The flux and impact of wastewater infrastructure microorganisms on human and ecosystem health

Abstract

Wastewater infrastructure is designed, in part, to remove microorganisms. However, many microorganisms are able to colonize infrastructure and resist treatment, resulting in an enormous flux of microorganisms to urban adjacent waters. These urban-associated microorganisms are discharged through three primary routes 1) failing infrastructure, 2) stormwater, and 3) treated wastewater effluent. Bacterial load estimates indicate failing infrastructure should be considered an equivalent source of microbial pollution as the other routes, but overall discharges are not well parameterized. More sophisticated methods, such as machine learning algorithms and microbiome characterization, are now used to track urban-derived microorganisms, including targets beyond fecal indicators, but development of methods to quantify the impact of these microbes/genes on human and ecosystem health is needed.

Graphical Abstract

Introduction

To meet the urban water demand, wastewater infrastructure was developed as a system of pipes and treatment processes. These engineered systems work, in a simplified view, to transport waste, including vast microbial assemblages, away from distributed sources to a centralized location for waste remediation before returning cleaned water to natural environments. Microorganisms are abundant at all points along these water conveyance and treatment systems. Although the bulk of the microbial biomass is removed by treatment, the enormous water volumes discharged result in immense loading of microorganisms to aquatic environments. Similarly, stormwater systems direct city water as runoff from the urban landscape to surface waters, but typically lack microorganism removal via formal treatment. Reliance on this water infrastructure is increasing; human demography projects more than 60% of the human population will be located in urban areas by 2030 [1]. This increasing urbanization pushes the boundaries of water treatment and reuse infrastructure. Understanding the impacts of this infrastructure on human and ecosystem health is therefore crucial to maintaining or improving life quality in cities.

Discharge estimates, the “who”, “when”, “where”, and “how much”, for urban wastewater microorganisms to aquatic systems are limited. This information gap constrains our understanding of the interactions between urban-derived microorganisms and natural ecosystems, especially beyond microorganisms used as fecal indicators and associated human waterborne pathogens. In this opinion, we identify recent advances in estimating the flux and load of microorganisms from wastewater infrastructure to surface waters and highlight how researchers are moving beyond traditional fecal indicator assays to track microbial-based water quality impacts. Within this framework, we discuss the current understanding of wastewater infrastructure associated microorganism dispersal and how these organism/gene fluxes may impact natural ecosystems and human health in cities.

The flux of wastewater microorganisms to water bodies

The U.S. population is served by wastewater infrastructure estimated to contain more than 800,000 miles of sewer pipes, 500,000 miles of private lateral pipes connected to homes, and 14,748 wastewater treatment plants (WWTPs) [2]. Collectively these plants treat and return to ecosystems 121 billion liters of wastewater per day [3]. At the same time, stormwater systems deliver on average 102 billion liters of water per day to the nation’s waterways [3]. Sewage overflows and failing sanitary sewer infrastructure are also ongoing challenges for urban areas. An estimated 3.4 trillion liters, representing 7.7% of U.S. wastewater, never reaches WWTPs [2]. All of this wastewater contains high microbial biomass, consisting of a mix of both transient microorganisms wasted in from external sources and what appears to be a resident microbial community [4]. Wastewater infrastructure therefore represents a primary source of urban microbial community development and a primary route by which microorganisms move through a city and into natural systems.

In our view, there are three major delivery routes for microorganisms from urban landscapes to water bodies: 1) non-point discharge from leaky or failing water infrastructure, 2) direct runoff via stormwater or overland flow, and 3) treated effluent from WWTPs. Of these dissemination routes, WWTP effluent is the best understood as environmental regulations require monitoring of various discharge parameters. In most cases, a high proportion of microorganisms (>90%) are removed from the influent wastewater before it is released into the environment [5]. However, with concentrations in raw sewage around 10⁹ bacterial 16S rRNA genes per mL [6,7], this means millions of residual microorganisms in every mL, including pathogens and antibiotic resistant bacteria, are released in the treated effluent discharged to waterways [8,9]. Direct runoff via stormwater or overland flow is much more difficult to characterize, as both quantity and composition are strongly influenced by local factors including weather patterns and impervious surface area [10–12], and concentrations of bacterial 16S rRNA genes in stormwater can range from 10⁶-10⁹ per mL [11,13]. Despite this, stormwater is widely recognized as a major contributor to surface water pollution in urban environments [11,14]. In particular, human fecal contamination is often detected in urban stormwater [12,14,15]. While the source of this contamination is not entirely clear, many researchers posit that it is due to non-point discharges from leaky or failing water infrastructure [11,15–17].

