Investigating the bacterial community of gray mangroves (Avicennia marina) in coastal areas of Tabuk region.

Mangrove vegetation, a threatened and unique inter-tidal ecosystem, harbours a complex and largely unexplored bacterial community crucial for nutrient cycling and the degradation of toxic pollutants in coastal areas. Despite its importance, the bacterial community composition of the gray mangrove (Avicennia marina) in the Red Sea coastal regions remains under-studied. This study aims to elucidate the structural and functional diversity of the microbiome in the bulk and rhizospheric soils associated with A. marina in the coastal areas of Ras Alshabaan-Umluj (Umluj) and Almunibrah-Al-Wajh (Al-Wajh) within the Tabuk region of Saudi Arabia. Amplicon sequencing targeting the 16S rRNA was performed using the metagenomic DNAs from the bulk and rhizospheric soil samples from Umluj and Al-Wajh. A total of 6,876 OTUs were recovered from all samples, of which 1,857 OTUs were common to all locations while the total number of OTUs unique to Al-wajh was higher (3,011 OTUs) than the total number of OTUs observed (1,324 OTUs) at Umluj site. Based on diversity indices, overall bacterial diversity was comparatively higher in rhizospheric soil samples of both sites. Comparing the diversity indices for the rhizosphere samples from the two sites revealed that the diversity was much higher in the rhizosphere samples from Al-Wajh as compared to those from Umluj. The most dominant genera in rhizosphere sample of Al-Wajh were Geminicoccus and Thermodesulfovibrio while the same habitat of the Umluj site was dominated by Propionibacterium, Corynebacterium and Staphylococcus. Bacterial functional potential prediction analyses showed that bacteria from two locations have almost similar patterns of functional genes including amino acids and carbohydrates metabolisms, sulfate reduction and C-1 compound metabolism and xenobiotics biodegradation. However, the rhizosphere samples of both sites harbour more genes involved in the utilization and assimilation of C-1 compounds. Our results reveal that bacterial communities inhabiting the rhizosphere of A. marina differed significantly from those in the bulk soil, suggesting a possible role of A. marina roots in shaping these bacterial communities. Additionally, not only vegetation but also geographical location appears to influence the overall bacterial composition at the two sites.

Harnessing de novo transcriptome sequencing to identify and characterize genes regulating carbohydrate biosynthesis pathways in Salvia guaranitica L.

Introduction: Carbohydrate compounds serve multifaceted roles, from energy sources to stress protectants, found across diverse organisms including bacteria, fungi, and plants. Despite this broad importance, the molecular genetic framework underlying carbohydrate biosynthesis pathways, such as starch, sucrose, and glycolysis/gluconeogenesis in Salvia guaranitica, remains largely unexplored. Methods: In this study, the Illumina-HiSeq 2500 platform was used to sequence the transcripts of S. guaranitica leaves, generating approximately 8.2 Gb of raw data. After filtering and removing adapter sequences, 38 million reads comprising 210 million high-quality nucleotide bases were obtained. De novo assembly resulted in 75,100 unigenes, which were annotated to establish a comprehensive database for investigating starch, sucrose, and glycolysis biosynthesis. Functional analyses of glucose-6-phosphate isomerase (SgGPI), trehalose-6-phosphate synthase/phosphatase (SgT6PS), and sucrose synthase (SgSUS) were performed using transgenic Arabidopsis thaliana. Results: Among the unigenes, 410 were identified as putatively involved in these metabolic pathways, including 175 related to glycolysis/gluconeogenesis and 235 to starch and sucrose biosynthesis. Overexpression of SgGPI, SgT6PS, and SgSUS in transgenic A. thaliana enhanced leaf area, accelerated flower formation, and promoted overall growth compared to wild-type plants. Discussion: These findings lay a foundation for understanding the roles of starch, sucrose, and glycolysis biosynthesis genes in S. guaranitica, offering insights into future metabolic engineering strategies for enhancing the production of valuable carbohydrate compounds in S. guaranitica or other plants.

Identification and Validation of Functional miRNAs and Their Main Targets in Sorghum bicolor.

