Seasonal shift in airborne microbial communities

Review of research advances in microbial sterilization technologies and applications in the built environment

As globalization accelerates, microbial contamination in the built environment poses a major public health challenge. Especially since Corona Virus Disease 2019 (COVID-19), microbial sterilization technology has become a crucial research area for indoor air pollution control in order to create a hygienic and safe built environment. Based on this, the study reviews sterilization technologies in the built environment, focusing on the principles, efficiency and applicability, revealing advantages and limitations, and summarizing current research advances. Despite the efficacy of single sterilization technologies in specific environments, the corresponding side effects still exist. Thus, this review highlights the efficiency of hybrid sterilization technologies, providing an in-depth understanding of the practical application in the built environment. Also, it presents an outlook on the future direction of sterilization technology, including the development of new methods that are more efficient, energy-saving, and targeted to better address microbial contamination in the complex and changing built environment. Overall, this study provides a clear guide for selecting technologies to handle microbial contamination in different building environments in the future, as well as a scientific basis for developing more effective air quality control strategies.

Characteristics of airborne bacteria over inland and coastal atmosphere influenced by systemic air mass in northern China

Regional aerosol pollution frequently occurs in winter and spring in northern China. Here, we surveyed four air pollution, categorized as episodes influenced by northerly or southerly air mass, and discussed the bacterial communities in inland and coastal cities. Influenced by northerly airmass, the predominant bacterial phyla were Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria both in the inland and coastal cities. The opportunistic pathogen in the genus Staphylococcus was predominant, and the relative proportion increased with the intensification of air pollution. Gut bacteria of the genus Lactobacillus and aquatic bacteria of the family Flavobacteriaceae were enriched in the coastal city. Influenced by southerly air mass, combined with the transmission of dust air masses in the northwest, air pollution in spring showed obvious sand dust characteristics. The prevalence of the members from the phylum Cyanobacteria was markedly greater in inland city compared to the coastal city, especially in dust samples. This indicated the possibility of soil Cyanobacteria members, subsequently being transported from terrestrial to coastal areas via dust movements. The bacterial community dynamics was intimately linked to meteorological factors and air pollutants. In both cities, pathogenic bacteria predominate in haze pollution influenced by northernly air masses, while a higher proportion of soil bacteria originating from natural sources predominate in southern air mass samples. The impact of varying air masses was particularly pronounced in inland city. Meteorological factors instigated by seasonal changes-especially the transition of wind direction from winter to spring, accompanied by elevated wind speeds and rising temperatures-play a pivotal role in shaping bacterial community structure. This study examined the sea-land variations in bacterial communities transported by systemic air masses during typical air pollution events. These insights lay the groundwork for future research into the distribution, sources, and health risks of bioaerosols during air pollution.

Assessing population exposure to airborne fungi in the UK over one year using high-throughput sequencing (HTS) metabarcoding methods

Airborne fungi are significant contributors to allergic and infectious disease. While microscopy remains the primary method for fungal identification, high-throughput sequencing (HTS) enables untargeted analysis of a much wider range of environmental taxa. This study used HTS to better characterise airborne fungal composition over a 12-month period in two UK locations, the city of Leicester in central England and a rural site in Chilton (Oxfordshire) approximately 115 km further south. Air samples were collected over a year. A subset of 240 samples (120 per location) were analysed by HTS with a combined internal transcribed spacer region (ITS2) and D1/D2 region of the large subunit (LSU) metabarcoding approach. With statistical imputation a representative 12-month dataset was created. Differences in fungal diversity and composition were explored, incorporating meteorological data. HTS analysis identified 272 fungal genera across locations and seasons, approximately 4-fold more than in other studies using traditional microscopy methods. Fungal diversity, richness and composition at the two locations were broadly similar with some taxa-specific differences likely reflecting land-use types (urban vs rural) and/or local meteorological variables. In particular, air temperature and precipitation significantly influenced fungal composition. This study demonstrates the value of HTS for characterising airborne fungi. While it does not provide absolute quantitation, HTS could be used as a screening tool to identify novel associations between fungal exposure and health outcomes, and should be used in combination with quantitative methods, such as microscopy and quantitative PCR (qPCR). Greater spatial and temporal understanding of the wide range of airborne fungal exposure is crucial for exploring associated health impacts and developing improved public health interventions and alert systems for susceptible individuals.

Temporal dynamics of airborne fungi in Swedish forest nurseries

In Sweden, reforestation of managed forests relies predominantly on planting nursery-produced tree seedlings. However, the intense production using containerized cultivation systems (e.g., high seedling density, irrigation from above, regular fertilization) creates favorable conditions for fungal infections. Despite the harmful role of diseases in forest nurseries, the origin and dispersal factors of fungal pathogens remain largely unknown. A better understanding of the airborne spread of pathogens could improve the prediction of fungal infection, ultimately optimizing preventative methods and decreasing the use of fungicides. This study investigated the temporal dynamics of airborne fungi in forest nurseries, with a focus on fungal pathogens. Airborne fungi were monitored in four Swedish forest nurseries over two growing seasons using spore traps and high-throughput sequencing. Fungal pathogens were identified using bioinformatics and quantified with quantitative PCR. Results showed strong temporal shifts of airborne fungal diversity and community composition following the growing seasons. The airborne spread included high abundances of important fungal pathogens (e.g., Cladosporium sp., Botrytis cinerea, Alternaria sp., Sydowia polyspora, and Melampsora populnea) with individual temporal and spatial variations. In general, the deposited spore loads of nursery pathogens correlated positively with increased temperature and negatively with higher precipitation. This was expressed the strongest for Cladosporium sp., Alternaria sp., and M. populnea, which suggests a higher availability of fungal inoculum in warm and dry periods. This study highlights the influence of seasonality on the temporal dynamics of economically important fungal pathogens in Swedish forest nurseries, which should be considered in the development of a local decision support system.IMPORTANCEFungal diseases in forest nurseries have significant environmental and economic impacts on the tree seedling production. This study highlights the role of seasonality in the airborne spread of fungal pathogens in Swedish forest nurseries. By analyzing airborne fungal spores using advanced sequencing and monitoring techniques, key fungal pathogens and their dispersal patterns over two growing seasons were identified. The findings indicate that warmer, drier periods may increase the spread of fungal pathogens, emphasizing the need for targeted preventative measures. Understanding these temporal dynamics can help optimize the use of fungicides in forest nurseries, thereby promoting more sustainable and environmentally friendly management practices. This research provides valuable insights for improving disease management in forest nurseries, ultimately supporting sustainable tree seedling production.

