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Ongoing Projects

The Sewerage Microbiome & Urban Microbial Ecology

We are investigating the microbial communities of sewage and sewer systems.  Pipe infrastructure is a relatively new habitat on this planet, and microbes have colonized these urban systems.  In fact, pipe infrastructure is a habitat or ecosystem where microbes exhibit community patterns similar to those of lakes, oceans, or soils, such as: seasonal dynamics, resident and transient members, and biogeography.  We are now working to more thoroughly characterize the sewage microbiome, the activities of the microbes therein, and how the unique selective pressures in these systems shape genomic content.  We have also begun projects to look at the impact these "pipe" microorganisms have on receiving water bodies.  Can pipe derived microbes survive in freshwaters, and if so for how long?  What about the genetic content of these microorganisms; does it spread into aquatic systems?  Is the human-derived pipe environment a new vector of genetic diversity to aquatic ecosystems? 


In collaboration with Dr. Sandra McLellan at the University of Wisconsin-Milwaukee, we are also using these systems to identify microorganisms that are abundant and common across human populations (i.e. cities) to develop more accurate and source-specific indicators of human fecal pollution.  See the McLellan lab website for more details. 

Microbial Communities of the Laurentian Great Lakes

In collaboration with Dr. Maureen Coleman at the University of Chicago, we are examining the genomic content of the microbial communities in the Laurentian Great Lakes.  For the past five years, samples have been collected aboard the R/V Lake Guardian from all five of the Great Lakes. Amplicon-based and metagenomic sequencing and analysis are ongoing so that we can better understand whether the microbial communities and populations in each lake are unique and/or differentiated from smaller inland lakes and oceans, how gene content is partitioned in these large systems, what unrecognized organisms or life traits are contributing to the nutrient cycling and population dynamics in these large systems, and much more.


See the Coleman lab website for further information. 


In our lab, we are examining two areas where microbes influence the health of intensive aquaculture systems.

The biofilter. Many recirculating aquaculture systems (RAS) employ a nitrifying biofilter to remove nitrogenous waste from fish excreta and undigested feed. We are characterizing the microbial communities in these biofilters, identifying what organisms are carrying out ammonia- and nitrite-oxidation, and examining whether the life traits of these organisms impact system start-up and typical operation conditions.

The gut. Typical aquaculture diets differ vastly from what reared animals encounter in nature and thus likely have a large impact on the microbial gut community. It is clear, gut microbial communities have a profound impact on animal health. It is not yet clear how aquaculture diets impact animal gut microbes or more importantly whether these changes impact animal health in these systems. In collaboration with Dong-Fang Deng at UW-Milwaukee, we are initiating trials to understand the interaction between diet in an aquaculture setting, gut microbial communities, and animal health.

Nutrient Input into ​Groundwater Systems

In collaboration with Dr. Tim Gundl at the University of Wisconsin-Milwaukee, we are investigating how macronutrients stemming from wastewater treatment systems enter shallow groundwater aquifers and whether this nutrient input alters the microbial community composition and bioactive processes carried out in these ecosystems.  The studied groundwater systems are used as a drinking water source and were once isolated from surface water infiltration, but changes in river flow resulting from wastewater discharge have allowed river water containing relatively high concentrations of macronutrients to enter the system. Yet some aquifers nearby remain un-impacted.  We are just beginning this project, but we believe the natural experiment setup will allow us to identify how alteration to surface water nutrient concentrations can impact microbial energetics in aquifers and whether this process could impact drinking water quality.