Bacterial community structure and secondary metabolite insights from halophiles at Oniru Beach, Lagos

This study examines the bacterial diversity and potential for secondary metabolite production of halophilic bacteria isolated from Oniru Beach, Lagos, Nigeria, a moderately saline marine environment. Using high-throughput next-generation sequencing, we profiled the bacterial community structure and complemented this with culture-dependent techniques to identify metabolite-producing strains. Physicochemical analysis revealed a slightly alkaline, oligotrophic, and low-oxygen environment enriched with bioactive metals, such as potassium, calcium, and iron, which may influence microbial adaptation and metabolic activity. Taxonomic profiling showed Proteobacteria (53.72%) as the dominant phylum, followed by Bacteroidetes (29.43%), Actinobacteria (3.88%), Deinococci (1.59%), and Firmicutes (1.37%), with Gammaproteobacteria (47.72%) being the most abundant class. Genus-level analysis highlighted Acinetobacter, Chryseobacterium, Stenotrophomonas, Enterobacter, and Pseudomonas as key constituents of this microbial community. Salt-tolerance assays and 16 S rRNA sequencing identified highly halophilic isolates, including Serratia marcescens, Staphylococcus edaphicus and Kurthia gibsonii, which displayed diverse physiological and biochemical adaptations. Gas chromatography-mass spectrometry (GC-MS) revealed a wide range of secondary metabolites, including osmolytes, fatty acids, and sugar alcohols, underscoring the metabolic versatility of these isolates. Overall, this work demonstrates that Oniru Beach hosts a complex halophilic microbiome with specialized ecological adaptations and biotechnological potential, particularly for novel bioactive compound discovery and bioremediation strategies.