DNA analysis of outdoor air reveals a high degree of fungal diversity, temporal variability, and genera not seen by spore morphology

Fungi are ubiquitous with many capable of causing disease by direct infection, toxicoses, or allergy. Fungal spores are present in outdoor air throughout the year, yet airborne diversity is poorly characterised. Airborne fungal spores are routinely counted by microscopy, enabling identification to genera at best. We generated traditional microscopic counts over a year, then used environmental sequencing techniques to assess and compare 3 d selected from the main fungal spore season. The days selected corresponded to one with a high quantity of spores unidentifiable by microscopy, and two representing dry and wet summer periods. Over 86 % of genera detected by sequencing were not routinely identifiable by microscopy. A high degree of temporal variability was detected, with the percentage of clones attributed to Basidiomycota or Ascomycota, and composition of genera within each phylum varying greatly between days. Throughout the year Basidiomycota spores were found at higher levels than Ascomycota, but levels fluctuated daily with Ascomycota comprising 11–84 % of total spores and Basidiomycota 7–81 %. No significant difference was found between the proportion of clones attributed to each morphological group detected by sequencing to that counted by microscopy (P = 0.477, 0.985, and 0.561). The majority of abundant genera detected by DNA analysis are not routinely identified by microscopy (>75 %). Of those, several are known human and plant pathogens, and may represent unrecognised aeroallergens.

► Fungal bioaerosols are ubiquitous, yet airborne diversity is poorly characterised.
► Outdoor microscopic fungal spore counts were generated over the course of a year.
► Environmental clone sequencing was used to determine fungal diversity on 3 d.
► >86 % of genera detected by sequencing were not routinely identifiable by microscopy.
► Levels of spores and DNA correlated & high degree of temporal variability detected.