The dynamics and assembly patterns of airborne pathogen communities in the municipal food waste treatment system and its risk implications

While municipal solid waste (MSW) provides an ideal habitat for pathogen propagation, the dynamics and assembly of airborne pathogen communities in these environments remain largely unknown. Here, we combined amplicon and metagenomics with spatiotemporal sampling to study inhalable particulate matter-carried potential pathogenic bacteria at full-scale food waste treatment plants (FWTPs), alongside comparisons to urban air in the area. The results showed that pathogenic bacteria constituted a notable portion (64.5 % ± 20.6 %, n = 75) of the total bacterial communities in FWTPs-impacted air, with species and relative abundance 2-4 times higher than that of urban air, and contributed over 50 % of pathogens to the outdoor air. Airborne pathogen community structures were highly shaped by sampling sites (i.e. treatment units), but conserved across seasons (summer vs. winter) and particle sizes (PM2.5vs. PM10). Notably, Acinetobacter johnsonii-dominated pathogens (i.e. biofilm-related species) presented high levels of aerosolization and consistently occupied the upper-representative niches in all neutral models, highlighting their persistent exposure risk. Furthermore, pathogen community assembly was strongly driven by stochastic processes (58.8 %-96.8 %), while environmental variables explained only limited variations (3.4 %-28.7 %). In particular, the relative importance of stochastic processes clearly increased along an outdoor-to-indoor gradient (84.9 %-96.5 % vs. 71.3 %-76 %), which might be related to indoor anthropogenic activities that weaken microbial network stability and environmental filtering effects. This work enhances our knowledge of the dynamic behaviors and risk of airborne pathogen communities in MSW disposal and underscores the role of FWTPs in disseminating airborne pathogens.

Indoor/Outdoor airborne microbiome characteristics in residential areas across four seasons and its indoor purification

Bioaerosols are more likely to accumulate in the residential environment, and long-term inhalation may lead to a variety of diseases and allergies. Here, we studied the distribution, influencing factors and diffusion characteristics of indoor and outdoor microbiota pollution in six residential buildings in Guangzhou, southern China over a period of one year. The results showed that the particle sizes of bioaerosol were mainly in the range of inhalable particle size (<4.7 μm) with a small difference among four seasons (74.61 % ± 2.17 %). The microbial communities showed obvious seasonal differences with high abundance in summer, but no obvious geographical differences. Among them, the bacteria were more abundant than the fungi. The dominant microbes in indoor and outdoor environments were similar, with Anoxybacillu, Brevibacillus and Acinetobacter as the dominant bacteria, and Cladosporium, Penicillium and Alternaria as the dominant fungi. The airborne microbiomes were more sensitive to temperature and particulate matter (PM2.5, PM10) concentrations. Based on the Sloan neutral model, bacteria were more prone to random diffusion than fungi, and the airborne microbiome can be randomly distributed in indoor and outdoor environments and between the two environments in each season. Bioaerosol in indoor was mainly from outdoor. The health risk evaluation showed that the indoor inhalation risks were higher than those outdoor. The air purifier had a better removal efficiency on 1.1-4.7 μm microorganisms, and the removal efficiency on Gram-negative bacteria was better than that on Gram-positive bacteria. This study is of great significance for the risk assessment and control of residential indoor bioaerosol exposure.

Global diversity of airborne pathogenic bacteria and fungi from wastewater treatment plants

Wastewater treatment plants (WWTPs) have been recognized as one of the major potential sources of the spread of airborne pathogenic microorganisms under the global pandemic of COVID-19. The differences in research regions, wastewater treatment processes, environmental conditions, and other aspects in the existing case studies have caused some confusion in the understanding of bioaerosol pollution characteristics. In this study, we integrated and analyzed data from field sampling and performed a systematic literature search to determine the abundance of airborne microorganisms in 13 countries and 37 cities across four continents (Asia, Europe, North America, and Africa). We analyzed the concentrations of bioaerosols, the core composition, global diversity, determinants, and potential risks of airborne pathogen communities in WWTPs. Our findings showed that the culturable bioaerosol concentrations of global WWTPs are 102-105 CFU/m3. Three core bacterial pathogens, namely Bacillus, Acinetobacter, and Pseudomonas, as well as two core fungal pathogens, Cladosporium and Aspergillus, were identified in the air across global WWTPs. WWTPs have unique core pathogenic communities and distinct continental divergence. The sources of airborne microorganisms (wastewater) and environmental variables (relative humidity and air contaminants) have impacts on the distribution of airborne pathogens. Potential health risks are associated with the core airborne pathogens in WWTPs. Our study showed the specificity, multifactorial influences, and potential pathogenicity of airborne pathogenic communities in WWTPs. Our findings can improve the understanding of the global diversity and biogeography of airborne pathogens in WWTPs, guiding risk assessment and control strategies for such pathogens. Furthermore, they provide a theoretical basis for safeguarding the health of WWTP workers and ensuring regional ecological security.

