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.

自养硝化剂通过催化氨氧化成硝酸盐，在全球氮循环中起着至关重要的作用。它们将二氧化碳 （CO₂） 转化为生物质，因此有望对大气中_CO2 浓度的增加做出积极反应。然而，在一项长期的自由空气 CO₂ 富集实验中，我们证明了大气中升高的 CO₂ 抑制了自养硝化剂的生长，导致水稻生态系统中的硝化作用减少。通过将稳定同位素探测与宏基因组学相结合，我们发现硝化剂的 CO₂ 抑制主要是 CO₂ 诱导的优势但以前未表征的自养硝化物种的功能丧失（基因组未从宏基因组中恢复）的结果。这些物种主要属于氨氧化古细菌和亚硝酸盐氧化细菌，占从活性硝化群落中鉴定出的占优势成员总数的 63%。我们进一步表明，这些新型硝化物质在 CO₂ 升高下的功能损失主要是由于 CO₂ 诱导的水稻土壤中缺氧胁迫加剧。我们的结果为气候变化下全球低地土壤和水系统中无机氮库的命运提供了见解。