The iPlant Collaborative is an NSF-funded cyberinfrastructure (CI) effort directed towards the plant sciences community. This paper enumerates the key concepts, middleware, tools, and extensions that create the unique capabilities of the iPlant Discovery Environment (DE) that provide access to our CI. The DE is a rich web-based application that brings flexible CI capabilities to a wide audience affiliated with the plant sciences, from computational biologists, bioinformaticians, applications developers, to bench biologists. The inherent interdisciplinary nature of plant sciences research produces diverse and complex data products that range from molecular sequences to satellite imagery as part of the discovery life cycle. With the constant creation of novel analysis algorithms, the advent and spread of large data repositories, and the need for collaborative data analysis, marshaling resources to effectively utilize these capabilities necessitates a highly flexible and scalable approach for implementing underlying CI. The iPlant infrastructure simultaneously supports multiple interdisciplinary projects providing essential features found in traditional science gateways as well as highly customized direct access to its underlying frameworks through use of APIs (Application Programming Interfaces). This allows the community to develop de novo applications. This approach allows us to serve broad community needs while providing flexible, secure, and creative utilization of our platform that is based on best practices and that leverages established computational resources.