The Differential Vertical Distribution of the Airborne Biological Particles Reveals an Atmospheric Reservoir of Microbial Pathogens and Aeroallergens

Unmanaged grasslands are a reservoir of Alternaria and other important fungal species with differing emission patterns

Alternaria is a ubiquitous fungal genus with many allergenic and pathogenic species inhabiting grasslands. We hypothesise that grasslands (natural/man-made) host a diversity of fungal species whose spores have varying emission patterns. Therefore, the purpose of this study was to examine the potential of grasslands for emission, diversity and composition of Alternaria and other fungal species. To test the hypothesis, Hirst-type and multi-vial Cyclone samplers collected air samples from two grassland sites (unmanaged and managed) and a non-grassland site at Lakeside campus of the University of Worcester, United Kingdom for the period May to September 2019. The unmanaged grassland was originally planted with grasses and left uncut for three years. The managed grassland was a roadside verge that was cut once every year, typically after most grasses have flowered. We used optical microscopy and Illumina MiSeq sequencing to investigate the emission, abundance, diversity and composition of the fungal spores from each site alongside meteorological variables. Kruskal-Wallis and Wilcoxon tests examined differences in the bi-hourly Alternaria concentrations between the sites. Shannon's and Simpson's Index determined the diversity of the fungal spores between the unmanaged and non-grassland sites. The results showed that grasslands are a strong source of Alternaria spores with considerably higher numbers of clinically important days compared with the non-grassland site. The managed grassland varied in Alternaria spore emission pattern from the unmanaged, probably due to differences in environmental variables and cutting frequency. The unmanaged grassland and non-grassland sites showed a high diversity of fungi including Alternaria, Cladosporium, Ascochyta, Botrytis and Aureobasidium. Overall, the study shows that grasslands are a strong source of fungal spores with allergenic and pathogenic potential and have varying emission patterns, compared with nearby urban areas where monitoring stations are located. This information is useful for atmospheric modelling of airborne fungal spore sources and has implications for allergy sufferers in particular.

Fungal Spore Richness and Abundance of Allergenic Taxa: Comparing a Portable Impactor and Passive Trap Indoors and Outdoors in an Urban Setting

Fungal spores are common airborne allergens, and fungal richness has been implicated in allergic disease. Amplicon sequencing of environmental DNA from air samples is a promising method to estimate fungal spore richness with semi-quantification of hundreds of taxa and can be combined with quantitative PCR to derive abundance estimates. However, it remains unclear how the choice of air sampling method influences these estimates. This study compared active sampling with a portable impactor and passive sampling with a passive trap over different durations to estimate fungal spore richness and the abundance of allergenic taxa. Air sampling was conducted indoors and outdoors at 12 residences, including repeated measurements with a portable impactor and passive traps with 1-day and 7-day durations. ITS2 amplicon sequence data were transformed to spore equivalents estimated by quantitative PCR, repeated active samples were combined, and abundance-based rarefaction was performed to standardize sample coverage for estimation of genus-level richness and spore abundance. Rarefied fungal richness was similar between methods indoors but higher for passive traps with a 7-day duration outdoors. Rarefied abundance of allergenic genera was similar between methods but some genera had lower abundance for passive traps with a 1-day duration, which differed indoors and outdoors indicating stochasticity in the collection of spores on collocated samplers. This study found that similar estimates of fungal spore richness and abundance of allergenic taxa can be obtained using a portable impactor or a passive trap within one day and that increased passive sample duration provides limited additional information.

Turtle species and ecology drive carapace microbiome diversity in three seasonally interconnected wetland habitats

Different species of freshwater turtles exhibit primary behaviours ranging from aerial basking to benthic bottom-walking, cycle between wet and dry conditions at different time intervals, and undertake short-distance overland movements between aquatic habitats. These behaviours in turn may impact the accumulation of microbes on external shell surfaces of turtles and provide novel niches for differentiation of microbial communities. We assessed microbial diversity using 16S and 18S rRNA metabarcoding on carapace surfaces of six species of freshwater turtles residing in three adjacent and seasonally interconnected wetland habitats in southeast Oklahoma (United States). Communities were highly diverse, with nearly 4200 prokaryotic and 500 micro-eukaryotic amplicon sequence variants recovered, and included taxa previously reported as common or differentially abundant on turtle shells. The 16S rRNA alpha diversity tended to be highest for two species of benthic turtles, while 18S rRNA alpha diversity was highest for two basking and one shallow-water benthic species. Beta diversity of communities was more strongly differentiated by turtle species than by collection site, and ordination patterns were largely reflective of turtle species' primary habits (i.e. benthic, basking, or benthic-basking). Our data support that freshwater turtles could play a role in microbial ecology and evolution in freshwater habitats and warrant additional exploration including in areas with high native turtle diversity and inter-habitat turtle movements.

