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.

Analysis of Microbial Communities and Pathogen Detection in Domestic Sewage Using Metagenomic Sequencing

“…In contrast, another study retrieved a minute concentration of viruses in wastewater [48]. Bacteriophages have been identified as the predominant members of the viral microbiomes studied [26,49]. They influence microbial communities through interactions with their specific bacterial hosts.…”

Tracking Double-Stranded DNA Bacteriophages and Their Hosts in a Deep Freshwater Lake by Integrating Metagenomics and The Hi-C Technique

“…S3). Interestingly, the bacteriophages whose taxonomic percentages were in the top three were Podoviridae, Siphoviridae and Myoviridae in Lake Fuxian, which coincided with those identi ed from the ocean virome GOV2.0 and wastewater viromes [7,18]. In Lake Fuxian, putative hosts for Myoviridae, Podoviridae and Siphoviridae were members of Caulobacter, Myxococcus and Enterobacteria.…”

“…In Lake Fuxian, putative hosts for Myoviridae, Podoviridae and Siphoviridae were members of Caulobacter, Myxococcus and Enterobacteria. In wastewater plants, the most abundant hosts were Acinetobacter, Arcobacter, and Moraxella [18]. This nding demonstrated that host structure could be more diverse than viral taxonomy structure among different habitats.…”

“…Bacteriophages can affect the diversity and function of aquatic microbial populations through the incorporation and expression of auxiliary metabolic genes (AMGs). Currently, phage-encoded AMGs are reported to include multiple types of genes involved in not only main nutrient cycle pathways, such as carbon metabolism [12][13][14], nitrogen [15], phosphorus [16] and sulfur cycling [17,18], but also some speci c pathways, such as acetate fermentation [19], methane oxidation [14], nucleotide metabolism [20] and oxidative stress responses [21]. Taken together, these ndings imply that viral AMGs in uence most, if not all, pathways of microbial metabolism.…”

Viromes in Marine Ecosystems Reveal Remarkable Invertebrate RNA Virus Diversity

“…The oceans, which cover 71% of the Earth, are the most valuable resource for investigating the ecological and geographical diversity of viruses. However, to date, aquatic viromic studies tended to study phages but already showed enormous genetic diversity and ecological distributions (Roux, et al 2016; Vlok, et al 2019; Guajardo-Leiva, et al 2020; Gulino, et al 2020; Moon, et al 2020; Zhang, et al 2020). Although some studies included aquatic invertebrates (Magbanua, et al 2000; Thakur, et al 2002; Shi, et al 2016; Rosani, et al 2019), there is a lack of systematic study of these animals in a whole.…”