Sediment

Ecology

Biology

Deposition (geology)

Nitrogen

Soil water

Long-term experiment

Nitrification

Paleontology

Organic chemistry

Environmental chemistry

Agronomy

Environmental science

Soil science

Chemistry

Nitrospira

Subtropics

Soil Biology and Biochemistry

The recent discovery of comammox Nitrospira capable of converting ammonia to nitrate in a single organism radically challenged our century-long perception of the classic two-step nitrification performed by ammonia oxidizers and nitrite oxidizers. However, our understanding of the niche separation of comammox Nitrospira and canonical nitrifiers in forest ecosystems remains limited, especially under a global scenario of elevated nitrogen (N) deposition. Here we evaluated the impacts of six-year N deposition on the dynamics of comammox Nitrospira, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in a subtropical forest soil. Soil inorganic N concentrations significantly increased under the six-year simulation of N deposition, while soil pH, available phosphorus, total carbon (C), C/N ratio and microbial biomass significantly decreased. Quantitative PCR showed that the amoA gene abundances of comammox Nitrospira clade B and AOA substantially increased under the increasing rates of N deposition. By contrast, the AOB amoA gene abundance significantly decreased with the higher levels of N deposition (100 and 150 kg N ha−1 yr−1). Increased 13CO2 incorporation into the AOA communities, rather than comammox Nitrospira or AOB, was demonstrated in a DNA-stable isotope probing microcosm, indicative of the capacity of AOA to assimilate 13CO2 through autotrophic nitrification in the investigated subtropical forest soil under long-term N deposition. Phylogenetic analysis revealed that the autotrophic AOA assemblages belonged to the Nitrosotalea cluster, and their capacity for assimilating CO2 through autotrophic nitrification was not affected by the long-term N deposition. Taken together, we provided new evidence for the niche separation of comammox Nitrospira and canonical ammonia oxidizers in soil nitrification under the long-term N deposition in the acidic subtropical forest soil.

Niche separation of comammox Nitrospira and canonical ammonia oxidizers in an acidic subtropical forest soil under long-term nitrogen deposition