Niche differentiation of Glade A comammox Nitrospira and canonical ammonia oxidizers in selected forest soils

Unravelling the ecological niche differentiation between comammox Nitrospira, ammonia-oxidizing archaea (AOA) and bacteria (AOB) is essential to understand forest nitrogen dynamics. Although genomic and physiological studies have suggested that comammox Nitrospira may outcompete AOA and AOB under oligotrophic conditions, empirical evidence is lacking in terrestrial ecosystems. Here we investigated the environmental prevalence and functional importance of comammox Nitrospira and their niche differentiation with AOA and AOB in forest soils from eastern Australia. Glade A comammox Nitrospira was widely detected in these forest soils, and their abundance was positively correlated with ammonium, total nitrogen and pH. The ammonium concentration was the most important driver of Glade A comammox Nitrospira abundance, based on random forest regression analysis. Glade B comammox Nitrospira was not detected in these forest soils and thus excluded from the downstream analyses. Urea application stimulated the growth of Glade A comammox Nitrospira and AOB, but not AOA, during a microcosm incubation. DNA-stable isotope probing revealed that Glade A comammox Nitrospira incorporated C-13-CO2 in the incubations, suggesting that Glade A comammox Nitrospira may contribute to autotrophic carbon fixation in these forest soils. Taken together, our findings indicate that Glade A comammox Nitrospira is prevalent and probably contributing to nitrification in forest soils of eastern Australia.