Seagrass-derived carbon suppresses nitrification and N₂O emissions by Comammox and canonical nitrifier communities

Seagrass meadows are critical regulators of coastal biogeochemical cycling, particularly through the exudation and accumulation of organic carbon that enriches their rhizosphere far beyond ambient marine levels. Microbially driven nitrification is a key process controlling nitrous oxide (N₂O) emissions, yet the ecological roles of complete ammonia oxidizers (Comammox) and canonical nitrifiers in seagrass ecosystems are poorly understood. Here, seagrass sediments (SS) exhibited significantly (P < .05) lower nitrification and N₂O production rates than non-seagrass sediments, where nitrification was the dominant N₂O source. We characterized Comammox for the first time in a seagrass ecosystem, revealing that they displayed potential nitrification rates lower than ammonia-oxidizing bacteria or ammonia-oxidizing archaea. Notably, Comammox showed the lowest potential N₂O production rates and negative CO₂ fluxes. Metagenomic profiles revealed lower relative abundances of genes associated with nitrification and N₂O-producing pathways in SS, while metatranscriptomic analysis identified significant (P < .05) down-regulation of the core nitrification genes. In contrast, genes involved in sugar transport and metabolism generally showed positive transcriptional changes. This study identifies a key microbial mechanism through which seagrass-derived carbon may contribute to lower nitrification and N₂O emissions, highlighting the potential of microbiome engineering in seagrass restoration and conservation for climate mitigation.