MicroRNAs (miRNAs) are typically non-coding RNAs of 18-26 nucleotides (nts) that are produced endogenously and regulated post-transcriptionally through degradation or translational repression. Since miRNAs are evolutionarily conserved, their preservation is essential for important regulatory functions in plant development, growth, and responses to environmental stress. Sorghum bicolor (sbi) is a valuable food and fodder crop which is grown worldwide. A range of sbi miRNAs were identified so far as being connected to plant development and stress responses. Herein, we employed a variety of bioinformatics tools for miRNA profiling in sbi and a PCR-based platform for the validation of these miRNAs. In total, 74 new conserved sbi miRNAs from 52 miRNA families have been predicted. Using the psRNA Target method, 10613 different protein targets of these predicted miRNAs have been attained. These targets include 54 GO-terms which have substantial targets in the biological, molecular, and cellular processes. We particularly found that the sbi-miR1861c and sbi-miR5050 are involved to regulate sulphur compound biosynthetic process, while the significant spliceosomal complex is regulated by sbi-miR815b and sbi-miR7768b. Also, we report that the pre-ribosome, electron transport chain, cell communication, cellular respiration, protein localization, and photosynthesis are controlled by sbi-miR2907b, sbi-miR530, sbi-miR7749, sbi-miR1858a, sbi-mi7729a, and sbi-miR417, respectively. The identification and validation of these novel sbi miRNAs shall contribute a lot in improving the crop yield and ensure sustainable agriculture.

Evaluation of the potential of two halophytes to extract Cd and Zn from contaminated saltwater.

The contamination of saltwater by toxic heavy metals has become a worldwide problem. The application of phytoextraction to remove these pollutants seems to be more efficient and cheaper compared to physicochemical methods. In this work, we evaluated the potential of two halophyte species to accumulate cadmium and zinc from contaminated water. Seedlings of Carpobrotus edulis L. and Sesuvium portulacastrum L. were cultivated during 1 month on pots filled with saltwater (200 mM NaCl) containing different concentrations of Cd2+ (0, 50, 100 µM) and of Zn2+ (0, 200, and 400 µM) applied separately. Results showed that both halophytes were more resistant to Zn2+ than Cd2+ and that Sesuvium better tolerates the two metals. Zn2+ and Cd2+ concentrations in the shoot as well as the values of translocation factors suggest that these species are able to absorb and to concentrate Cd2+ and Zn2+ in their roots and shoots. Hence, after 1 month of culture on 50 µM Cd2+, plants were able to extract 31% and 21% of Cd, respectively, in S. portulacastrum and C. edulis. The Zn-extraction efficiency was less important and reached 18 and 19%, respectively, in S. portulacastrum and C. edulis cultivated under 200 µM Zn2+. Given together, data demonstrate the efficiency of the use of halophytes, especially S. portulacastrum, to extract Zn2+ and Cd2+ from salt wastewater.

Biogenic Nanoparticles Silver and Copper and Their Composites Derived from Marine Alga Ulva lactuca: Insight into the Characterizations, Antibacterial Activity, and Anti-Biofilm Formation.

