Alternative carbon and energy metabolisms linked to hydrocarbon degradation are widely distributed across the different microbial communities from deep-sea sediments of the Gulf of Mexico.

In marine sediments, microorganisms' roles in recycling organic and inorganic molecules, including hydrocarbons, are critical for ecosystem function. Genomic studies in the Gulf of Mexico (GoM) reveal that microbial community composition and function are shaped by environmental gradients, with hydrocarbon degradation relying on consortia dynamics rather than single species, highlighting their collective ecological importance. Our study evaluated the prokaryotic microbial community in deep-sea GoM sediments, under a depth gradient, in Coatzacoalcos and Perdido regions, two areas influenced by crude-oil efflux and petroleum extraction. Findings indicated depth was the primary driver of microbial community structure, with distinct compositional shifts between shallow (< 1000 m) and deep (> 1200 m) sediments, showcasing microbial adaptation to deep-sea nutrient-limited conditions. Furthermore, functional gene analysis revealed depth-specific metabolic partitioning, with Deltaproteobacteria dominating amino acid and energy metabolism in shallow sediments, while Alphaproteobacteria and Thaumarchaeota prevailed in deeper zones. This underlines the importance of microbial community shifts in composition and structure in ensuring environmental resilience. In addition, relatively low-abundance but critical hydrocarbon degradation genes were detected, primarily in shallow/transition zones, indicating niche-specific potential for bioremediation despite their apparent limited representation. This research contributes to advancing our understanding of alternative carbon and energy metabolisms linked to hydrocarbon degradation that are widely distributed across different microbial communities inhabiting deep-sea marine sediments.