Our research program is focused on understanding microorganisms and molecular processes involved in the decomposition of plant material, particular the recalcitrant structures in the plant cell wall. This research has important implications for climate change research, developing cellulosic biofuels and animal health and nutrition. A prominent component of our research is using genomic and computational methods to understand variation at the molecular and organismal levels. Our laboratory is set up for standard molecular biology and microbial physiology research and contains specialized equipment for working with anaerobic bacteria. The research we do is currently funded by the National Science Foundation, Department of Energy, United States Department of Agriculture, and the Morris Animal Foundation. Below are overviews of some of our current funded project areas.
Global warming and forest soil microbiomes
Human activities are having a major impact on the global balance of exchange between carbon reservoirs. Three quarters of the carbon in terrestrial ecosystems is found as organic matter in soils, most of which is derived from plant litter. Accurate models capable of predicting the flux of carbon on a global scale, must be informed by a complete understanding of the complexity of carbon flow in soil, and the mechanisms of carbon transformation through communities of microbes. Our ability to understand carbon cycling by microbial communities is being transformed by rapid advances in DNA sequencing technology. We are developing new bioinformatic approaches for understanding microbial communities and their evolution. We also use microcosms, small experimental ecological systems representing aspects of the natural environment, to conduct replicated, controlled experiments in which system parameters are varied. Microcosms are particularly tractable to metagenomics, metatranscriptomic and other genome-enabled approaches and offer opportunities to apply genomics to analyze the physiological ecology of single cells and microbial consortia. Our research involves laboratory studies and field research at the Harvard Forest.
Renewable biofuels from plant litter using C. phytofermentans (Cphy) and other newly discovered microorganisms
Our primary long-term goal is to contribute to the production of biofuels derived from ecologically and economically sustainable plant feedstocks. Using genome-based technologies we are able to measure changes in the DNA sequences and gene expression levels of all of these parts as they change in response to environmental cues and as they evolve over time. These data are then integrated in genetic and physiological models to improve biofuel production and tested using molecular genetic and biochemical approaches. The questions we are asking include: What are the enzymes used by C. phytofermentans to deconstruct plant cell walls? Why is ethanol the primary product? What is the structure and function of polyhedral microcompartments? How does the cellular energetics constrain engineering for other products?