Fungal Cells Recovery From Air Samples: A Tale of Loss And Gain

Abstract

There are limitations in establishing a direct link between fungal exposure and health effects due to the methodology used, amongst other reasons. Culture methods ignore the nonviable/uncultivable fraction of airborne fungi. Molecular methods allow for a better understanding of the environmental health impacts of microbial communities. However, there are challenges when applying these techniques to bioaerosols, particularly to fungal cells. This study reveals that there is a loss of fungal cells when samples are recovered from air using wet samplers and aimed to create and test an improved protocol for concentrating mold spores via filtration prior to DNA extraction. Results obtained using the new technique showed that up to 3 orders of magnitude more fungal DNA was retrieved from the samples using qPCR. A sequencing approach with MiSeq revealed a different diversity profile depending on the methodology used. Specifically, eight fungal families were highlighted to be differentially abundant in centrifuged and filtered samples, out of 19 families tested. An experiment using laboratory settings showed the same spore loss during centrifugation for Aspergillus niger and Penicillium roquefortii strains. We believe that this work helped identify and address fungal cell loss during processing of air samples including centrifugation step and and propose an alternative method for a more accurate evaluation of fungal exposure and diversity.ImportanceThis work shed light on a significant issue regarding the loss of fungal spores when recovered from air samples using liquid medium and centrifugation to concentrate air particles before DNA extraction. We provide proof that the loss affect the overall fungal diversity of aerosols, and that some taxa are differentially more affected than others. Furthermore, a laboratory experiment confirmed the environmental results obtained during the field sampling. The filtration protocol described in this work offers a better description of the fungal diversity of aerosols and should be used in fungal aerosol studies.