Pandemics rarely begin “at home,” but rather with emergence of a new infectious disease in a pathogen evolution hotspot, followed by dissemination through the global transportation network. Chicago’s role as a global air hub means that rapid response depends critically on both early detection of local outbreaks (from new emergence or global spread) and on robust communication among science, policy, utilities, and community stakeholders, cities, and regions.
Wastewater based epidemiology (WBE)—monitoring potential pathogens in sewers and waterways—provides a rapid and cost-effective means to monitor COVID-19 infections in cities. As sewers and treatment plants collect wastewater from entire urban regions, WBE provides a means to monitor COVID-19 across large geographic areas and millions of people. Because SARS-CoV-2 RNA is excreted by pre- and asymptomatic individuals, WBE provides advance warning and more complete assessments of the COVID-19 epidemic than traditional testing. Combining distributed wastewater sampling with hydraulic modeling enables early-stage tracing of outbreaks back to local source locations with high infection rates. Moreover, deep gene sequencing enables tracking strain-level variation in SARS-CoV-2 and other viruses, distinguishing local outbreaks from new imported cases.
Wastewater treatment plants (WWTPs) represent hotspots for the concentration of nutrients, compounds of emerging concern, and microorganisms. The direct release of WWTP effluent into surrounding aquatic environments impacts these systems both biologically and chemically in ways that are not fully understood. One of the great challenges in urbanized aquatic systems that receive WWTP effluent is to better understand the fate, transport, and metabolism of potentially harmful contaminants and nutrients that are introduced along with the effluent. Assessing these effects is of considerable environmental consequence, especially in areas under the influence of high population pressure and stress to the health of freshwater systems.
This is especially important because microorganisms (bacteria and archaea) represent the largest component of biodiversity on earth in terms of total biomass as well as gene and sequence diversity; the hundreds or thousands of distinct species of microbes in any given aquatic system are responsible for biogeochemical transformations in the environment and play an important role in biodegradation. This project aims to study the microbial community from both a taxonomic and functional perspective to understand how populations of aquatic microorganisms and their biodegradation potential in the environment are influenced by effluent inputs. Although potential ecosystem effects of effluent discharge on nutrient loading, chemical loading, and eutrophication have been investigated, the overall impact of WWTP effluent on microbial community composition and metabolic potential in aquatic systems is poorly studied and has far-reaching impacts.
Taking advantage of the upcoming disinfection of effluent in a WWTP on the North Shore Chanel of the Chicago River, we are working to identify the taxonomic diversity and ecological contributions (functional gene potential and expression) of effluent-derived microorganisms and examine patterns of assembly and distribution throughout the system within the framework of disinfection and biodegradation potential. This project will contribute to the overall understanding of microbial community composition and dynamics in an effluent-dominated urban aquatic system.
Microorganisms have been the primary source of clinically used antibiotics for nearly a century, though the constant rediscovery of known compounds using traditional drug discovery approaches has not kept pace with evolving resistance to existing antibiotic treatments. Since nature is a reservoir for antibiotics and antibiotic resistance genes, it is critical that we understand how these genes are distributed in the environment in order to reveal patterns of co- occurrence, and develop a targeted approach to antibiotic-lead discovery from environmental microorganisms.
In this study, we will use advanced sequencing techniques and data analysis to map the occurrence of antibiotic production and resistance genes emanating from wastewater treatment plants that discharge into Lake Michigan and Lake Erie. This information will be used to predict how antibiotic production and resistance genes are transmitted in nature and will facilitate the development of a more targeted approach toward the discovery of antimicrobials. This research is at the crossroads of ecology, environmental engineering, and drug discovery. This systems biology approach makes our work truly novel, but also difficult to fund by federal programs.
We are measuring the input of genetic pollutants into Lakes Michigan and Erie, tracing their dissemination, and using gene distribution maps to not only understand the evolutionary relationship between antibiotic production genes (APG) and resistance genes (ARG), but also to revolutionize the manner in which we mine the environment for new antibiotic drug leads.
