Dataset Information

Initial Mapping of the New York City Wastewater Virome.

ABSTRACT: Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.

SUBMITTER: Gulino K

PROVIDER: S-EPMC7300365 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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Initial Mapping of the New York City Wastewater Virome.

Gulino K K Rahman J J Badri M M Morton J J Bonneau R R Ghedin E E

mSystems 20200616 3

Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest ...[more]

PMID: 32546676

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Project description:According to current surveys and overdoses data, there is a drug crisis in the USA. Wastewater-based epidemiology (WBE) is an evolving discipline that analyses wastewater samples to detect drugs and metabolites to estimate drug consumption in a certain community. This study demonstrates how drug relative presence could be tracked by testing wastewater, providing real-time results, in different boroughs in New York City throughout 1 year. We developed and fully validated two analytical methods, one for 21 drugs and metabolites, including nicotine, cocaine, amphetamines, opioids and cannabis markers; and another for the normalization factor creatinine. Both methods were performed by liquid chromatography tandem mass spectrometry (LC-MS/MS) using positive electrospray ionization, achieving a limit of quantification of 5-10 ng/L for drugs and metabolites, and 0.01 mg/L for creatinine. These methods were applied to 48 one-time grab wastewater samples collected from six wastewater treatment plants in New York City (Manhattan, The Bronx, Queens and Brooklyn), eight different times throughout 2016, before and after major holidays, including Memorial Day, 4th of July, Labour Day and New Year's. In this study, the drug group normalized concentrations present in the wastewater samples, in decreasing order, were cocaine, nicotine, opioids, cannabis and amphetamines. When looking at individual compounds, the one with the highest normalized concentration was benzoylecgonine (BE), followed by cotinine, morphine and 11-nor-9-carboxy-tetrahydrocannabinol (THCCOOH). To estimate community use, these concentrations were multiplied by the corresponding correction factor, and the most present were THCCOOH, followed by BE, cotinine and morphine. When comparing the treatment plants by drug group (nicotine, cocaine, amphetamines, opioids and cannabis), samples collected from The Bronx had the highest normalized concentrations for nicotine, cocaine and opioids; The Bronx and Manhattan for cannabis; and Manhattan and Queens for amphetamines. In most of the cases, no effect due to holiday was observed. This study provides the first snapshot of drug use in New York City and how that changes between key calendar dates employing wastewater analysis.

Dataset Information

Initial Mapping of the New York City Wastewater Virome.

Publications

Initial Mapping of the New York City Wastewater Virome.

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