Bioaerosol Sampler Choice Should Consider Efficiency and Ability of Samplers To Cover Microbial Diversity

Abstract

Bioaerosol studies tend to describe the microbial content and understand the aerosolization processes linked to diseases. Air samplers are used to collect, identify and quantify bioaerosols. Studies comparing the performance of air samplers have typically used a culture approach or have targeted a specific microorganism in laboratory settings. The objective of this study was to use environmental field samples to compare the efficiency of 3 high airflow rate samplers for describing bioaerosol diversity using a next-generation sequencing approach. Two liquid cyclonic impactors and one electrostatic filter dry sampler were used in four wastewater treatment plants to target bacterial diversity and in five dairy farms to target fungal diversity. The dry electrostatic sampler was consistently more powerful in collecting more fungal and bacterial OTUs. Substantial differences in OTU abundance between liquid and dry sampling were revealed. The majority of the diversity revealed by dry electrostatic sampling was not identified using the cyclonic liquid impactors. The findings on this work suggest that the choice of a bioaerosol sampler should include information about the efficiency and ability of samplers to cover microbial diversity. Although these results suggest that electrostatic filters result in better coverage of the microbial diversity amongst the tested air samplers, further studies are needed to confirm this hypothesis. While it is difficult to determine a single universally optimal air sampler, this work provides an in-depth look at some of the considerations that are essential when choosing an air sampler for studying the microbial ecology of bioaerosols. Associating bioaerosol exposure and health problems is challenging and adequate exposure monitoring is a priority for scientist in the field. Conclusions that can be drawn from bioaerosol exposure studies are highly dependent on the design of the study and the methodologies used. The air sampling strategy is the first methodological step leading to an accurate interpretation of what is present in the air. Applying new molecular approaches to evaluate the efficiency of the different types of samplers used in the field is a necessary work around the traditional approaches and the biases they introduce to such studies. The results and conclusions provided in this manuscript should be taken in considerations when conducting a bioaerosol study.

Comparison of the performance of ITS1 and ITS2 as barcodes in amplicon-based sequencing of bioaerosols

“…In this work, the choice of barcode was the principal factor responsible for detecting trends in the fungal composition of samples from compost, biomethanization facilities and dairy farms. These observations argue against the notion that environmental factors (e.g., source of bioaerosols) are the main variables that influence fungal composition, as previously described (Mbareche et al, 2017;Mbareche et al, 2018a;Mbareche et al, 2018b;Mbareche et al, 2019a;Mbareche et al, 2019b). In addition, even when all the samples were considered in one PCoA plot, the choice of the barcode was the best predicator of the microbial content of the samples.…”

“…The samples used in this study are a part of published work in three different publications assessing workers' exposure in composting sites, biomethanization facilities, and dairy farms (Mbareche et al, 2017;Mbareche et al, 2018a;Mbareche et al, 2018b;Mbareche et al, 2019a). The internal transcribed spacer (ITS) region has been proposed as a standard genetic marker for fungi (Schoch et al, 2012).…”

“…Samples were collected from two different biomethanization facilities during the summer of 2015 and the winter of 2016. As previously described in Mbareche et al (2018a); Mbareche et al (2018b), the first facility (BF1) treats primary and secondary sludge from wastewater treatment plants, and industrial waste. The second facility (BF2) treats domestic municipal waste.…”

“…The amplification primers chosen for amplicon-based HTS were based on Tedersoo and his colleagues in their analyses of primer biases in fungal metabarcoding (Tedersoo et al, 2015a;Tedersoo et al, 2015b). As previously described in Mbareche et al, (2018aMbareche et al, ( , 2018bMbareche et al, ( , 2019a. Amplification of the amplicons, equimolar pooling and sequencing were performed at the Plateforme d'analyses génomiques (IBIS, Université Laval, Quebec City, Canada).…”

“…These conditions are created by the presence of decaying materials such as hay, peat, wood dust, manure, biosolids, and organic wastes, like compost (Gilbert & Duchaine, 2009). Dairy farms and waste treatment sites are examples of such environments where humans are exposed to a wide variety of fungi (Mbareche et al, 2017;Mbareche et al, 2018a;Mbareche et al, 2019a). Fungi can also become airborne in environments where they are deliberately introduced, such as in the food industry where fungi are used for production (Morell et al, 2011;Simon & Duquenne, 2014).…”