Exogenous application of agmatine improves water stress and salinity stress tolerance in turnip (Brassica rapa L.)

This study was carried out to determine the consequence of foliar application of agmatine (0 and 0.5 mM), on growth, physiological and biochemical traits, and yield of turnip (Brassica rapa L.) plants grown under water stress or salt stress conditions. The effect of three irrigation regimes (100%, 80% and 40% of field capacity) and three salt concentrations (0, 100 and 200 mM NaCl) on turnip plants grown in pots under greenhouse conditions were studied.  Water deficit developed at 40% Field capacity (FC) and salinity stress, especially at 200 mM, resulted in significant decreases in all growth parameters when compared to control plants (100% FC) including root length and diameter as well as shoot weights per plant. Water stress and high salt stress negatively affected most physiological and biochemical characteristics such as total chlorophyll, photosynthetic rate, stomatal conductance, and transpiration rate. Water use efficiency (WUE) increased under 80% FC or 100 mM NaCl. Antioxidant enzymes activity, catalase and peroxidase and glutathione reductase, increased with water stress and salt stress. Foliar application of agmatine seemed to alleviate the adverse effects of water stress and salt stress on turnip. Alleviating harmful effects of salt stress and enhancing water stress tolerance by agmatine was associated with improving leaf gas exchange, antioxidant enzymes and protein profile

G3BPs in Plant Stress

The sessile nature of plants enforces highly adaptable strategies to adapt to different environmental stresses. Plants respond to these stresses by a massive reprogramming of mRNA metabolism. Balancing of mRNA fates, including translation, sequestration, and decay is essential for plants to not only coordinate growth and development but also to combat biotic and abiotic environmental stresses. RNA stress granules (SGs) and processing bodies (P bodies) synchronize mRNA metabolism for optimum functioning of an organism. SGs are evolutionarily conserved cytoplasmic localized RNA-protein storage sites that are formed in response to adverse conditions, harboring mostly but not always translationally inactive mRNAs. SGs disassemble and release mRNAs into a translationally active form upon stress relief. RasGAP SH3 domain binding proteins (G3BPs or Rasputins) are “scaffolds” for the assembly and stability of SGs, which coordinate receptor mediated signal transduction with RNA metabolism. The role of G3BPs in the formation of SGs is well established in mammals, but G3BPs in plants are poorly characterized. In this review, we discuss recent findings of the dynamics and functions of plant G3BPs in response to environmental stresses and speculate on possible mechanisms such as transcription and post-translational modifications that might regulate the function of this important family of proteins

Microbiome structure and response to watering in rhizosphere of Nitrosalsola vermiculata and surrounding bulk soil

The plant rhizosphere microbiomes were thought to help the plant stands adverse condition. The study aims at deciphering signatures of rhizosphere soil microbiomes of the medicinal plant Nitrosalsola vermiculata and those of the surrounding bulk soil as well as to detect influence of watering in restructuring soil microbes that can improve the plant’s ability to tolerate drought stress. Amplicon sequencing of partial 16S rRNA gene indicated that alpha diversity indices are higher in rhizosphere than in bulk soils, while no distinctive differences were observed due to the watering. Relative abundance of phylum Cyanobacteria and its descendent unidentified genus is the highest among phyla and genera of bulk soil. Relative abundance of phyla Euryarchaeota, Chloroflexi, Actinobacteria, Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria and Gemmatimonadetes as well as genera Bacillus, Ammoniphilus, Sphingomonas, Microvirga, Pontibacter, Adhaeribacter and Arthrobacter was significantly higher in rhizosphere soil. The latter taxa were reported to act as plant growth-promoting bacteria (PGPB) through symbiotic associations. We speculate that relative abundance and mutual dominance of these taxa in rhizosphere of N. vermiculata were due to the intensity and type of plant root exudates. Other factors include soil pH where microbes favoring high soil pH can show better growth in rhizosphere soil. Also, co-existence of phyla that promote sustainability of cohabiting phyla in the rhizosphere and have high synergism prevalence in biofilm formation can be one extra factor. Quorum sensing (QS) also mediates bacterial population density in a given environment and elicit specific plant responses. The low abundance of Cyanobacteria in rhizosphere soil can be due to the inhibitory effect of highly abundant members of Firmicutes, especially those of genus Bacillus. The latter conclusion was confirmed by the occurrence of high expression rate of comQ gene triggering QS in genus Bacillus. Highly abundant microbes whose abundance was not changed due to watering are phyla Firmicutes, Proteobacteria, Chloroflexi and Cyanobacteria and their descendent genera Bacillus, Ammoniphilus, Sphingomonas, Microvirga and unidentified genus of Cyanobacteria. We speculate that non-responsive taxa to watering were drought tolerant and can help plants stand adverse conditions of water scarce. In conclusion, insights on the factors involved in shaping microbiome signatures and those eliciting differential plant responses to drought stress are raised and warrant further investigations