Fungal community shows more variations by season and particle size than bacteria

The global concern regarding the health risk associated with airborne microorganisms has prompted research in this field. However, there is a lack of systematic investigation into the particle-size distribution of airborne bacterial and fungal communities associated with seasons, which determines where they are deposited in the human respiratory tract. To address this gap, we conducted a study in Nanchang, located in central China, where we collected both coarse and fine particles during summer and winter seasons. The results demonstrated that microbial community exhibited obvious seasonal and particle-size variations except bacterial community in fine particles. Certain taxa (e.g., Bacteroidales, Ktedonobacterales, Capnodiales) displayed either seasonal and/or particle-size preferences. Furthermore, airborne microorganisms in coarse particles were more sensitive to season and particle size compared to those in fine particles, with fungal community being more susceptible than bacterial community. The susceptibility can be attributed to their high vulnerability to air pollutants and meteorological conditions, primarily PM2.5 and PM10. Additionally, a greater relative abundance of pathogenic fungi was observed in fine particles, even though microbial diversity in coarse particles was noticeably higher than that in fine particles. Furthermore, some predominant pathogens such as Alternaria, Nigrospora, and Escherichia-Shigella not only had particle size and/or seasonal preferences, but also were strongly correlated with environmental factors. This study advances our understanding of atmospheric pathogenic microorganisms and highlights the fungal health threat.

Stochastic microbial dispersal drives local extinction and global diversity

Airborne dispersal of microorganisms is a ubiquitous migration mechanism, allowing otherwise independent microbial habitats to interact via biomass exchange. Here, we study the ecological implications of such advective transport using a simple spatial model for bacteria-phage interactions: the population dynamics at each habitat are described by classical Lotka-Volterra equations; however, species populations are taken as integer, that is, a discrete, positive extinction threshold exists. Spatially, species can spread from habitat to habitat by stochastic airborne dispersal. In any given habitat, the spatial biomass exchange causes incessant population density oscillations, which, as a consequence, occasionally drive species to extinction. The balance between local extinction events and dispersal-induced migration allows species to persist globally, even though diversity would be depleted by competitive exclusion, locally. The disruptive effect of biomass dispersal thus acts to increase microbial diversity, allowing system-scale coexistence of multiple species that would not coexist locally.

Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors

In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.

Temporal variations of antimicrobial resistance genes in aerosols: A one-year monitoring at the puy de Dôme summit (Central France)

The recent characterization of antibiotic resistance genes (ARGs) in clouds evidenced that the atmosphere actively partakes in the global spreading of antibiotic resistance worldwide. Indeed, the outdoor atmosphere continuously receives large quantities of particles of biological origins, emitted from both anthropogenic or natural sources at the near Earth's surface. Nonetheless, our understanding of the composition of the atmospheric resistome, especially at mid-altitude (i.e. above 1000 m a.s.l.), remains largely limited. The atmosphere is vast and highly dynamic, so that the diversity and abundance of ARGs are expected to fluctuate both spatially and temporally. In this work, the abundance and diversity of ARGs were assessed in atmospheric aerosol samples collected weekly between July 2016 and August 2017 at the mountain site of puy de Dôme (1465 m a.s.l., central France). Our results evidence the presence of 33 different subtypes of ARGs in atmospheric aerosols, out of 34 assessed, whose total concentration fluctuated seasonally from 59 to 1.1 × 105 copies m-3 of air. These were heavily dominated by genes from the quinolone resistance family, notably the qepA gene encoding efflux pump mechanisms, which represented >95 % of total ARGs concentration. Its abundance positively correlated with that of bacteria affiliated with the genera Kineococcus, Neorhizobium, Devosia or Massilia, ubiquitous in soils. This, along with the high abundance of Sphingomonas species, points toward a large contribution of natural sources to the airborne ARGs. Nonetheless, the increased contribution of macrolide resistance (notably the erm35 gene) during winter suggests a sporadic diffusion of ARGs from human activities. Our observations depict the atmosphere as an important vector of ARGs from terrestrial sources. Therefore, monitoring ARGs in airborne microorganisms appears necessary to fully understand the dynamics of antimicrobial resistances in the environment and mitigate the threats they may represent.

The atmosphere: a transport medium or an active microbial ecosystem?

The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.

Linkage between Airborne Particulate Matter and Viral Pandemic COVID-19 in Bucharest

The long-distance spreading and transport of airborne particulate matter (PM) of biogenic or chemical compounds, which are thought to be possible carriers of SARS-CoV-2 virions, can have a negative impact on the incidence and severity of COVID-19 viral disease. Considering the total Aerosol Optical Depth at 550 nm (AOD) as an atmospheric aerosol loading variable, inhalable fine PM with a diameter ≤2.5 µm (PM2.5) or coarse PM with a diameter ≤10 µm (PM10) during 26 February 2020-31 March 2022, and COVID-19's five waves in Romania, the current study investigates the impact of outdoor PM on the COVID-19 pandemic in Bucharest city. Through descriptive statistics analysis applied to average daily time series in situ and satellite data of PM2.5, PM10, and climate parameters, this study found decreased trends of PM2.5 and PM10 concentrations of 24.58% and 18.9%, respectively compared to the pre-pandemic period (2015-2019). Exposure to high levels of PM2.5 and PM10 particles was positively correlated with COVID-19 incidence and mortality. The derived average PM2.5/PM10 ratios during the entire pandemic period are relatively low (<0.44), indicating a dominance of coarse traffic-related particles' fraction. Significant reductions of the averaged AOD levels over Bucharest were recorded during the first and third waves of COVID-19 pandemic and their associated lockdowns (~28.2% and ~16.4%, respectively) compared to pre-pandemic period (2015-2019) average AOD levels. The findings of this research are important for decision-makers implementing COVID-19 safety controls and health measures during viral infections.

