Mohamed Barakat

King Saud University | KKUH · Center of Excellence in Biotechnology Research

The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly processes, a...

Background The rhizosheath, a cohesive soil layer firmly adhering to plant roots, plays a vital role in facilitating water and mineral uptake. In pearl millet, rhizosheath formation is genetically controlled and influenced by root exudates. Here, we investigated the impact of root exudates on the microbiota composition, interactions, and assembly p...

Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved...

Hypersaline ecosystems host a particular microbiota, which can be specifically recruited by halophytes. In order to broaden our knowledge of hypersaline ecosystems, an in natura study was conducted on the microbiota associated with the halophyte Halocnemum strobilaceum from alkaline-saline arid soil in Algeria. We collected and identified a total o...

Bauxite residue is the alkaline byproduct generated during alumina extraction and is commonly landfilled in open-air deposits. The growth in global alumina production have raised environmental concerns about these deposits since no large-scale reuses exist to date. Microbial-driven techniques including bioremediation and critical metal bio-recovery...

Uranium is a naturally occurring radionuclide. Its redistribution, primarily due to human activities, can have adverse effects on human and non-human biota, which poses environmental concerns. The molecular mechanisms of uranium tolerance and the cellular response induced by uranium exposure in bacteria are not yet fully understood. Here, we carrie...

Aims: The interactions between plant roots and the associated microbiota impact soil aggregation, water retention and plant nutrient availability. Thus, selection of plant genotypes that promote microbial species involved in root-adhering soil aggregation and rhizosheath formation could help improve yield sustainably. Here, we tested pearl millet g...

Two-component systems (TCSs) are ubiquitous signaling pathways, typically comprising a sensory histidine kinase (HK) and a response regulator, which communicate via intermolecular kinase-to-receiver domain phosphotransfer. Hybrid HKs constitute non-canonical TCS signaling pathways, with transmitter and receiver domains within a single protein commu...

Drought is a common abiotic stress factor that seriously affects wheat production in many parts of the world. To identify stable QTLs associated with three morphophysiological traits and four spectral reflectance indices (SRIs) in F6 (previous research) and F7 generations, recombinant inbred line (RIL) population from the cross between drought-sens...

Silver nanomaterials with different shapes (spheres, plates, wires, rods, cubes) are valued by industries and scientists for their shape-dependent properties which make them useful for diverse applications. In a safer-by-design perspective, controlling the shape of Ag nanomaterials could be an option to increase their properties while lowering eith...

Wheat flour quality is a complex group of traits of tremendous importance to wheat producers, end-users and breeders. Eight flour quality traits; flour protein content, wet gluten content, gluten index, dry gluten content, falling number, ash content, test weight and flour moisture were measured in two doubled haploid populations (Yecora Rojo X Ksu...

QTL analysis for grain failing rate and related traits in doubled haploid population of wheat under heat stress conditions

Farinograph and mixograph-related parameters are key elements in wheat end-products quality. Understanding the genetic control of these traits and the influence of environmental factors such as heat stress, and their interaction are critical for developing cultivars with improved for those traits. To identify QTL for six farinograph and three mixog...

Objective Carbapenemase producing bacteria poses serious threat to public. This study was performed to understand the emergence and genetic features of NDM-producers in hospital setting. Materials and Methods Samples were collected from tertiary care hospital. Isolate identification was carried out by 16S rRNA sequencing. The genome of Citrobacter...

The bread-making quality traits of bread wheat underlie into genetic make-up of a variety and are influenced by environmental factors and their interaction. Identifying QTL that control bread-making traits in wheat under heat stress may help to develop cultivars that are improved for those traits. Two doubled haploid (DH) populations (Yecora Rojo ×...

Toxoplasma gondii has a complex life cycle that is typified by asexual development that takes place in vertebrates, and sexual reproduction, which occurs exclusively in felids and is therefore less studied. The developmental transitions rely on changes in the patterns of gene expression, and recent studies have assigned roles for chromatin shapers,...

