Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia

• Published in: Plants (Basel) Vol. 12; no. 11; p. 2176
• Main Authors: Baeshen, Naseebh N, Baz, Lina, Shami, Ashwag Y, Ashy, Ruba A, Jalal, Rewaa S, Abulfaraj, Aala A, Refai, Mohammed, Majeed, Mazen A, Abuzahrah, Samah S, Abdelkader, Hayam, Baeshen, Nabih A, Baeshen, Mohammed N
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 30-05-2023; MDPI
• Subjects: 16S rRNA gene; Abiotic stress; alpha diversity; Amaranthaceae; Bacteria; Bioinformatics; Comparative analysis; Deserts; Diversity indices; Environmental aspects; Environmental changes; Environmental conditions; Fungi; Genetic aspects; Halopeplis perfoliata; Halophytes; Identification and classification; Industrial applications; ITS rRNA gene; Measurement; Medical innovations; Metagenomics; microbial communities; Microbiomes; Microorganisms; Next-generation sequencing; Physiological aspects; Plant communities; Plant growth; Quality assessment; Quality control; Rhizosphere; rRNA 16S; Saline soils; Soil investigations; Soil microbiology; Soil microorganisms; Statistical analysis; Tamarisks; Tamarix aphylla; Taxonomy; Saudi Arabia; United States > US; beta diversity; Halopeplis perfoliata; ITS rRNA gene; alpha diversity; microbial communities; Tamarix aphylla; 16S rRNA gene
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12112176

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
and
. 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
was the most prevalent in the soil samples examined, followed by the phylum
. 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
and
, 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.