Ecology is quickly changing into a data intensive science. Powerful new data storage and computing capabilities allow scientists to explore environments through diverse and large-scale datasets ranging from microbial DNA to satellite images of natural ecosystems. At the forefront are computational infrastructures, in which scientists can share data and knowledge, computational resources and analysis tools for ecological research. Through the iMicrobe project, we extend an existing computational infrastructure called CyVerse to create a data commons for microbial data sets taken from diverse environments. We will also develop methods for scientists to find, tag and reuse data sets based on standard terms and ontology, and develop Apps for analyzing metagenomic samples (see protocols.io). This project strives to enhance the use of shared microbial data sets and computational infrastructure and code to promote large-scale studies of microbial ecology to understand the Earth system.