Less is known about the flux of microorganisms from non-point raw wastewater pollution. It appears non-point flux of untreated wastewater to the environment is tied closely to precipitation, where increasing precipitation levels and likely intensity increase the amount of wastewater microorganisms entering waterways, even in the absence of sewer overflow events [14,18–20]. In cases where non-point raw wastewater pollution is linked to precipitation, stormwater can become a vehicle for transport of this pollution to surface waters, making non-point raw wastewater and stormwater pollution intrinsically linked. However, few cities have been examined in this way, so it is not clear whether this relationship applies widely or is more locally/regionally specific. Using data for each of three major wastewater paths to the environment, we estimate there are 10²⁰ – 10²³ bacteria per day entering water bodies via wastewater infrastructure in the U.S. (See Table 1 for details and source breakdown). Studies quantifying the flux, load, and timing of wastewater microorganism and associated gene discharge are needed to understand the risks imposed by each dissemination route and to direct resources where they are the most effective in preventing water quality degradation. We echo other recent voices in advocating for support in understanding the multi-faceted links between water infrastructure and human and ecosystem health [21–23].

Table 1.

Estimated bacterial loads in U.S. wastewaters discharged to water bodies

	Raw Sewage1	Stormwater	WWTP Effluent
Bacterial 16S rRNA Gene Concentration (copies per mL)2	108 - 1010	106 - 109	107 - 108
Daily Discharge (L)3	9.3 billion	101 billion	121 billion
Daily Bacterial Load4	10220 - 1022	1020 - 1023	1021 - 1022

1. Wastewater discharged from sanitary sewers prior to treatment, including sewer overflows and leaking sewer systems.

2. Raw sewage estimates from [6,7], Stormwater estimates from [11,13], WWTP effluent estimates from [5,6]. Data ranges are indicated.

3. Discharge estimates are from [2,3]

4. Total load estimate for U.S. water bodies

Tracking wastewater microorganisms into natural systems

Traditionally, urban discharges into natural water bodies have been monitored by measuring fecal pollution with fecal indicator bacteria (FIB), such as fecal coliforms, E. coli, or enterococci [24]. This method of monitoring urban discharge is grounded in protecting public health, as levels of FIB have been observed to correlate with gastrointestinal illness risk in certain conditions [25–27]. The primary cited drawback of these traditional fecal indicators is that they are common to nearly all warm-blooded animal guts, including humans; therefore, their detection does not provide fecal pollution source information [28]. Human-derived waste has a much higher burden of human pathogens than waste from other sources such as wildlife [29], so source detection is imperative for determining human health risks in contaminated waters.

This FIB monitoring limitation has led, in recent years, to the development of novel indicators for tracking the presence of a human, wastewater, or urban “signal” in surface waters surrounding urban centers. These assays include: 1) culture-based methods targeting alternate indicators such as coliphage [30]; 2) PCR-based detection of genes related to human health concerns, such as antibiotic resistance genes (ARGs), mobile genetic elements, or source-specific bacteria and phages [31–33], and 3) evaluation of microbial communities, either based on similarity to specific pollution sources with programs like SourceTracker [34], by monitoring spatiotemporal changes in community metrics [35,36], or via taxon co-occurrence patterns [37]. Development of these methods has required the improved characterization of microbial communities from common surface water fecal pollution sources, including sewage and other urban discharges, reviewed by [38]. These studies use modern high-throughput sequencing technologies to obtain microbial community information for development of source-specific pollution indicators; common examples include gene markers for source-specific bacteria in the Bacteroides genus and Lachnospiraceae family [33] and new sequence classifier approaches using machine learning [14,39]. Using these methods, researchers have concluded that urban microbial pollution can be widespread, reaching up to 8 km offshore from an urban center [40], that stormwater outfall assemblages may consist largely (up to 75%) of organisms washed in from urban impervious surfaces [14], and that a significant proportion of sediment communities in rivers, lakes, oceans around WWTPs consist of urban-derived microorganisms [41,42].

With the development of new source-specific monitoring methods, studies have observed significant differences between the microbiota of human fecal samples, raw sewage, and treated wastewater [4,43]. This suggests that various points along the urban water infrastructure continuum, such as sewer pipes and WWTPs, are unique habitats with mature and distinct microbial communities. Together these data also indicate FIB are not specific or abundant enough to provide reliable tracking and assessment of wastewater discharge impacts on natural systems. Validations of urban discharge indicators or community-based tracking measures are needed. We suggest further characterization and cross-site comparison of various urban water microbiomes is still necessary as microbial assemblages in these systems have many potential source environments, making ubiquitous pollution indicators more difficult to identify.

Implications of microorganism discharge on human and ecosystem health

The microorganisms and chemicals from water contact are now recognized as a significant component of an individual’s cumulative interaction with the environment [44], which is thought to be responsible for 70%-90% of all human illnesses [45]. More specifically, untreated sewage escaping sewer systems ends up in groundwater or surface waters within city limits, where people can be exposed through recreation or intrusion into drinking water distribution systems [20,46]. One study estimates there are 90 million cases of waterborne illness in the U.S. per year from recreational water exposures, costing $2.2 – 3.7 billion [47]. Studies have evaluated the persistence and/or decay of common human pathogenic organisms in surface waters, recently reviewed in [23]. However, the influence of resident microbiota on pathogen decay is rarely considered [48,49], and the prevalence of emerging wastewater infrastructure-associated pathogens such as Arcobacter spp. remains relatively understudied [50].

