Abdelhadi Abdallah Abdelhadi

Climate change is intensifying soil salinization, posing a major threat to crop establishment and productivity, particularly in arid and semi-arid regions. Barley (Hordeum vulgare L.), one of the most salt-tolerant cereals, offers valuable genetic resources for improving salinity resilience at early growth stages. This study exploited the genetic diversity of the Nested Association Mapping (NAM) population Halle Exotic Barley-25 (HEB-25) to dissect salinity tolerance during germination and seedling developmental stages. First, the HEB-25 parental lines (25 wild barley genotypes and cv. Barke) were evaluated under salinity treatment to identify contrasting responses. Based on this screening, four HEB families (01, 04, 09, and 22) were selected out of 25 HEB families for detailed phenotypic and genomic analysis. Seeds of the selected HEB families were subjected to 40% seawater salinity stress and control treatments to assess germination percentage and seedling traits, including shoot length, root length, fresh weight (FW), dry weight (DW), DW/FW ratio, root–shoot ratio, and salt tolerance index (STI). Substantial variation was observed among families for all measured traits under salinity stress. STI values enabled clear differentiation among families: Family 01 exhibited the most consistent overall tolerance profile, Family 22 showed the strongest sensitivity in biomass traits, and Family 04 displayed a trait-specific response with sensitivity at the family-mean level but exceptional within-family diversity, harboring some of the highest individual TI values across the population. A genome-wide association study was conducted using 32,995 SNP markers. A total of 27 significant SNPs were identified, corresponding to 20 quantitative trait loci (QTLs). Of these, 12 QTLs were detected under control conditions, 16 under seawater treatment, and 21 based on tolerance indices, indicating both constitutive and stress-responsive genetic effects. Gene annotation within these regions revealed approximately 23 candidate genes associated with abiotic stress tolerance, including genes involved in ion transport, osmotic adjustment, kinases and stress signaling pathways. HEB_22_003, HEB_04_087, and HEB_01_013 represent the most promising genotypes for salinity breeding. These findings highlight the effectiveness of combining precise phenotyping with high-resolution genomic analysis in the HEB-25 population to uncover the genetic architecture of salinity tolerance at early developmental stages. We identified 20 salinity-responsive QTLs, including five major-effect loci on chromosomes 2H, 4H, 5H, and 7H that consistently explained the largest share of phenotypic variation. These loci co-localized with candidate genes linked to ion homeostasis, Ca²⁺-mediated signaling, protein glycosylation, epigenetic regulation, and root system plasticity, revealing key mechanisms underlying early-stage salt adaptation in barley. The strong and contrasting responses of Family 01 and Family 04 provide an excellent genetic framework for functional validation of tolerance alleles. Collectively, these genomic resources establish a robust foundation for QTL pyramiding, marker-assisted breeding, and the development of climate-resilient barley cultivars for saline agroecosystems.

Whole-genome sequencing (WGS) of microbial isolates is a valuable tool for mapping the genomes of novel organisms and is helpful for understanding plant-bacteria interactions. The close relationships between bacteria and plants are essential for maintaining healthy ecosystems, whether the bacteria reside the plant or in the rhizosphere surrounding its roots. In this study, isolation, characterization, and WGS were performed to identify promising plant growth-promoting rhizobacteria (PGPR) using the rhizospheric soil sample of jatropha tree roots. Out of 100 isolates, six (FACU 2024, 2, 3, 4, 5, and 6) exhibited phosphate-solubilizing bacteria (PSB) traits, including solubilizing phosphate and producing indole acetic acid (IAA), and the ability of other plant growth-promoting (PGP) traits was tested. Isolate FACU 2024 exhibited the highest values for IAA production (12.1 µg/ml), soluble phosphate release (300 µg/ml), and phosphate solubilization index (6.7). Therefore, FACU 2024 was molecularly identified as Escherichia coli. The WGS analysis revealed that E. coli FACU 2024 possesses one chromosome and one plasmid with a total length of 4.8 Mb and were submitted on GenBank under accession numbers CP147009 and CP147010. The bacterial genome contained about 142 PGP genes, ranging from 258 to 3744 bp and associated with phosphate solubilization, siderophore production, indole acetic acid (IAA) production, nitrogen metabolism, nitrogen fixation, and nitrite/nitrate reduction. Moreover, genomic islands (GIs) were enriched with genes associated with horizontal gene transfer (HGT), stress response, and environmental adaptation, and prophage analyses were carried out. In addition, 15 heavy metal resistance genes were annotated, such as those for As, Cd, Zn, Pb, Cu, Fe, and Co, ranging from 426 to 2505 bp. This study provides the first comprehensive genetic evidence linking E. coli to key PGPR traits alongside genes conferring resistance to multiple heavy metals. This strain demonstrates potential as a PGPR in addition to heavy metal bioremediation.

