Wael S. El-Sayed

Isolation and identification of a novel strain of the genus Ochrobactrum with phenol-degrading activity

A bacterial strain AS1 belonging to the genus Ochrobactrum, was isolated from an enriched phenol-activated sludge in Egypt. This strain grew aerobically on phenol as the sole carbon source using the meta-cleavage pathway at high phenol-degrading rates compared with those in a previous report.

Isolation and Characterization of Phenol-catabolizing Bacteria from a Coking Plant

New phenol degrading bacteria with high biodegradation activity and high tolerance were isolated as Burkholderia cepacia PW3 and Pseudomonas aeruginosa AT2. Both isolates could grow aerobically on phenol as a sole carbon source even at 3 g/l. The whole-cell kinetic properties for phenol degradation by strains PW3 and AT2 showed a Vmax of 0.321 and 0.253 mg/l/min/(mg protein), respectively. The metabolic pathways for phenol biodegradation in both strains were assigned to the meta-cleavage activity of catechol 2,3-dioxygenase.

In vitro antagonistic activity, plant growth promoting traits and phylogenetic affiliation of rhizobacteria associated with wild plants grown in arid soil

The role of plant growth-promoting rhizobacteria (PGPR) in adaptation of plants in extreme environments is not yet completely understood. For this study native bacteria were isolated from rhizospeheric arid soils and evaluated for both growth-promoting abilities and antagonistic potential against phytopathogenic fungi and nematodes. The phylogentic affiliation of these representative isolates was also characterized. Rhizobacteria associated with 11 wild plant species from the arid soil of Almadinah Almunawarah, Kingdom of Saudi Arabia (KSA) were investigated. From a total of 531 isolates, only 66 bacterial isolates were selected based on their ability to inhibit Fusarium oxysporum, and Sclerotinia sclerotiorum. The selected isolates were screened in vitro for activities related to plant nutrition and plant growth regulation as well as for antifungal and nematicidal traits. Isolated bacteria were found to exhibit capabilities in fix atmospheric nitrogen, produce ammonia, indoleacetic acid (IAA), siderophores, solubilize phosphate and zinc, and showed an antagonistic potential against some phytopathogenic fungi and one nematode species (Meloidogyne incognita) to various extent. Isolates were ranked by their potential ability to function as PGPR. The 66 isolates were genotyped using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequence analysis. The taxonomic composition of the representative genotypes from both rhizosphere and rhizoplane comprised Bacillus, Enterobacter and Pseudomonas. Out of the 10 genotypes, three strains designated as PHP03, CCP05, and TAP02 might be regarded as novel strains based on their low similarity percentages and high bootstrap values. The present study clearly identified specific traits in the isolated rhizobacteria, which make them good candidates as PGPR and might contribute to plant adaption to arid environments. Application of such results in agricultural fields may improve and enhance plant growth in arid soils.

New eco-friendly 1-alkyl-3-(4-phenoxybutyl) imidazolium-based ionic liquids derivatives: a green ultrasound-assisted synthesis, characterization, antibacterial activity and POM analyses.

In view of the emerging importance of the ILs as “green” materials with wide applications and our general interests in green processes, a series of a twenty five new 1-alkyl-3-(4-phenoxybutyl) imidazolium-based ionic liquids (ILs) derivatives is synthesized using a facile and green ultrasound-assisted procedure. Their structures were characterized by FT-IR, 1H-NMR, 13C-NMR, 11B, 19F, 31P, and mass spectrometry. Antimicrobial screens of some selected ILs were conducted against a panel of Gram-positive and Gram-negative bacteria. The antimicrobial activity of each compound was measured by determination of the minimal inhibitory concentration (MIC) yielding very interesting and promising results. Their antibacterial activities are reported, and, on the basis of the experimental and virtual POM screening data available, attempt is also made to elucidate the structure activity relationship.

