The utilization of natural microbial diversity in biotechnology is hindered by our inability to culture the vast majority of microorganisms and the observation that laboratory engineered bacteria rarely function in the wild. It is now clear that an understanding of the community structure, function and evolution of bacteria in their natural environments is required to meet the promise of microbial biotechnology. To meet these new challenges, microbiologists are applying the tools of genomics and related high-throughput technologies to both cultured microbes and environmental samples. This work will lead to new views on ecosystems and biological function together with the biotechnology enabled by this science.