Metaproteomic Insights into Bioenergy Conversion Enzymes of Bathypelagic Microbial Communities in the South China Sea

Marine microorganisms inhabiting the bathypelagic zone (1000-4000 m) exhibit distinctive environmental adaptability and serve as a valuable reservoir of bioenzymes. However, a limited understanding of deep-sea microbial community composition and metabolic activities hinders the broad application of their enzymatic potential. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities in the bathypelagic layers of the South China Sea (SCS), and we compared them with the corresponding metagenomic data. Our findings revealed a strong phylum-level correlation between metaproteomic and metagenomic datasets, along with a significant enrichment of proteins associated with inorganic ion metabolism and energy conversion. Deep-sea microbial communities are characterized by unique dominant taxa, such as Propionibacteriales, and exhibit diverse strategies for energy utilization. Notably, we identified several enzymes involved in energy conversion, including RuBisCO and carbon monoxide dehydrogenase in Proteobacteria and ammonia monooxygenase in Thaumarchaeota for carbon fixation. These enzymes catalyze reactions utilizing various inorganic substrates as energy sources. Additionally, the deep-sea environment significantly enhanced the expression of methane monooxygenase in methylotrophs, suggesting that such conditions may promote the development of methane-utilizing cell factories. This study not only deepens our understanding of energy conversion mechanisms in deep-sea microorganisms but also offers valuable enzymatic resources for the development of novel bioenergy technologies.