In this paper we introduce results obtained from the Program for Research on Oxidants: PHotochemistry, Emissions, and transport (PROPHET) program that is being conducted at the University of Michigan Biological Station in northern Michigan. PROPHET is an independent consortium of individually funded scientists whose mutual interests and varied experiences have created a synergistic collaboration focused on studies of atmospheric chemical and meteorological processes linked to tropospheric ozone. Since 1997, the PROPHET science team has combined expertise to characterize the important atmospheric issues in this region and to begin to push the limits of our knowledge of the links between the biosphere and the atmosphere. The opportunity to conduct research in the physical context of the Biological Station enables this team to interact with a tremendous range of activities related to forest and ecosystem health and uniquely positions PROPHET to make contributions to the emerging field of biosphere-atmosphere interactions. Among other findings in this special section, Faloona et al. report on surprising measurements of the OH radical at night and discuss the possibility that biogenic emissions play a heretofore unappreciated role in nighttime chemistry and that our understanding of radical production in forests may be incomplete. Grossenbacher et al. report the first field measurements of isoprene nitrates and suggest that isoprene oxidation in this forest is slower, on average, than in areas with lower NOx burdens. Westberg et al. report on results of several approaches aimed at quantifying isoprene fluxes in this environment. It is our hope that the experiments described in this special section and future PROPHET experiments are paving the way toward a better understanding of natural forest systems and their interaction with anthropogenic inputs.