Many microorganisms are advected in the lower atmosphere from one habitat to another with scales of motion being hundreds to thousands of kilometers. The concentration of these microbes in the lower atmosphere at a single geographic location can show rapid temporal changes. We used autonomous unmanned aerial vehicles (UAVs) equipped with microbe-sampling devices to collect fungi in the genus Fusarium one hundred meters above ground level at a single sampling location in Blacksburg, Virginia, USA. Some Fusarium species are important plant and animal pathogens, others saprophytes, and still others are producers of dangerous toxins. We correlated punctuated changes in the concentration of Fusarium, to the movement of atmospheric transport barriers (ATBs) identified as finite-time Lyapunov exponent-based Lagrangian coherent structures (LCSs). An analysis of the FTLE field for periods surrounding 73 individual flight collections of Fusarium showed a relationship between punctuated changes in concentrations of Fusarium and the passage times of LCSs, particularly repelling LCSs. This work has implications for understanding the atmospheric transport of invasive microbial species into previously unexposed regions, and may contribute to information systems for pest management and disease control in the future.