Abundant Cyanobacteria in Autumn Adhering to the Heating, Ventilation, and Air-Conditioning (HVAC) in Shanghai

Cyanobacteria are ever-present, mainly flourishing in aquatic environments and surviving virtually in other habitats. The microbiota of indoor dust on the pre-filter of heating, ventilation, and air-conditioning (HVAC) systems, which reflect indoor microbial contamination and affect human health, has attracted attention. Contemporary studies on cyanobacteria deposited on the pre-filter of HVAC remain scant. By the culture-independent approach of qPCR and high throughput sequencing technologies, our results documented that the cyanobacterial concentrations were highest in autumn, occurred recurrently, and were about 2.60 and 10.57-fold higher than those in winter and summer. We proposed that aquatic and terrestrial cyanobacteria contributed to the pre-filter of HVAC by airborne transportation produced by wave breaks, bubble bursts, and soil surface by wind force, owing to the evidence that cyanobacteria were commonly detected in airborne particulate matters. The cyanobacteria community structure was characterized in Shanghai, where Chroococcidiopsaceae, norank_cyanobacteriales, Nostocaceae, Paraspirulinaceae, and others dominated the dust on the pre-filter of HVAC. Some detected genera, including Nodularia sp., Pseudanabaena sp., and Leptolyngbya sp., potentially produced cyanobacterial toxins, which need further studying to determine their potential threat to human health. The present work shed new insight into cyanobacteria distribution in the specific environment besides aquatic habitats.

Peculiar weather patterns effects on air pollution and COVID-19 spread in Tokyo metropolis

As a pandemic hotspot in Japan, between March 1, 2020-October 1, 2022, Tokyo metropolis experienced seven COVID-19 waves. Motivated by the high rate of COVID-19 incidence and mortality during the seventh wave, and environmental/health challenges we conducted a time-series analysis to investigate the long-term interaction of air quality and climate variability with viral pandemic in Tokyo. Through daily time series geospatial and observational air pollution/climate data, and COVID-19 incidence and death cases, this study compared the environmental conditions during COVID-19 multiwaves. In spite of five State of Emergency (SOEs) restrictions associated with COVID-19 pandemic, during (2020-2022) period air quality recorded low improvements relative to (2015-2019) average annual values, namely: Aerosol Optical Depth increased by 9.13% in 2020 year, and declined by 6.64% in 2021, and 12.03% in 2022; particulate matter PM2.5 and PM10 decreased during 2020, 2021, and 2022 years by 10.22%, 62.26%, 0.39%, and respectively by 4.42%, 3.95%, 5.76%. For (2021-2022) period the average ratio of PM2.5/PM10 was (0.319 ± 0.1640), showing a higher contribution to aerosol loading of traffic-related coarse particles in comparison with fine particles. The highest rates of the daily recorded COVID-19 incidence and death cases in Tokyo during the seventh COVID-19 wave (1 July 2022-1 October 2022) may be attributed to accumulation near the ground of high levels of air pollutants and viral pathogens due to: 1) peculiar persistent atmospheric anticyclonic circulation with strong positive anomalies of geopotential height at 500 hPa; 2) lower levels of Planetary Boundary Layer (PBL) heights; 3) high daily maximum air temperature and land surface temperature due to the prolonged heat waves (HWs) in summer 2022; 4) no imposed restrictions. Such findings can guide public decision-makers to design proper strategies to curb pandemics under persistent stable anticyclonic weather conditions and summer HWs in large metropolitan areas.

Greener residential environment is associated with increased bacterial diversity in outdoor ambient air

In urban areas, exposure to greenspace has been found to be beneficial to human health. The biodiversity hypothesis proposed that exposure to diverse ambient microbes in greener areas may be one pathway leading to health benefits such as improved immune system functioning, reduced systemic inflammation, and ultimately reduced morbidity and mortality. Previous studies observed differences in ambient outdoor bacterial diversity between areas of high and low vegetated land cover but didn't focus on residential environments which are important to human health. This research examined the relationship between vegetated land and tree cover near residence and outdoor ambient air bacterial diversity and composition. We used a filter and pump system to collect ambient bacteria samples outside residences in the Raleigh-Durham-Chapel Hill metropolitan area and identified bacteria by 16S rRNA amplicon sequencing. Geospatial quantification of total vegetated land or tree cover was conducted within 500 m of each residence. Shannon's diversity index and weighted UniFrac distances were calculated to measure α (within-sample) and β (between-sample) diversity, respectively. Linear regression for α-diversity and permutational analysis of variance (PERMANOVA) for β-diversity were used to model relationships between vegetated land and tree cover and bacterial diversity. Data analysis included 73 ambient air samples collected near 69 residences. Analysis of β-diversity demonstrated differences in ambient air microbiome composition between areas of high and low vegetated land (p = 0.03) and tree cover (p = 0.07). These relationships remained consistent among quintiles of vegetated land (p = 0.03) and tree cover (p = 0.008) and continuous measures of vegetated land (p = 0.03) and tree cover (p = 0.03). Increased vegetated land and tree cover were also associated with increased ambient microbiome α-diversity (p = 0.06 and p = 0.03, respectively). To our knowledge, this is the first study to demonstrate associations between vegetated land and tree cover and the ambient air microbiome's diversity and composition in the residential ecosystem.

