Emerging Infectious Diseases

Microbial Population and Community Dynamics

Bioenergy and Biobased-technologies

The energy crisis offers a tremendous opportunity to develop novel technologies for the use of sustainable, domestic resources to provide fuel, power, and chemical needs from plants and plant-derived materials. Increased funding is available for developing and improving technologies for biomass power; for making biofuels (such as ethanol from biomass residues as well as grain) and renewable diesel; and for making plastics and chemicals from renewable, biobased materials. Indeed, MSU was recently awarded its largest grant ever for such research as part of the new Great Lakes Bioenergy Research Center (GLBRC). Of foremost importance is the study of the microbial populations and communities that process biomass in the relevant environments. Additionally, it is critical to develop new strains and consortia of microbes for enhanced bioprocessing capabilities and increased efficiency of energetic conversion, probably by using a combination of targeted genetic engineering and experimental evolution approaches (as currently being planned for the GLBRC) . Three potential areas of expertise for future hires include: a geneticist devoted to engineering and evolving fermentative organisms for increased biomass degradation and enhanced biofuel production, a biological engineer with expertise in microbial fuel cells, and an environmental microbiologist using metagenomics analysis to analyze microbial diversity and the energetic yields of natural consortia.

Metabolomics in Microbes and Microbial Communities

Metabolites include the intermediary and end products of gene expression in any organism. The metabolome, therefore, represents the set of all metabolites produced by a given organism. The burgeoning field of metabolomics emphasizes the numerous small, but fundamentally important, molecules that are the building-blocks and by-products of metabolism. The interactions of metabolites within and between species are of particular importance in microbial communities, where some metabolites may promote coexistence of species while others (including antibiotics) serve as potent inhibitors of competing species. Specific cellular processes leave behind unique chemical fingerprints, and metabolomic techniques can be used to explore these important interactions and relationships. This position would have a strong focus on analytical chemistry tools for characterizing and quantifying metabolites, on integrated data analysis for interpreting metabolic interactions and networks, or both. For example, nuclear magnetic resonance and mass spectrometric methods would likely play a critical role in allowing comprehensive measurements of cellular components, while the mathematical integration and analysis of genomic, proteomic, transcriptomic, and metabolomic information can provide a more complete and dynamic picture of a living organism or microbial community than is possible using any single approach. An individual working in this area would ideally integrate laboratory experimentation with mathematical modeling, and would interact closely with the Quantitative Biology and Modeling Initiative at MSU.

Genomic Evolution

This area encompasses some of the most fundamental questions in biology as well as areas of tremendous biomedical and economic importance, including in developing new approaches related to bioenergy and strain improvement. Investigators in this field address issues ranging from the history of life to the mechanisms of adaptation and diversification while relating their findings to food safety, the emergence of new pathogens, and the spread of antibiotic resistance. The successful candidate might study evolutionary processes that structure the genomes of Bacteria, Archaea, or unicellular Eukaryotes, while addressing fundamental questions concerning, for example, genome organization, roles of horizontal gene transfer, molecular mechanisms of recombination and mutation, minimal genomes, selfish DNA, or the origin of gene regulons and networks. Experimental approaches to genomic evolution have seen particular interest and success in recent years on several fronts, including to address basic questions about the dynamics of evolution, for tracking genome-wide changes in microbial pathogens, and for strain improvement for technological purposes, including bioenergy, where leading research groups are increasingly combining genetic engineering and experimental evolution strategies. Of particular interest in all these areas are questions related to evolvability and robustness. What genomic features ñ such as biochemical pathways that govern mutation rates, and gene-regulatory networks that influence patterns of gene interaction ñ promote rapid evolution, as would be desirable for strain improvement? And how does evolvability affect the robustness of an organism to environmental and genetic perturbations, and thus the stability of the desired phenotype? This position will complement those groups involved in microbial evolution and microbial genomics at MSU.

Archaea, the Third Domain of Life

The study of the Archaea, which includes many organisms that live in extreme environments, will yield a vast range of novel physiological and biochemical features, undoubtedly including some with great biotechnological potential. The study of extremophilic organisms in this Domain represents a significant gap in research not only at MSU but also nationwide. In addition to basic questions related to the mechanisms of growth and survival of thermophilic, acidophilic, and halophilic representatives, this extensive group of microbes has been a rich resource for the isolation of novel enzymes of industrial interest. This position would encompass integrative research extending from metagenomes in extreme environments to the analysis of the biochemistry of the archaeal proteome and metabolome. The overarching goals would include exploration and discovery for biotechnological applications, while broadening our current understanding of both physiological diversity and evolutionary mechanisms.

Microbial Biogeochemistry

Microorganisms in the earth and in water play essential roles related to global climate change and stability, nutrient pollution and management, waste recycling and bioremediation. Biogeochemical processes are a major focus of NSF and DOE microbial programs. Many economically valuable geologic deposits from oils to ores result from or are enhanced by microbial activity. A position in this area will continue MSU's long tradition in ecosystem studies centered on the carbon, nitrogen, and sulfur cycles, and may extend that expertise to mineralization and geological fingerprinting, which is of particular interest in the search for evidence of early life processes on earth and on other planets. Furthermore, research in soil and water microbial ecosystems forms a critical component of the efficiency of plant growth, which will be a key part of emerging efforts to develop a sustainable bioeconomy.