Simulated Urban Soils Can Alter the Diversity of Crenarchaeal Genes for Ammonia Monooxygenase.

Common landscaping practices involve the removal of vegetation followed by mulching to prevent weed invasion and reduce evapotranspiration.  These practices can induce changes in the soil’s biogeochemistry, including N cycling.  The objective of this study was to evaluate the diversity of Crenarchaeal genes for ammonia monooxygenase (enzyme driving the rate-limiting step of nitrification) in simulated urban soils that were previously shown to differ in nitrous oxide emissions.  Soil samples (Opequon series) were collected from replicated plots of unmowed vegetation, bark-mulched and gravel-covered soils.  Our hypothesis was that the diversity of Crenarchaeal amoA genes would differ between urban landscape covers after three years of treatment establishment.  Soil samples were also analyzed for C, N, Ca, Mg, P, and K contents. Soil DNA was extracted using the MoBio UltraClean™ Soil DNA Kit.  Environmental amoA amplicons were cloned and sequenced.  Rarefaction analysis was performed using DOTUR, while clone library composition was compared using ∫-LIBSHUFF.  Crenarchaeal amoA copies were found consistently in all soil samples analyzed.  A total of 161 amplicons, clustering in 27 OTUs (97% sequence similarity), were analyzed from replicated treatments.  Six OTUs, of which one comprised 54% of the amplicons, included sequences from all treatments.  Clone library composition differed significantly (p-value <0.05) between the gravel-covered and bark-mulched treatments.  The latter results indicate that both gravel and bark landscape cover may be selecting for different communities of Crenarchaea with ammonia monooxygenase genes.  Such selection may have arisen due to the introduction of new populations or to the soil environmental conditions characteristic of each treatment.  Soil nutrient concentrations, for example, were found to vary significantly across treatments.  Further efforts need to focus on understanding the environmental factors that determine the establishment, abundance and distribution of different putative Crenarchaeal ammonia oxidizers, and the relationship with to N-oxide fluxes in urban soils.