Comammox <i>Nitrospira</i> act as key bacteria in weakly acidic soil via potential cobalamin sharing

The discovery of comammox <i>Nitrospira</i> in low pH environments has reshaped the ammonia oxidation process in acidic settings, providing a plausible explanation for the higher nitrification rates observed in weakly acidic soils. However, the response of comammox <i>Nitrospira</i> to varying pH levels and its ecological role in these environments remains unclear. Here, a survey across soils with varying pH values (ranging from 4.4 to 9.7) was conducted to assess how comammox <i>Nitrospira</i> perform under different pH conditions. Results showed that comammox <i>Nitrospira</i> dominate ammonia oxidation in weakly acidic soils, functioning as a K-strategy species characterized by slow growth and stress tolerance. As a key species in this environment, comammox <i>Nitrospira</i> may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox <i>Nitrospira</i> uniquely encode a metabolic pathway that compensates for cobalamin imbalance in weakly acidic soils, where 86.8% of metagenome-assembled genomes (MAGs) encode cobalamin-dependent genes. Additionally, we used DNA stable-isotope probing (DNA-SIP) to demonstrate its response to pH fluctuations to reflect how it responds to the decrease in pH. Results confirmed that comammox <i>Nitrospira</i> became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox <i>Nitrospira</i> will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox <i>Nitrospira</i> perform in weakly acidic soil and its response to pH changes.