses composed the total existed mass where each group of courses composed a layer. Each layer started with thicker course and ended in thinner ones. Higher layers got lesser courses. So far, one should start thinking now why there were layers; why thicker and thinner courses existed. In the mean time as mortar was not in use by that time, pyramids –as in Saqqara- were formed in inclined walls, as shown in the adjacent photo. In addition, inclined walls must have formed the whole structure of Khufu pyramid.

Genetic variabilities and relationships among some egyptian Aspergillus spp. based on microscopic characters, isozyme profiles and random amplification of polymorphic DNA

Twelve Aspergillus spp. were isolated from the Egyptian soils and were studied morphologically and microscopically. Isozyme profiles and random amplified polymorphic DNA (RAPD) were also employed for determination of the genetic relationship among the tested Aspergillus spp. Results of RAPD revealed genetic similarity level above 80% between A. terreus and A. aculeatus. The species A. niger, A. candidus, A. terreus and A. aculeatus were joined with a similarity level of 65%. Unique bands were displayed by certain fungi and can be taken as a positive marker for isolate identification. Five isozyme systems; peroxidase, alcohol dehydrogenase, α esterase, β esterase and superoxide dismutase were studied to detect the genetic variabilities among the tested isolates. Subsequently, comparing the three dendrograms which belong to morphological characters, isoymes and RAPD revealed a great relationship between A. terreus and A. niveus from one side and A. candidus and A. terreus from the other side.

Effect of Crop Sequence, Compost and Plant Residues on Maize Yield Production, Sandy Soil Fertility and Reduce N-Mineral Fertilizer

Continuous population growth gives rise to food problems in developing countries, which requires enhancement in quantity and quality of agricultural products as well as reduce fertilizer use. Therefore a cropping system study was carried out to establish good agricultural practices that decrease soil degradation and building up fertility of desert soils in Egypt. Accordingly, two rotation cycles were established to investigate the effect of inclusion legume crop (pea) in the rotation compared to heavy feeder crop (potato)

Is the Partial Root Drying Irrigation Method Suitable for Sandy Soils? Field Experiment and Modelling Using the Saltmed Model

AbstractThis study investigated the impact of regulated deficit irrigation (RDI) and partial root drying (PRD) on soil moisture, dry matter, and yield and water productivity of maize grown in sandy soil in Egypt. The experiment was conducted in 2013 and included eight treatments of RDI and PRD. Four RDI treatments [100% full irrigation requirement, FI (control), 80% FI, 60% FI and 40% FI] and four PRD treatments [100% PRD, 80% PRD, 60% PRD and 40% PRD] were conducted. The experimental and simulated results using the SALTMED model showed that maize yields obtained under RDI were higher than those obtained under PRD; this may be due to the fact that the soil is sandy and the PRD treatment received relatively less irrigation water. The latter perhaps have led to a smaller and narrower wetted soil volume within the root zone, and possibly some of the water was partly lost below the root zone due to the high infiltration rate commonly associated with sandy soils. The correlation between the observed and simulated grain yield showed that the SALTMED model was able to simulate grain yield and water productivity for all treatments with high accuracy, producing an average R2 of 0.98 and 0.95, respectively. © 2018 John Wiley & Sons, Ltd.

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.