eDNA metabarcoding reveals halophilic and halotolerant bacterial assemblages in the salt flats of the northern Red Sea coast

The salt flats (sabkhas in Arabic), located in NEOM, Saudi Arabia, along the northern Red Sea coast, are ecologically significant yet vulnerable arid ecosystems that harbor unique microbial biodiversity. These environments are increasingly exposed to varying salinity levels and anthropogenic pressures that may alter microbial community structure. Despite their recognized ecological significance, salt flats remain poorly studied in terms of bacterial diversity using molecular approaches. This study applied environmental DNA (eDNA) metabarcoding of 16 S rRNA gene to assess bacterial community diversity and composition across 30 sabkha soil samples from inland and coastal sites. High-throughput sequencing generated 285,900 high-quality reads, resulting in the identification of 363 operational taxonomic units (OTUs), spanning 219 genera, 49 families, 34 orders, and 8 phyla. The microbial community was dominated by halophilic and halotolerant taxa such as Halomonas , Caldalkalibacillus , Klebsiella , and Vibrio . The most abundant phyla identified were Pseudomonadota and Bacillota. Inland sabkhas contained fewer but highly specialized taxa, whereas coastal sabkhas supported more diverse assemblages, including marine-associated genera. Alpha and beta diversity metrics showed spatial variation, while multivariate analyses indicated soil texture as the key driver of community patterns. These findings represent the first molecular insight into bacterial communities of NEOM sabkhas, providing a baseline for long-term ecological monitoring. The findings support evidence-based conservation and sustainable development efforts and emphasize the utility of eDNA-based monitoring as a tool for guiding ecosystem management in the face of environmental change.