Microbiome research is one the most exciting areas of science today. Our laboratory’s long-term research goal is to contribute to the understanding of forest microbial communities and their response to climate change. We particularly enjoy discovering new forest microbes in the Pioneer Valley, North Quabbin Woods and at our research sites at the Harvard Forest. Our fundamental revelations into how microbes work together to decompose forest leaf litter and cycle nutrients has led to applied applications in biofuels, probiotics and biotechnology. Our research is currently supported by the National Science Foundation, Department of Energy, and New England BioLabs.
Discovery and Classification of New Lineages of Microbial Life
Our lab has a long history in microbial genomics and evolution. We have isolated new bacterial species from the surrounding forests, most recently a new genus Kineothrix whose members are turning up in many human gut microbiome studies and maybe responsible for the Love Bug Effect. This is a prime example of how basic science and taxonomic classification can provide benefits to human well-being. We also use environmental genomics to discover genomes of the bacteria that have never been cultured including intracellular and host-dependent bacteria. For most of our Harvard Forest metagenomes less than 3% of the DNA mapped to existing genomes which demonstrates vast discovery space still exists in soil communities.
Revealing the Hidden Diversity of Terrestrial Giant Viruses
Unexpectedly, we discovered 16 giant viruses in our climate warming study at Harvard Forest, including the world’s 2nd largest giant virus genome, 6 ranking in the top 100 and all 16 representing new species, genera or families. We are using environmental genomics to discovery new lineages of viral life and establishing cultures systems so to study them further in the laboratory. The TEM image (colorized) of a Harvard Forest giant virus comes from our collaborators Matthias Fisher and Ulli Mersdorf at the Max Planck Institute in Heidelberg.
Ecological and evolutionary genetic responses to long-term experimental soil warming
The Barre Woods experimental warming site at Harvard Forrest was established in 2002 by Jerry Melillo. Several challenges remain to directly link soil communities to changes in soil CO2 efflux. We are using metatranscriptomic approaches in conjunction with the experimental toggling of temperature in the warming site to understand the response of the microbial communities and building reference genomes from this community to identify adaptions in response to warming.
Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT)
The Ecological Metagenome-derived Reference Genomes and Traits (EMERGENT) synthesis project connects genomic information about the soil microbiome with the broader ecological context. This National Science Foundation Long Term Ecological Research synthesis working group will advance efforts to harmonize molecular information for microbial taxa and their functional traits. For more information see the EMERGENT GitHub project site.
Integrating Microbiome Data from National Ecological Observatory Network Eco-climatic Regions
In this project we are utilizing soils from the NEON Biorepository and EMSL/JGI capabilities to conduct continental scale ecosystem research along climate/vegetation gradients. Through this effort we hope to close the gap between genomic studies and large ecosystem synthesis efforts that have been valuable in understanding how carbon cycling and soil respiration respond to warming