Bacterial pathogens cause pain and death, add significantly to the expense of healthcare globally, and pose a serious concern in many aspects of daily life. Additionally, they raise significant issues in other industries, including pharmaceuticals, clothing, and food packaging. Due to their unique properties, a great deal of attention has been given to biogenic metal nanoparticles, nanocomposites, and their applications against pathogenic bacteria. This study is focused on biogenic silver and copper nanoparticles and their composites (UL/Ag2 O-NPS, Ul/CuO-NPs, and Ul/Ag/Cu-NCMs) produced by the marine green alga Ulva lactuca. The characterization of biogenic nanoparticles UL/Ag2 O-NPS and Ul/CuO-NPs and their composites Ul/Ag/Cu-NCMs has been accomplished by FT-IR, SEM, TEM, EDS, XRD, and the zeta potential. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) experiments were conducted to prove antibacterial activity against both Gram-positive and Gram-negative bacteria and anti-biofilm. The FTIR spectroscopy results indicate the exiting band at 1633 cm-1, which represents N-H stretching in nanocomposites, with a small shift in both copper and silver nanoparticles, which is responsible for the bio-reduction of nanoparticles. The TEM image reveals that the Ul/Ag/Cu-NCMs were hexagonal, and the size distribution ranged from 10 to 35 nm. Meanwhile, Ul/CuO-NPs are rod-shaped, whereas UL/Ag2 O-NPS are spherical. The EDX analysis shows that Cu metal was present in a high weight percentage over Ag in the case of bio-Ag/Cu-NCMs. The X-ray diffraction denotes that Ul/Ag/Cu-NCMs, UL/CuO-NPs, and UL/Ag2 O-NPS were crystalline. The results predicted by the zeta potential demonstrate that Ul/Ag/Cu-NCMs were more stable than Ul/CuO-NPs. The antibacterial activity of UL/Ag2 O-NPS, Ul/Ag/Cu-NCMs, and UL/CuO-NPs was studied against eleven Gram-negative and Gram-positive multidrug-resistant bacterial species. The maximum inhibition zones were obtained with UL/Ag2 O-NPS, followed by Ul/Ag/Cu-NCMs and Ul/CuO-NPs in all the tested bacteria. The maximum anti-biofilm percentage formed by E. coli KY856933 was obtained with UL/Ag2 O-NPS. These findings suggest that the synthesized nanoparticles might be a great alternative for use as an antibacterial agent against different multidrug-resistant bacterial strains.

The Expression of Triticum aestivum Cysteine-Rich Receptor-like Protein Kinase Genes during Leaf Rust Fungal Infection.

Understanding the role of cysteine-rich receptor-like kinases (CRKs) in plant defense mechanisms is crucial for enhancing wheat resistance to leaf rust fungus infection. Here, we identified and verified 164 members of the CRK gene family using the Triticum aestivum reference version 2 collected from the international wheat genome sequencing consortium (IWGSC). The proteins exhibited characteristic features of CRKs, including the presence of signal peptides, cysteine-rich/stress antifungal/DUF26 domains, transmembrane domains, and Pkinase domains. Phylogenetic analysis revealed extensive diversification within the wheat CRK gene family, indicating the development of distinct specific functional roles to wheat plants. When studying the expression of the CRK gene family in near-isogenic lines (NILs) carrying Lr57- and Lr14a-resistant genes, Puccinia triticina, the causal agent of leaf rust fungus, triggered temporal gene expression dynamics. The upregulation of specific CRK genes in the resistant interaction indicated their potential role in enhancing wheat resistance to leaf rust, while contrasting gene expression patterns in the susceptible interaction highlighted potential susceptibility associated CRK genes. The study uncovered certain CRK genes that exhibited expression upregulation upon leaf rust infection and the Lr14a-resistant gene. The findings suggest that targeting CRKs may present a promising strategy for improving wheat resistance to rust diseases.

Utilization of Genetic Resources, Genetic Diversity and Genetic Variability for Selecting New Restorer Lines of Rice (Oryza sativa L.).

Exploration of and understanding diversity and variability in genotypes of germplasm determines the success of rice improvement programs. One of the most important determinants of the success of breeding programs is genetic diversity and inheritance of traits. Genetic variability analysis helps breeders to determine the appropriate selection method and standards to be used to improve the preferred trait. The aim of this study was to estimate genetic components, heritability and to obtain information about genetic diversity using cluster analysis and principal component analysis. Twenty rice genotypes with three replicates in a randomized complete block design were analyzed at the Experimental Farm at Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the period from 2017 to 2020. The results of the analysis of variance showed that highly significant variations were recorded between the studied genotypes for all traits. The genotypic coefficient of variation (GCV%) and phenotypic (PCV%) coefficient of variation were moderate for plant height, panicles/plant, panicle weight, spikelets/panicle, filled grains/panicle, grain yield/plant and amylose content percentage for the first-year, second-year and combined data. This indicates the existence of beneficial genetic variability that can be exploited to improve these traits. The broad-sense estimates of heritability were high and recorded values higher than 60% for all the studied traits for the two-year and combined data, except for hulling percentage. This indicates that the selection of traits that have high heritability and are less affected by the environment leads to an acceleration of the improvement of these traits. The results from the cluster analysis and principal component analysis revealed a high level of genotypic variation among the studied genotypes and genetic diversity between them. One of the most important outcomes of this study is the successful utilization of genetic resources (germplasm) from ancient varieties and lines of rice in selecting and identifying 17 new restoration lines of rice, which have various improvement purposes in rice and hybrid rice breeding programs.

