Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in low pH soils. This study aimed to investigate the effect of different fertilisation histories on community composition and activity of acidophilic AOA in soils. High-throughput sequencing of ammonia monooxygenase gene (amoA) was performed on six low pH agricultural plots originating from the same soil but amended with different types of fertilisers for over 20 years and nitrification rates in those soils were measured. In these fertilised acidic soils, nitrification was likely dominated by Nitrososphaerales AOA and ammonia-oxidising bacteria, while Ca. Nitrosotaleaceae AOA activity was non-significant. Within Nitrososphaerales AOA, community composition differed based on the fertilisation history, with Nitrososphaerales C11 only representing a low proportion of the community. This study revealed that long-term soil fertilisation selects for different acidophilic nitrifier communities, potentially through soil pH change or through direct effect of nitrogen, potassium and phosphorus. Comparative community composition among the differently fertilised soils also highlighted the existence of AOA phylotypes with different levels of stability to environmental changes, contributing to the understanding of high AOA diversity maintenance in terrestrial ecosystems
We thank Prof Yuanqiu He (now deceased) at the State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences for his contribution to this study. In addition, we thank the staff of the Analysis Center at the Institute of Soil Science for technical support, including Ms Rong Huang and Mr Zuohao Ma for 454-pyrosequencing, Mr Ruhai Wang for the ammonia and nitrate and nitrite content assays, Mr Guoxing Lu for the SOM assay. We also thank Dr Jian Cui and Dr Xiaoli Liu for assistance in soil sampling in the fields.
This work was supported by the National Natural Science Foundation of China (41530857, 91751204 and 41977056). JZ was funded by a Natural Environment Research Council grant (NE/K016342/1) and CGR was supported by a Royal Society University Research Fellowship (URF150571).