DIVERSITY OF BACILLUS GENOTYPES IN SOIL SAMPLES FROM EL-OMAYED BIOSPHERE RESERVE IN EGYPT

Sequencing of the 16S rDNA hypervariant region was applied to determine the presence and composition of Bacillus species in 40 soil samples randomly collected from different habitats in El-Omayed biosphere reserve, Egypt. Although purified cultures showed 18 different phenotypes that were morphologically distinct on a sporulation medium plate, only 4 different nucleotide sequences designated Seq A, B, C and D were revealed. Computational analysis of DNA sequence data suggested that 17 of these isolates are closely related members of the Bacillus cereus/thuringiensis group (Seq B, C and D) and one isolate is belonging to the Bacillus subtilis group (Seq A). Further phenotypic investigations confirmed the diversity of the 17 novel Bacillus cereus/thuringiensis isolates and indicated that the new Bacillus subtilis group isolate is a Bacillus amyloliquefaciens strain. A simple phenotypic discrimination key that can be applied for distinguishing between such closely related Bacillus cereus/thuringiensis members is presented

Conversion of Uric Acid into Ammonium in Oil-Degrading Marine Microbial Communities: a Possible Role of Halomonads

Uric acid is a promising hydrophobic nitrogen source for biostimulation of microbial activities in oil-impacted marine environments. This study investigated metabolic processes and microbial community changes in a series of microcosms using sediment from the Mediterranean and the Red Sea amended with ammonium and uric acid. Respiration, emulsification, ammonium and protein concentration measurements suggested a rapid production of ammonium from uric acid accompanied by the development of microbial communities containing hydrocarbonoclastic bacteria after 3 weeks of incubation. About 80 % of uric acid was converted to ammonium within the first few days of the experiment. Microbial population dynamics were investigated by Ribosomal Intergenic Spacer Analysis and Illumina sequencing as well as by culture-based techniques. Resulting data indicated that strains related to Halomonas spp. converted uric acid into ammonium, which stimulated growth of microbial consortia dominated by Alcanivorax spp. and Pseudomonas spp. Several strains of Halomonas spp. were isolated on uric acid as the sole carbon source showed location specificity. These results point towards a possible role of halomonads in the conversion of uric acid to ammonium utilized by hydrocarbonoclastic bacteria.With exception of XH and JC, all authors were supported by the FP7 Project ULIXES (FP7-KBBE-2010-266473). This work was further funded by grant BIO2011-25012 from the Spanish Ministry of the Economy and Competitiveness. FM was supported by Università degli Studi di Milano, European Social Fund (FSE) and Regione Lombardia (contract BDote Ricerca^). DD acknowledges support of KAUST, King Abdullah University of Science and Technology. PG acknowledges the support of the European Commission through the project Kill-Spill (FP7, Contract Nr 312139).Peer Reviewe

Bacterial Diversity and Bioremediation Potential of the Highly Contaminated Marine Sediments at El-Max District (Egypt, Mediterranean Sea)

Coastal environments worldwide are threatened by the effects of pollution, a risk particularly high in semienclosed basins like the Mediterranean Sea that is poorly studied from bioremediation potential perspective especially in the Southern coast. Here, we investigated the physical, chemical, and microbiological features of hydrocarbon and heavy metals contaminated sediments collected at El-Max bay (Egypt). Molecular and statistical approaches assessing the structure of the sediment-dwelling bacterial communities showed correlations between the composition of bacterial assemblages and the associated environmental parameters. Fifty strains were isolated on mineral media supplemented by 1% crude oil and identified as a diverse range of hydrocarbon-degrading bacteria involved in different successional stages of biodegradation. We screened the collection for biotechnological potential studying biosurfactant production, biofilm formation, and the capability to utilize different hydrocarbons. Some strains were able to grow on multiple hydrocarbons as unique carbon source and presented biosurfactant-like activities and/or capacity to form biofilm and owned genes involved in different detoxification/degradation processes. El-Max sediments represent a promising reservoir of novel bacterial strains adapted to high hydrocarbon contamination loads. The potential of the strains for exploitation for in situ intervention to combat pollution in coastal areas is discussed

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Effective multi-functional biotechnological applications of protease/keratinase enzyme produced by new Egyptian isolate (Laceyella sacchari YNDH)

Abstract Background Due to a multitude of industrial applications of keratinolytic proteases, their demands are increasing. The present investigation studied the production and monitoring of the most possible multi-functional applications of YNDH thermoalkaline keratin-degrading enzyme. Results This work is considered the first that reported YNDH strain closely related to Laceyella sacchari strain; YNDH is a producer of protease/keratinase enzyme and able to degrade natural keratin such as feathers, wool, human hairs, and nails. Experimental design Plackett-Burman (PBD) was applied to evaluate culture conditions affecting the production of thermoalkaline protease/keratinase. Afterwards, Box-Behnken design (BBD) was applied to find out the optimum level of significant variables namely, NH4Cl, yeast extract, and NaNO3 with a predicted activity of 1324.7 U/ml. Accordingly, the following medium composition and parameters were calculated to be optimum (%w/v): NH4Cl, 0.08; feather, 1; yeast extract, 0.04; MgSO4.7H2O, 0.02; NaNO3, 0.016; KH2PO4, 0.01; K2HPO4, 0.01; pH, 8; inoculum size; 5%, cultivation temperature (Temp.) 45 °C and incubation time 48 h. The studied enzyme can degrade keratin-azure, remove proteinaceous materials, and is able to remove hairs from goat hides. These interesting characteristics make this enzyme a good candidate in many applications especially in detergent (Det.), in leather industries, and in pharmaceuticals particularly in nail treatment. Conclusion The promising properties of the newly keratin-degrading protease enzyme from Laceyella sacchari strain YNDH would underpin its efficient exploitation in several industries to cope with the demands of worldwide enzyme markets