Characterizations of Alpha-Cellulose and Microcrystalline Cellulose Isolated from Cocoa Pod Husk as a Potential Pharmaceutical Excipient.

Cellulose is a non-toxic, bio-degradable, and renewable biopolymer which is abundantly available in nature. The most common source of commercial microcrystalline cellulose is fibrous wood pulp. Cellulose and its derivatives have found wide commercial applications in the pharmaceutical, cosmetic, food, paper, textile, and engineering industries. This study aims to isolate and characterize cellulose forms from cocoa pod husk (CPH) and to assess its mechanical and disintegration properties as a direct compression excipient in metronidazole tablets. Two isolated cellulose types (i.e., cocoa alpha-cellulose (CAC) and cocoa microcrystalline cellulose (C-MCC)) were compared with avicel (AV). CAC and C-MCC were characterized for their physicochemical properties using Scanning Electron Microscopy (SEM), FTIR spectroscopy, Differential Scanning Calorimetry (DSC), and X-Ray Powder Diffraction (XRD). Metronidazole tablets were produced by direct compression with cellulose. The mechanical and disintegration properties of the tablets were evaluated. CAC and C-MCC yield was 42.3% w/w and 38.25% w/w, respectively. Particle diameters were significantly different with CAC (282.22 µm) > C-MCC (161.32 µm) > AV (72.51 µm). CAC and C-MCC had a better flow than AV. SEM revealed the fibrous nature of the cellulose. FTIR and XRD analysis confirmed the presence of cellulose with crystallinity index of 69.26%, 43.83%, and 26.32% for AV, C-MCC, and CAC, respectively. C-MCC and AV are more crystalline and thermally stable at high temperatures compared to CAC. The mechanical and disintegration properties of C-MCC and AV tablets complied with pharmacopeia specifications. Taken together, C-MCC isolated from CPH displayed some fundamental characteristics suitable for use as a pharmaceutical excipient and displayed better properties compared to that of AV.

Molecular Identification of Zantedeschia Culture with Determination of Its Morphometric and Metabolic Activities for Mediterranean Acclimatization.

Calla lily (Zantedeschia albomaculata (Hook.) Baill.) is an herbaceous or semi-evergreen perennial grown from rhizomes. It is commonly named "Spotted Arum". Ribosomal RNAs (rRNAs) are found in all known organisms and are known for being functionally equivalent in all of them. A completely new in vitro culture protocol was applied to Z. albomaculata with two hormones, 6-Benzylaminopurine (BAP) and kinetin, to obtain full growth and multiplication. Due to their highly conserved sequences, the analysis of small-subunit rRNAs (16S-18S rRNAs) can provide precise statistical evaluation of a wide variety of phylogenetic connections. As a result, the plant's 18S rRNA gene allowed for identification and partial sequencing. Also, the traditional floral method and the novel application technique for identification were applied to Z. albomaculata. In this paper we systemically describe the structural strategies of the plant's adaptation to the surroundings at the morphological, physiological, and anatomical scale. Most the essential oils and fatty acids found in Z. albomaculata are omega fatty acids, octadecenoic acid, linoleic acid, and palmitic acid. All these fatty acids have industrial, medicinal, and pharmaceutical applications. The significant findings are the spadix sheathing leaves, and the precipitation of raphides calcium oxalate. The mitotic index showing the division activity was recorded, and it was 17.4%. The antimicrobial activity of Z. albomaculata ethanol extract was performed via the well diffusion method. This extract has shown high activity against Escherichia coli and Pseudomonas aeruginosa, compared to its lower activity against Bacillus cereus. By defining these characteristics and in vitro culture conditions, we will be able to acclimatize the plant in greenhouses, and then transfer it to the open field. The findings of this work identified the general characteristics of Zantedeschia albomaculata as an ornamental and medicinal plant in order to acclimatize this plant for cultivation in the Mediterranean climate.