Faculty Members

Our lab asks questions at the interface of population, community and evolutionary ecology. Working in lakes and ponds, we ask how microbes and crustacean zooplankton interact both as hosts and parasites and as grazers and resources.

Karin Dahmen studies biological problems which are difficult to model because spatial heterogeneity and noise due to discreteness effects are of fundamental significance to transport and reaction kinetics. Most recently she and her group focussed on a generalization of a simple model for how genes spread in a population, when reproduction may only occur in small patches ("oases"), and where organisms die and compete for resources everywhere else. They calculated the probability density function for the transit time between a populated oasis and an unpopulated oasis, developing the theory of stochastic reaction-diffusion equations with quenched disorder. The results are expected to be of broad applicability to other problems characterized by interactions between genes, population dynamics and environmental fluctuations, such as the growth of microbial populations near sea floor vents, the spread of disease in corals, and the seasonal variation of the distribution of phytoplankton populations in the oceans.

Our laboratory investigates microbial communities and populations in contaminated subsurface environments and how the selective pressure of contamination influences community composition. We also explore how unique microorganisms (i.e. novel genera and species) develop as new metabolic niches form resulting from contamination and its effects on local geochemistry.
https://netfiles.uiuc.edu/finneran/www/

Nigel Goldenfeld is a theoretical physicist who is explores collective effects in biology through the following ongoing projects. (1) The role of microbes on the formation of travertine terraces at Yellowstone's geothermal hot spring system. (2) The large-scale impact of horizontal gene transfer on ecosystem stability, with emphasis on the interactions between microbes and phages, and the dynamics of microbial "speciation" at the genome level. (3) Nigel also uses computer modeling to study the evolution of the genetic code and the emergence of complexity in biological systems. Nigel's work is performed in collaboration with Bruce Fouke, Zan Luthey-Schulten and Carl Woese and supported by the National Science Foundation and the Department of Energy.

The Kent lab is interested in the ecology of microbial communities involved in ecosystem processes in terrestrial and aquatic ecosystems. We are particularly interested in exploring microbial contributions to environmental quality and sustainability.

My research focuses on mixed culture biotechnology with applications in biological water and wastewater treatment processes. Biological wastewater treatment is worldwide the largest biotechnology application, treating billions of liters of water per day. Yet, most of today's treatment processes are based on a limited and often empirical understanding of the underlying mechanisms. The primary goal of my research is to elucidate key biological processes in water and wastewater treatment to optimize reactor performance through intelligent operation. Process applications include municipal, industrial wastewater, and agricultural wastewater treatment, biological drinking water treatment, and energy production from organic process streams.

Analysis of genomes and genome evolution, including the roles and effects of horizontal gene transfer. Analysis of host-associated microbial communities.

One of my main research interests is the role of soil microorganisms in seed banks, with the goal of developing more biological-based approaches for weed management in agroecosystems. Another area of my research is in the biodegradation of herbicides in soil, with specific emphasis on anaerobic microbial processes. A third area of interest investigates the molecular ecology of antibiotic resistance (ABR) genes in the environment, where the diversity, persistence, and dissemination of ABR genes are tracked from agricultural sources through groundwater and soil systems.

My research focuses on the Microbial Ecology of biogeochemical processes, particularly those that occur in the subsurface. The emphasis of my experimental work has been in three areas. First, several projects focus on characterizing the role of respiratory anaerobic organisms, such as those that utilize halogenated compounds and metals, in polluted ecosystems. This has led to a collaborative genomics project looking at the population ecology, evolution and physiological diversity of the anaerobic versaphile Anaeromyxobacter dehalogenans. In my second research area we investigate the microbial community diversity in relation to geochemical parameters in anaerobic groundwater where natural arsenic concentrations are high, such as the Mahomet aquifer in east-central Illinois. Lastly, I have become involved in an investigation of the complex microbial communites in calcium carbonate depositing environments such as Mammoth Hot Springs in Yellowstone National Park and Coral Reefs. We are particularly interested in the mechanistic relationship between the geochemical system and physiology of key microorganisms in each environment.

My current research interest involves the investigation of the biochemical, physiological, molecular and evolutionary aspects of an organelle found in Agrobacterium tumefasciens and Rhodospirillum rubrum containing pyrophosphate (PPi), polyphosphate (polyP), calcium, magnesium, and potassium. This organelle is enclosed by a unit membrane, and possess a calcium-accumulating activity, and a proton translocating pyrophosphatase (H+-PPase) that acidifies their content. These characteristics are similar to those described for the acidocalcisomes of early eukaryotes, such as Chlamydomonas reinhardtii, malaria parasite, Toxoplasma gondii, and trypanosomatids. The elucidation of the function of bacterial acidocalcisomes may provide new insights in the understanding of important issues, such as bacterial pathogenesis and bacterial adaptive mechanism to stress.

In addition, I am interested in the evolution process of prokaryotic and early branching eukaryotic organisms, and whether this organelle originated previously to the basal branching of the universal tree of life. The discovery of an organelle shared by prokaryotes and eukaryotes opens a new window into previously unsuspected genomic interactions among the domains of the tree of life.

Our goal is to understand the forces that shape diversity as microorganisms evolve. Our approach uses comparative genomics and metagenomics to reconstruct the natural history of a species of thermophilic Archaea that live in island populations and to understand how horizontal gene flow, natural selection shape microbial genomes over recent history. We are also investigating how interactions between microorganisms and mobile genetic elements like viruses and plasmids are shaping diversity and driving speciation. Finally we are investigating the effect of disturbance such as virus predation or environmental instability shape diversity and drive adaptation in dynamics microbial populations in humic lakes.

Our major research interests are in the genomics, metagenomics and molecular ecology of lignocellulose degradation, using the rumen and Ruminococcus flavefaciens as the model system. We are also interested in microbiome technologies for studying communities from production species (poultry, swine and cattle) as well as other mammals (humans and primates).

Host-Microbe Systems: Evolutionary Medicine, Comparative Biology and Women’s Vaginal Health. We have launched a new research program to study the dynamic interactions between the host and its commensal as well as pathogenic microbes to elucidate basic processes of disease. This research focuses on the complex ecosystem of the vaginal microbiota and its impact on health and disease in women, as part of our IGB Host-Microbe Systems Theme on women’s vaginal health (http://www.igb.uiuc.edu/research_themes/hostmicrobe.html). The HMS Theme is developing analytical and functional genomic technologies for determining the microbial, immunologic, and metabolic content of the vaginal ecosystem and for identifying specific host biomarkers in response to colonization with normal versus harmful microbes, as well as toxicity and infection. We are taking a novel evolutionary medicine, “life-history” and comparative biology approach toward defining predictive models of vaginal ecosystem dynamics and developing nonhuman primate models for studying human disease.

Dr. Zilles studies how dynamic environmental conditions and complex communities influence microbial ecology and physiology in a variety of engineered and agricultural systems.