Industrial workplaces, particularly those involved in ore processing or smelting, pose a high risk of exposure to cadmium, a highly toxic metal. This study isolated and identified eight cadmium-resistant strains from industrial wastewater for their ability to resist cadmium. Enterobacter roggenkampii FACU2 demonstrated exceptional cadmium removal capabilities during our analysis, successfully eliminating 62% of the cadmium. Additionally, transmission electron microscopy (TEM) was utilized to examine the morphological change between the most and least efficient strains that responded to cadmium stress at the cellular level. Compared to the control bacteria, the treated bacteria exhibited notably higher levels of cadmium adsorption and accumulation within their cells. A complete genome analysis revealed that E. roggenkampii FACU2 has one chromosome and one plasmid with a size of 4,856,454 bp and 80,926 bp, respectively, in addition to harboring numerous heavy metal-resistant genes related to cadmium and other heavy metals. Moreover, the gene expression of four cadmium-resistant genes (czcA, cadA, czcC and czcD) showed that the high cadmium concentration led to a significant increase in czcA and cadA mRNA levels, thus indicating the activation of cadmium-resistant genes in the E. roggenkampii FACU2 compared to Enterobacter sp. strain FACU. Due to its ability to remove cadmium and other heavy metals, this strain holds promise as a source of genes for biological treatment methods. This application could contribute to environmental purification, ultimately benefiting human health.

Many organisms have adapted to survive in environments with high levels of arsenic (As), a naturally occurring metalloid with various oxidation states and a common element in human activities. These organisms employ diverse mechanisms to resist the harmful effects of arsenic compounds. Ten arsenic-resistant bacteria were isolated from contaminated wastewater in this study. The most efficient bacterial isolate able to resist 15,000 ppm Na₂HAsO₄·7H₂O was identified using the 16S rRNA gene and whole genome analysis as Enterobacter cloacae FACU. The arsenic E. cloacae FACU biosorption capability was analyzed. To further unravel the genetic determinants of As stress resistance, the whole genome sequence of E. cloacae FACU was performed. The FACU complete genome sequence consists of one chromosome (5.7 Mb) and two plasmids, pENCL 1 and pENCL 2 (755,058 and 1155666 bp, respectively). 7152 CDSs were identified in the E. cloacae FACU genome. The genome consists of 130 genes for tRNA and 21 for rRNAs. The average G + C content was found to be 54%. Sequencing analysis annotated 58 genes related to resistance to many heavy metals, including 16 genes involved in arsenic efflux transporter and arsenic reduction (five arsRDABC genes) and 42 genes related to lead, zinc, mercury, nickel, silver, copper, cadmium and chromium in FACU. Scanning electron microscopy (SEM) confirmed the difference between the morphological responses of the As-treated FACU compared to the control strain. The study highlights the genes involved in the mechanism of As stress resistance, metabolic pathways, and potential activity of E. cloacae FACU at the genetic level.