Increased global warming, caused by climate change and human activities, will seriously hinder plant development, such as increasing salt concentrations in soils, which will limit water availability for plants. To ensure optimal plant growth under such changing conditions, microorganisms that improve plant growth and health must be integrated into...

Pearl millet is a cereal crop that is given a little attention by researchers despite its tremendous capabilities with respect to its pears (wheat, barley, ...). This plant cultivated in arid and semi-arid areas in Western Africa and Sahel resisting low rainfall and poor soil conditions is the main food and cheapest nutritive source for people livi...

The Asian tiger mosquito Aedes albopictus is a major public health concern because of its invasive success and its ability to transmit pathogens. Given the low availability of treatments against mosquito‐borne diseases, vector control remains the most suitable strategy. The methods used thus far are becoming less effective, but recent strategies ha...

Stress induced by high temperature represents a major constraint over wheat production in many production areas. Here, the comprehensive coverage of the wheat genome achievable using single nucleotide polymorphism markers was exploited to carry out a genetic analysis targeting yield components in plants exposed to high temperature stress. The mappi...

Ramlibacter tataouinensis TTB310, a non-photosynthetic betaproteobacterium isolated from a semi-arid region of southern Tunisia, forms both rods and cysts. Cysts are resistant to desiccation and divide when water and nutrients are available. Rods are motile and capable of dissemination. Due to the strong correlation between sunlight and desiccation...

Taxonomic affiliation of OTUs retrieved from heavy-DNA fractions (root exudate consumers): (file 1) shared by exploitative plants (DG, TF, BE, and AO) and representing the core microbiota; (file 2) present in AO only; (file 3) present in BE only; (file 4) present in DG only; (file 5) present in TF only.

Taxonomic affiliation of OTUs retrieved from light-DNA fractions (SOM degraders): (file 1) shared by conservative plants (FP and SC) and representing the core microbiota; (file 2) present in FP only; (file 3) present in SC only.

Taxonomic affiliation of OTUs retrieved from heavy-DNA fractions (root exudate consumers): (file 1) shared by exploitative (DG, BE, AO and TF) and conservative plants (FP and SC) and representing the core microbiota; (file 2) present in exploitative plants only; (file 3) present in conservative plants only.

Taxonomic affiliation of OTUs retrieved from root-DNA fractions (root exudate consumers): (file 1) shared by exploitative (DG, BE, AO and TF) and conservative plants (FP and SC) and representing the core microbiota; (file 2) present in exploitative plants only; (file 3) present in conservative plants only.

Principal coordinate analysis (PCoA) profile of the active bacterial diversity (using Bray–Curtis distances) colonizing the RAS and inhabiting the root tissues of Bromus erectus (BE), Anthoxanthum odoratum (AO), Dactylis glomerata (DG), Trisetum flavescens (TF), Festuca paniculata (FP), and Sesleria caerulea (SC). (A) PCoA of active microbiota obta...

Taxonomic affiliation of OTUs retrieved from light-DNA fractions (SOM degraders): (file 1) shared by exploitative (DG, BE, AO, and TF) and conservative plants (FP and SC) and representing the core microbiota; (file 2) present in exploitative plants only; (file 3) present in conservative plants only.

Table of the different bacteria present in the co-occurrence analysis (Figure 5). Each sheet displays the taxonomic affiliation of the bacterial communities uncovered for the RAS, including root exudate consumers of exploitative plant species (Exploit_heavy DNA fractions), root exudate consumers of conservative plant species (Cons_heavy DNA fractio...

Bacterial diversity in the rhizosphere of Bromus erectus (BE), Anthoxanthum odoratum (AO), Dactylis glomerata (DG), Trisetum flavescens (TF), Festuca paniculata (FP) and Sesleria caerulea (SC), as characterized by rarefaction curves of OTUs clustered using the swarm method with d = 3. H: heavy-DNA fraction; L: light-DNA fraction; R: root-DNA.

