Metagenomics-centric assembly of nitrifying communities in three pH-distinct soils with the same origin of parent material

Abstract:

[Objective] Aimed to reveal the community compositions of nitrifiers and its response to pH in typical agricultural upland purple soils. [Methods] Metagenomics was used to investigate the abundances and communities of soil nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB) and complete ammonia oxidizers (Comammox) in three purple soils that developed from the same parent material but varied in pH. [Results] The abundances of nitrifiers accounted for 2.130%-6.082% of the total microorganisms. The relative abundance of AOA in acid soil was significantly higher than that of alkaline soil, whereas AOB was the opposite; the relative abundance of NOB in neutral soil was the highest. A specie of Comammox named Candidatus Nitrospira inopinata (Ca. N. inopinata) was found in all soil samples, and its relative abundance was the highest in neutral soil, accounting for 0.203% of the total microorganisms. The community composition analyses of nitrifier showed that:the Nitrososphaera and Nitrospira were the dominant AOA and NOB in all soil samples; Nitroscoccus was predominant in AOB populations in acid soil, whereas in neutral and alkaline soils the dominant AOB was Nitrosospira. Pearson correlation analysis reveals that the abundances of these nitrifiers were driven by soil pH and NH₄⁺. [Conclusion] Comammox existed in all soil samples and had a preference for a neutral environment; the relative abundances and community compositions of AOA, AOB, and NOB all showed a significant difference, soil pH and NH₄⁺ were the two most influential factors.