Bacterial Degradation of the Saturate Fraction of Arabian Light Crude oil: Biosurfactant Production and the Effect of ZnO Nanoparticles

The aim of this research was to study the influence of nanoparticles and the initial oil amount on the biodegradation of crude oil. Production of biosurfactants was also assessed. Crude oil-utilizing bacteria were isolated from oilfields via enrichment in chemically defined medium with crude oil a sole carbon source. The isolates could be affiliated to the genera Bacillus, Pseudomonas, Achromobacter, and Microbacterium by 16S rDNA sequencing and phylogenetic analysis. GC/FID analysis revealed 52 to 98% degradation of the oil saturate fraction within one month. Nanoparticles of ZnO inhibited growth and crude oil biodegradation by one isolate. (NBHCO4). Two strains, NBHCO2 and NCEOW, emulsified and utilized water-in-oil emulsions (chocolate mousse). Two bacterial strains, I-19 and NBHCO2 grew with crude oil in cultures containing up to 20% oil. Degradation extent in the I-19 culture increased as the oil amount increased. On the contrary, the NBHCO2 culture exhibited a decrease in degradation extent as the oil amount increased. Biosurfactant production in only one crude oil culture (I-19) could be confirmed by the observed reduction in surface tension. Some isolates produced biosurfactants from water-soluble substrates such as glucose. The NBHCO2 strain produced a lipopeptide biosurfactant which reduced the surface tension of the growth medium from 72 to 27mN/m. A gene of catechol dioxygenase was detected in the I-19, NBHCO4, and NCEOW isolates. In conclusion, metal oxide nanoparticles can interfere with crude oil biodegradation. Biosurfactants are not necessarily a prerequisite for crude oil biodegradation. The initial oil amount is a significant determinant of oil biodegradability. The isolates can by applied for bioaugmentation of petroleum-polluted soil and biosurfactants production.

Deterioration to extinction of wastewater bacteria by non-thermal atmospheric pressure air plasma as assessed by 16S rDNA-DGGE fingerprinting

The use of cold plasma jets for inactivation of a variety of microorganisms has recently been evaluated via culture-based methods. Accordingly, elucidation of the role of cold plasma in decontamination would be inaccurate because most microbial populations within a system remain unexplored owing to the high amount of yet uncultured bacteria. The impact of cold atmospheric plasma on the bacterial community structure of wastewater from two different industries was investigated by metagenomic-based polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) utilizing 16S rRNA genes. Three doses of atmospheric pressure dielectric barrier discharge plasma were applied to wastewater samples on different time scales. DGGE revealed that the bacterial community gradually changed and overall abundance decreased to extinction upon plasma treatment. The bacterial community in food processing wastewater contained 11 key operational taxonomic units that remained almost completely unchanged when exposed to plasma irradiation at 75.5 mA for 30 or 60 s. However, when exposure time was extended to 90 s, only Escherichia coli, Coliforms, Aeromonas sp., Vibrio sp., and Pseudomonas putida survived. Only E. coli, Aeromonas sp., Vibrio sp., and P. putida survived treatment at 81.94 mA for 90 s. Conversely, all bacterial groups were completely eliminated by treatment at 85.34 mA for either 60 or 90 s. Dominant bacterial groups in leather processing wastewater also changed greatly upon exposure to plasma at 75.5 mA for 30 or 60 s, with Enterobacter aerogenes, Klebsiella sp., Pseudomonas stutzeri, and Acidithiobacillus ferrooxidans being sensitive to and eliminated from the community. At 90 s of exposure, all groups were affected except for Pseudomonas sp. and Citrobacter freundii. The same trend was observed for treatment at 81.94 mA. The variability in bacterial community response to different plasma treatment protocols revealed that plasma had a selective impact on bacterial community structure at lower doses and potential bactericidal effects at higher doses.

Diversity and phylogenetic analysis of endosymbiotic bacteria of the date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae)

BackgroundThe date palm root borer Oryctes agamemnon (Coleoptera: Scarabaeidae) is one of the major pests of palms. In Saudi Arabia, both larvae and adults of Oryctes are particularly troublesome, especially during the establishment of young date palm orchards. Endosymbiotic bacteria are known to have a key role in food digestion and insecticide resistance mechanisms, and therefore are essential to their host insect. Identification of these bacteria in their insect host can lead to development of new insect pest control strategies.ResultsMetagenomic DNA from larval midgut of the date palm root borer, O. agamemnon, was analyzed for endosymbiotic bacterial communities using denatured gradient gel electrophoresis (DGGE) utilizing 16S rRNA genes. The DGGE fingerprints with metagenomic DNA showed predominance of eleven major operational taxonomic units (OTUs) identified as members of Photobacterium, Vibrio, Allomonas, Shewanella, Cellulomonas, and Citrobacter, as well as uncultured bacteria, including some uncultured Vibrio members. DGGE profiles also showed shifts in the dominant bacterial populations of the original soil compared with those that existed in the larval midguts. The endosymbiotic bacterial community was dominated by members of the family Vibrionaceae (54.5%), followed by uncultured bacteria (18.2%), Enterobacteriaceae (9.1%), Shewanellaceae (9.1%), and Cellulomonadaceae (9.1%). Phylogenetic studies confirmed the affiliation of the dominant OTUs into specified families revealed by clustering of each phylotype to its corresponding clade. Relative frequency of each phylotype in larval midguts revealed predominance of Vibrio furnisii and Vibrio navarrensis, followed by uncultured bacterial spp., then Cellulomonas hominis, Shewanella algae, and Citrobacter freundii.ConclusionAnalysis of metagenomic DNA for endosymbiotic bacterial communities from the midgut of Oryctes larvae showed strong selection of specific bacterial populations that may have a key role in digestion, as well as other benefits to the larvae of O. agamemnon. Determination of the distinct endosymbiotic community structure and its possible biological functions within the insect could provide us with basic information for future pest control research.

