In order to predict the impact of global changes on terrestrial ecosystems, it is becoming clear that specific study of the soil microbial community must be included. However, this has been difficult to achieve due to: 1) technical challenges in studying what cannot be seen with the naked eye; and 2) differences in research approach of ecosystem versus microbial ecologists. Recent advances in methods are making it possible to study soil microorganisms in detail, but how to best use the information to protect and manage ecosystems remains unclear. This workshop will bring together scientists from a range of disciplines to identify the most important questions about threats to ecosystems that require microbiology to answer, and determine what strategies and possible future techniques will allow scientists to answer these questions? The workshop will be significant in gathering both young and experienced visionary experts from several scientific areas. One of the outcomes, in addition to a concrete research agenda, will be the creation of an interdisciplinary research community and increased communication among science disciplines. Because issues in ecosystem ecology are rarely confined within a discipline, this type of interdisciplinary collaboration and communication is critical for future efforts in global change research.