1. Microbial diversity: My lab seeks to understand the causes of microbial diversity, the importance of diversity for ecosystem function, and the relationship between taxonomic and functional diversity. Environmental sandboxes will include the Grand River watershed, agricultural soils, and the rare Charitable Research Reserve. We develop molecular and bioinformatics methods for profiling microbial communities and have already discovered extreme phylogenetic novelty associated with the “rare biosphere”. The rare biosphere is common because most microbial species exist at low abundance, resist cultivation, and have escaped detection by DNA-based analyses. These organisms are likely contributors to community stability and function, and represent an enormous pool of uncharacterized genes and enzymes, useful for medical and industrial applications.

2. Linking function and phylogeny: New organisms and enzymes involved in carbon cycling are continually being discovered in soil and aquatic environments. By combining stable isotope probing and functional metagenomics, my lab seeks to better understand the organisms and pathways involved in the degradation and assimilation of greenhouse gases and plant-derived compounds in different environments and under diverse conditions. Stable-isotope probing provides targeted access to genes of active organisms that would otherwise escape detection by alternative cultivation-based techniques.

3. Nitrogen cycle: The nitrogen cycle is core to Earth’s biogeochemistry and represents an area of exciting microbiological discovery. We explore the nitrogen cycle in engineered aquatic environments to identify organisms and enzymes involved in both oxic and anoxic nitrogen conversion processes. By combining both culture-dependent and culture-independent approaches, we study ammonia-oxidizing archaea and bacteria, anaerobic ammonium-oxidizing bacteria, and denitrifiers. Although much of our work in this area involves studying these processes in commonplace engineered environments (e.g., wastewater, aquarium filters), we are also interested in nitrogen cycle processes responsible for metabolizing nitrogen in contaminated groundwater and agricultural soils.