Community and functional shifts in sediment microbiomes driven by coral-algal proximity in the Northern Red Sea

Coral–algy -55al interfaces are hotspots of biogeochemical activity, yet the structure and functional roles of sediment microbiomes associated with these habitats remain poorly resolved, particularly in the environmentally extreme northern Red Sea. This study characterizes how microbial community composition and functional potential vary with coral–algal proximity across three coastal sites (Alshreah, Saweehal, Marwan Cave). Shotgun metagenomic sequencing was performed on 18 sediment samples collected from two contrasting habitats at each site: (i) far-from-algae zones (≥500 m) and (ii) close-to-algae zones (≤10 m). Across all locations, eight dominant bacterial species structured the sediment microbiome, including Shewanella algae, Arenibacter algicola, Vibrio algicola, Zobellia alginiliquefaciens , and Prochlorococcus marinus . Species-level patterns showed strong spatial heterogeneity, with Marwan Cave consistently dominated by S. algae , while other sites exhibited clear habitat-dependent shifts. A. algicola and S. algae were more abundant near coral–algal habitats, whereas V. algicola was more prevalent in distant sediments. Further analysis indicated that both geographic location and algal proximity contributed to community structuring, with proximity effects most apparent at Alshreah and Saweehal. Functional profiles revealed clear habitat partitioning. Close-to-algae sediments were enriched in genes for chemotaxis, glycerol transport, and anaerobic metabolism, indicative of bacterial exploitation of algal exudates and low-oxygen microzones, while far-from-algae sediments showed higher representation of ABC transport systems, amino-acid metabolism, and stress-response pathways, reflecting nutrient-limited and more environmentally variable conditions. Overall, proximity to coral–algal assemblages emerged as a major ecological gradient shaping both the taxonomic and functional attributes of Red Sea sediment microbiomes, operating alongside strong site-level environmental differences. These findings highlight the biogeochemical influence of benthic algae and provide baseline insights into microbial processes that may reinforce coral–algal regime shifts in warming reef systems.