Sulfur-cycling diazotrophs dominate nitrogen fixation in seagrass sediments

Diazotrophs, the microbes capable of fixing dinitrogen, are essential for providing bioavailable nitrogen that supports marine primary production. Traditionally, nitrogen fixation in seagrass sediments has been linked primarily to heterotrophic sulfate reduction, leaving the roles of other metabolic processes, like sulfur oxidation, largely unexplored. Here, we employed metagenomic and metatranscriptomic approaches to explore the distribution, metabolic capabilities, and activity of diazotrophs in sediments dominated by the seagrass Halophila ovalis in a subtropical bay in Hong Kong. Our results revealed significantly higher nitrogen fixation rates in seagrass-vegetated sediments compared to adjacent bare sediments, with peak rates occurring in subsurface layers, suggesting that seagrass sediments may serve as hotspots for nitrogen fixation. We recovered 305 metagenome-assembled genomes, including those of diazotrophic sulfur-cycling bacteria. Notably, sulfur-oxidizing Gammaproteobacteria and sulfate-reducing Desulfobacterota emerged as the dominant and active members of the diazotroph community in seagrass sediments, expressing specific genes related to both nitrogen and sulfur metabolic pathways. Furthermore, our findings suggest that sulfate-reducing Desulfobacterota likely drive the high nitrogen fixation rates observed in deeper sediment layers, while sulfur-oxidizing Gammaproteobacteria may play a crucial role in surface layers. This study underscores the important roles of both sulfate-reducing and sulfur-oxidizing bacteria in nitrogen fixation within seagrass sediments, revealing a complex interplay between nitrogen fixation and sulfur metabolism.IMPORTANCESeagrass meadows are vital blue carbon ecosystems found in coastal and estuarine regions, playing a crucial role in carbon sequestration and supporting marine diversity. Traditionally, biological nitrogen fixation, an essential process for supplying bioavailable nitrogen to living organisms, has been primarily associated with heterotrophic sulfate reduction in these ecosystems. Our research offers novel insights into the nitrogen-fixing microorganisms present in the sediments dominated by the seagrass Halophila ovalis. We found that both sulfur-oxidizing and sulfate-reducing bacteria contribute to nitrogen fixation processes in seagrass sediments. This study highlights the intricate connections between nitrogen and sulfur metabolic pathways, providing a more comprehensive understanding of nutrient cycling in coastal ecosystems.