Niche differentiation of ammonia-oxidizing microbial communities and their function in soil

Soil archaea and bacteria are known to oxidize ammonia to nitrite in a key step of nitrification, which may be affected by N inputs from natural (e.g., mineralization) or anthropogenic (e.g., atmospheric deposition) sources. Most research has shown that N enrichment changes community composition of ammonia-oxidizing microorganisms, increases population density, and elevates ammonia oxidation (AO) rates. However, differential adaptations to environmental change within the archaea and bacteria (and subgroups within these groups) may alter the enzymatic potential of ammonia-oxidizers that can lead to distinct ecosystem responses.

We asked if N enrichment affects the ecology of ammonia-oxidation through selective effects on particular microorganisms and their function at the physiological level (i.e., through niche differentiation). We measured AO in soils from N fertilized (NH₄NO₃ added at 60 kg N ha^-1 yr^-1 since 2005) and unfertilized Sonoran Desert soils near Phoenix, Arizona, using the nitrite-accumulation method. Soils were collected in common patch types in aridlands, away from plants and under the canopy of creosote bush shrubs. In the lab, we measured potential AO rates using shaken-slurries and actual net rates using static incubations. Rates were measured under a range of starting ammonium concentrations for each method to evaluate the enzyme kinetics of ammonia-oxidizing communities. Additionally, ammonia-oxidizers were quantified using real-time PCR and identified to the species level using clone libraries and pyrosequencing. 

Several patterns emerged from the effects of long-term N fertilization on ammonia-oxidizing communities and their function. We found that one archaeal population made up the bulk (74-95%) of all the ammonia-oxidizers across treatments and patch types. As predicted, N fertilization increased rates of potential and actual AO in soil, and increased the population size of ammonia-oxidizers. Interestingly, rate increases in response to N fertilization were positively associated with specific AO rates per cell (i.e., AO efficiency). N fertilization also increased diversity (richness and evenness) of the ammonia-oxidizing community. In addition, inspection at a fine level of phylogenetic resolution revealed that individual clades differentially respond to N enrichment. These results suggest that environmental N addition in aridland soils changes ammonia-oxidizing communities at the population level through shifts in the community structure and population size, resulting in enhanced nutrient cycling rates at the ecosystem scale.