Wastewater treatment plants (WWTPs) release treated effluent containing mobile genetic elements (MGEs), antibiotic resistance genes (ARGs), and microorganisms into the environment, yet little is known about their influence on nearby microbial communities and the retention of these factors in receiving water bodies. Our research aimed to characterize the genes and organisms from two different WWTPs that discharge into Lake Michigan, as well as from surrounding lake sediments to determine the dispersal and fate of these factors with respect to distance from the effluent outfall. Shotgun metagenomics coupled to distance-decay analyses showed a higher abundance of genes identical to those in WWTP effluent genes in sediments closer to outfall sites than in sediments farther away, indicating their possible WWTP origin. We also found genes attributed to organisms, such as those belonging to Helicobacteraceae, Legionellaceae, Moraxellaceae, and Neisseriaceae, in effluent from both WWTPs and decreasing in abundance in lake sediments with increased distance from WWTPs. Moreover, our results showed that the WWTPs likely influence the ARG composition in lake sediments close to the effluent discharge. Many of these ARGs were located on MGEs in both the effluent and sediment samples, indicating a relatively broad propensity for horizontal gene transfer (HGT). Our approach allowed us to specifically link genes to organisms and their genetic context, providing insight into WWTP impacts on natural microbial communities. Overall, our results suggest a substantial influence of wastewater effluent on gene content and microbial community structure in the sediments of receiving water bodies.IMPORTANCE Wastewater treatment plants (WWTPs) release their effluent into aquatic environments. Although treated, effluent retains many genes and microorganisms that have the potential to influence the receiving water in ways that are poorly understood. Here, we tracked the genetic footprint, including genes specific to antibiotic resistance and mobile genetic elements and their associated organisms, from WWTPs to lake sediments. Our work is novel in that we used metagenomic data sets to comprehensively evaluate total gene content and the genetic and taxonomic context of specific genes in environmental samples putatively impacted by WWTP inputs. Based on two different WWTPs with different treatment processes, our findings point to an influence of WWTPs on the presence, abundance, and composition of these factors in the environment.
Urban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and storm flow events represent one such source of complex physical, chemical, and biological perturbations. Microorganisms are important components of these streams from both ecological and public health perspectives. Analysis of the effect of perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced storm flow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high-rainfall event, with potential environment and public health implications. Previous work in this area has focused on specific genes/organisms or has not assessed immediate storm flow impact.
Lake Michigan is one of the largest lakes in the world and the second largest of the North American Great Lakes by volume. Over the last two decades, the lake has witnessed significant ecological changes due to proliferation of invasive quagga mussels into its deeper offshore regions. The impact of these changes on the labile dissolved organic matter pool available for bacterial consumption and the relative importance of terrestrially derived DOM (t‐DOM) for bacterial metabolism across Lake Michigan in the post‐mussel period is poorly understood. Here, we investigated Lake Michigan bacterial community structure and activity in offshore and coastal regions near the mouth of Kalamazoo River, one of the largest tributaries to southern Lake Michigan. In addition, we evaluated short‐term bacterioplankton response to a pulse of t‐DOM (leaf litter leachate) in shipboard mesocosms set up using nearshore and offshore lake‐water. The bacterial community composition and activity for the natural and t‐DOM enriched samples were characterized using combined metagenomics and metatranscriptomics. We observed four‐fold more transcripts for Cyanobacteria in the offshore bacterial community compared to nearshore, highlighting the importance of Cyanobacterial primary production in supporting microbial food web of the oligotrophic offshore. However, despite this and certain differences in DOM related transporter gene transcripts between the two regions, the nearshore and offshore bacterial communities showed a similar response to t‐DOM, primarily in the form of increased transcriptional activity for aromatic compound metabolism. The use of metagenome assembled genomes identified populations within the Bacteroidetes phylum that play an important role in t‐DOM response.
22Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological 23 health and water quality. Microbial communities in streams play important functional roles and 24 their composition and metabolic potential can help assess ecological state and water quality. 25Although these environments are highly heterogenous, little is known about the influence of 26 isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, 27we examined the microbial community composition and diversity in an urban stream during dry 28 and wet weather conditions with both 16S rRNA gene sequencing across multiple years and 29shotgun metagenomics to more deeply analyze a single stormflow event. Metagenomics was 30 used to assess population-level dynamics as well as shifts in the microbial community taxonomic 31 profile and functional potential before and after a substantial rainfall. Results demonstrated 32 general trends present in the stream under stormflow vs. baseflow conditions across years and 33 seasons and also highlighted the significant influence of increased effluent flow following rain in 34 shifting the stream microbial community from abundant freshwater taxa to those more associated 35 with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to 36 changes in functional gene content, particularly for transmembrane transport and organic 37 substance biosynthesis. We also observed an increase in relative abundance of genes encoding 38 degradation of organic pollutants and antibiotic resistance after rain. Overall, this study provided 39 evidence of stormflow impacts on an urban stream microbiome from an environmental and 40 public health perspective. 41
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