Lecithinase-producing bacteria in commercial and home-made foods: Evaluation of toxic properties and identification of potent producers

Abstract The aim of this study was to determine bacterial contamination in 28 refrigerated and unrefrigerated, commercial and home-made food items in Al Madinah Al Munawarah, Saudi Arabia. Of the 60 bacterial strains isolated, 53 were recovered from food samples refrigerated for 7 days and 7 from fresh, unrefrigerated food. The isolated bacteria were screened for lecithinase enzyme (toxin) production by the cup plate clearing zone technique. All isolates were positive on the basis of their ability to grow aerobically on egg yolk agar, giving black colonies as a characteristic feature of lecithinase production and opaque zones with diameters of 4–27 mm. Isolates were categorized into low, moderate and high lecithinase producers. Potent lecithinase-producing strains isolated from refrigerated green pepper (PS1) and lettuce (LS1) had a remarkably large zone measuring 27 ± 1.9 mm. All isolates also had additional toxic properties, including caseinase and haemolytic activities. Genotypic characterization by amplified ribosomal DNA restriction analysis showed that strains PS1 and LS1 were from same genus. Phenotypic characterization with biochemical tests and the Phoenix identification system suggested their affiliation to the Bacillus group. 16S rDNA sequence analysis of both strains showed them to be Bacillus cereus, with 99% sequence similarity to B. cereus strain J8B-67.

Molecular characterization of the alpha subunit of multicomponent phenol hydroxylase from 4-chlorophenol-degrading Pseudomonas sp. strain PT3

Multicomponent phenol hydroxylases (mPHs) are diiron enzymes that use molecular oxygen to hydroxylate a variety of phenolic compounds. The DNA sequence of the alpha subunit (large subunit) of mPH from 4-chlorophenol (4-CP)-degrading bacterial strain PT3 was determined. Strain PT3 was isolated from oil-contaminated soil samples adjacent to automobile workshops and oil stations after enrichment and establishment of a chlorophenol-degrading consortium. Strain PT3 was identified as a member of Pseudomonas sp. based on sequence analysis of the 16S rRNA gene fragment. The 4-CP catabolic pathway by strain PT3 was tentatively proposed to proceed via a meta-cleavage pathway after hydroxylation to the corresponding chlorocatechol. This hypothesis was supported by polymerase chain reaction (PCR) detection of the LmPH encoding sequence and UV/VIS spectrophotometric analysis of the culture filtrate showing accumulation of 5-chloro-2-hydroxymuconic semialdehyde (5-CHMS) with λmax 380. The detection of catabolic genes involved in 4-CP degradation by PCR showed the presence of both mPH and catechol 2,3-dioxygenase (C23DO). Nucleotide sequence analysis of the alpha subunit of mPH from strain PT3 revealed specific phylogenetic grouping to known mPH. The metal coordination encoding regions from strain PT3 were found to be conserved with those from the homologous dinuclear oxo-iron bacterial monooxygenases. Two DE(D)XRH motifs was detected in LmPH of strain PT3 within an approximate 100 amino acid interval, a typical arrangement characteristic of most known PHs.

Microwave-Assisted Synthesis of Some Potential Bioactive Imidazolium-Based Room-Temperature Ionic Liquids

An environmentally-friendly and easy synthesis of a series of novel functionalized imidazolium-based ionic liquids (ILs) is described under both the conventional procedure and microwave irradiation. The structures of newly synthesized room-temperature ionic liquids (RTILs) were established by different spectral analyses. All ILs (1–14) were screened for their in vitro antimicrobial activity against a panel of clinically isolated bacteria. The results of the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) showed that some of the tested ILs are very promising anti-bacterial agents especially those containing an alkyl chain with a phenyl group (most notably 1, 2, 12, and 13).