Temporal patterns of variability for prokaryotic and eukaryotic diversity in the urban air of Madrid (Spain)

Abstract

Although many microorganisms are ubiquitously present in the air, airborne microbial communities have been much less characterized than those in soil or aquatic environments. Besides its ecological importance, detection and monitoring of the wide diversity of these aerosolized microorganisms (bacteria, viruses, fungi and pollen) is relevant for understanding allergy and disease outbreaks, especially in highly populated cities. In this study, we describe the simultaneous biodiversity of bacteria, fungi and plants present in the urban atmosphere of Madrid (Spain) along different seasonal periods, using DNA sequencing. Sampling in two different locations (downtown and peri-urban) we found that changes in the composition of each community are mainly driven by environmental factors, rather than by the features of the specific sampling microenvironments. While pollen particles are dominated by a few taxa characteristic of each season, bacteria and fungi show a high diversity but stable core communities along the year. The prokaryotic core is governed by soil and leaf surface bacteria, with predominance of Actinobacteria (Frankiales and Micrococcales) and Alphaproteobacteria (Sphingomonadales, Rhodobacterales, Rhizobiales and Acetobacterales). Fungal diversity is characterized by the steady presence of members of Capnodiales and Pleosporales. Pathogenic bacterial and fungal taxa were also detected across the year. We also correlated the airborne biodiversity with environmental variables. Air temperature has a strong influence on the community composition of bacteria, while pollen and fungi seasonal variations are mainly correlated with precipitation. Our results contribute to the characterization of airborne prokaryotic and eukaryotic communities in urban areas and show the suitability of this method for biosurveillance strategies.

Spatio-temporal variations in bacterial and fungal community associated with dust aerosol in Kuwait

“…These results were corroborated by the observations of the observed OTUs which recorded the highest for bacterial and lowest for fungal genera. This can be attributed to the fact that the summer season promotes the multiplication of bacteria whereas it is less conducive for fungal growth [ 52 ]. Similarly, spring and autumn probably being the periods of moderate temperatures regimes, favors fungal growth, but are less preferred by the bacterial populations and hence less diverse populations [ 53 ].…”

Seasonal Changes of the Airborne Microbiome in a Large Urban Area

“…Since spurious OTUs with very low counts may appear due to PCR and sequencing errors [52,53], we estimated a 'noise floor' following the statistical procedure outlined in [28], which resulted in one and two counts for bacteria and fungi, respectively. As a pre-analysis step, we thus removed singletons (OTUs present with an abundance of one count in one sample and zero in the rest) for bacteria, as well as singletons and doubletons for fungi.…”

“…To establish the core of bacterial and fungal genera (taxa, at the Genus level, present in at least 95% of all samples) we considered a more restrictive criterion of 'presence' taking into account experimental variability with duplicate and simultaneously running spore traps, as described in [28]. This sets a threshold of 0.032% in relative abundance for an OTU to be reliably observed in a given sample, which we used as a criterion for presence/absence.…”

“…OTUs assigned to chloroplast, mitochondria, "Unassigned" or that did not reach a defined taxonomic rank at Phylum level were filtered out. For bacteria, we conducted an additional manual revision to search for potential contaminations from insect or human-skin microbiota during manipulation, as in [28], identifying a total of 9 OTUs that were removed for further analyses.…”

“…Thus, urban parks provide soil and plant-related niches, in addition to fauna-related microbes, while ponds and fountains are sources of aquatic microbial life [20]. In addition, it is known that environmental changes drive important variations in the airborne communities both at short-term [21][22][23] and associated to seasonal variability [4,[24][25][26][27][28]. Especially relevant are the latter.…”