Research

Below are our current active areas of research

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.

Giant Viruses, Chlamydia, Vampire Bacteria and the Unexpected Diversity in Soil Microbial Life at Harvard Forest

Several challenges remain to directly link soil communities to changes in soil CO2 efflux. Consequently, it is essential that we develop alternative methods for analyzing community composition and function of active community members. We have used an approach, termed mini-metagenomics to reveal a surprising diversity of microbial life. Sixteen new lineages of giant viruses were discovered for the first time in a forest soil ecosystem.  Intracellular and host-dependent bacteria (Chlamydiae, Legionellales, Bacteriodetes, Rickettsiales and TM6/Dependentiae) were enriched in the data set relative to abundances in our traditional metagenomics. We are developing methods to directly detect and isolate this unusual organisms.

Genome-based predictive models of trophic modes influencing biogeochemical cycles

We are using integrative approaches supported by computational tools and analyses that iterate between models that capture microbial community dynamics and experiments in a natural forest ecosystem. Our prior -omics data reveals the importance of considering trophic modes involving eukaryotes, archaea, bacteria and viruses to understand key microbe-mediated biogeochemical cycling processes in terrestrial systems. Our experimental approaches and the development of computational models will enable testing hypotheses relating fundamental ecological concepts and will be useful in predicting and scaling responses to long-term soil warming

Ecological and evolutionary genetic responses to long-term experimental soil warming

New bacterial genotypes can be selected within days using a strong selective force (e.g. antibiotics) and within a few months in response to moderate changes in climate-related parameters (e.g. temperature). Thus, we expect 25 years of experimental warming at the Prospect Hill site at Harvard Forest to provide ample time for natural selection of genotypes better adapted to the altered environment. Our goal for this proposal is to detect natural selection in microbial communities resulting from 25 years of experimental forest soil warming starting with comprehensive reference genomes. The key questions we are addressing include: Has long-term warming changed population structure of active microorganisms? Is there evidence of selection in response to warming?