A microbial blueprint for nitrogen conservation: Overpowering N-loss with DNRA and diazotrophy in deep-sea sediments

Deep-sea sediments play a vital role in the global nitrogen cycle, yet how microbial communities regulate nitrogen transformations under extreme oligotrophy remains unclear. Using 15N isotope labeling and molecular analyses, we investigated vertical patterns of microbial nitrogen-cycling processes in two deep-sea sediment cores. Nitrification, predominantly mediated by ammonia-oxidizing archaea (97.82+/-5.33%), declined in surface layers but increased again with depth. In contrast, dissimilatory nitrate reduction to ammonium became more prominent in deeper layers, whereas biological nitrogen fixation decreased on average but remained active throughout. By comparison, denitrification and anammox rates were consistently negligible. Substrate limitation and structured DNRA-associated networks sustained DNRA and BNF across the sediment cores, while vertical reorganization of nrfA and nosZ communities reinforced this nitrogen-retention strategy. These findings indicated that microbial networks reorganized to favor nitrogen conservation pathways over nitrogen-loss processes in the oligotrophic deep-sea sediments. This adaptive nitrogen retention strategy enhanced nitrogen use efficiency and sustained ecosystem functioning under N-limitation, providing critical insights into microbial-driven biogeochemical cycling in the deep-sea biosphere.