Metabolic relationships and niche differentiation between ammonia-oxidizing microorganisms and complete ammonia oxidizers in soil ecosystems

Abstract Background: Ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammox) play a crucial role in nitrification, which is an essential process in terrestrial nitrogen cycling. However, partitioning of their ecological niches has never previously been demonstrated. In this study, we conducted batch incubation and applied a combination of 13C-stable isotopes and multiple inhibitor methods for the first time to elucidate the metabolic pathways and interactions of AOA, AOB, and comammox in soil subjected to different durations of winter irrigation. Results: The results showed that the proportion of organic 13C-labeled AOA and comammox increased by 14.4–75.5% after adding 13C-labeled organic matter. Meanwhile, the abundance of 13C-AOA and 13C-comammox increased by 80.3% and 64.2%, respectively, whereas AOA inhibition reduced 13C-labeled comammox abundance. The combined nitrification potential of AOA and AOB was lower than the sum of the independent nitrification potentials of AOA and AOB, and AOA and AOB co-occurrence increased the nitrification potential of comammox from 42–45% to 55–58%. Conclusions: Our findings proved that AOA and comammox can directly or indirectly utilize organic substances and exert complex metabolic mechanisms, and indicated that AOA and comammox are synergistic and have common C metabolism pathways. These results provided the first evidence of niche partitioning among AOA, AOB, and comammox in soils. The study provides a reference for future studies attempting to elucidate the genetic and metabolic associations among these three microbial functional groups.