Vertically stratified carbon fixation and coupling processes in deep-sea sediment

Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH₄⁺) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.