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Research Opportunities

 Alison Buchan  Alison Buchan, Microbiology
Students will participate in research examining viruses that infect members of the ecologically important Roseobacter clade of heterotrophic marine bacteria and the influences that viral infection have on host activities and the fate of microbial carbon and nutrients released by viral activity. Using our recently established and environmentally relevant phage-host model systems, students will participate in metabolomics studies to examine the effect of virus infection on host metabolism. Students will also participate in metabolomics studies of microbial isolates and mixed populations consuming cellular components released by phage-mediated lysis of roseobacters.
 Jennifer DeBruyn  Jennifer DeBruyn, Biosystems Engineering and Soil Science
Students will research microbial ecology of soil and terrestrial systems, with intent to understand carbon cycling dynamics.  Focus areas will include microbial communities involved in crop ecosystems and decomposition (composting) of cadavers.  Students will use molecular techniques and chemistry to further our understanding of soil community structures, carbon cycling and taphonomy.
 Annette Engel  Annette Engel, Earth and Planetary Sciences
Students will conduct field, laboratory, and computational research in the general area of aqueous geochemistry and subsurface geomicrobiology. Students will be able to sample a variety of settings, including surface soils, aquifer wells, and caves, using aqueous and microbial geochemistry techniques, and then will analyze the samples using laboratory approaches. Students will processes the data using bioinformatics techniques to determine how geochemical conditions influence the diversity of metabolic pathways and associated taxonomy of microbial groups, and to evaluate models that are being developed for understanding the interactions between subsurface geochemical and microbial ecosystems.
Heidi Goodrich-Blair Heidi Goodrich-Blair, Microbiology
Students will use bacterial genetics, genomics, microscopy, and molecular and biochemical approaches to investigate the symbiotic interactions of the bacterium Xenorhabdus with its animal hosts. Xenorhabdus is a mutualist of Steinernema nematodes and a pathogen of a wide range of insects, and experimentation on this system will give students experiences in a broad range of skills in bacteriology, nematology, and entomology. Students will explore research questions that address evolutionary, ecological, and physiological principles underlying symbiotic associations.
 Terry Hazen Terry Hazen, Microbiology
Systems Biology Approach (Ecosystems to Molecular Level) for Oil bioremediation, Aerobic Landfill Engineering, Characterization of Hazardous Waste Sites.
Perturbation studies of deep-sea water from 8 sites around the world with crude oil for risk assessment of deep drilling.
Aerobic Landfill Engineering cost analysis and modeling with thermal recovery vs. methane production optimization.
Characterization of Hazardous Waste sites to take into account treatment-train final outcomes.
 Qiang He Qiang He, Civil & Environmental Engineering.
Students will conduct research on the microbial ecology of biofilms in drinking water distribution systems. Biofilms pose public health risks by impairing water quality integrity and serving as a reservoir of harmful microorganisms. The focus of this study is the microbial functional characteristics underlying the development and persistence of biofilms in disinfected water.  Students will employ molecular techniques to identify microbial functional groups predominant and persistent in drinking water distribution systems and determine the biochemical functional features enable biofilm development, which could be used to develop more effective water quality control strategies.
 Sarah L. Lebeis Sarah L. Lebeis, Microbiology
The research that students will perform will examine plant-associated microbial communities, which can profoundly affect plant health. Students will use a collection of bacterial isolates and plant immune system mutants to separate how plant-microbe and microbe-microbe interactions each contribute to the assembly and stability of root microbiome. Students will implement a variety of molecular, genomic, and microscopy techniques, which will contribute to our understanding of how plant-microbe relationships can be exploited to promote plant health during environmental changes.
 Karen Lloyd Karen Lloyd, Microbiology
Students will use cutting edge bioinformatics to explore genomes of marine microorganisms to look for particular environmental functions.  Students will gain familiarity with the breadth and diversity of microbial life that does not exist in laboratory cultures, and will use techniques of primer design, PCR, and quantitative PCR to assay the relevance of particular genes in the marine environment.
 Frank Löffler  Frank Löffler, Microbiology and Civil & Environmental Engineering
Undergraduate students will have opportunities to work on defined research projects under direct guidance of a graduate or postdoctoral student.  Undergraduate students will have opportunities to learn enrichment procedures to obtain microbes of interest from the environment, apply cultivation and cultivation-independent approaches to explore microbial community structure, function and response to perturbations, use experimental and computational tools to explore genomes, transcriptomes and proteomes of defined cultures and environmental communities, and work at the interface of basic and applied microbial ecology research.