The rapid industrial revolution significantly increased heavy metal pollution, becoming a major global environmental concern. This pollution is considered as one of the most harmful and toxic threats to all environmental components (air, soil, water, animals, and plants until reaching to human). Therefore, scientists try to find a promising and eco-friendly technique to solve this problem i.e., bacterial bioremediation. Various heavy metal resistance mechanisms were reported. Omics technologies can significantly improve our understanding of heavy metal resistant bacteria and their communities. They are a potent tool for investigating the adaptation processes of microbes in severe conditions. These omics methods provide unique benefits for investigating metabolic alterations, microbial diversity, and mechanisms of resistance of individual strains or communities to harsh conditions. Starting with genome sequencing which provides us with complete and comprehensive insight into the resistance mechanism of heavy metal resistant bacteria. Moreover, genome sequencing facilitates the opportunities to identify specific metal resistance genes, operons, and regulatory elements in the genomes of individual bacteria, understand the genetic mechanisms and variations responsible for heavy metal resistance within and between bacterial species in addition to the transcriptome, proteome that obtain the real expressed genes. Moreover, at the community level, metagenome, meta transcriptome and meta proteome participate in understanding the microbial interactive network potentially novel metabolic pathways, enzymes and gene species can all be found using these methods. This review presents the state of the art and anticipated developments in the use of omics technologies in the investigation of microbes used for heavy metal bioremediation.

Sustainable agriculture is essential to attain food security and address increasing climate change concerns. Population, abiotic and biotic stresses and limited agricultural water supplies and land are important barriers to cereal crops production, in addition to extreme weather. These factors influence their quality and productivity. Therefore, there is a pressing need for effective methods of food production under these conditions. For many individuals in low- and middle-income nations, cereals represent a key food source. Developing cereal crops with enhanced flexibility, high yields, and the ability to tolerate these biotic and abiotic problems is therefore essential. Modern OMICS techniques, next-generation sequencing, bioinformatics tools and the most recent improvements in genome editing tools (GET) have made targeted mutagenesis conceivable. By altering a crop variety's endogenous genome, which is free of any foreign genes, genome editing (GE) enhances the crop variety. Therefore, crops that have undergone GE but have not integrated foreign genes are not considered genetically modified organisms (GMOs) in a number of countries. GE is being used by researchers to promote the nutritional value of cereal crops and increase their tolerance to biotic and abiotic stresses. This review critically discusses the activities of GET, the role of bioinformatics tools and its application to sustainable agriculture for cereal crops.

This study was carried out to identify the relationship between miRNAs/ targets and phytohormone-related genes associated with Rhizophagus irregularis/ F. oxysporum f. sp. lycopersici (Fol) interaction through post-infection of tomato roots at different stages. Furthermore, to address the role of miRNA-mediated families in regulating plant hormone crosstalk during plant-microbe interactions, including salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), auxin (AUX) and 5 ethylene (ET). In this study, Expression levels of ethylene-responsive genes reflect antagonism between arbuscular mycorrhizal fungi (AMF) and ET, re-modulating immunoregulatory capacity in tomato. On the other hand, our data reinforce that overexpression of AP2 and ERF1 delay senescence in Fol-infected tomato plants by downregulating the expression level of SPL3. Moreover, a balance between TCP4, miR164, and miR319b transcript levels suggests that their interaction attenuates senescence under AMF infection. Measurements of phytohormone production under AMF/Fol infection at 30 days post-inoculation (dpi) showed significantly lower hormone production in the resistant genotype (Heinz 'Hz') compared to the susceptible genotype (Castle Rock 'CR') by 36, 17, and 14% for ET, ABA, and JA, respectively. These findings potentially imply that modifications in Heinz’s hormonal signaling are prompting host changes, which lead to decreased phytohormone levels. This study provides an applied basis for further research on the molecular mechanism and challenges associated with the continuous cropping of tomato by R. irregulari under the deleterious effects of Fusarium on late stages of root infection.

