Disturbance reshapes functional redundancy and accelerates nitrification in soil nitrifying communities.

Statistical and culture-based models propose that environmental disturbances reshape competitive interactions among functionally redundant microbial taxa. However, the mechanisms driving these changes and their impact on biogeochemical processes remain largely untested in soil, owing to the challenge of linking functions to specific taxa in highly diverse and functionally complex soil microbiomes. Here, we simulated environmental disturbance in microcosms containing organic carbon-rich or sandy soils. Using bacterial and archaeal nitrifiers, a functionally tractable microbial guild, we examined how disturbance restructures competition among diverse microbial taxa within this guild. In both soils, ammonia-oxidizing archaea (AOA) predominated numerically and functionally under steady climax conditions. Following disturbance, ammonia-oxidizing bacteria (AOB) and complete ammonia oxidizers (comammox) rapidly gained a growth-related competitive advantage, likely due to increased per-cell ammonium availability supporting their intrinsic high growth rates. AOB recolonization was essential for full post-disturbance nitrogen turnover, resulting in elevated nitrification rates and increased nitrous oxide emissions. Nitrification rate did not fully recover when AOB were inhibited. In contrast, AOA and comammox played a dispensable role in recovering post-disturbance nitrification, limited by slower growth and lower per-cell activity, respectively. Competitive regrowth ability of microbial species showed a tradeoff with pre-disturbance abundance, highlighting the enhanced post-disturbance role of rare-abundance AOA, in addition to AOB phylotypes. Our findings demonstrate that bacterial and archaeal nitrifiers constitute a continuous spectrum between r- and K-strategists. Disturbance reshapes competition through differential growth and activity traits among functionally redundant taxa, favoring AOB and thereby transforming community assembly while intensifying nutrient cycling and greenhouse gas fluxes.