Microbial diversity and functional potential of arid and semi-arid soils in Algeria: A metagenomic approach

Abstract

Despite covering over 40% of Earth's land area, the microbial diversity and adaptive mechanisms of arid and semi-arid regions remain poorly understood. This gap is notable in Algeria, where prior studies focused on limited ecological aspects and used varying sequencing depths, leaving regions like Djanet largely unexplored. This research targets these environments, specifically Setif and Djanet, to investigate microbial community structures and functions in these tough conditions. Soil samples were analyzed for physicochemical properties, including pH, electrical conductivity, and elemental composition, using standard methods. Bacterial diversity and adaptation traits were examined through 16S rRNA gene amplicon sequencing (Illumina MiSeq V3–V4), revealing a detailed microbial profile. Significant differences (p < 0.05) appeared in calcium carbonate, organic matter, and calcium ions across sites. The sequencing yielded 255,206 quality reads, identifying 27 phyla, 71 classes, 151 orders, 205 families, 353 genera, and 7409 species. Actinobacteria and Chloroflexi were dominant, with Acidimicrobiota and Thermobilia also present. An unclassified Actinobacteria family (AKIW781, 15.2%) was most common in RM2 (Tassili Djanet) and RM3 (Forest Elouricia), while Nocardioides was prevalent in RM1 (Oasis Djanet, at 5.35%). Unique genera such as Skermanella and Agromyces appeared in RM1, whereas Bacillus was restricted to RM2. Alpha diversity was highest in RM1 and lower in RM2 and RM3. Overall, the study highlights significant variations in microbial diversity, gene potential, and soil properties among the sites. β-diversity analysis showed distinct microbial communities, with RM1 having a unique composition compared to RM2 and RM3. Functional prediction tools such as PICRUSt and KEGG pathways indicated that, in these arid zones, microbial metabolic pathways favored antioxidant production and osmotic regulation, both vital for survival in extreme conditions. Notably, functional shifts along the arid gradient revealed that RM1 possesses unique adaptive traits supporting the desert–oasis transition. This research provides essential data for bioprospecting microbial resources in Algeria's arid zones and enhances understanding of microbial adaptation in extreme environments.