Inhibition of autotrophic nitrifiers in a nitrogen-rich paddy soil by elevated CO2

Autotrophic nitrifiers, by catalysing the oxidation of ammonia to nitrate, play a vital role in the global nitrogen cycle. They convert carbon dioxide (CO₂) into biomass and, therefore, are expected to respond positively to increasing atmospheric CO₂ concentrations. 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 (genomes not recovered from metagenomes) of dominant but previously uncharacterized autotrophic nitrifying species. These species belonged mainly to ammonia-oxidizing archaea and nitrite-oxidizing bacteria and comprised 63% of total dominant members identified from the active nitrifying communities. We further showed that the functional 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 climate change.