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Microbial respiration of particulate organic carbon (POC) is one of the key processes controlling the magnitude of POC export from the surface ocean and its storage on long timescales in the deep. Metabolic processes are a function of temperature, such that warming sea temperatures should increase microbial respiration, potentially reducing POC export. To investigate this in the Southern Ocean, we measured microbial oxygen consumption of large particles over a 10 degrees C temperature range (summer maximum +8 degrees C) to then estimate the decrease in export by 2100. Our results showed that POC-normalised respiration increased with warming. We estimate that POC export (scaled to primary production) could decrease by 17 +/- 7 % (SE) by 2100, using projected regional warming (+1.9 degrees C) from the IPCC RCP 8.5 ('business-as-usual' scenario) for our subAntarctic site. Increased microbial respiration is one of many processes that will be altered by future climate change, which could all modify carbon storage in the future. Our estimate of the potential decline in carbon sequestration is within previous estimates from lab and field experiments, but higher than simple mechanistic models. To explore our results further, we used the metabolic theory of ecology (MTE) to determine the activation energy of microbial respiration, which was 0.9 eV. This is higher than classical MTE (0.6-0.7 eV), suggesting that sub-Antarctic microbes are particularly sensitive to temperature change. Such regional characteristics in the response of organisms to increased temperatures should be accounted for in large-scale or global model analyses to ensure that the results do not underestimate microbial responses to warming.