The phenylurea herbicides are persistent in soil and water, necessitating the creation of methods for removing them from the environment. This study aimed to examine the soil microbial diversity, searching for local bacterial isolates able to efficiently degrade the phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1, 1-dimethylurea (IPU). The best isolates able to effectively degrade IPU were selected, characterized, and identified as Pseudomonas putida and Acinetobacter johnsonii. The catechol 1, 2-dioxygenase enzyme's catA gene was amplified, cloned, and expressed in E. coli M15. The Expressed E. coli showed high degradation efficiency (44.80%) as analyzed by HPLC after 15 days of inoculation in comparison to P. putida (21.60%). The expression of the catA gene in P. putida and expressed E. coli was measured using quantitative polymerase chain reaction (qPCR). The results displayed a significant increase in the mRNA levels of the catA gene by increasing the incubation time with IPU. Hydrophilic interaction chromatography (HILIC) mass spectrometry analysis revealed that three intermediate metabolites, 1-(4-isopropylphenyl)-3-methylurea (MDIPU), 4-Isopropylaniline (4-IA) and 1-(4-isopropylphenyl) urea (DDIPU) were generated by both P. putida and expressed E. coli. In addition, IPU-induced catA activity was detected in both P. putida and expressed E. coli. The supernatant of both P. putida and expressed E. coli had a significant influence on weed growth. The study clearly exhibited that P. putida and expressed E. coli were capable of metabolizing IPU influentially and thus could be utilized for bioremediation and biodegradation technology development.

Background: Arterial catheters are frequently needed to optimize the intensive care in the sick newborn. Umbilical Arterial Catheters (UAC) is more popular than peripheral arterial catheterization. They are utilized to provide continuous accurate arterial blood pressure monitoring, frequent assessment of gas exchange efficiency, frequent blood sampling and rarely for exchange blood transfusion. Umbilical Arterial Catheters may be used in emergencies to infuse fluids or medications in the absence of venous access. Malposition of the Umbilical Arterial Catheter requires immediate attention. The main complication of UAC malposition is obstruction of the arterial lumen of a small caliber branching artery. This may lead to impedance of arterial flow and predisposes to arterial thrombosis and embolism. Case Presentation: We present a rare case of bilateral UAC catheterization where the second umbilical artery was erroneously catheterized instead of the intended umbilical vein. Conclusion: This case reinforces the need for thorough assessment of the position and course of any recently inserted umbilical vascular catheter. Conclusion: This case reinforces the need for thorough assessment of the position and course of any recently inserted umbilical vascular catheter.Background: Arterial catheters are frequently needed to optimize the intensive care in the sick newborn. Umbilical Arterial Catheters (UAC) is more popular than peripheral arterial catheterization. They are utilized to provide continuous accurate arterial blood pressure monitoring, frequent assessment of gas exchange efficiency, frequent blood sampling and rarely for exchange blood transfusion. Umbilical Arterial Catheters may be used in emergencies to infuse fluids or medications in the absence of venous access. Malposition of the Umbilical Arterial Catheter requires immediate attention. The main complication of UAC malposition is obstruction of the arterial lumen of a small caliber branching artery. This may lead to impedance of arterial flow and predisposes to arterial thrombosis and embolism. Case Presentation: We present a rare case of bilateral UAC catheterization where the second umbilical artery was erroneously catheterized instead of the intended umbilical vein. Conclusion: This case reinforces the need for thorough assessment of the position and course of any recently inserted umbilical vascular catheter.Background: Arterial catheters are frequently needed to optimize the intensive care in the sick newborn. Umbilical Arterial Catheters (UAC) is more popular than peripheral arterial catheterization. They are utilized to provide continuous accurate arterial blood pressure monitoring, frequent assessment of gas exchange efficiency, frequent blood sampling and rarely for exchange blood transfusion. Umbilical Arterial Catheters may be used in emergencies to infuse fluids or medications in the absence of venous access. Malposition of the Umbilical Arterial Catheter requires immediate attention. The main complication of UAC malposition is obstruction of the arterial lumen of a small caliber branching artery. This may lead to impedance of arterial flow and predisposes to arterial thrombosis and embolism. Case Presentation: We present a rare case of bilateral UAC catheterization where the second umbilical artery was erroneously catheterized instead of the intended umbilical vein. Conclusion: This case reinforces the need for thorough assessment of the position and course of any recently inserted umbilical vascular catheter.