Habitat- and depth-dependent functional partitioning of AOA, AOB, and comammox under contrasting salinity and redox conditions.

Nitrification is mediated by ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (comammox), yet their functional partitioning across habitats with contrasting salinity and redox conditions remains poorly resolved. Here, we integrated amoA gene abundance, amoA transcript abundance, and dual-inhibitor-derived potential ammonia oxidation rates to compare the three guilds in intertidal sediments, saline soils, and agricultural soils. In high-salinity intertidal sediments, comammox had the highest gene and transcript abundances and accounted for approximately 54-85% of estimated ammonia oxidation, indicating strong agreement among population-, transcription-, and process-level indicators. In saline soils, AOA contributed the largest proportion of ammonia oxidation at all depths, accounting for approximately 47-59%, despite greater AOB gene abundance. Agricultural soils showed pronounced depth-dependent functional partitioning. Comammox contributed most at 0-5 cm at approximately 45%, AOA dominated at 5-10 cm at approximately 50%, and AOA and AOB contributed comparably at 10-15 cm at approximately 39% and 37%, respectively. Cross-level decoupling also differed among habitats. Intertidal AOB showed high transcript abundance relative to its small gene pool, whereas agricultural-soil AOA showed high gene abundance but comparatively low transcript abundance. Salinity and oxidation-reduction potential were associated with shifts in abundance, transcription, and functional contribution, together with variation in pH, organic carbon, and inorganic-N availability. These findings show that contrasting salinity and redox settings were associated with habitat-dependent reorganization, rather than uniform suppression, of ammonia oxidation. Integrating DNA-, RNA-, and process-level evidence provides a more reliable framework for identifying functionally important ammonia oxidizers in coastal transition zones and salt-affected soils.