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  1. Foundation species, which help maintain habitat and ecosystem functioning, are declining due to anthropogenic impacts. Within the rocky intertidal ecosystem, studies have investigated the effects of foundation species on community structure and some resource fluxes; however, how intertidal foundation species loss will affect multiple facets of ecosystem functioning in concert remains unknown. We studied the direct and indirect effects of foundation species loss of mussels Mytilus californianus and surfgrass Phyllospadix spp. on community structure, fluxes (light, temperature, dissolved oxygen [DO], dissolved inorganic nutrients, pH T ), and ecosystem metabolism (net ecosystem calcification [NEC] and net ecosystem production [NEP]) in central Oregon using in situ tide pool manipulations. Surfgrass loss increased microalgae cover, increased average maximum light by 142% and average maximum temperature by 3.8°C, increased DO and pH T values, and indirectly increased NEP and NEC via increased maximum temperature and pH T respectively. Mussel loss increased microalgae cover, increased average maximum light by 5.8% and average maximum temperature by 1.3°C, increased DO and pH T values, and indirectly increased NEP via increased producer cover. Shifts in baseline nutrient concentrations and temperature values from coastal upwelling influenced ecosystem metabolism in pools with intact foundation species. Our results indicate that as communities respond to foundation species loss, ecosystem functioning depends on the dominant community present and biologically or physically driven shifts in biogeochemistry. This study highlights the importance of the connection between community and ecosystem ecology in understanding the magnitude of changes occurring with anthropogenically-driven intertidal foundation species loss. 
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