Zhao Yuxiang, Hu Jiajie, Wang Jiaqi, Yao Xiangwu, Zhang Tong, Hu Baolan
Key Laboratory of Environment Remediation and Ecological Health, Ministry of Education, College of Environmental Resource Sciences Zhejiang University Hangzhou China.
College of Environmental and Resource Sciences Zhejiang University Hangzhou China.
Imeta. 2025 Feb 4;4(1):e271. doi: 10.1002/imt2.271. eCollection 2025 Feb.
The discovery of comammox 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 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 perform under different pH conditions. Results showed that comammox 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 may promote bacterial cooperation under low pH conditions. Genomic evidence suggested that cobalamin sharing is a potential mechanism, as comammox 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 became dominant ammonia oxidizers in the soil after the decrease in pH. We suggested that comammox will become increasingly important in global soils, under the trend of soil acidification. Overall, our work provides insights that how comammox perform in weakly acidic soil and its response to pH changes.
在低pH环境中发现的完全氨氧化菌重塑了酸性环境中的氨氧化过程，为在弱酸性土壤中观察到的较高硝化速率提供了一个合理的解释。然而，完全氨氧化菌对不同pH水平的响应及其在这些环境中的生态作用仍不清楚。在此，我们对pH值不同（范围为4.4至9.7）的土壤进行了一项调查，以评估完全氨氧化菌在不同pH条件下的表现。结果表明，完全氨氧化菌在弱酸性土壤中主导氨氧化过程，作为一种以生长缓慢和耐胁迫为特征的K策略物种发挥作用。作为这种环境中的关键物种，完全氨氧化菌可能在低pH条件下促进细菌间的合作。基因组证据表明，钴胺素共享是一种潜在机制，因为完全氨氧化菌独特地编码了一条代谢途径，可补偿弱酸性土壤中钴胺素的失衡，在该土壤中，86.8%的宏基因组组装基因组（MAG）编码依赖钴胺素的基因。此外，我们使用DNA稳定同位素探测（DNA-SIP）来证明其对pH波动的响应，以反映它对pH降低的反应。结果证实，pH降低后，完全氨氧化菌在土壤中成为占主导地位的氨氧化菌。我们认为，在土壤酸化趋势下，完全氨氧化菌在全球土壤中将变得越来越重要。总体而言，我们的工作提供了关于完全氨氧化菌在弱酸性土壤中的表现及其对pH变化的响应的见解。
