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Comparative metagenome of a stream impacted by the urbanization phenomenon.

ABSTRACT: Rivers and streams are important reservoirs of freshwater for human consumption. These ecosystems are threatened by increasing urbanization, because raw sewage discharged into them alters their nutrient content and may affect the composition of their microbial community. In the present study, we investigate the taxonomic and functional profile of the microbial community in an urban lotic environment. Samples of running water were collected at two points in the São Pedro stream: an upstream preserved and non-urbanized area, and a polluted urbanized area with discharged sewage. The metagenomic DNA was sequenced by pyrosequencing. Differences were observed in the community composition at the two sites. The non-urbanized area was overrepresented by genera of ubiquitous microbes that act in the maintenance of environments. In contrast, the urbanized metagenome was rich in genera pathogenic to humans. The functional profile indicated that the microbes act on the metabolism of methane, nitrogen and sulfur, especially in the urbanized area. It was also found that virulence/defense (antibiotic resistance and metal resistance) and stress response-related genes were disseminated in the urbanized environment. The structure of the microbial community was altered by uncontrolled anthropic interference, highlighting the selective pressure imposed by high loads of urban sewage discharged into freshwater environments.

SUBMITTER: Medeiros JD

PROVIDER: S-EPMC5052392 | biostudies-literature | 2016 Oct - Dec

REPOSITORIES: biostudies-literature

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Comparative metagenome of a stream impacted by the urbanization phenomenon.

Medeiros Julliane Dutra JD Cantão Maurício Egídio ME Cesar Dionéia Evangelista DE Nicolás Marisa Fabiana MF Diniz Cláudio Galuppo CG Silva Vânia Lúcia VL Vasconcelos Ana Tereza Ribeiro de AT Coelho Cíntia Marques CM

Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 20160704 4

Rivers and streams are important reservoirs of freshwater for human consumption. These ecosystems are threatened by increasing urbanization, because raw sewage discharged into them alters their nutrient content and may affect the composition of their microbial community. In the present study, we investigate the taxonomic and functional profile of the microbial community in an urban lotic environment. Samples of running water were collected at two points in the São Pedro stream: an upstream prese ...[more]

PMID: 27522532

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Project description: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.

Project description:A variety of antibiotics are ubiquitous in all freshwater ecosystems that receive wastewater. A wide variety of antibiotics have been developed to kill problematic bacteria and fungi through targeted application, and their use has contributed significantly to public health and livestock management. Unfortunately, a substantial fraction of the antibiotics applied to humans, pets and livestock end up in wastewater, and ultimately many of these chemicals enter freshwater ecosystems. The effect of adding chemicals that are intentionally designed to kill microbes, on freshwater microbial communities remains poorly understood. There are reasons to be concerned, as microbes play an essential role in nutrient uptake, carbon fixation and denitrification in freshwater ecosystems. Chemicals that reduce or alter freshwater microbial communities might reduce their capacity to degrade the excess nutrients and organic matter that characterize wastewater. We performed a laboratory experiment in which we exposed microbial community from unexposed stream sediments to three commonly detected antibiotics found in urban wastewater and urban streams (sulfamethoxazole, danofloxacin, and erythromycin). We assessed how the form and concentration of inorganic nitrogen, microbial carbon, and nitrogen cycling processes changed in response to environmentally relevant doses (10 μg/L) of each of these antibiotics individually and in combination. We expected to find that all antibiotics suppressed rates of microbial mineralization and nitrogen transformations and we anticipated that this suppression of microbial activity would be greatest in the combined treatment. Contrary to our expectations we measured few significant changes in microbially mediated functions in response to our experimental antibiotic dosing. We found no difference in functional gene abundance of key nitrogen cycling genes nosZ, mcrA, nirK, and amoA genes, and we measured no treatment effects on NO3- uptake or N2O, N2, CH4, CO2 production over the course of our seven-day experiment. In the mixture treatment, we measured significant increases in NH4+ concentrations over the first 24 hours of the experiment, which were indistinguishable from controls within six hours. Our results suggest remarkable community resistance to pressure antibiotic exposure poses on naïve stream sediments.

Project description:Streams collect runoff, heat, and sediment from their watersheds, making them highly vulnerable to anthropogenic disturbances such as urbanization and climate change. Forecasting the effects of these disturbances using process-based models is critical to identifying the form and magnitude of likely impacts. Here, we integrate a new biotic model with four previously developed physical models (downscaled climate projections, stream hydrology, geomorphology, and water temperature) to predict how stream fish growth and reproduction will most probably respond to shifts in climate and urbanization over the next several decades.The biotic submodel couples dynamics in fish populations and habitat suitability to predict fish assemblage composition, based on readily available biotic information (preferences for habitat, temperature, and food, and characteristics of spawning) and day-to-day variability in stream conditions.WE ILLUSTRATE THE MODEL USING PIEDMONT HEADWATER STREAMS IN THE CHESAPEAKE BAY WATERSHED OF THE USA, PROJECTING TEN SCENARIOS: Baseline (low urbanization; no on-going construction; and present-day climate); one Urbanization scenario (higher impervious surface, lower forest cover, significant construction activity); four future climate change scenarios [Hadley CM3 and Parallel Climate Models under medium-high (A2) and medium-low (B2) emissions scenarios]; and the same four climate change scenarios plus Urbanization.Urbanization alone depressed growth or reproduction of 8 of 39 species, while climate change alone depressed 22 to 29 species. Almost every recreationally important species (i.e. trouts, basses, sunfishes) and six of the ten currently most common species were predicted to be significantly stressed. The combined effect of climate change and urbanization on adult growth was sometimes large compared to the effect of either stressor alone. Thus, the model predicts considerable change in fish assemblage composition, including loss of diversity.Synthesis and applications. The interaction of climate change and urban growth may entail significant reconfiguring of headwater streams, including a loss of ecosystem structure and services, which will be more costly than climate change alone. On local scales, stakeholders cannot control climate drivers but they can mitigate stream impacts via careful land use. Therefore, to conserve stream ecosystems, we recommend that proactive measures be taken to insure against species loss or severe population declines. Delays will inevitably exacerbate the impacts of both climate change and urbanization on headwater systems.

Dataset Information

Comparative metagenome of a stream impacted by the urbanization phenomenon.

Publications

Comparative metagenome of a stream impacted by the urbanization phenomenon.

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