Although the vast majority of microbes in nature resist laboratory cultivation, they represent an almost limitless reservoir of genetic diversity and metabolic innovation. Next generation sequencing technologies are rapidly expanding our capacity to access genotypic and phenotypic information directly from environmental samples. However, to effectively interpret and apply this increasing volume of information, new analytical tools and services must be developed with the end user in mind. Here, I explore problems and solutions in environmental sequence analysis spanning different levels of biological organization from genomes to biomes. I highlight emerging open source tools for integrating and visualizing multimolecular (DNA, RNA and protein) and environmental parameter data and consider the future of data intensive computation and environmental sensing as it relates to pathway reconstruction, ecosystem modeling and synthetic ecology.