Funding: Chicago Biomedical Consortium
Microbes in freshwater ecosystems play a pivotal role in terrestrial carbon cycling and are expected to be highly sensitive to climate change drivers. The millions of microbes that inhabit each milliliter of water are crucial players in the Earth’s carbon cycle. Among many possible roles, arguably the most important one for bacteria in the carbon cycle is the use of dissolved organic carbon (DOC) and other components of the dissolved organic material (DOM) pool.
DOC is one of the largest carbon pools in the biosphere. The flux of carbon through the DOM pool is also quite large, equivalent to roughly half of primary production in many aquatic ecosystems. In aquatic ecosystems that experience allocthonous inputs of organic matter, bacterial secondary production can equal or exceed phytoplankton primary production. Carbon assimilation by microorganisms serves as the first step in the microbial food web; carbon flux through DOM is determined by assimilation and respiration by heterotrophic bacteria and ultimately by the rest of the microbial loop. How phylogenetic and genetic diversity impact this flux is not clear and is a major unsolved problem in microbial ecology.
Supplements of carbon and nutrients from adjacent land drive high rates of microbial activity, leading to elevated respiratory rates and exchange of greenhouse gases between the water and the atmosphere. The concentration of human activities along coastlines causes direct and indirect perturbations to these natural processes through pollution, eutrophication, water withdrawal, and wetland loss. These increased stresses on the coastal carbon cycle impact productivity, food web structure, atmospheric CO2 exchange, and other key processes in ways that are very poorly understood.
Despite the importance of microorganisms in carbon flux, and the importance of DOM flux through bacterioplankton to the pelagic food web, only a handful of studies have used modern –omics techniques to study freshwater microbial communities and their members and none of these have been in Lake Michigan. The microbial food web has largely been ignored by the federal agencies involved in Lake Michigan monitoring, however nutrient inputs from terrestrial environments, the invasive dreissenid mussels, and growth/abundance of primary producers including cyanobacteria, picoeukaryotes, and phytoplankton have all been known to affect lake food web dynamics. The microbial community is often the first to respond to related small and large-scale perturbations such as pulses of nutrients and organic matter or shifts in their quality, quantity, and distribution.
This project aims to explore the microbial community composition (i.e., What is the diversity, genetic potential, and taxonomic structure?) and activity (i.e., What genes are being used, a proxy for metabolism?) in Lake Michigan as microbes break down and assimilate different organic matter sources that are then made available to other components of the lake food web.
Funding: Illinois-Indiana SeaGrant
Aquaculture conditions can support the growth of bacteria in culture tanks, which can benefit or harm fish depending on the balance of pathogens and beneficial microorganisms. Most diseases can result from opportunistic pathogens found in the water, but in situ conditions can influence the host’s immune system and promote the proliferation of pathogenic organisms. We hypothesize that culture conditions (algal paste and clay additions) alter the culture environment in different ways, shifting the microbial community composition, which includes both pathogens and beneficial organisms. We are investigating this shift in order to identify pathogenic and beneficial bacteria and the conditions that promote their growth, and test whether we can create an optimal amendment that will include or favor beneficial bacteria.
We are also investigating the role of Dimethylsulfoniopropionate (DMSP), an organic sulfur compound produced by marine phytoplankton and found high concentrations in areas with high productivity, in shaping the microbial communities and influencing fish growth and survival. DMSP is released into the dissolved organic matter pool upon algal grazing and lysis where it is converted to dimethylsulfide (DMS) primarily by marine bacteria that use it as a major sulfur and carbon source. Animals higher up the food chain can eavesdrop on DMSP/DMS olfactory cues from algal consumption to find their food. DMS stimulates feeding behavior in a range of animals, including birds and marine fish.
The use of DMS precursors can also stimulate feeding behavior and greater growth in aquaculture. In aquaculture, algal cells in greenwater could potentially release DMSP as dead algae decompose (or are eaten by rotifers in warm water environments).