The health risk posed by improper sanitation is not restricted to waterborne pathogens; treated and untreated sewage carries with it a plethora of chemicals, hormones, and antibiotic resistant bacteria and resistance conferring genes [22]. Given the incredibly high flux of urban microorganisms into natural water bodies, widespread colonization of natural systems by wastewater microorganisms or dissemination of their associated genes seems likely. For example, a continental-scale assessment of Chinese estuaries revealed 18 ARGs were present in all sediment samples over a 4000-km coastline, and the authors linked these genes directly to human activities [51]. Exact gene variants from common wastewater infrastructure organisms (e.g. Acinetobacter, Legionella, Neisseria) were identified in both WWTP effluent and receiving water sediments, and these genes increased as one neared the discharge points [41]. Studies have also identified high ARG abundances in water and sediments near WWTP effluents [22,52]. The interaction between natural ecosystems and urban infrastructure is now recognized as an important pathway for ARG spread globally, but there is a great need for integration of monitoring and mitigation efforts across agencies and countries [22].

The focus on characterizing pathogens and ARGs associated with urban water infrastructure is founded in a desire to protect public health, but other ecological impacts of urban discharges on natural microbiota should be given similar attention. Many chemicals, including emerging contaminants like nanomaterials, are found in wastewater, and any of these could disrupt or stimulate typical community activity. For example, WWTP effluents have been shown to alter the composition of ammonia oxidizers in downstream water bodies [53], thus altering rates of nitrate supply. Off the coast of southern Florida, Staley et al determined that land-based discharges, such as wastewater, impact the microbiome of corals and coral reef waters [35], contributing to the disruption of coral microbiomes and increasing their susceptibility to infection. Much work remains in the effort to quantify and ultimately understand the impact of infrastructure microorganism immigration to natural ecosystems, especially when considering the concomitant impacts from altered water chemistry, primary nutrient concentrations, and chemical pollutants in discharged waters. Metagenomic and other ‘omic techniques hold promise to further our understanding in this area. So far, most studies have focused on antibiotic resistance and mobile genetic elements, but these approaches could be expanded to target any activity that may be altered by a high flux of urban-associated microorganisms [41]. Despite the extent of microbial discharge from urban areas to water bodies, there remains relatively little information on how urban microorganisms interact with resident microbiota of fresh or marine ecosystems, if they are capable of taking up residence in these systems, and what conditions promote their maintenance or proliferation. Wastewaters contain many microorganisms and their associated genetic content, including ARGs and mobile elements that are not typical of natural aquatic ecosystems [40,41]. It remains to be determined the extent to which these genes persist or are mobilized into the resident communities. Likewise, there is virtually no information about ecosystem tipping points related to urban microbial discharge, though advanced community analysis methods for determining such parameters are becoming available. At what point does continuous immigration of wastewater-associated microorganisms overwhelm natural aquatic microbial community stability, thereby fundamentally altering community structure and potentially ecosystem related outputs? In situ and experimental observations are greatly needed in this area.

Conclusions & Perspective

Sewers and stormwater represent unique environments for microbial communities, which are influenced by selective pressures from a laundry list of modern pharmaceuticals, chemicals, and household and industrial food waste dumped into these systems. Microorganisms with capabilities, both “old” and “new”, of interacting with these waste products are discharged in massive quantities every day from urban water infrastructure to aquatic systems. Ultimately, the fate of these organisms and their genes is largely unknown. We highlighted three main routes for wastewater microorganism release: 1) failing infrastructure, 2) stormwater, and 3) treated wastewater effluent. In our estimates, each of these routes contributes similarly large microbial loads to aquatic ecosystems. However, each route contains different microbial assemblages and thus presents a unique risk and/or interaction with its receiving water body [4,14,43]. The release of microorganisms in failing water infrastructure needs further attention, as it is likely to increase in magnitude in the coming years and is a major source of pathogens and antibiotic resistance dissemination. Eliminating microorganism discharge from urban infrastructure to the natural environment is not a realistic goal. Instead, the impacts and risks of these pollutants should be identified and quantified to establish microbial loading thresholds that are grounded in human health and ecosystem protection, and to identify priorities for treatment and infrastructure investment. Overall, we advocate for a shift in perspective, from considering water infrastructure as isolated unit processes to an interconnected urban water microbiome. We believe this framework facilitates an understanding of microbial community development and movement through cities, which will improve quantification of microbial loads and fluxes and identify locations of primary risk to human and ecosystem health. Advances in microbiome tracking and quantitative analysis methods are opening new doors in the developing field of urban microbial ecology, but integration among engineering design and epidemiological and ecological monitoring frameworks are needed to move the work from descriptive to predictive, and to incorporate microbial communities into macro-scale urban planning.

Highlights.

• New pollution indicators improve tracking of urban impacts on water quality

• In the U.S., urban wastewater releases >10²¹ bacteria per day to water bodies

• Failing water infrastructure may have a big impact on urban water quality

• Urban microorganisms are sources of gene transfer events in aquatic ecosystems

• Urban water infrastructure should be considered an interconnected water microbiome