The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3–V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.
Plant leaves and roots are home to diverse communities of bacteria, which play a significant role in plant health and growth. Although one of the most unfriendly environments for plant growth is deserts, desert plants can influence their surrounding microbial population and choose favorable bacteria that encourage their growth under these severe circumstances. Senna italica is known for its excellent medicinal values as a traditional medical plant, but little is known about its associated endophytic bacterial community under extreme conditions. In the present study, metagenomic sequencing of 16S rRNA was used to report the diversity of endophytic bacterial communities associated with the leaves and roots of the desert medicinal plant Senna italica that was collected from the Asfan region in northeast Jeddah, Saudi Arabia. Analyses of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to five phyla, including Cyanobacteria, Proteobacteria, Actinobacteria, Firmicutes, and unclassified phyla. Results indicated that the most common phyla were Cyanobacteria/Chloroplast and Actinobacteria. Analysis of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to twelve genera at the taxonomic genus level. The most abundant ones were highlighted for further analysis, including Okibacterium and Streptomyces found in Actinobacteria, which were the dominant genus in roots samples. However, Streptophyta found in Cyanobacteria/Chloroplast was the dominant genus in leaf samples. Metagenomic analysis of medicinal plants leads to identifying novel organisms or genes that may have a role in abiotic stress resistance in the plant. The study of endophytic microbiome taxonomic, phylogenetic, and functional diversity will better know innovative candidates that may be selected as biological agents to enhance agricultural and industrial processes, especially for crop desert agricultural improvement.
Natural microbial communities associated with desert plants are found in soils that face nutrient deficiencies and extreme environments, including salinity and drought. In this study, 16S rRNA metagenomic sequencing was used to screen and identify bacterial assemblies associated with the desert plant Senna italica, obtained from diverse soil samples located in the Asfan region, northeast of Jeddah, Saudi Arabia. Several studies found Senna italica as a valuable medicinal plant for treating different diseases; however, a few studies were done on its association with bacterial communities under drought conditions. This study aimed to identify bacterial communities present in the drought soil environment of the Senna italica plants. To approach our goals, we applied metagenomic techniques, discovering a new bacterial strain beneficial for biotechnological applications. Our results showed that the analysis of the 16S rRNA sequences at the taxonomic phylum level detected 15 phyla of bacterial populations in the soil samples. The most prevalent was kept for further research. Our findings demonstrated that rhizospheric bacteria may be used as indicators of plant growth rate and survival ability in hostile environments. Studying the soil microbiome's taxonomic, phylogenetic, and functional diversity will facilitate identifying new candidates for biological agents that can be used to improve agricultural and industrial processes.
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