Expression Profiling of Salt-Responsive Genes and Transcription Factors in Leaf Transcriptome of <i>Arabidopsis thaliana</i>

This investigation discerns the expression profiles of genes within the leaf transcriptome of Arabidopsis thaliana subjected to salt stress (200 mM NaCl). Notably, the pivotal role of indole acetic acid emerged as a keystone orchestrating a multifaceted cascade of regulatory events aimed at enhancing the plant’s adaptability under salt-induced stress. Cluster analysis elucidated upregulation of gene families with pivotal roles in supporting the availability of carbon dioxide, ameliorating photosynthetic processes and mitigating the deleterious effects of reactive oxygen species under salt stress. Analysis also unveiled the participation of several transcription factor families in the orchestration of a multitude of genes under salt stress. The investigation singled out a solitary TF, denominated as BH100, which was validated through RNA-Seq and qPCR, utilizing a VIGS line featuring the knockdown of the BH100 gene. This transcription factor was implicated in the upregulation of the FRO gene, thereby establishing a link between the synchronized expression of these two genes and their role in promoting iron acquisition under salt stress. In summation, our study unveiled the regulatory frameworks and salt-responsive genes underpinning the response of Arabidopsis to salt stress. We present compelling arguments for the potential applicability of this information in the realm of molecular breeding programs

Metagenomic analysis reveals the fate of antibiotic resistance genes in a full-scale wastewater treatment plant in egypt

Wastewater treatment plants (WWTPs) are recognized as hotspots for the dissemination of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in the environment. Our study utilized a high-throughput sequencing-based metagenomic analysis approach to compare the ARG abundance profiles of the raw sewage, treated effluent and activated sludge samples from a full-scale WWTP in Egypt. In addition, the difference in microbial community composition due to the treatment process was assessed. As a result, 578 ARG subtypes (resistance genes) belonging to 18 ARG types (antibiotic resistance classes) were identified. ARGs encoding for resistance against multidrug, aminoglycoside, bacitracin, beta-lactam, sulfonamide, and tetracycline antibiotics were the most abundant types. The total removal efficiency percentage of ARGs in the WWTP was found to be 98% however, the ARG persistence results indicated that around 68% of the ARGs in the influent could be found in the treated effluent. This finding suggests that the treated wastewater poses a potential risk for the ARG dissemination in bacterial communities of the receiving water bodies via horizontal gene transfer (HGT). The community composition at phylum level showed that Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most abundant phyla in all datasets. Although the relative abundance of several pathogenic bacteria in the influent declined to less than 1% in the effluent, the taxonomic assignments at species level for the effluent and sludge metagenomes demonstrated that clinically important pathogens such as Escherichia coli, Klebsiella pneumonia, and Aeromonas caviae were present. Overall, the results of this study would hopefully enhance our knowledge about the abundance profiles of ARGs and their fate in different wastewater treatment compartments that have never been examined before

The Assessment of the Risk Ranking and Mobility Potential Associated with Environmental Resistomes in Wastewater Using Metagenomic Assembly

