Active Soil Nitrifying Communities Revealed by <i>In Situ</i> Transcriptomics and Microcosm-Based Stable-Isotope Probing
Weiwei Xia, Jun Zhao, Yan Zheng, Huimin Zhang, Jiabao Zhang, Rui-Rui Chen, Xiangui Lin, Zhongjun Jia
Abstract
The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics and microcosm-based stable-isotope probing. The results showed that chronic N enrichment led to competitive advantages of Nitrosospira cluster 3-like AOB over N. viennensis -like AOA in soils under field conditions. Microcosm labeling revealed similar results for active AOA and AOB, although an apparent discrepancy was observed for nitrite-oxidizing bacteria. This study suggests that the soil microbiome represents a relatively stable community resulting from complex evolutionary processes over a large time scale, and microcosms can serve as powerful tools to test the theory of environmental filtering on the key functional microbial guilds.