Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria in Diverse Chinese Paddy Soils

Abstract

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) in three types of paddy soils of China before and after rice plantation were investigated by using an integrated approach including geochemistry, 454 pyrosequencing, and quantitative polymerase chain reaction (PCR). The abundances of AOA amoA gene were 1∼2 orders of magnitude higher than AOB amoA gene. The types of paddy soils had important impacts on the diversities of both AOA and AOB via clay mineralogy (smectite or illite-rich) and bioavailability of ammonium. The Nitrososphaera subcluster 5 and Nitrosopumilis cluster of AOA, and Nitrosomonas subcluster 5 and Nitrosospira subcluster 3 of AOB were well adapted to soils with high ammonium concentrations. AOA and AOB community structures were different before and after rice plantation, likely due to changes of pH and ammonium fertilization. The Nitrosospira subclusters 2 and 9 were well adapted to acidic paddy soils. However, the sensitivity of AOA and AOB community structures to these factors may be complicated by other geochemical conditions. The results of this study collectively demonstrated that multiple environmental factors, such as clay mineralogy, ammonium content and total organic carbon as well as soil pH, shaped AOA and AOB community structure and abundance.

Keywords:

• abundance
• AOA
• AOB
• Chinese paddy soil
• diversity
• flooding

Acknowledgments

This work was supported by the National Program on Key Basic Research Project (973 Program) (2012CB822000) and the Scientific Research Funds for the 1000 “Talents” Program Plan from China University of Geosciences-Beijing. The authors are grateful to Mr. Joseph P. Peacock from the University of Nevada, Dr. Marco J. L. Coolen from Woods Hole Oceanographic Institute and Dr. James T. Hollibaugh from the University of Georgia for their suggestions on 454 pyrosequencing data analysis. We are grateful to two anonymous reviewers whose comments improved the quality of this manuscript.