Functional microbial community structures and chemical properties indicated mechanisms and potential risks of urban river eco-remediation

To investigate the mechanisms and potential risks of river eco-remediation, river water, sediment, and biofilms in remediation facilities were sampled from a 2-year full scale eco-remediation site in an urban river in southeastern China. The samples from both remediated and adjacent control areas were analyzed for chemical properties and functional microbial community structures. The eco-remediation significantly changed the community structures in the river and introduced much more diverse functional microorganisms in facility biofilms. Corresponding to effective reduction of organics and ammonium in river water, some labile-organics-degrading and ammonia-oxidizing gene families showed higher abundances in river water of remediated area than control area, and were obviously more abundant in facility biofilms than in river water and sediment. The eco-remediation facilities showed obvious absorption of N, P, and heavy metals (Mn, Cr^VI, Fe, Al, As, Co), contributing to nutrients and metals removal from river water. The eco-remediation also increased transparency and sedimentation of some heavy metals (Cu, Pb, Zn), which probably associated with colloids breakdown. Various metal-resistance microorganisms showed different abundances between facility biofilms and sediment, in accordance with relative metals. Most detected pathogens were not significantly affected by eco-remediation. However, our measurements in sediment and facilities showed heavy metals accumulation and development of some pathogens and several antibiotic-resistance pathogens, alerting us to investigate and control these potential risks to ecosystem and human health.

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

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.

Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition

Urbanization strongly influences headwater stream chemistry and hydrology, but little is known about how these conditions impact bacterial community composition. We predicted that urbanization would impact bacterial community composition, but that stream water column bacterial communities would be most strongly linked to urbanization at a watershed-scale, as measured by impervious cover, while sediment bacterial communities would correlate with environmental conditions at the scale of stream reaches. To test this hypothesis, we determined bacterial community composition in the water column and sediment of headwater streams located across a gradient of watershed impervious cover using high-throughput 16S rRNA gene amplicon sequencing. Alpha diversity metrics did not show a strong response to catchment urbanization, but beta diversity was significantly related to watershed impervious cover with significant differences also found between water column and sediment samples. Samples grouped primarily according to habitat—water column vs. sediment—with a significant response to watershed impervious cover nested within each habitat type. Compositional shifts for communities in urbanized streams indicated an increase in taxa associated with human activity including bacteria from the genus Polynucleobacter, which is widespread, but has been associated with eutrophic conditions in larger water bodies. Another indicator of communities in urbanized streams was an OTU from the genus Gallionella, which is linked to corrosion of water distribution systems. To identify changes in bacterial community interactions, bacterial co-occurrence networks were generated from urban and forested samples. The urbanized co-occurrence network was much smaller and had fewer co-occurrence events per taxon than forested equivalents, indicating a loss of keystone taxa with urbanization. Our results suggest that urbanization has significant impacts on the community composition of headwater streams, and suggest that processes driving these changes in urbanized water column vs. sediment environments are distinct.