The air mycobiome is decoupled from the soil mycobiome in the California San Joaquin Valley

Dispersal is a key force in the assembly of fungal communities and the air is the dominant route of dispersal for most fungi. Understanding the dynamics of airborne fungi is important for determining their source and for helping to prevent fungal disease. This understanding is important in the San Joaquin Valley of California, which is home to 4.2 million people and where the airborne fungus Coccidioides is responsible for the most important fungal disease of otherwise healthy humans, coccidioidomycosis. The San Joaquin Valley is the most productive agricultural region in the United States, with the principal crops grown therein susceptible to fungal pathogens. Here, we characterize the fungal community in soil and air on undeveloped and agricultural land in the San Joaquin Valley using metabarcoding of the internal transcribed spacer 2 variable region of fungal rDNA. Using 1,002 individual samples, we report one of the most extensive studies of fungi sampled simultaneously from air and soil using modern sequencing techniques. We find that the air mycobiome in the San Joaquin Valley is distinct from the soil mycobiome, and that the assemblages of airborne fungi from sites as far apart as 160 km are far more similar to one another than to the fungal communities in nearby soils. Additionally, we present evidence that airborne fungi in the San Joaquin Valley are subject to dispersal limitation and cyclical intra-annual patterns of community composition. Our findings are broadly applicable to understanding the dispersal of airborne fungi and the taxonomic structure of airborne fungal assemblages.

A systematic review of enteric pathogens and antibiotic resistance genes in outdoor urban aerosols

Aerosol transport of enteric microbiota including fecal pathogens and antimicrobial resistance genes (ARGs) has been documented in a range of settings but remains poorly understood outside indoor environments. We conducted a systematic review of the peer-reviewed literature to summarize evidence on specific enteric microbiota including enteric pathogens and ARGs that have been measured in aerosol samples in urban settings where the risks of outdoor exposure and antibiotic resistance (AR) spread may be highest. Following PRISMA guidelines, we conducted a key word search for articles published within the years 1990-2020 using relevant data sources. Two authors independently conducted the keyword searches of databases and conducted primary and secondary screenings before merging results. To be included, studies contained extractable data on enteric microbes and AR in outdoor aerosols regardless of source confirmation and reported on qualitative, quantitative, or viability data on enteric microbes or AR. Qualitative analyses and metric summaries revealed that enteric microbes and AR have been consistently reported in outdoor aerosols, generally via relative abundance measures, though gaps remain preventing full understanding of the role of the aeromicrobiological pathway in the fate and transport of enteric associated outdoor aerosols. We identified remaining gaps in the evidence base including a need for broad characterization of enteric pathogens in bioaerosols beyond bacterial genera, a need for greater sampling in locations of high enteric disease risk, and a need for quantitative estimation of microbial and nucleic acid densities that may be applied to fate and transport models and in quantitative microbial risk assessment.

Microbial Activity and Community Structure in PM2 .5 at Different Heights in Ground Boundary Layer of Beijing Atmosphere under Various Air Quality Levels

The outbreak of the COVID-19 epidemic is a reminder that aerosols have important health effects as a potential route for disease transmission. Biological components in aerosols (especially PM_2.5 ) may pose potential threats to humans as pathogens and allergens. Research on PM_2.5 and biological components currently focuses mainly on polluted conditions, with less emphasis on clean environments. Sampling has also been primarily based on a single point with a lack of data at different positions. In this study, a modified fluorescein diacetate hydrolysis method was used to measure microbial activity in PM_2.5 at different altitudes over a year in Beijing, China. A high-throughput sequencing method was used to study the microbial community. Results showed that microbial activity 1.5 m (0.0465 ng m^-3 ) above the ground was higher than 31.5 m (0.0348 ng m^-3 ). There was higher microbial activity at both heights during spring. Furthermore, a positive correlation was observed between microbial activity and relative abundance of dominant species. Microbial activity increased during autumn and winter increased alongside the pollution level, but in spring higher levels of microbial activity were observed in excellent or good weather conditions. The results from this study are valuable for further research regarding the biological components of atmospheric PM, the prevention of biological pollution, and establishing a comprehensive air quality evaluation system. This article is protected by copyright. All rights reserved.

