Insight into the role of competition in niche differentiation between ammonia-oxidizing archaea and bacteria in ammonium-rich alkaline soil: A network-based study

Abstract

Interspecific competition between ammonia-oxidizing archaea (AOA) and bacteria (AOB) has been documented, however, its significance in niche differentiation between these nitrifiers under ammonia-rich conditions remains elusive. A network-oriented microcosm incubation study was established to improve our understanding of their interspecific competition. A high ammonium concentration was maintained during the incubation by regularly supplementing urea, and the growth of AOB was retarded to different extents using the AOB inhibitors 1-octyne (OC) and 3,4-dimethylpyrazole phosphate (DMPP) as amendments. In parallel, a 13CO2-stable isotope probing (SIP) incubation study was conducted to investigate the metabolic activity of AOA and AOB under ammonium-rich conditions, with and without DMPP amendment. The results of the network-oriented microcosm incubation indicated that the growth of AOA was highly and negatively correlated with the growth of AOB (r = −0.94, P < 0.001). Network analysis of the whole prokaryotes showed that the majority of AOA phylotypes formed a module independent of AOB phylotypes, indicating their distinct niche preferences. In another distinctive module, we found the remaining AOA to have a coexclusion pattern with AOB, indicating a competitive relationship and a positive connection between AOB and many taxa capable of nitrite/nitrate metabolism, in particular denitrification. The SIP study confirmed that all AOA and AOB phylotypes retained in the network were autotrophically active. It was also shown that the phylotype susceptible to AOB competition was closely related to Nitrososphaera viennensis EN76. Overall, the results demonstrate that both niche preference and interspecific competition contribute to niche partitioning between AOA and AOB. Our results also showed that a tight connection between AOB and other nitrogen-cycling microorganisms may be responsible for substantial nitrogen loss.