Comparative Metagenomics to Study the Impact of Soil Salinity on Microbial Diversity in Al-Madinah, KSA

Abstract

Abstract The chemical properties and fertility of soil are greatly influenced by soil microbes, which are essential to the biogeochemical cycle. Analyzing the microbial structure of soil is important for efficient use of the soil, whether it be for agricultural purposes or other uses. Sabkhat Al-Madinah in Saudi Arabia has soil with high salinity and plants that thrive in that environment. The microbial makeup of the soil in this area has not been extensively researched. This study aimed to analyze the microbial structure of two locations in Sabkhat Al-Madinah's soil and examine the correlation with soil properties. The 16S rRNA gene's V3-V4 region was targeted for metagenomic analysis using Illumina MiSeq. The soil chemical properties including EC, pH as well the concentration of some soil elements were determined. The microbial composition of both sites were investigated at different taxonomic levels using MG-RAST and QIIME2 pipelines. There was a significant difference in salt concentration between the two sites that were derived from the same sabkha. The second sample had higher sodium content, leading to increased E.C measures. Moreover, The two samples had different microbial compositions. The first sample was dominated by Bacteroidetes (18.37%), Firmicutes (13.57%) and Proteobacteria (13.57%), while the second one contained Proteobacteria (25.01%), Actinobacteria (12.03%) and Firmicutes (11.36%). Firmicutes were newly recorded and found only in saline habitats in KSA. Acidobacteria, Thermodesulfobacteria and Streptophyta were present only in the first sample, while Verrucomicrobia sequences were identified only in the second sample which had higher salt content. On the genus level, 16 genera were found across both samples with Bacillus being the most prevalent at 5.17% followed by Marinoscillum (4%), Fibrobacter (3.57%) and Rubrobacter (3.45%) in the first sample. The second soil sample had a dominant genus, Halomonas, making up 10.64% of the total sequences. Other genera present included Fibrobacter (3.96%), Nitrospira (3.92%), Rubrobacter (3.36%) and Methylophaga (3%). In conclusion, the analysis of bacteria in the two sites revealed notable differences in soil properties and bacterial diversity.