Superior anti-pulmonary viral potential of Natrialba sp. M6-producing surfactin and C50 carotenoid pigment with unveiling its action modes

Abstract Background Respiratory viruses, particularly adenoviruses (ADV), influenza A virus (e.g., H1N1), and coronaviruses (e.g., HCoV-229E and SARS-CoV-2) pose a global public health problem. Therefore, developing natural wide-spectrum antiviral compounds for disrupting the viral life cycle with antioxidant activity provides an efficient treatment approach. Herein, biosurfactant (Sur) and C50 carotenoid pigment (Pig) of haloalkaliphilic archaeon Natrialba sp. M6 which exhibited potent efficacy against hepatitis and anti-herpes simplex viruses, were investigated against pulmonary viruses. Methods The cytotoxicity of the extracted Sur and Pig was examined on susceptible cell lines for ADV, HIN1, HCoV-229E, and SARS-CoV-2. Their potential against the cytopathic activity of these viruses was detected with investigating the action modes (including, virucidal, anti-adsorption, and anti-replication), unveiling the main mechanisms, and using molecular docking analysis. Radical scavenging activity was determined and HPLC analysis for potent extract (Sur) was performed. Results All current investigations stated higher anti-pulmonary viruses of Sur than Pig via mainly virucidal and/or anti-replicative modes. Moreover, Sur had stronger ADV’s capsid protein binding, ADV’s DNA polymerase inhibition, suppressing hemagglutinin and neuraminidase of H1N1, and inhibiting chymotrypsin-like (3CL) protease of SARS-CoV-2, supporting with in-silico analysis, as well as radical scavenging activity than Pig. HPLC analysis of Sur confirmed the predominate presence of surfactin in it. Conclusion This study declared the promising efficacy of Sur as an efficient pharmacological treatment option for these pulmonary viruses and considered as guide for further in vivo research

Diversity of Bacillus genotypes in soil samples from El-Omayed Biosphere Reserve in Egypt

Sequencing of the 16S rDNA hypervariant region was applied to determine the presence and composition of Bacillus species in 40 soil samples randomly collected from different habitats in El-Omayed biosphere reserve, Egypt. Although purified cultures showed 18 different phenotypes that were morphologically distinct on a sporulation medium plate, only 4 different nucleotide sequences designated Seq A, B, C and D were revealed. Computational analysis of DNA sequence data suggested that 17 of these isolates are closely related members of the Bacillus cereus/thuringiensis group (Seq B, C and D) and one isolate is belonging to the Bacillus subtilis group (Seq A). Further phenotypic investigations confirmed the diversity of the 17 novel Bacillus cereus/thuringiensis isolates and indicated that the new Bacillus subtilis group isolate is a Bacillus amyloliquefaciens strain. A simple phenotypic discrimination key that can be applied for distinguishing between such closely related Bacillus cereus/thuringiensis members is presented

Production, Purification, and Characterization of Thermostable α-Amylase Produced by Bacillus licheniformis Isolate AI20

An optimization strategy, based on statistical experimental design, is employed to enhance the production of thermostable α-amylase by a thermotolerant B. licheniformis AI20 isolate. Using one variant at time (OVAT) method, starch, yeast extract, and CaCl2 were observed to influence the enzyme production significantly. Thereafter, the response surface methodology (RSM) was adopted to acquire the best process conditions among the selected variables, where a three-level Box-Behnken design was employed to create a polynomial quadratic model correlating the relationship between the three variables and α-amylase activity. The optimal combination of the major constituents of media for α-amylase production was 1.0% starch, 0.75% yeast extract, and 0.02% CaCl2. The predicted optimum α-amylase activity was 384 U/mL/min, which is two folds more than the basal medium conditions. The produced α-amylase was purified through various chromatographic techniques. The estimated enzyme molecular mass was 55 kDa and the α-amylase had an optimal temperature and pH of 60–80°C and 6–7.5, respectively. Values of Vmax and Km for the purified enzyme were 454 mU/mg and 0.709 mg/mL. The α-amylase enzyme showed great stability against different solvents. Additionally, the enzyme activity was slightly inhibited by detergents, sodium dodecyl sulphate (SDS), or chelating agents such as EDTA and EGTA. On the other hand, great enzyme stability against different divalent metal ions was observed at 0.1 mM concentration, but 10 mM of Cu2+ or Zn2+ reduced the enzyme activity by 25 and 55%, respectively

Industrial Bioprocessing Strategies for Cultivation of Local Streptomyces violaceoruber Strain SYA3 to Fabricate Nano-ZnO as Anti-Phytopathogens Agent

Recently, applying industrial bio-processing strategies are being a promised tool that used to produce large quantities of bioactive metabolites from different microbial cells. So in this study, the statistical experimental designs (Plackett–Burman and Box–Behnken) were used for optimization of local S. violaceoruber SYA3 biomass production (18g/l) and fabrication the highest nano-ZnO mass weight (15g/l). Since the nano-ZnO was fabricated by using the extracted periplasmic metabolites as a reducing agent and Zn(NO3 ) 2 .6 H2 O as a precursor. The morphological properties and size of the nano-ZnO were evaluated using SEM and TEM analysis. Large-scale production was studied via batch fermentation mode using semi-industrial scale bioreactor (8.9L). The biomass production and the fabricated nano-ZnO was (22.8g/l) and (56.8g/l), respectively. Finally, this work reported developing a new cheap and eco-friendly nano-ZnO fabrication method and applying nano-ZnO as a strong anti-phytopathogens agent