Inhibition of autotrophic nitrifiers in soil by elevated CO2

Abstract Autotrophic nitrifiers, by catalyzing the oxidation of ammonia to nitrate, play a vital role in the global nitrogen cycle ¹–⁵. They convert carbon dioxide (CO₂) into biomass ¹,³,⁶ and, therefore, are expected to respond positively to increasing atmospheric CO₂ concentrations ¹,³,⁶. However, in a long-term free-air CO₂ enrichment experiment, we demonstrated that elevated atmospheric CO₂ inhibited the growth of autotrophic nitrifiers, resulting in a reduction in nitrification in a rice ecosystem. By coupling stable isotope probing with metagenomics, we found that the CO₂ inhibition of nitrifiers was mainly a consequence of CO₂-induced functional loss (that is, incapable of recovering genomes) of dominant but previously uncharacterized autotrophic nitrifying species, especially those of ammonia-oxidizing archaea and nitrite-oxidizing bacteria, which comprised 63% of total dominant members identified from the active nitrifying communities. We further found that the loss of these novel nitrifying species under elevated CO₂ was due largely to the CO₂-induced aggravation of anoxic stress in the paddy soil. Our results provide insight into the fate of inorganic nitrogen pools in global lowland soil and water systems under future climate change scenarios.