Taxonomic affiliation of OTUs retrieved from light-DNA fractions (SOM degraders): (file 1) shared by exploitative plants (DG, TF, BE, and AO) and representing the core microbiota; (file 2) present in AO only; (file 3) present in BE only; (file 4) present in DG only; (file 5) present in TF only.

Taxonomic affiliation of OTUs retrieved from heavy-DNA fractions (root exudate consumers): (file 1) shared by conservative plants (FP and SC) and representing the core microbiota; (file 2) present in FP only; (file 3) present in SC only.

Taxonomic affiliation of OTUs retrieved from root-DNA fractions (root exudate consumers): (file 1) shared by conservative plants (FP and SC) and representing the core microbiota; (file 2) present in FP only; (file 3) present in SC only.

Sample coverage, species richness and species diversity indices.

Taxonomic affiliation of OTUs retrieved from root-DNA fractions (root exudate consumers): (file 1) shared by exploitative plants (DG, TF, BE, and AO) and representing the core microbiota; (file 2) present in AO only; (file 3) present in BE only; (file 4) present in DG only; (file 5) present in TF only.

Silver phytoavailability in exposure scenarios close to predicted environmental concentrations (PEC) has rarely been studied. The ISO-standardized RHIZOtest, based on a root mat technique, was used to expose tall fescue (Festuca arundinacea) to silver at a concentration close to (0.0015 mg.kg-1) and 100 times higher (0.15 mg.kg-1) than PEC in soils...

Table corresponding to Figure 9D containing the normalized expression distribution of T. gondii genes in the tachyzoite stage subdivided into four ranges of expression (clusters Q1 to Q4).

An unusual genome architecture characterizes the two related human parasitic pathogens Plasmodium falciparum and Toxoplasma gondii. A major fraction of the bulk parasite genome is packaged as transcriptionally permissive euchromatin with few loci embedded in silenced heterochromatin. Primary chromatin shapers include histone modifications at the nu...

A doubled haploid (DH) production system for wheat using a microspore culture method produced seeds and subsequently regenerated haploid wheat plants derived from the F1 plants of two wheat populations (Irena × Ksu102 and Klasic × Ksu105). 68 DH were obtained from both populations. Field trials of these DH lines were conducted over two seasons. Gen...

The ISO-standardized RHIZOtest is used here for the first time to decipher how plant species, soil properties, physical-chemical properties of the nanoparticles and their transformation regulate the phytoavailability of nanoparticles. Two plants, tomato and fescue, were exposed to two soils with contrasted properties: a sandy soil poor in organic m...

Root exudation contributes to soil carbon allocation and also to microbial C and energy supply, which subsequently impacts soil aggregation around roots. Biologically-driven soil structural formation is an important driver of soil fertility. Plant genetic determinants of exudation and more generally of factors promoting rhizosphere soil aggregation...

The analysis of microbial diversity highlights the idea that tolerance of desiccation is more important than tolerance of temperature as an adaptive microbial trait for desert conditions. The culture-independent analysis of this microbial diversity in deserts revealed that 70–80 % of 16S-rDNA sequences do not match with described bacterial species,...

Soils act as nanoceria sinks via agricultural spreading and surface waters. Canola plants were grown for one month in soil spiked with nanoceria (1 mg.kg-1). To define the role of nanomaterials design on environmental impacts, we studied nanoceria with different sizes (3.5 or 31 nm) and coating (citrate). We measured microbial activities involved i...

We present a reliable PCR-based method to avoid the biases related to identification based on the conventional phenotypes currently used in the identification of Pseudomonas syringae sensu lato, a ubiquitous environmental bacterium including plant pathogens. We identified a DNA target suitable for this purpose by applying a comparative genomic pipe...

The P2CS database (http://www.p2cs.org/) is a comprehensive resource for the analysis of Prokaryotic Two-Component Systems (TCSs). TCSs are comprised of a receptor histidine kinase (HK) and a partner response regulator (RR) and control important prokaryotic behaviors. The latest incarnation of P2CS includes 164 651 TCS proteins, from 2758 sequenced...

