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.

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, “Cellular Processes”, “Environmental Information Processing”, “Genetic Information Processing”, and “Metabolism”, in the rhizosphere microbiome. Most of the enriched enzymes in rhizobacteria are assigned to the pathway “Amino acids metabolism”, 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 “Tryptophan metabolism”. 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’s ability to benefit from soil nutrients when they are not in the form available for plant root absorption.

Tinospora sagittata is a columbin-rich medicinal plant, but its columbin levels are reduced under artificial cultivation conditions. The objective of this study was to analyze the effects of inoculations with Diversispora versiformis (Dv), Funneliformis mosseae (Fm), Rhizophagus intraradices (Ri), and mixed inoculation (Dv + Fm + Ri) (Mix) on growth performance, root morphology, leaf photosynthetic physiology, and root columbin levels in T. sagittata. These arbuscular mycorrhizal fungi (AMF) were able to colonize the roots, as evidenced by a root mycorrhizal colonization rate ranging from 17% to 48% and soil hyphal lengths ranging from 17.51 cm/g to 32.02 cm/g, with the Mix treatment being the greatest. AMF inoculations improved plant height (16–151%), leaf number (119–283%), shoot (37–211%), and root biomass (22–318%) to varying extents, with Ri and Mix treatments being the most prominent. AMF-treated plants presented relatively greater root total length, projected area, surface area, volume, and average diameter, especially those treated with Ri and Mix. AMF inoculations also significantly improved the leaf nitrogen balance index, transpiration rate, and stomatal conductance, while the photosynthesis rate and chlorophyll index varied by AMF species, along with a decrease in intercellular CO₂ levels. Root columbin levels ranged from 0.524 mg/g to 5.389 mg/g, and AMF inoculation significantly increased root columbin levels by 228–928%, with Ri being the most significant. Root columbin levels were significantly positively correlated with soil hyphal length, root total length, root projected area, root surface area, root volume, and root average diameter, but not root AMF colonization rate. This study demonstrates for the first time that AMF, especially Ri, can be employed as a biostimulant to promote growth as well as root columbin levels in T. sagittata, where AMF-triggered improvement in root morphology is an important reason for promoting root columbin levels.

Moringa oleifera, known for its nutritional and therapeutic properties, exhibits a complex relationship with its rhizospheric soil microbiome. This study aimed to elucidate the microbiome's structural composition, molecular functions, and its role in plant growth by integrating Clusters of Orthologous Genes (COG) analysis with enzymatic functions previously identified through KEGG, CAZy, and CARD databases. Metagenomic sequencing and bioinformatics analysis were performed from the rhizospheric soil microbiome of M. oleifera collected from the Mecca district in Saudi Arabia. The analysis revealed a role for the rhizospheric microbiome in energy production, storage, and regulation, with glucose serving as a crucial precursor for NADH synthesis and subsequent ATP production via oxidative phosphorylation. Key orthologous genes (OGs) implicated in this process include NuoD, NuoH, NuoM, NuoN, NuoL, atpA, QcrB/PetB, and AccC. Additionally, OGs involved in ATP hydrolysis, such as ClpP, EntF, YopO, and AtoC, were identified. Taxonomic analysis highlighted Actinobacteria and Proteobacteria as the predominant phyla, with enriched genera including Blastococcus, Nocardioides, Streptomyces, Microvirga, Sphingomonas, and Massilia, correlating with specific OGs involved in ATP hydrolysis. This study provides insights into the molecular mechanisms underpinning plant–microbe interactions and highlights the multifaceted roles of ATP-dependent processes in the rhizosphere. Further research is recommended to explore the potential applications of these findings in sustainable agriculture and ecosystem management.

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.

High-throughput data are produced on a big scale and at several levels in order to comprehend complex diseases including cancer, diabetes, and kidney disorders. A significant obstacle still exists, nonetheless, in extracting useful information from huge datasets for a thorough comprehension of cell phenotypes and disease pathogenesis. Big data is created to address biological concerns as a result of technological advancements, and it is always easy for biologists and computer scientists to collaborate to streamline the massive datasets and extract the information that is relevant and physiologically important. In order to achieve this, we have classified using expression datasets and inferred the corresponding functional annotation using a computational technique. In order to analyze changes in gene expression and functional annotation, we employed a dataset of prostate cancer patients with normal and variable tumor percentages. We have chosen a gene expression omnibus (GEO) dataset that includes human samples with a range of tumor percentages (0–85%). We arranged the samples according to tumor proportion in ascending order and compared them to the control group (samples with no tumor) to look for changes in gene expression and developed functions as the tumor percentage increased. When the tumor percentage is less than 50%, we see some fluctuation in the number of differentially expressed genes (DEGs), but after that, it increases exponentially. In terms of the pathways, there is a lot of variation in the number of enriched pathways, with tumor < 50% not increasing, while several cancer-associated pathways seem to be enriched for nearly all the different tumor percentages. Our analysis leads us to the conclusion that whereas a number of cancer-associated pathways are consistently enriched for all tumor percentages, the number of differentially expressed genes (DEGs) grows as the tumor percentage rises while the enriched pathways do not. Insulin resistance, acute myeloid leukemia, basal TFs, HIF1-a, neurotrophin, base excision repair, ErbB, VEGF, and mTOR signaling pathways are among the top-ranked enriched pathways. RPP30, SRP14, CCNE1, PRKAR1A, ABCF2, PCMT1, TUBA1C, STOML2, PPP2R4, and TPI1 are possible pathway components.