Riverine microbial communities impacted by per- and polyfluoroalkyl substances (PFAS) emissions from a fluoropolymer-manufacturing plant

Per- and polyfluoroalkyl substances (PFAS) are widespread pollutants that can influence microorganisms. To unveil the effects of PFAS in natural microecosystems, a study that focused on the bacterial, fungal, and microeukaryotic communities around the PFAS point source was conducted in China. A total of 255 specific taxa were significantly different between the upstream and downstream samples, 54 of which were directly correlated with PFAS concentration. Stenotrophomonas (99.2 %), Ralstonia (90.7 %), Phoma (21.9 %), and Alternaria (97.6 %) were the dominant genera in sediment samples from the downstream communities. In addition, most of the dominant taxa were significantly correlated with PFAS concentration. Furthermore, the type of microorganism (bacteria, fungi, and microeukaryotes) and habitat (sediment or pelagic) also influence the microbial community responses to PFAS exposure. Pelagic microorganisms featured more PFAS-correlated biomarker taxa (36 pelagic microeukaryotic biomarkers and 8 pelagic bacteria biomarkers) than the sediments (9 sediment fungi biomarkers and 5 sediment bacteria biomarker). In general, around the factory, the microbial community was more variable in pelagic, summer, and microeukaryotic conditions than in other types. Attention needs to be paid to these variables in the future effect of PFAS on microorganisms.

The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome

The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.

Antibiotic Resistance Genes in Aerosols: Baseline from Kuwait

Antimicrobial resistance (AMR) is one of the biggest threats to human health worldwide. The World Health Organization (WHO, Geneva, Switzerland) has launched the "One-Health" approach, which encourages assessment of antibiotic-resistant genes (ARGs) within environments shared by human-animals-plants-microbes to constrain and alleviate the development of AMR. Aerosols as a medium to disseminate ARGs, have received minimal attention. In the present study, we investigated the distribution and abundance of ARGs in indoor and outdoor aerosols collected from an urban location in Kuwait and the interior of three hospitals. The high throughput quantitative polymerase chain reaction (HT-qPCR) approach was used for this purpose. The results demonstrate the presence of aminoglycoside, beta-lactam, fluoroquinolone, tetracycline, macrolide-lincosamide-streptogramin B (MLSB), multidrug-resistant (MDR) and vancomycin-resistant genes in the aerosols. The most dominant drug class was beta-lactam and the genes were IMP-2-group (0.85), Per-2 group (0.65), OXA-54 (0.57), QnrS (0.50) and OXA-55 (0.55) in the urban non-clinical settings. The indoor aerosols possessed a richer diversity (Observed, Chao1, Shannon's and Pielou's evenness) of ARGs compared to the outdoors. Seasonal variations (autumn vs. winter) in relative abundances and types of ARGs were also recorded (R² of 0.132 at p < 0.08). The presence of ARGs was found in both the inhalable (2.1 µm, 1.1 µm, 0.7 µm and < 0.3 µm) and respirable (>9.0 µm, 5.8 µm, 4.7 µm and 3.3 µm) size fractions within hospital aerosols. All the ARGs are of pathogenic bacterial origin and are hosted by pathogenic forms. The findings present baseline data and underpin the need for detailed investigations looking at aerosol as a vehicle for ARG dissemination among human and non-human terrestrial biota.

Quantification of antibiotic resistance genes (ARGs) in clouds at a mountain site (puy de Dôme, central France)

Antibiotic resistance in bacteria is becoming a major sanitary concern worldwide. The extensive use of large quantities of antibiotics to sustain human activity has led to the rapid acquisition and maintenance of antibiotic resistant genes (ARGs) in bacteria and to their spread into the environment. Eventually, these can be disseminated over long distances by atmospheric transport. Here, we assessed the presence of ARGs in clouds as an indicator of long-distance travel potential of antibiotic resistance in the atmosphere. We hypothesized that a variety of ARGs can reach the altitude of clouds mainly located within the free troposphere. Once incorporated in the atmosphere, they are efficiently transported and their respective concentrations should differ depending on the sources and the geographical origin of the air masses. We deployed high-flow rate impingers and collected twelve clouds between September 2019 and October 2021 at the meteorological station of the puy de Dôme summit (1465 m a.s.l., France). Total airborne bacteria concentration was assessed by flow cytometry, and ARGs subtypes of the main families of antibiotic resistance (quinolone, sulfonamide, tetracycline; glycopeptide, aminoglycoside, β-lactamase, macrolide) including one mobile genetic element (transposase) were quantified by qPCR. Our results indicate the presence of 29 different ARGs' subtypes at concentrations ranging from 1.01 × 10³ to 1.61 × 10⁴ copies m^-3 of air. Clear distinctions could be observed between clouds in air masses transported over marine areas (Atlantic Ocean) and clouds influenced by continental surfaces. Specifically, quinolones (mostly qepA) resistance genes were prevalent in marine clouds (54 % of the total ARGs on average), whereas higher contributions of sulfonamide, tetracycline; glycopeptide, β-lactamase and macrolide were found in continental clouds. This study constitutes the first evidence for the presence of microbial ARGs in clouds at concentrations comparable to other natural environments. This highlights the atmosphere as routes for the dissemination of ARGs at large scale.

