First shotgun metagenomic survey of depth-stratified microbial communities in the oligotrophic Jordanian Gulf of Aqaba (Red Sea) reveals depth-structured communities and nitrifier enrichment

IntroductionThe oligotrophic Gulf of Aqaba is characterized by strong vertical hydrographic gradients, yet depth-resolved metagenomic information on microbial community structure in the Jordanian sector remains limited. This study examined the microbial community composition across the water column.MethodsDuring the summer 2022 OceanXplorer expedition, seawater samples were collected at seven stations in the Jordanian Gulf of Aqaba from surface, deep chlorophyll maximum (DCM) and deep-water layers exceeding 800 m. High-resolution conductivity, temperature, and depth (CTD) profiles were used to characterize physicochemical gradients. Microbial DNA was subjected to shotgun metagenomic sequencing to assess community composition, diversity metrics, and depth-associated differences in microbial assemblages.ResultsCTD profiles revealed strong summer stratification and pronounced physicochemical gradients across the water column. GC content increased from 39.4% in surface samples to 46.1% in deep-water samples, indicating major taxonomic turnover with depth. Microbial community composition was strongly structured by depth, which explained 81.3% of Bray–Curtis dissimilarity variation (PERMANOVA: F = 36.89, p = 0.0001), whereas station-level variation was minimal. Alpha diversity also increased with depth, with observed richness rising 1.35-fold from surface to deep waters. Surface communities were dominated by Prochlorococcus_A and Pelagibacter, while the DCM hosted transitional assemblages containing of both surface-associated phototrophic taxa and deeper-water nitrifier-associated lineages. Deep waters were enriched in ammonia-oxidizing archaea, including Nitrosopelagicus, which averaged 4.86% in deep samples and 1.48% in the DCM, but was absent from the dominant surface genera.DiscussionThese findings identify depth-associated hydrographic stratification as the primary driver of microbial zonation in the Jordanian Gulf of Aqaba. The transition from phototroph-dominated surface communities to nitrifier-enriched deep-water assemblages suggests strong vertical partitioning of microbial functional potential. This study provides the first water-column-scale metagenomic dataset for microbial communities in the oligotrophic Jordanian Gulf of Aqaba and establishes a baseline for understanding their contribution to regional biogeochemical cycling.