Outdoor Atmospheric Microbial Diversity is Associated with Urban Landscape Structure and Differs from Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial Analysis

Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples. Importance Global nutrient cycling and human health depend on the rich biodiversity of microorganisms. The influence of the urban environment on microbiomes remains poorly described despite cities being the fastest growing ecosystems. All life is exposed to the atmosphere and thus discerning what microbes are present and what their functions may be is critical to create resistant and resilient cities under climate change. This study combines a spatially explicit analysis of urban structure with mobile monitoring of the atmospheric microbiome.