Airborne bacterial communities in residences: similarities and differences with fungi

Abstract

Genetic analysis of indoor air has uncovered a rich microbial presence, but rarely have both the bacterial and fungal components been examined in the same samples. Here we present a study that examined the bacterial component of passively settled microbes from both indoor and outdoor air over a discrete time period and for which the fungal component has already been reported. Dust was allowed to passively settle in five common locations around a home - living room, bedroom, bathroom, kitchen, and balcony - at different dwellings within a university-housing complex for a one-month period at two time points, once in summer and again in winter. We amplified the bacterial 16S rRNA gene in these samples and analyzed them with high-throughput sequencing. Like fungal OTU-richness, bacterial OTU-richness was higher outdoors then indoors and was invariant across different indoor room types. While fungal composition was structured largely by season and residential unit, bacterial composition varied by residential unit and room type. Bacteria from putative outdoor sources, such as Sphingomonas and Deinococcus, comprised a large percentage of the balcony samples, while human-associated taxa comprised a large percentage of the indoor samples. Abundant outdoor bacterial taxa were also observed indoors, but the reverse was not true; this is unlike fungi, in which the taxa abundant indoors were also well-represented outdoors. Moreover, there was a partial association of bacterial composition and geographic distance, such that samples separated by even a few hundred meters tended have greater compositional differences than samples closer together in space, a pattern also observed for fungi. These data show that while the outdoor source for indoor bacteria and fungi varies in both space and time, humans provide a strong and homogenizing effect on indoor bacterial bioaerosols, a pattern not observed in fungi.

Figure 1. Bacterial richness (A) and fungal richness (B) across sample locations.

Both bacterial and fungal OTU richness was higher outdoors than indoors. Solid lines represent the median, boxes the quartiles, and bars the interquartile range. Outliers are circles.

Figure 2. Visualization of differences in bacterial (A) and fungal (B) community composition based on binary Bray-Curtis index.

Principal coordinates plot showing relationship among samples, where summer samples are circles, winter samples are squares, and room locations are color-coded.

Figure 3. Heat map of the mean relative percentage of bacteria from a particular source (top row) at each sampling locations (left column).

A red shade indicates a great influence of a particular source at a particular site, and a blue shad a less influence. Soil and leaf bacterial communities are a greater influence on balcony samples than indoor rooms. Conversely, human-associated bacteria are a greater influence on indoor samples than outdoor samples. Due to uncertainty in the source tracking approach, in which each taxon could not be assigned to a particular source (soil, leaf, human, or otherwise), this heatmap shows the different relative contributions of identified sources to different rooms, not different sources for a given room. In other words, the data should be read as columns, not rows.

Figure 4. Taxonomic summary plots of bacterial orders across the different sampling locations.

Movement from the left to the right of the graph follows typical steps from the doorway in the dwellings, where kitchens were closest to the front door and bathrooms were the most internal.