Advancing transcriptomic profiling of airborne bacteria

Aerobiology research focusing on bioaerosol particle dynamics has catalogued the identity, distribution, and abundance of airborne microbes in a broad variety of indoor environments and, more recently, indoor disinfection methods for medically relevant microbes. Given their importance in environmental health and our constant exposure to airborne microbes in our daily lives, surprisingly little is known about the activity of live bioaerosols and their metabolic responses to aerosolization and suspension stress. In this context, microbial messenger RNA (mRNA) is a powerful information source of near-real-time organismal responses that cannot be attained through genomic, proteomic, or metabolomic studies. This review discusses current knowledge from transcriptomic studies describing airborne bacterial cellular activity in response to a myriad of environmental stresses imparted rapidly upon aerosolization and continued suspension as a microscopic bioaerosol. In the context of transcriptome profiling, potential artifacts associated with aerosolization/collection of bioaerosols are discussed from the perspective of preserving mRNA and maintaining its fidelity as it exists in airborne microbes. Recommendations for advancing live bioaerosol metabolic profiling through gene expression studies are presented to mitigate inherent artifacts and challenges with modern bioaerosol experiments. These recommendations include the use of larger experimental chambers, temperature control during aerosolization processes, and liquid capture bioaerosol sampling into a nucleic acid preservative to improve the fidelity of collected RNA and better capture the transcriptional activity of airborne microorganisms. Eventually, improvements in profiling bioaerosol activity can contribute toward answering fundamental questions on the aerobiome such as: is the atmosphere a temporary highway or a habitat for microorganisms?