Urban soils immobilize harmful microbes and antibiotic resistance genes

Exposure to harmful microbiomes and antibiotic resistance genes (ARGs) can negatively affect human health. However, the contribution of vegetation and soils to the airborne microbiota transferred indoors (AMTI) remains unclear. We used our newly-developed airborne microbial sampler (VenTube) to collect AMTI samples from 72 neighborhoods in Shanghai. The AMTI sampling coincided with simultaneous adjacent phyllosphere and soil microbes. We characterized the microbial communities using next-generation sequencing and quantitative PCR, and employed traceability analysis to identify the sources of AMTI. Our findings revealed that both bacterial and fungal communities in AMTI predominantly originated from phyllosphere, which was estimated to contribute up to 52.3 % and 67.2 % of the bacterial and fungal communities, respectively. Notably, there was extensive co-transfer of potential human pathogens (PHP) between phyllosphere microbes and AMTI. Surprisingly, although the soil harbored higher levels of PHP and respiratory diseases (RDs)-associated ARGs than AMTI, it contained fewer RDs-associated microbes overall. Furthermore, soil sulfur enrichment due to an increase in Ligustrum trees influenced the release of RDs-associated microorganisms from the soil. Collectively, our study emphasizes that the elevated levels of RDs-associated microbes in AMTI primarily derived from phyllosphere microbes. We also highlight that soils may limit the spread of RDs-associated microbes and ARGs.