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The risks of invasions of remote ecosystems by new microorganisms is a major threat as they are likely to impact the diversity and function of resident communities and local ecosystems. In the Antarctic, aerial transport is the primary source of new biological inputs. Airborne communities are believed to be influenced by environmental and climatic conditions, which are already changing rapidly on a global scale, but especially in the Polar regions. Yet, the influence of climate change, weather patterns and environmental conditions on these airborne communities are still unclear. One of the key challenges in understanding these processes is the high heterogeneity and variability of airborne samples. Following the Antarctic Expedition (ACE), in which daily samples were taken around the Antarctic continent to provide spatial distribution of airborne microorganisms, a time series was conducted at one of the ACE field sites (South Georgia) over a period of two weeks, at both high and low altitude to establish the daily variability between aerobiological sample sets. Results showed that although there was indeed a high heterogeneity and variability within the sample sets and across sample types, reliable patterns in the overall diversity could still be determined, and hence single daily samples can still provide useful assessment of aerial diversity over spatial and temporal scales in the Antarctic.