Spatial heterogeneity of denitrification genes in a highly homogenous urban stream

Human modification of natural streams by urbanization has led to more homogeneous channel surfaces; however, the influence of channel simplification on in situ microbial distribution and function is poorly characterized. For example, denitrification, a microbial process that reduces soluble nitrogen (N) levels, requires peripheral anoxic zones that might be lost in artificial channels such as those with a concrete lining. To examine how microbial function might be influenced by channel simplification, we quantified denitrification rates and conditions in microbial mats within an urban concrete channel. We quantified spatial and diurnal patterns of nitrate uptake, diurnal dissolved oxygen (DO) levels, and nutrient conditions, along with the spatial distribution of DO, solids, chlorophyll a, and genes associated with denitrification (nirS and nirK), ammonia-oxidizing bacteria (AOB), cyanobacteria, and algal chloroplasts. Despite the channel being superficially homogeneous, nir genes were distributed in a patchy manner. Two types of gene patches were observed: one associated with nirK, which had diurnally variable DO levels and high nocturnal nitrate uptake rates, and the other associated with nirS, which had elevated AOB genes, thicker layers of mud, and an apparent 24 h nitrate uptake. All active nir patches had elevated microbial photosynthetic genes. Results imply that even artificial channels, with reduced macroscale heterogeneity, can sustain significant rates of denitrification, although the responsible communities vary with space and time. This patchiness has significant implications to extending local data to landscape level predictions and field sampling strategies but also suggests alternate channel designs to increase N retention rate