Isoprene (2-methyl-1,3-butadiene) emission from plants sits at the center of advances in both plant physiology and atmospheric chemistry.  Recent studies demonstrate that isoprene production by plants helps protect them against damage by ozone, and isoprene emission from plants into air with high levels of fossil fuel combustion products increases ozone concentrations in the troposphere.  These advances suggest the possibility that emissions of isoprene from plants, in conjunction with fossil fuel combustion, create a positive feedback loop that drives changes in both biological diversity and atmospheric chemistry.  This feedback loop stands as one of the first examples of a situation where species-specific metabolism has impacts on tropospheric chemistry and where those impacts, in turn, alter both biological diversity and ecosystem metabolism.  We investigate this positive feedback loop using species-specific physiological data on isoprene emission & ozone impacts and models of both community ecology & atmospheric chemistry.  We find that under conditions of anthropogenically influenced air, where nitrogen oxide concentrations are well above background levels, isoprene emission from plants causes an increases in tropospheric ozone and that this rise in ozone differentially affects isoprene emitters and non-emitters, with isoprene emitters, on the whole, less affected by ozone.  These differences in ozone impacts lead to differences in growth and survival that alter community composition and, in turn, ecosystem-scale isoprene emission rate.  In contrast, isoprene emission into uncontaminated air leads to no significant changes in atmospheric chemistry, species growth and mortality, or community composition.