Long-Term Studies of Biological Components of Atmospheric Aerosol: Trends and Variability

Background: Biological components of atmospheric aerosol affect the quality of atmospheric air. Long-term trends in changes of the concentrations of total protein (a universal marker of the biogenic component of atmospheric aerosol) and culturable microorganisms in the air are studied. Methods: Atmospheric air samples are taken at two locations in the south of Western Siberia and during airborne sounding of the atmosphere. Sample analysis is carried out in the laboratory using standard culture methods (culturable microorganisms) and the fluorescence method (total protein). Results: Negative trends in the average annual concentration of total protein and culturable microorganisms in the air are revealed over more than 20 years of observations. For the concentration of total protein and culturable microorganisms in the air, intra-annual dynamics is revealed. The ratio of the maximum and minimum values of these concentrations reaches an order of magnitude. The variability of concentrations does not exceed, as a rule, two times for total protein and three times for culturable microorganisms. At the same time, for the data obtained in the course of airborne sounding of the atmosphere, a high temporal stability of the vertical profiles of the studied concentrations was found. The detected biodiversity of culturable microorganisms in atmospheric air samples demonstrates a very high variability at all observation sites. Conclusions: The revealed long-term changes in the biological components of atmospheric aerosol result in a decrease in their contribution to the atmospheric air quality index.

Monitoring techniques for pollen allergy risk assessment

Understanding airborne pollen allergens trends is of great importance for the high prevalence and the socio-economic impact that pollen-related respiratory diseases have on a global scale. Pursuing this aim, aeropalynology evolved as a broad and complex field, that requires multidisciplinary knowledge covering the molecular identity of pollen allergens, the nature of allergen-bearing particles (pollen grains, pollen sub-particles, and small airborne particles), and the distribution of their sources. To estimate the health hazard that urban vegetation and atmospheric pollen concentrations pose to allergic subjects, it is pivotal to develop efficient and rapid monitoring systems and reliable allergic risk indices. Here, we review different pollen allergens monitoring approaches, classifying them into I) vegetation-based, II) pollen-based, and III) allergen-based, and underlining their advantages and limits. Finally, we discuss the outstanding issues and directions for future research that will further clarify our understanding of pollen aeroallergens dynamics and allergen avoidance strategies.

Bioaerosols in urban environments: Trends and interactions with pollutants and meteorological variables based on quasi-climatological series

Pollen grains emitted by urban vegetation are the main primary biological airborne particles (PBAPs) which alter the biological quality of urban air and have a significant impact on human health. This work analyses the interactions which exist between pollen-type PBAPs, meteorological variables, and air pollutants in the urban atmosphere so that the complex relationships and trends in future scenarios of changing environmental conditions can be assessed. For this study, the 1992-2018 pollen data series from the city of Granada (southeast Spain) was used, in which the dynamics of the total pollen as well as the 8 main pollen types (Cupressaceae, Olea, Pinus, Platanus, Poaceae, Populus, Quercus and Urticaceae) were analysed. The trend analysis showed that all except Urticaceae trended upward throughout the series. Spearman's correlations with meteorological variables showed that, in general, the most influential variables on the pollen concentrations were the daily maximum temperature, relative humidity, water vapor pressure, global radiation, and insolation, with different effects on different pollen types. Parallel analysis by neural networks (ANN) confirmed these variables as the predominant ones, especially global radiation. The correlation with atmospheric pollutants revealed that ozone was the pollutant with the highest influence, although some pollen types also showed correlation with NO₂, SO₂, CO and PM₁₀. The Generalized Linear Models (GLM) between pollen and pollutants also indicated O₃ as the most prominent variable. These results highlight the active role that pollen-type PBAPs have on urban air quality by establishing their interactions with meteorological variables and pollutants, thereby providing information on the behaviour of pollen emissions under changing environmental conditions.

