Air monitoring by nanopore sequencing
While the air microbiome and its diversity are essential for human health and ecosystem resilience, comprehensive air microbial diversity monitoring has remained rare, and little is known about the air microbiome's composition, distribution, or functionality. Here we 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 both controlled indoor greenhouse environments and natural outdoor environments. Based on de novo assemblies from long sequencing reads, we identify the taxa of several air microbiota down to the species level and annotate their ecosystem functions. Extending our study to urban settings, we conducted a comprehensive air sampling campaign in Barcelona, Spain, revealing distinct microbial communities across various urban locations. As nanopore sequencing for air monitoring can be easily employed, is automatable, fast, and portable for in situ applications worldwide, we envision that this approach can help holistically explore the role of the air microbiome (Reska T. et al., 2024, ISME Commun. 4(1), doi:10.1093/ismeco/ycae099) (Explanation of the files, barcoding scheme, and processing can be found here: https://github.com/ttmgr/Air_Metagenomics/).