The environmental pollution of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) is a growing public health concern. In the current study, de novo metagenomic assembly and bioinformatics analysis approaches were utilized to estimate the quantitative risk index of the environmental resistomes in wastewater influent (INF) and effluent (EFF) of a conventional wastewater treatment plant (WWTP) in Egypt. Furthermore, the risk indices of the local INF and EFF resistomes were compared to those calculated for the selected publicly available wastewater datasets from eight countries worldwide. Additionally, a classification framework prioritizing the public health hazard level of the discharged non-redundant highly mobilized ARGs was introduced. This integrative outline considered the estimated mobility potential percentage, host pathogenicity, and annotation category (perfect, strict, and loose) of the detected ARGs on their assembled contigs. Moreover, high-quality metagenome-assembled genomes (MAGs) were extracted and the putative genome bins with acquired ARGs were determined. The comprehensive resistome risk scores of the local WWTP showed that INF resistome had a slightly higher risk index (47.87) compared to the average score of the other examined counterparts (41.06). However, the estimated risk value of EFF resistome (26.80) was ranked within the global average (26.06) of the selected international WWTPs. Furthermore, the determination of the samples’ risk ranking showed that most of the effluent resistomes were clustered in a lower risk rank compared to the other selected samples for raw sewage, influent, and hospital wastewater, indicating the impact of the wastewater treatment process on reducing the ARG mobilization potential in downstream environments. The evaluation of the ARGs’ genetic context in their ARG-carrying contigs (ACCs) indicated that a total of 161/648 (25%) non-redundant ARGs were co-located with sequences of mobile genetic determinants on the same ACC in both the INF and EFF assemblies. These ARGs comprised the pan mobile resistome of the studied WWTP. Of them, 111 ARGs with a mobility potential percent (M%) less than 95% were grouped at the least risk level 5. The remaining 50 highly mobilized ARGs (M% ≥ 95%) were extracted and classified into four higher risk levels. Those of risk levels 1 and 2 (39 ARGs) represented the current ARG dissemination threats for further monitoring in downstream environments, where they were all carried by pathogenic hosts and annotated to the perfect and strict categories by the resistance gene identifier software (RGI). A total of 10 highly mobilized ARGs were assigned to risk rank 3, as they comprised the loose hits of the RGI analysis. Finally, the risk level 4 ARGs constituted genes that co-existed with the non-pathogenic sequence on the ACCs and were represented by one gene in the current analysis framework. The two previous categories constituted new highly mobilized ARGs of emergent threat to public health. On the other hand, a total of 35 and 118 MAGs were recovered from INF and EFF assembled metagenomes, respectively, using selection cutoff thresholds of a minimum completeness of 70% and a maximum contamination of 10%. While none of the INF MAGs carried any acquired ARGs, six EFF genome bins (5%) were associated with ten acquired ARGs, as indicated by the ResFinder software. These results suggest that potential horizontal gene transfer (HGT) events have evolved among the community members of the studied EFF samples

The Assessment of the Risk Ranking and Mobility Potential Associated with Environmental Resistomes in Wastewater Using Metagenomic Assembly

The environmental pollution of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) is a growing public health concern. In the current study, de novo metagenomic assembly and bioinformatics analysis approaches were utilized to estimate the quantitative risk index of the environmental resistomes in wastewater influent (INF) and effluent (EFF) of a conventional wastewater treatment plant (WWTP) in Egypt. Furthermore, the risk indices of the local INF and EFF resistomes were compared to those calculated for the selected publicly available wastewater datasets from eight countries worldwide. Additionally, a classification framework prioritizing the public health hazard level of the discharged non-redundant highly mobilized ARGs was introduced. This integrative outline considered the estimated mobility potential percentage, host pathogenicity, and annotation category (perfect, strict, and loose) of the detected ARGs on their assembled contigs. Moreover, high-quality metagenome-assembled genomes (MAGs) were extracted and the putative genome bins with acquired ARGs were determined. The comprehensive resistome risk scores of the local WWTP showed that INF resistome had a slightly higher risk index (47.87) compared to the average score of the other examined counterparts (41.06). However, the estimated risk value of EFF resistome (26.80) was ranked within the global average (26.06) of the selected international WWTPs. Furthermore, the determination of the samples&rsquo; risk ranking showed that most of the effluent resistomes were clustered in a lower risk rank compared to the other selected samples for raw sewage, influent, and hospital wastewater, indicating the impact of the wastewater treatment process on reducing the ARG mobilization potential in downstream environments. The evaluation of the ARGs&rsquo; genetic context in their ARG-carrying contigs (ACCs) indicated that a total of 161/648 (25%) non-redundant ARGs were co-located with sequences of mobile genetic determinants on the same ACC in both the INF and EFF assemblies. These ARGs comprised the pan mobile resistome of the studied WWTP. Of them, 111 ARGs with a mobility potential percent (M%) less than 95% were grouped at the least risk level 5. The remaining 50 highly mobilized ARGs (M% &ge; 95%) were extracted and classified into four higher risk levels. Those of risk levels 1 and 2 (39 ARGs) represented the current ARG dissemination threats for further monitoring in downstream environments, where they were all carried by pathogenic hosts and annotated to the perfect and strict categories by the resistance gene identifier software (RGI). A total of 10 highly mobilized ARGs were assigned to risk rank 3, as they comprised the loose hits of the RGI analysis. Finally, the risk level 4 ARGs constituted genes that co-existed with the non-pathogenic sequence on the ACCs and were represented by one gene in the current analysis framework. The two previous categories constituted new highly mobilized ARGs of emergent threat to public health. On the other hand, a total of 35 and 118 MAGs were recovered from INF and EFF assembled metagenomes, respectively, using selection cutoff thresholds of a minimum completeness of 70% and a maximum contamination of 10%. While none of the INF MAGs carried any acquired ARGs, six EFF genome bins (5%) were associated with ten acquired ARGs, as indicated by the ResFinder software. These results suggest that potential horizontal gene transfer (HGT) events have evolved among the community members of the studied EFF samples

Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering

The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes

Functional Interpretation of Cross-Talking Pathways with Emphasis on Amino Acid Metabolism in Rhizosphere Microbiome of the Wild Plant Moringa oleifera

The functional processes and mutual benefits of the wild plant Moringa oleifera and its rhizosphere microbiome were studied via metagenomic whole-genome shotgun sequencing (mWGS) in comparison with a bulk soil microbiome. The results indicated high gene abundance of the four KEGG categories, &ldquo;Cellular Processes&rdquo;, &ldquo;Environmental Information Processing&rdquo;, &ldquo;Genetic Information Processing&rdquo;, and &ldquo;Metabolism&rdquo;, in the rhizosphere microbiome. Most of the enriched enzymes in rhizobacteria are assigned to the pathway &ldquo;Amino acids metabolism&rdquo;, where soil-dwelling microbes use amino acids as a defense mechanism against phytopathogens, while promoting growth, colonizing the cohabiting commensal microbes and conferring tolerance against abiotic stresses. In the present study, it was proven that these beneficial microbes include Bacillus subtilis, Pseudomonas fluorescens, and Escherichia coli. Mineral solubilization in these rhizobacteria can make nutrients available for plant utilization. These rhizobacteria extensively synthesize and metabolize amino acids at a high rate, which makes nitrogen available in different forms for plants and microbes. Amino acids in the rhizosphere might stand mainly as an intermediate switcher for the direction of the soil nitrogen cycle. Indole acetic acid (IAA) was proven to be synthesized by these beneficial rhizobacteria via route indole-3-pyruvate (IPyA) of the pathway &ldquo;Tryptophan metabolism&rdquo;. This hormone might stand as a shuttle signaling molecule between M. oleifera and its rhizobacteria. Tryptophan is also metabolized to promote other processes with important industrial applications. Rhizobacteria were also proven to breakdown starch and sucrose into glucose, which is the primary metabolic fuel of living organisms. In conclusion, we assume that the metabolic processes in the rhizosphere microbiome of this wild plant can be eventually utilized in boosting the sustainability of agriculture applications and the plant&rsquo;s ability to benefit from soil nutrients when they are not in the form available for plant root absorption

Functional annotation of rhizospheric phageome of the wild plant species Moringa oleifera

IntroductionThe study aims to describe phageome of soil rhizosphere of M.oleifera in terms of the genes encoding CAZymes and other KEGG enzymes.MethodsGenes of the rhizospheric virome of the wild plant species Moringa oleifera were investigated for their ability to encode useful CAZymes and other KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes and to resist antibiotic resistance genes (ARGs) in the soil.ResultsAbundance of these genes was higher in the rhizospheric microbiome than in the bulk soil. Detected viral families include the plant viral family Potyviridae as well as the tailed bacteriophages of class Caudoviricetes that are mainly associated with bacterial genera Pseudomonas, Streptomyces and Mycobacterium. Viral CAZymes in this soil mainly belong to glycoside hydrolase (GH) families GH43 and GH23. Some of these CAZymes participate in a KEGG pathway with actions included debranching and degradation of hemicellulose. Other actions include biosynthesizing biopolymer of the bacterial cell wall and the layered cell wall structure of peptidoglycan. Other CAZymes promote plant physiological activities such as cell-cell recognition, embryogenesis and programmed cell death (PCD). Enzymes of other pathways help reduce the level of soil H2O2 and participate in the biosynthesis of glycine, malate, isoprenoids, as well as isoprene that protects plant from heat stress. Other enzymes act in promoting both the permeability of bacterial peroxisome membrane and carbon fixation in plants. Some enzymes participate in a balanced supply of dNTPs, successful DNA replication and mismatch repair during bacterial cell division. They also catalyze the release of signal peptides from bacterial membrane prolipoproteins. Phages with the most highly abundant antibiotic resistance genes (ARGs) transduce species of bacterial genera Pseudomonas, Streptomyces, and Mycobacterium. Abundant mechanisms of antibiotic resistance in the rhizosphere include “antibiotic efflux pump” for ARGs soxR, OleC, and MuxB, “antibiotic target alteration” for parY mutant, and “antibiotic inactivation” for arr-1.DiscussionThese ARGs can act synergistically to inhibit several antibiotics including tetracycline, penam, cephalosporin, rifamycins, aminocoumarin, and oleandomycin. The study highlighted the issue of horizontal transfer of ARGs to clinical isolates and human gut microbiome