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

Abstract

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. Clade 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 clade A comammox Nitrospira abundance, based on random forest regression analysis. Clade B comammox Nitrospira was not detected in these forest soils and thus excluded from the downstream analyses. Urea application stimulated the growth of clade A comammox Nitrospira and AOB, but not AOA, during a microcosm incubation. DNA-stable isotope probing revealed that clade A comammox Nitrospira incorporated 13C–CO2 in the incubations, suggesting that clade A comammox Nitrospira may contribute to autotrophic carbon fixation in these forest soils. Taken together, our findings indicate that clade A comammox Nitrospira is prevalent and probably contributing to nitrification in forest soils of eastern Australia.