Vertical variations in the concentration and community structure of airborne microbes in PM2.5

With the recent rapid development of urbanization, severe air pollution events frequently occur in China. Subsequently, variations of bioaerosols during air pollution events have attracted increasing attention in recent years. However, most published studies on bioaerosols mainly focus on the characteristics of airborne bacteria and fungi at a certain height near the ground surface. The vertical variations in microbial aerosols at different heights are not well understood. In this study, PM_2.5 samples at three heights (1.5 m, 100 m and 229.5 m) were collected from September 2019 to January 2020 in Xi'an, China. The samples were then analyzed by a fluorescence staining and high-throughput sequencing to explore the vertical variations in the concentration and community structure of the airborne bacteria. The results show that the microbial concentration in PM_2.5 decreased with increasing height on polluted days, while there was no significant difference at different heights on non-polluted days (p > 0.05). The bacterial community structures were similar at different heights on polluted days; however, on non-polluted days, the bacterial community structure at 229.5 m was significantly different from that at the other heights. Importantly, meteorological factors had more significant effects on the bacterial community at 229.5 m than at 1.5 m and 100 m. The present results can improve the understanding of vertical distribution of bioaerosols and their diffusion process.

Bacterial diversity in aqueous/sludge phases within diesel fuel storage tanks

Diesel fuel storage tanks are not hostile environments for microorganisms and tend to form sludges in the water deposited at the bottom of the tanks. The lack of nutrient, carbon and energy limitations within these habitats boost the abundance and the metabolic activity of microorganisms providing microbial hotspots with high growing rates of diesel degradation (0.10 ± 0.021 d^-1). Five different Phyla (Thermotogae, Spirochaetes, Firmicutes, Bacteroidetes Proteobacteria) were identified within the aqueous/sludge phase from in situ diesel storage tanks, by cultured independent molecular surveys using the 16S rDNA gene fragment. The identified dominant strains were Geotoga aestuarianus, Flavobacterium ceti, Spirochaeta thermophila, Propionispira arboris, Sporobacterium olearium and Dysgonomonas genera. The altitude where the storage tanks are located and the organic carbon concentration within the aqueous/sludge phases affected the bacterial diversity. Therefore, the more diverse the microbial communities are, the more probability of the presence of bacteria with capacity to metabolized diesel and eliminate organic matter. Despite, only phosphate showed an effect on the bacterial distribution within the storage tanks, there was an apparent lack of deterministic process in structuring microbial communities. Consequently, preventative protocols are a priority to avoid the microbial growth within diesel fuel storage tanks. A new focus of this worldwide problem within the oil industry would be to explore deeply the wide range of metabolic and adaptive capacities of these microorganisms. These microbial consortia are potential tools with new specific services to apply in bioremediation among others.

Atmospheric Biodetection Part I: Study of Airborne Bacterial Concentrations from January 2018 to May 2020 at Saclay, France

Background: The monitoring of bioaerosol concentrations in the air is a relevant endeavor due to potential health risks associated with exposure to such particles and in the understanding of their role in climate. In this context, the atmospheric concentrations of bacteria were measured from January 2018 to May 2020 at Saclay, France. The aim of the study was to understand the seasonality, the daily variability, and to identify the geographical origin of airborne bacteria. Methods: 880 samples were collected daily on polycarbonate filters, extracted with purified water, and analyzed using the cultivable method and flow cytometry. A source receptor model was used to identify the origin of bacteria. Results: A tri-modal seasonality was identified with the highest concentrations early in spring and over the summer season with the lowest during the winter season. Extreme changes occurred daily due to rapid changes in meteorological conditions and shifts from clean air masses to polluted ones. Conclusion: Our work points toward bacterial concentrations originating from specific seasonal-geographical ecosystems. During pollution events, bacteria appear to rise from dense urban areas or are transported long distances from their sources. This key finding should drive future actions to better control the dispersion of potential pathogens in the air, like persistent microorganisms originating from contaminated areas.