While the air microbiome and its diversity are known to be essential for human health and ecosystem resilience, the current lack of holistic air microbial diversity monitoring means that little is known about the air microbiome's composition, distribution, or functional effects. We here show that nanopore shotgun sequencing can robustly assess the air microbiome in combination with active air sampling through liquid impingement and tailored computational analysis. We provide laboratory and computational protocols for air microbiome profiling, and reliably assess the taxonomic composition of the core air microbiome in controlled and natural environments. Based on de novo assemblies from the long sequencing reads, we further identify the taxa of several air microbiota down to the species level and annotate their ecosystem functions, including their potential role in natural biodegradation processes. As air monitoring by nanopore sequencing can be employed in an automatable, fast, and portable manner for in situ applications all around the world, we envision that this approach can help holistically explore the role of the air microbiome.

Air monitoring by nanopore sequencing