Nitrosospira cluster 3-like bacterial ammonia oxidizers and Nitrospira-like nitrite oxidizers dominate nitrification activity in acidic terrace paddy soils

Abstract

The isolation of acid-adapted ammonia-oxidizing bacteria (AOB) has suggested the functional importance of AOB in acidic soils. However, there is, currently, no convincing evidence that links AOB activity to nitrification in acidic paddy soils. Here we demonstrated the incorporation of 13CO2 into the genomes of ammonia-oxidizing archaea (AOA), AOB and nitrite-oxidizing bacteria (NOB) following urea application by using stable isotope probing (SIP) in three acidic terrace paddy soils with altitudes of 200 m (E200), 600 m (E600) and 1100 m (E1100), respectively. Nitrification activity increased from E200 to E600 and then to E1100, accompanied with significant growth of AOB over the 56-day incubation, while the abundance of archaeal amoA gene declined significantly in all soils after incubation. DNA-SIP demonstrated that active AOB outnumbered AOA and were much more heavily labeled than AOA and NOB, implying their more significant contributions to nitrification in these soils. Phylogenetic analysis indicated that Nitrosospira cluster 3-like AOB predominantly catalyzed bacterial ammonia oxidation. 13C-labeled NOB was dominated by Nitrospira moscoviensis in E1100, while in E200 and E600, Nitrospira marina and Nitrospira japonica were as prevalent as Nitrospira moscoviensis, respectively. Canonical correlation analysis and the Mantel test indicated the importance of soil physiochemical properties (e.g., pH, available phosphorus (AP) and soil oxidation capacity (OXC)) in determining the composition of the active nitrifying populations. These results suggest a greater functional importance of AOB in ammonia oxidation in the tested acidic paddy soils and the existence of a broader ecological niche for AOB than previously considered.