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Understanding microbial interactions is key to the study of global warming, biodegradation of harmful compounds, and the exploration of complex microbial communities in their natural environment. The DOE has placed an increased emphasis on the role microbes play in modifying their environment and their impact on energy security. The MME group has responded to these needs by aggressively seeking out new projects and expanding its staff to develop new core capabilities. One of the key challenges has been to harness the explosion of microbial DNA sequence information to accurately measure the microbial dynamics in extreme environments. Since less than one percent of the microbial species can be cultured from these environments, our knowledge of what these organisms may be doing is limited to where they are observed and the similarity of their genomes to studied organisms. By understanding the ecological structure of microbial communities and the fine-scale dynamics resulting from subtle perturbations, it may be possible to identify novel functional pathways and use the diverse microbial capabilities to assist in key DOE missions. The molecular tools being developed in the ESD’s Center for Environmental Biotechnology will position us to be leaders in this area.