Microstrobilinia castrans, a new genus and species of the Sclerotiniaceae parasitizing pollen cones of Picea spp

The fungal pathogens of spruce are well known in Europe and elsewhere. Therefore, it was surprising to discover a new fungal species and genus in Central Europe that attacks the pollen cones of three spruce species. The new ascomycete forms apothecia on stromatized pollen cones of Norway spruce (Picea abies) and Serbian spruce (Picea omorika) in mountain areas and on West Himalayan spruce (Picea smithiana) planted in urban lowland regions of Switzerland, Germany, and Italy. It was also detected in France, based on metabarcode sequences deposited in the GlobalFungi database. Its sudden appearance and the different origins of the host trees in Europe and Asia leave the origin of the fungus unclear. The new fungus might be a neomycete for Europe. A phylogenetic analysis using SSU, LSU, ITS, RPB2, and TEF1 sequences classified the fungus as a member of Sclerotiniaceae (Helotiales, Leotiomycetes). However, it differs morphologically from the other genera of this family in having an ascus without apical apparatus containing four mainly citriform spores with 16 nuclei each. Furthermore, it is the only known cup fungus that parasitizes pollen cones of conifers by stromatizing their tissue and infecting pollen grains. The fungus does not seem to cause major damage to the spruce populations, as only a few pollen cones per tree are affected. All this leads us to describe the newly discovered fungus as the new species and new genus Microstrobilinia castrans, the fungus that castrates pollen cones of spruce.

Seasonal variation of airborne fungal diversity and community structure in urban outdoor environments in Tianjin, China

Airborne fungi are ubiquitous in human living environments and may be a source of respiratory problems, allergies, and other health issues. A 12 months study was performed to investigate the diversity, concentration and community structure of culturable airborne fungi in different outdoor environments of Tianjin City, using an HAS-100B air sampler. A total of 1,015 fungal strains belonging to 175 species and 82 genera of Ascomycota 92.5%, Basidiomycota 7%, and Mucoromycota 0.3% were isolated and identified using morphological and molecular analysis. The most abundant fungal genera were Alternaria 35%, Cladosporium 18%, Penicillium 5.6%, Talaromyces 3.9%, Didymella 3%, and Aspergillus 2.8%, while the most frequently occurring species were A. alternata (24.7%), C. cladosporioides (11%), A. tenuissima (5.3%), P. oxalicum (4.53%), and T. funiculosus (2.66%). The fungal concentration ranged from 0 to 340 CFU/m³ during the whole study. Environmental factors, including temperature, relative humidity, wind speed, and air pressure exerted a varying effect on the presence and concentration of different fungal taxa. The four analyzed seasons showed significantly different airborne fungal communities, which were more strongly influenced by air temperature and relative humidity in spring and summer, whereas wind speed and air pressure had a stronger effect in autumn and winter. Fungal communities from green and busy sites did not show significant differences over the four analyzed seasons, which may be due to the effect of the surrounding environments characterized by high human activities on the air of the relatively small parks present in Tianjin. The present study provided valuable information on the seasonal dynamics and the environmental factors shaping the diversity and concentration of the analyzed outdoor airborne fungal communities, which can be of help for air quality monitoring, microbial contamination control, and health risk assessment in urban environments.

Aerobiology over the Southern Ocean - Implications for bacterial colonization of Antarctica

Parts of the Antarctic are experiencing dramatic ecosystem change due to rapid and record warming, which may weaken biogeographic boundaries and modify dispersal barriers, increasing the risk of biological invasions. In this study, we collected air samples from 100 locations around the Southern Ocean to analyze bacterial biodiversity in the circumpolar air around the Antarctic continent, as understanding dispersal processes is paramount to assessing the risks of microbiological invasions. We also compared the Southern Ocean air bacterial biodiversity to non-polar ecosystems to identify the potential origin of these Southern Ocean air microorganisms. The bacterial diversity in the air had both local and global origins and presented low richness overall but high heterogeneity, compatible with a scenario whereby samples are composed of a suite of different species in very low relative abundances. Only 4% of Amplicon Sequence Variants (ASVs) were identified in both polar and non-polar air masses, suggesting that the polar air mass over the Southern Ocean can act as a selective dispersal filter. Furthermore, both microbial diversity and community structure both varied significantly with meteorological data, suggesting that regional bacterial biodiversity could be sensitive to changes in weather conditions, potentially altering the existing pattern of microbial deposition in the Antarctic.

Cumulative effects of air pollution and climate drivers on COVID-19 multiwaves in Bucharest, Romania

Over more than two years of global health crisis due to ongoing COVID-19 pandemic, Romania experienced a five-wave pattern. This study aims to assess the potential impact of environmental drivers on COVID-19 transmission in Bucharest, capital of Romania during the analyzed epidemic period. Through descriptive statistics and cross-correlation tests applied to time series of daily observational and geospatial data of major outdoor inhalable particulate matter with aerodynamic diameter ≤ 2.5 µm (PM2.5) or ≤ 10 µm (PM10), nitrogen dioxide (NO2), ozone (O3), sulfur dioxide (SO2), carbon monoxide (CO), Aerosol Optical Depth at 550 nm (AOD) and radon (222Rn), we investigated the COVID-19 waves patterns under different meteorological conditions. This study examined the contribution of individual climate variables on the ground level air pollutants concentrations and COVID-19 disease severity. As compared to the long-term average AOD over Bucharest from 2015 to 2019, for the same year periods, this study revealed major AOD level reduction by ~28 % during the spring lockdown of the first COVID-19 wave (15 March 2020-15 May 2020), and ~16 % during the third COVID-19 wave (1 February 2021-1 June 2021). This study found positive correlations between exposure to air pollutants PM2.5, PM10, NO2, SO2, CO and 222Rn, and significant negative correlations, especially for spring-summer periods between ground O3 levels, air temperature, Planetary Boundary Layer height, and surface solar irradiance with COVID-19 incidence and deaths. For the analyzed time period 1 January 2020-1 April 2022, before and during each COVID-19 wave were recorded stagnant synoptic anticyclonic conditions favorable for SARS-CoV-2 virus spreading, with positive Omega surface charts composite average (Pa/s) at 850 mb during fall- winter seasons, clearly evidenced for the second, the fourth and the fifth waves. These findings are relevant for viral infections controls and health safety strategies design in highly polluted urban environments.

