Distinct biogeography of nitrite- and nitrate-dependent anaerobic methane oxidizing microorganisms in the yellow sea and yellow river

• Distinct n-DAMO biogeography between the Yellow River and Sea. • Divergent roles of n-DAMO bacteria and archaea in CH4 oxidation between ecosystems • Yellow Sea shows higher n-DAMO archaea abundance and nitrate-DAMO rates. • Salinity drives spatial variation in n-DAMO microbial communities. Nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) processes represent a critical methane sink to mitigate greenhouse gas emissions. However, it remains unclear whether there are ecological and interactional differences between n-DAMO bacteria and n-DAMO archaea in freshwater and marine environments. This study investigated n-DAMO microorganisms in China’s Yellow River (freshwater) and Yellow Sea (marine). We used stable isotope tracers and molecular techniques to analyze their distribution and activity. Active n-DAMO processes were detected in sediments from both ecosystems. Specifically, the nitrite-DAMO process was more predominant for methane oxidation in the Yellow River, while the nitrate-DAMO process was more significant in the Yellow Sea, with nitrate availability (NO 3 − -N) identified as a key influencing factor. The mcr A gene abundance of n-DAMO archaea was 19.9-fold higher in the Yellow Sea (average 2.94 × 10 8 copies g −1 dry weight) than in the Yellow River ( p < 0.05). Conversely, the pmo A genes of n-DAMO bacteria in Yellow River sediments showed marginally lower abundance compared to Yellow Sea sediments. n-DAMO microbial communities in the two ecosystems demonstrated distinct divergence, with salinity identified as the principal environmental driver, explaining 28.03% bacterial and 26.19% archaeal variance (RDA, p < 0.05). Phylogenetic niche partitioning was observed: Group A lineage of n-DAMO bacteria exclusively dominated Yellow River sediments (100% relative abundance), whereas Group B prevailed in Yellow Sea ecosystems, likely attributed to osmo-tolerance adaptations. These findings demonstrated biogeochemical conditions, especially salinity and substrate availability, determine the niche and functional differentiation of n-DAMO microbes.