In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species‐specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over‐harvesting. Through a series of case studies, we show that the loss of foundation tree species changes the local environment on which a variety of other species depend; how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow; and dramatically alters the dynamics of associated aquatic ecosystems. Forests in which dynamics are controlled by one or a few foundation species appear to be dominated by a small number of strong interactions and may be highly susceptible to alternating between stable states following even small perturbations. The ongoing decline of many foundation species provides a set of important, albeit unfortunate, opportunities to develop the research tools, models, and metrics needed to identify foundation species, anticipate the cascade of immediate, short‐ and long‐term changes in ecosystem structure and function that will follow from their loss, and provide options for remedial conservation and management.

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Dissolved organic matter (DOM) is recognized as a major component in the global carbon cycle and is an important driver in aquatic ecosystem function. Climate, land use, and forest cover changes all impact stream DOM and alter biogeochemical cycles in terrestrial environments. We determined the temporal variation in DOM quantity and quality in headwater streams at a reference watershed (REF), a watershed clear-cut 30 years ago (CC), and a watershed converted to a white pine plantation 50 years ago (WP) at the US Forest Service, Coweeta Hydrologic Laboratory, in the Nantahala Mountains of western North Carolina, USA. Average stream dissolved organic carbon (DOC) concentrations in CC or WP were 60 and 80% of those in REF, respectively. Stream DOM composition showed that the difference was mainly due to changes in humiclike components in chromophoric DOM. In addition, excitation-emission matrix fluorescence data with parallel factor analysis indicate that although the concentration of protein-like components did not differ significantly among watersheds, their relative abundance showed an enrichment in CC and WP compared to REF. The ratio of humic acid-type to fulvic acid-type components was highest and lowest at REF and WP, respectively. Our data suggest that forest ecosystem disturbance history affects the DOM quantity and quality in headwater streams over decades as a result of changes in watershed soil organic matter characteristics due to differences in organic matter inputs.