Impacts of exposure to air pollution, radon and climate drivers on the COVID-19 pandemic in Bucharest, Romania: A time series study

During the ongoing global COVID-19 pandemic disease, like several countries, Romania experienced a multiwaves pattern over more than two years. The spreading pattern of SARS-CoV-2 pathogens in the Bucharest, capital of Romania is a multi-factorial process involving among other factors outdoor environmental variables and viral inactivation. Through descriptive statistics and cross-correlation analysis applied to daily time series of observational and geospatial data, this study aims to evaluate the synergy of COVID-19 incidence and lethality with air pollution and radon under different climate conditions, which may exacerbate the coronavirus' effect on human health. During the entire analyzed period 1 January 2020-21 December 2021, for each of the four COVID-19 waves were recorded different anomalous anticyclonic synoptic meteorological patterns in the mid-troposphere, and favorable stability conditions during fall-early winter seasons for COVID-19 disease fast-spreading, mostly during the second, and the fourth waves. As the temporal pattern of airborne SARS-CoV-2 and its mutagen variants is affected by seasonal variability of the main air pollutants and climate parameters, this paper found: 1) the daily outdoor exposures to air pollutants (particulate matter PM2.5 and PM10, nitrogen dioxide-NO₂, sulfur dioxide-SO₂, carbon monoxide-CO) and radon - ²²²Rn, are directly correlated with the daily COVID-19 incidence and mortality, and may contribute to the spread and the severity of the pandemic; 2) the daily ground ozone-O₃ levels, air temperature, Planetary Boundary Layer height, and surface solar irradiance are anticorrelated with the daily new COVID-19 incidence and deaths, averageingful for spring-summer periods. Outdoor exposure to ambient air pollution associated with radon is a non-negligible driver of COVID-19 transmission in large metropolitan areas, and climate variables are risk factors in spreading the viral infection. The findings of this study provide useful information for public health authorities and decision-makers to develop future pandemic diseases strategies in high polluted metropolitan environments.

Fungal Spore Richness in School Classrooms is Related to Surrounding Forest in a Season-Dependent Manner

Airborne fungal spores are important aeroallergens that are remarkably diverse in terms of taxonomic richness. Indoor fungal richness is dominated by outdoor fungi and is geographically patterned, but the influence of natural landscape is unclear. We aimed to elucidate the relationship between indoor fungal spore richness and natural landscape by examining the amount of surrounding forest cover. Passive sampling of airborne fungal spores was conducted in 24 schools in Taiwan during hot and cool seasons, and amplicon sequencing was used to study fungal spore (genus) richness targeting the internal transcribed spacer 2 (ITS2) region. In total, 693 fungal genera were identified, 12 of which were ubiquitous. Despite overall similarity of fungal spore richness between seasons, Basidiomycota and Ascomycota richness increased during the hot and cool seasons, respectively. Fungal spore richness in schools had a strong positive correlation with the amount of surrounding forest cover during the cool season, but not during the hot season. Fungal assemblages in schools were more similar during the hot season due to the increased ubiquity of Agaricomycetes genera. These observations indicate dispersal limitation at the kilometer scale during the cool season and increased long-distance dispersal during the hot season. Several allergenic fungi were commonly identified in schools, including some previously overlooked by conventional methods, which may be targeted as sensitizing agents in future investigations into atopic conditions. More generally, the relative importance of fungal spore richness in the development, chronicity, and severity of atopic conditions in children requires investigation.

A systematic review of outdoor airborne fungal spore seasonality across Europe and the implications for health

Fungal spores make up a significant proportion of organic matter within the air. Allergic sensitisation to fungi is associated with conditions including allergic fungal airway disease. This systematic review analyses outdoor fungal spore seasonality across Europe and considers the implications for health. Seventy-four studies met the inclusion criteria, the majority of which (n = 64) were observational sampling studies published between 1978 and 2020. The most commonly reported genera were the known allergens Alternaria and Cladosporium, measured in 52 and 49 studies, respectively. Both displayed statistically significant increased season length in south-westerly (Mediterranean) versus north-easterly (Atlantic and Continental) regions. Although there was a trend for reduced peak or annual Alternaria and Cladosporium spore concentrations in more northernly locations, this was not statistically significant. Peak spore concentrations of Alternaria and Cladosporium exceeded clinical thresholds in nearly all locations, with median peak concentrations of 665 and 18,827 per m3, respectively. Meteorological variables, predominantly temperature, precipitation and relative humidity, were the main factors associated with fungal seasonality. Land-use was identified as another important factor, particularly proximity to agricultural and coastal areas. While correlations of increased season length or decreased annual spore concentrations with increasing average temperatures were reported in multi-decade sampling studies, the number of such studies was too small to make any definitive conclusions. Further, up-to-date studies covering underrepresented geographical regions and fungal taxa (including the use of modern molecular techniques), and the impact of land-use and climate change will help address remaining knowledge gaps. Such knowledge will help to better understand fungal allergy, develop improved fungal spore calendars and forecasts with greater geographical coverage, and promote increased awareness and management strategies for those with allergic fungal disease.

