Quantitative Biology / Gene Expression in Development & Disease Seminar

Friday, 12 April 2013 at 11:30am

Room 1400 Biomedical and Physical Sciences Bldg.

Refreshments at 11:30

Speaker:  Jack Gilbert, Department of Ecology and Evolution, University of Chicago

Title:  The Earth Microbiome Project: Characterizing the Microbial World!

The understanding of Earth's climate and ecology requires multi-scale observations of the biosphere, of which microbial life are a major component. However, to acquire and process physical samples of soil, water and air that comprise the appropriate spatial and temporal resolution to capture the immense variation in microbial dynamics, would require a herculean effort and immense financial resources dwarfing even the most ambitious projects to date.

To overcome this hurdle we created the Earth Microbiome Project, a crowd-sourced effort to acquire physical samples from researchers around the world that are, importantly, contextualized with physical, chemical and biological data detailing the environmental properties of that sample in the location and time it was acquired. The EMP leverages these existing efforts to target a systematic analysis of microbial taxonomic and functional dynamics across a vast array of environmental parameter gradients. The EMP uses the data standards format to capture the environmental gradients, location, time and sampling protocol information about every sample donated by our valued collaborators. Physical samples are then processed using a standardized DNA extraction, PCR, and shotgun sequencing protocol to generate comparable data regarding the microbial community structure and function in each sample.

To date we have processed over 10,000 samples, and have more than 20,000 in the process of being analyzed. One of the key goals of the EMP is to map the spatiotemporal variability of microbial communities to capture the changes in important processes that need to be appropriately expressed in models to provide reliable forecasts of ecosystem phenotype across our changing planet. This is essential if we are to develop economically sound strategies to be good stewards of our Earth. The EMP recognizes that environments are comprised of complex sets of interdependent parameters and that the development of useful predictive computational models of both terrestrial and atmospheric systems requires recognition and accommodation of sources of uncertainty.