Niche specialization and prevalence of comammox Nitrospira in the alkaline sediments of thermokarst lakes on the Tibetan Plateau.

Complete ammonia-oxidizing (comammox) Nitrospira are recognized as key players in the nitrogen cycle, yet their ecological roles in extreme environments remain poorly understood. Here, we show that comammox Nitrospira occupy distinct ecological niches in Tibetan Plateau thermokarst lakes (pH 7.5-10.2) using stable isotope probing, metagenomics, and metatranscriptomics. While gross nitrification rates are significantly higher in subalkaline lakes due to the active presence of ammonia-oxidizing archaea (AOA) and bacteria (AOB), these canonical nitrifiers are inhibited under elevated pH. In contrast, comammox Nitrospira activity is significantly higher in alkaline than in subalkaline lakes, becoming the predominant nitrifiers with activities exceeding those of AOA and AOB by over 6- and 15-fold, respectively. This niche transition, coupled with the inherently low N2O yield of comammox, results in significantly attenuated nitrous oxide (N2O) production in alkaline lakes. Under saline-alkaline stress, these bacteria maintained high expression of carbon fixation and sulfur metabolism genes while upregulating compatible solute biosynthesis, cation transporters, and protein chaperones. Altogether, these findings identify comammox bacteria as key mediators of nitrogen cycling in permafrost-affected thermokarst lakes, expanding their known physiological range and providing mechanistic insights into their adaptations to extreme environments.