Assessing the impact of air pollution and climate seasonality on COVID-19 multiwaves in Madrid, Spain

While the COVID-19 pandemic is still in progress, being under the fifth COVID-19 wave in Madrid, over more than one year, Spain experienced a four wave pattern. The transmission of SARS-CoV-2 pathogens in Madrid metropolitan region was investigated from an urban context associated with seasonal variability of climate and air pollution drivers. Based on descriptive statistics and regression methods of in-situ and geospatial daily time series data, this study provides a comparative analysis between COVID-19 waves incidence and mortality cases in Madrid under different air quality and climate conditions. During analyzed period 1 January 2020-1 July 2021, for each of the four COVID-19 waves in Madrid were recorded anomalous anticyclonic synoptic meteorological patterns in the mid-troposphere and favorable stability conditions for COVID-19 disease fast spreading. As airborne microbial temporal pattern is most affected by seasonal changes, this paper found: 1) a significant negative correlation of air temperature, Planetary Boundary Layer height, and surface solar irradiance with daily new COVID-19 incidence and deaths; 2) a similar mutual seasonality with climate variables of the first and the fourth COVID-waves from spring seasons of 2020 and 2021 years. Such information may help the health decision makers and public plan for the future.

OUP accepted manuscript

The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.

Rainfalls sprinkle cloud bacterial diversity while scavenging biomass

Bacteria circulate in the atmosphere, through clouds and precipitation to surface ecosystems. Here, we conducted a coordinated study of bacteria assemblages in clouds and precipitation at two sites distant of ∼800 m in elevation in a rural vegetated area around puy de Dôme Mountain, France, and analysed them in regard to meteorological, chemical and air masses' history data. In both clouds and precipitation, bacteria generally associated with vegetation or soil dominated. Elevated ATP-to-cell ratio in clouds compared with precipitation suggested a higher proportion of viable cells and/or specific biological processes. The increase of bacterial cell concentration from clouds to precipitation indicated strong below-cloud scavenging. Using ions as tracers, we derive that 0.2 to 25.5% of the 1.1 × 107 to 6.6 × 108 bacteria cell/m2/h1 deposited with precipitation originated from the source clouds. Yet, the relative species richness decreased with the proportion of inputs from clouds, pointing them as sources of distant microbial diversity. Biodiversity profiles, thus, differed between clouds and precipitation in relation with distant/local influencing sources, and potentially with bacterial phenotypic traits. Notably Undibacterium, Bacillus and Staphylococcus were more represented in clouds, while epiphytic bacteria such as Massilia, Sphingomonas, Rhodococcus and Pseudomonas were enriched in precipitation.

Exploring the linkage between seasonality of environmental factors and COVID-19 waves in Madrid, Spain

Like several countries, Spain experienced a multi wave pattern of COVID-19 pandemic over more than one year period, between spring 2020 and spring 2021. The transmission of SARS-CoV-2 pandemics is a multi-factorial process involving among other factors outdoor environmental variables and viral inactivation.This study aims to quantify the impact of climate and air pollution factors seasonality on incidence and severity of COVID-19 disease waves in Madrid metropolitan region in Spain. We employed descriptive statistics and Spearman rank correlation tests for analysis of daily in-situ and geospatial time-series of air quality and climate data to investigate the associations with COVID-19 incidence and lethality in Madrid under different synoptic meteorological patterns. During the analyzed period (1 January 2020-28 February 2021), with one month before each of three COVID-19 waves were recorded anomalous anticyclonic circulations in the mid-troposphere, with positive anomalies of geopotential heights at 500 mb and favorable stability conditions for SARS-CoV-2 fast diffusion. In addition, the results reveal that air temperature, Planetary Boundary Layer height, ground level ozone have a significant negative relationship with daily new COVID-19 confirmed cases and deaths. The findings of this study provide useful information to the public health authorities and policymakers for optimizing interventions during pandemics.

Seasonal changes dominate long-term variability of the urban air microbiome across space and time

Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km² around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both groups characteristic of seasonal periods, but not of specific sampling sites or plant coverage. The present study suggests that the near surface atmosphere of urban environments contains an ecosystem stable across relatively large spatial and temporal scales, with a rather homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.

Characterization of fungal aerosol in a landfill and an incineration plants in Guangzhou, Southern China: The link to potential impacts

To understand the characteristics and potential impacts of fungal aerosols in waste disposal treatments, we performed observations at a landfill and an incineration plants in Guangzhou, Southern China. Size-segregated airborne fungal concentrations were measured based on culture-dependent method, and fungal compositions in PM_2.5 were obtained using high-throughput sequencing method. Concentrations of airborne fungi varied from 376 to 9318 CFU/m³ in the landfill plant and from 53 to 8491 CFU/m³ in the incineration plant, respectively. The temporal and spatial variations of fungal aerosols indicate that waste disposal operation, garbage transport, air mixing, and meteorological factors can significantly influence the variations of airborne fungi in the outdoor environment in both plants. Among the meteorological factors, light/moderate rain could significantly increase the airborne fungal concentrations while heavy rain could decrease the concentrations due to wet scavenge. We observed that culturable fungal aerosols predominantly resided in the size range of 2.1-3.3 μm. Different fungal community structures in PM_2.5 were found between the landfill and the incineration plants, suggesting the influence of different waste sorts and treatment procedures. We further identified the pathogenic/allergenic fungal taxa (e.g., Alternaria, Epicoccum sp. and Stachybotrys sp.) in the two plants, implying the potential human health risks with long-term exposure for on-site workers and surrounding residents. The fungal genera producing microbial volatile organic compounds (MVOCs, e.g., Cladosporium, Fusarium sp., Penicillium sp. and Candida) were found in both plants. These MVOCs generation related fungal genera could contribute to the odor in the plants and, more importantly, affect the downwind area after aerosolization and transportation.

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.