The microbiome of urban waters

Abstract

More than 50% of the world's population lives in urban centers. As collection basins for landscape activity, urban waters are an interface between human activity and the natural environment. The microbiome of urban waters could provide insight into the impacts of pollution, the presence of human health risks, or the potential for long-term consequences for these ecosystems and the people who depend upon them. An integral part of the urban water cycle is sewer infrastructure. Thousands of miles of pipes line cities as part of wastewater and stormwater systems. As stormwater and sewage are released into natural waterways, traces of human and animal microbiomes reflect the sources and magnitude of fecal pollution and indicate the presence of pollutants, such as nutrients, pathogens, and chemicals. Non-fecal organisms are also released as part of these systems. Runoff from impervious surfaces delivers microbes from soils, plants and the built environment to stormwater systems. Further, urban sewer infrastructure contains its own unique microbial community seemingly adapted to this relatively new artificial habitat. High microbial densities are conveyed via pipes to waterways, and these organisms can be found as an urban microbial signature imprinted on the natural community of rivers and urban coastal waters. The potential consequences of mass releases of non-indigenous microorganisms into natural waters include creation of reservoirs for emerging human pathogens, altered nutrient flows into aquatic food webs, and increased genetic exchange between two distinct gene pools. This review highlights the recent characterization of the microbiome of urban sewer and stormwater infrastructure and its connection to and potential impact upon freshwater systems.

Keywords: aquatic food webs; human health; infrastructure and sanitation; next generation sequencing; urban freshwaters.

Fig. 1.

Sanitary sewers act as collectors of organisms from “indoor” microbiomes, including bacteria associated with the human body and waste, food, and pipes. Stormwater sewers collect organisms from “outdoor” microbiomes, such as soil, impervious surfaces, plants, and animal feces. Sewers serve as transporters that deliver bacteria to aquatic environments; but microbial communities are also transformed within the sewers, including death of some organisms and growth of others within the pipe.

Fig. 2.

Network analysis of the family Lachnospiraceae in fecal communities of animals, humans, and sewage. Large dots represent individual samples, small dots represent operational taxonomic units (OTUs). Lines connect samples and OTUs to show connections among different individuals from the same and from different host species. Sewage samples from Spain, Brazil, Malawi, and the USA are indicated by distinct shades of green. Clear trends within host species are present, as well as OTUs that are shared among hosts or associated with an individual sample.

Fig. 3.

Dominant bacterial taxa found in (A) stormwater (n = 30) and (B) untreated sewage influent (n = 6). Several abundant taxa were shared between the two environments and were mainly of non-fecal origin. Both communities were very diverse, with a total of 1709 and 1491 designated taxa in stormwater and untreated sewage, respectively. (Figure adapted from Fisher et al. [15].)