Profiling the microeukaryote diversity in arid sabkha soils in NEOM, Saudi Arabia, using 18S rRNA-based eDNA metabarcoding

The sabkhas or salt flats in NEOM, Saudi Arabia are ecologically significant yet fragile environments that play a vital role in biodiversity conservation and ecosystem functioning. However, these arid ecosystems are increasingly exposed to urbanization and anthropogenic pressures that may alter their soil microbial communities, particularly eukaryotic microbes, which are essential indicators of ecosystem health and resilience. Despite their ecological importance, the diversity and composition of microbial eukaryotes in sabkhas remain poorly understudied by molecular-based tools. This study presents the first application of environmental DNA (eDNA) metabarcoding targeting the 18S rRNA gene to assess the biodiversity and community structure of microeukaryote communities across four sabkha sites: NEOM Bay (NB), Inland Gayal (IG), Coastal Gayal (CG), and the Intertidal Area (IA). A total of 20 soil samples were analyzed, revealing 35 genera across 32 families, 21 orders, and six phyla. The dominant phyla identified were Ascomycota (fungi) and Bacillariophyta (microalgae), with Phaeodactylum and Thalassiosira emerging as the most prevalent genera. Alpha diversity metrics indicated spatial variation across sites, while multivariate analyses revealed that community variation was influenced by environmental gradients and indicated taxon-environment associations. These results represent the first molecular insight into microeukaryote diversity in NEOM sabkhas, providing a baseline for future ecological monitoring. Moreover, this study demonstrates the utility of eDNA metabarcoding as a rapid and scalable approach for biodiversity assessment, with implications for informing sustainable development and conservation strategies in arid coastal ecosystems under increasing environmental pressure.