Physical-chemists, (micro)biologists, and ecologists need to conduct meaningful experiments to study the environmental risk of engineered nanomaterials with access to relevant mechanistic data across several spatial and temporal scales. Indoor aquatic mesocosms (60L) that can be tailored to virtually mimic any ecosystem appear as a particularly wel...

Engineered nanomaterials (ENMs) are used to enhance the properties of many manufactured products and technologies. Increased use of ENMs will inevitably lead to environmental release. An important route of exposure is through the waste stream where ENMs will enter wastewater treatment plants (WWTPs), undergo transformations, and be discharged with...

Microbial anodes were formed under polarization at -0.3V/SCE on graphite plates in effluents from a pulp and paper mill. The bioanodes formed with the addition of acetate led to the highest current densities (up to 6A/m(2)) but were then unable to oxidize the raw effluent efficiently (0.5A/m(2)). In contrast, the bioanodes formed without acetate ad...

Background Regulatory proteins (RPs) such as transcription factors (TFs) and two-component system (TCS) proteins control how prokaryotic cells respond to changes in their external and/or internal state. Identification and annotation of TFs and TCSs is non-trivial, and between-genome comparisons are often confounded by different standards in annotat...

After invading host cells, Toxoplasma gondii multiplies within a parasitophorous vacuole (PV) that is maintained by parasite proteins secreted from organelles called dense granules. Most dense granule proteins remain within the PV, and few are known to access the host cell cytosol. We identify GRA16 as a dense granule protein that is exported throu...

This study was conducted to detect quantitative trait loci QTL associated with drought tolerance in wheat genotypes by the SSR markers and to provide valuable information for marker assisted selection. SSR markers linked to flag leaf senescence (FLS) was identified in two DNA pools, which were established using F2 mapping population resulting from...

Hydrogen production by microorganisms is often described as a promising sustainable and clean energy source, but still faces several obstacles, which prevent practical application. Among them, oxygen sensitivity of hydrogenases represents one of the major limitations hampering the biotechnological implementation of photobiological production proces...

Background Transcription factors (TFs) are DNA-binding proteins that regulate gene expression by activating or repressing transcription. Some have housekeeping roles, while others regulate the expression of specific genes in response to environmental change. The majority of TFs are multi-domain proteins, and they can be divided into families accord...

Classification of TF categories: Schematic representation of the conserved domain architectures.

Classification of TF families: List of domain architectures.

The mutS-rpoS region is known to be a highly polymorphic segment of the chromosome owing to horizontal gene transfer and evolutionary processes. In Pseudomonas, mutS-fdxA-rsmZ-rpoS organization is highly conserved, as well as the promoter region of the RsmZ small RNA (sRNA)-encoding gene. One exception to this conservation is in Pseudomonas brassic...

Prokaryotic microorganisms are known to be highly adaptable to diverse environmental conditions and to thrive in harsh environments. Halophilic microorganisms (Bacteria and Archaea) tolerate and grow in the presence of salt concentrations 10 times higher than seawater, whereas acidophiles withstand a pH of 1, and hyperthermophiles face temperatures...

Comparison of the Ramlibacter tataouinensis TTB310 genome against the closest proteobacterial genomes. Similarity searches were carried out between strain TTB310 and all the complete proteomes present in NCBI database, using BLASTP. The figure was generated with the results of the thirteen most similar genomes (12 betaproteobacteria, 1 alphaproteob...

Genes of Ramlibacter tataouinensis TTB310 potentially involved in peroxide scavenging pathways. (TIFF)

Biosynthesis of even- and odd-numbered, straight and branched chain fatty acids from acetyl-CoA, propionyl-CoA and branched chain amino acids derivatives as starting units in Ramlibacter tataouinensis TTB310. Determining steps for the distribution of fatty acid molecular species in the final profile include the branched chain amino acid transaminas...