 Jill Mikucki  Jill Mikucki, Microbiology
Students will study the microbial ecology of icy Antarctic ecosystems with a focus on subglacial lake and sedimentary environments. Students will employ microscopy, molecular and culture techniques to examine the relationship between microbial diversity, the subice environment and the cycling of key metabolic substrates to understand how microorganisms survive and grow under extreme cold and dark conditions.  Students will work with Antarctic samples to isolate and characterize ecologically relevant microorganisms and evaluate how isolates respond to changing environmental parameters. Students will also help develop and test appropriate ‘clean access’ techniques for sampling pristine frozen environments for application to future subglacial drilling projects.
 Mark Radosevich  Mark Radosevich, Biosystems Engineering and Soil Science
Students will conduct research in soil microbial ecology. Possible topics for investigation will include the role of bacterial quorum-sensing on lysogenic interactions of bacteriophage and host bacteria in soil ecosystems, niche specialization of ammonia-oxidizing prokaryotes, the adaptations and ecological function of soil bacteria within the phylum Gemmatimonedetes, and development of molecular assays to  assess phosphorus-stress in soil bacteria.  Students will employ a range of process-level and molecular approaches to address these topics.
 Todd Reynolds  Todd Reynolds, Microbiology
Students will conduct research studying how fungi in the genus Candida interact with one another and their normal environment.  Candida species are part of the normal flora of humans (commensals), but are also the most common opportunist fungal pathogen pathogen of people that are immunocompromised.  We will focus on how  Candida yeast cells participate in intercellular communication with one another or the host via quorum sensing factors, cell wall interactions, and response to nutrient in their immediate environment.
 Steven Ripp  Steven Ripp, Microbiology
Students will conduct research in synthetic biology and the bioengineering of recombinant bacterial, viral, and mammalian reporters for food/waterborne pathogen identification, the detection of harmful environmental pollutants, and biomedical imaging. Students will be challenged with molecular cloning techniques and the modeling of reporter response kinetics to produce new tools for environmental surveillance, food safety, and clinical diagnostics.
Sean M. Schaeffer, Biosystems Engineering and Soil Science
Students will conduct research in the areas of soil ecology and biogeochemistry, with an emphasis on climate change and functional diversity of microbial communities. Current research areas include bacterial nitrogen transformations and greenhouse gas production in agroecosystems, the physiological response of microbial communities to drought, and the effects of climate change on soil microbial functional diversity in High Arctic ecosystems. Students will have the opportunity to learn field and lab-based techniques to measure microbial activity, substrate decomposition, and fluxes of energy and nutrients through the soil-plant-atmosphere continuum. Student research will contribute our understanding of how microbes adapt to a changing environment and the critical roles they play in mediating global biogeochemical cycles.
 Drew Steen  Drew Steen
I’m interested in interactions between heterotrophic microorganisms and dissolved organic matter in aquatic environments, including lakes, rivers, the coastal ocean, and deep marine sediments (hundreds of meters below the seafloor). My particular focus is on how Bacteria and Archaea use extracellular enzymes to access complex organic matter, a process which has important implications for the global carbon cycle. I have recently received samples from up to 200 meters deep in sediments from the Baltic Sea, in which the pace of microbial life is many orders of magnitude slower than “typical” microbial environments. I’m interested in working with an undergraduate student to characterize the activities of enzymes (with a special focus on peptidases) in these samples. This will represent the first time that extracellular enzymes have been assayed in such deep sediments
 Chunlei Su Chunlei Su, Microbiology
Students will conduct research in the area of population genetics and evolution of virulence in the protozoan parasite Toxoplasma gondii.  The goals are to understand the origin, the global transmission patterns, the mechanisms of clonal expansion of a few predominant lineages of T. gondii. Students will employ molecular techniques to identify and genotype Toxoplasma strains collected from domestic animals, wildlife and humans.   Students will also help develop a global geographical information database to integrate Toxoplasma population diversity data collected in our laboratory.
 Steven W. Wilhelm Steven W. Wilhelm, Microbiology
Students will have opportunities to conduct research in several areas including how viruses shape microbial communities,  the interactions between viruses and prokaryotes influences biogeochemical cycles, and investigations into the root causes of toxic algal blooms.  Students will employ molecular techniques.  Students will help develop new approaches so that relationships can be extended to new model organisms from freshwater and marine systems. State-of-the-art molecular and bioinformatics tools are available to provide training tractable to any area of the biological and environmental sciences.
 Erik R. Zinser Erik R. Zinser, Microbiology
Students will conduct research in the general area of microbial ecology of aquatic systems, with a focus on how biotic and abiotic factors impinge on the growth and physiology of the globally-abundant marine cyanobacterium, Prochlorococcus.   Students will use classical as well as modern molecular approaches to characterize the genetic underpinnings of the responses of Prochlorococcus to variations in environmental parameters, such as temperature and light, and will also characterize their interactions with other members of the marine microbial community, including heterotrophic bacteria and other primary producers, such as Synechococcus.   For the latter studies, metabolomics will also be employed to investigate mechanisms of nutrient cross-feeding between members of different trophic groups.


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