Reassembly of active ammonia oxidizing bacteria following invasion of exogenous microbiome in an acidic soil

Abstract

Ammonia oxidation is the rate-limiting step of the global nitrogen cycle, and it is mainly catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). AOA can carry out nitrification even in acidic soils, whereas AOB activity was not consistently observed in acidic soils. In this study, we manipulated two environmental variables, i.e., the microbial composition and ammonium source (urea and ammonium sulphate), in an acidic forest soil and tested their impacts on AOB abundance, diversity and activity. Soil microcosms were established either using the native forest soil (FS) or after amending the forest soil with 5% (w/w) agricultural soil (AFS) to inoculate new, exogenous microbes. Under the same microcosm incubation condition for 28 days, AOB did not grow in FS but they grew in AFS, suggesting that exogenous microbial invasion could stimulate AOB activity in the acidic soil. Urea amendment led to higher growth of AOB than ammonium sulphate amended in AFS microcosms. DNA-based stable isotope probing revealed that the active AOB lineages were dominated by Nitrosospira cluster 3a.2 and Nitrosospira cluster 10 in the ammonium sulphate supplied soil, but shifted to co-dominance of Nitrosospira cluster 3a.2 and Nitrosospira cluster 1 after urea amendment, demonstrating differential preferences of ammonia sources of phylogenetically distinct AOB lineages. Additionally, AOB abundance showed lower stability than AOA in soils subjected to these two environmental changes, suggesting AOB are more important in determining the fate of soil nitrification following short-term environmental disturbances.