The institutional repository (IR) is fast being embraced as a necessary service of the academic library. Most often, the IR is implemented as an isolated software system and by definition it contains a limited range of content (i.e., institutionally-produced works). At the same time, non-institutionally-produced digital collections that the library owns typically sit separately - perhaps they have special audiences, contributors, needs, and likely they have unique development histories. What identity unifies them for presentation to users? Do they need to be tied together somehow? Organizationally, how should they be effectively and efficiently managed and preserved? Technically, are there ways to leverage systems to manage diverse collections found in IRs and in subject-based or special collections? The answer for the University of Minnesota is the University Digital Conservancy, a new program that encompasses data management, preservation, delivery, and the development of new born-digital or previously-digitized collections. This paper focuses on the opportunities and challenges posed by the construction of a holistic framework for developing, managing, preserving, and delivering digital collections. It discusses the complexities involved in: bringing together disparate collections with distinct contributors and audiences; integrating and replacing legacy systems with current technology; developing policy and workflow for digital archival collections, institutional repository-type content, and subject-based repository content that originates in- and/or outside of the institution. The paper focuses on three examples relevant to the agricultural, environmental, and natural resource sciences, including: AgEcon Search, an existing digital collection of 20,000 applied economics working papers contributed by faculty from around the world; agricultural extension publications; and, works of the new Institute for the Environment at the University of Minnesota. Discussion of the unique opportunities and challenges posed by each of these collections will help inform librarians working to develop their own institutional solutions around digital information.