Our Research

Microbiome research is among the most exciting and promising areas of science today due to many technological advances that allow us to determine in complex environments which microbes are present and their metabolism. Our laboratory’s primary long-term research goal is to contribute to the understanding of microbial communities and their evolution by developing and applying genome-based technology. Working in the fields of evolutionary biology and climate change, we are sensitive to how scientific results can be difficult to reconcile with our belief systems and seek to increase public understanding of scientific data. Our research is supported by the National Science Foundation, Department of Energy, and New England BioLabs. Below are overviews of some of our current project areas.

Long-term experimental evolution and ecology

A central feature of our laboratory has been the use of long-term experimental evolution and ecology approaches on scales from individual microbes to ecological communities with the application of next generation sequence technologies to identify mutations in evolved strains and determine changes in microbial community composition. Our was among the first to ask questions using environmental metagenomic data and to determine selection by sequencing bacterial populations instead of individual isolates.

Microbial communities for environmental and animal health

We established a paradigm of using experimental microcosms and community genomics that led to the isolation of novel anaerobic bacteria and their application to environmental and animal health. By sequencing the genomes of scores of these bacteria we have identified novel features including bacterial microcompartments and are making overdue taxonomic revisions to the Clostridia. These microbes (and we helped too) launched several companies.

The Harvard Forest Experimental Warming Plots

Most of our research is now centered at the Harvard Forest Long Term Ecological Research site in Petersham, MA is home to long-term experimental soil warming sites where our current field work is based. The oldest of these warming sites was established by Jerry Melillo in 1991 to measure the effects of global warming by running cables 10 cm under the forest floor and heating the soil 5° C above the control plot temperature throughout the year. After 25 years of continuous warming there has been a measurable changes increase in the flux of carbon dioxide from carbon in the soil to the atmosphere through increase microbial respiration. This has been accompanied by changes in soil chemistry, the microbial communities and the forest plants.