A comparative study of ammonia-oxidizing archaea and bacteria in acidic and alkaline purple soils

Abstract

Soil pH has been suggested as one of the most important factors affecting the ecological characteristics of soil ammonia-oxidizers (AO), which mediate the conversion of ammonia to nitrate via nitrite and contribute significantly to the leaching of nitrate to groundwater and the production of atmospheric nitrous oxide (N2O). However, the dynamics of the AO community in acidic purple soils, which are widely distributed in Southwest China, remain largely unknown. In this study, two typical purple soils with different pH values (acidic: ACI; alkaline: ALK) were collected and studied. The abundance of amoA (gene encoding ammonia monooxygenase) of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and that of the cbbL gene (encoding ribulose-1,5-biphosphate carboxylase/oxygenase) were determined by real-time PCR, and the community structures of AOB and AOA were investigated by cloning and sequencing. The results revealed that abundances of AOB and AOA were significantly lower in the ACI purple soil sample than in the ALK sample, but a higher ratio of AOA to AOB was found in the ACI purple soil sample. No significant difference in the abundance of cbbL was found between the two soils, but the ratio of AOB and AOA amoA to cbbL genes in the ACI soil samples was higher than that in the ALK sample. Moreover, the ALK and ACI soils harbored contrasting community compositions of AO. AOB in the ALK were dominated by cluster 3a (87 %), while the percentage of cluster 3a decreased and clusters 9 and 10 accounted for almost 77 % of the AOB community in the ACI soil. Nitrososphaera and Nitrosotalea were the major AOA phylotypes in the ALK and ACI soils, respectively. In conclusion, our results revealed the potential relations among pH, AO, and total chemoautotrophic bacteria in soil and that pH might have an essential impact on the adaptation and selection of AO in purple soils.