Microbial activity is one of the most important processes to mediate the flux of organic carbon from the ocean surface to the seafloor.However,little is known about the microorganisms that underpin this key step of the global carbon cycle in the deep oceans.Here we present genomic and transcriptomic evidence that five ubiquitous archaeal groups actively use proteins,carbohydrates,fatty acids and lipids as sources of carbon and energy.Applying random shotgun sequencing,de novo genome assembly and advanced tetranucleotide-based binning approaches,we reconstructed a total of 59 near-complete genomes of uncultured marine archaea at depths ranging from 800 to 4950 m in hydrothermal vent plumes and pelagic background seawater across three different ocean basins,including Guaymas Basin,Lau Basin,and the Mid-Cayman Rise.