Streams, as low-lying points in the landscape, are strongly influenced by the stormwaters, pollutants, and warming that characterize catchment urbanization. River restoration projects are an increasingly popular method for mitigating urban insults. Despite the growing frequency and high expense of urban stream restoration projects, very few projects have been evaluated to determine whether they can successfully enhance habitat structure or support the stream biota characteristic of reference sites. We compared the physical and biological structure of four urban degraded, four urban restored, and four forested streams in the Piedmont region of North Carolina to quantify the ability of reach-scale stream restoration to restore physical and biological structure to urban streams and to examine the assumption that providing habitat is sufficient for biological recovery. To be successful at mitigating urban impacts, the habitat structure and biological communities found in restored streams should be more similar to forested reference sites than to their urban degraded counterparts. For every measured reach- and patch-scale attribute, we found that restored streams were indistinguishable from their degraded urban stream counterparts. Forested streams were shallower, had greater habitat complexity and median sediment size, and contained less-tolerant communities with higher sensitive taxa richness than streams in either urban category. Because heavy machinery is used to regrade and reconfigure restored channels, restored streams had less canopy cover than either forested or urban streams. Channel habitat complexity and watershed impervious surface cover (ISC) were the best predictors of sensitive taxa richness and biotic index at the reach and catchment scale, respectively. Macroinvertebrate communities in restored channels were compositionally similar to the communities in urban degraded channels, and both were dissimilar to communities in forested streams. The macroinvertebrate communities of both restored and urban degraded streams were correlated with environmental variables characteristic of degraded urban systems. Our study suggests that reach-scale restoration is not successfully mitigating for the factors causing physical and biological degradation.

Summary A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer‐scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0%–83% developed watershed area) in the Raleigh‐Durham area of North Carolina (USA). Using statistical approaches derived from macro‐organismal ecology, we found that more bacterial taxa were classified as intolerant than as tolerant to increasing watershed urbanization (143 vs 48 OTUs), and we identified a threshold of 12.1% developed watershed area beyond which the majority of intolerant taxa were lost from streams. Two bacterial families strongly decreased with urbanization: Acidobacteriaceae (Acidobacteria) and Xanthobacteraceae (Alphaproteobacteria). Tolerant taxa were broadly distributed throughout the bacterial phylogeny, with members of the Comamonadaceae family (Betaproteobacteria) presenting the highest number of tolerant taxa. Shifts in microbial community structure were strongly correlated with a stream biotic index, based on macroinvertebrate composition, suggesting that microbial assemblages could be used to establish biotic criteria for monitoring aquatic ecosystems. In addition, our study shows that classic methods in community ecology can be applied to microbiome datasets to identify reliable microbial indicator taxa and determine the environmental constraints on individual taxa distributions along environmental gradients.

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Watershed urbanization introduces a variety of physical, chemical, and thermal stressors to receiving streams and leads to well-documented declines in the diversity of fish and macroinvertebrates. Far less knowledge is available about how these urban stressors affect microbial communities and microbially mediated ecosystem properties. We examined 67 chemical, physical, and biological attributes of streams draining 47 watersheds in the metropolitan area surrounding Raleigh, North Carolina. Watersheds ranged from undeveloped to 99.7% developed watershed area. In contrast to prior investigators, we found no consistent changes in habitat structure, channel dimensions, or bed sediment size distributions along the urbanization gradient. Watershed urbanization led to large and consistent changes in receiving stream chemistry (increases in NO 3 2 , bioavailable and algal-derived dissolved organic C, and the trace metals Pb, Cd, and Zn) and thermal regimes. These chemical and thermal changes were not associated with any consistent shifts in microbial community structure or taxonomic richness, based on terminalrestriction fragment length polymorphism and pyrosequencing methods, despite the fact that these urban stressors were associated with commonly reported declines in macroinvertebrate taxonomic richness and altered macroinvertebrate community composition. Chemical and thermal changes as a function of % developed watershed area also were unrelated to shifts in microbially mediated biogeochemical processes (C mineralization, denitrification potential, and substrate-induced respiration). A broad urbanization gradient sampled in this region suggests that stream ecosystem responses to watershed urbanization can follow diverse trajectories.