High-Flow-Rate Impinger for the Study of Concentration, Viability, Metabolic Activity, and Ice-Nucleation Activity of Airborne Bacteria

Microfluidics for the biological analysis of atmospheric ice-nucleating particles: Perspectives and challenges

Atmospheric ice-nucleating particles (INPs) make up a vanishingly small proportion of atmospheric aerosol but are key to triggering the freezing of supercooled liquid water droplets, altering the lifetime and radiative properties of clouds and having a substantial impact on weather and climate. However, INPs are notoriously difficult to model due to a lack of information on their global sources, sinks, concentrations, and activity, necessitating the development of new instrumentation for quantifying and characterizing INPs in a rapid and automated manner. Microfluidic technology has been increasingly adopted by ice nucleation research groups in recent years as a means of performing droplet freezing analysis of INPs, enabling the measurement of hundreds or thousands of droplets per experiment at temperatures down to the homogeneous freezing of water. The potential for microfluidics extends far beyond this, with an entire toolbox of bioanalytical separation and detection techniques developed over 30 years for medical applications. Such methods could easily be adapted to biological and biogenic INP analysis to revolutionize the field, for example, in the identification and quantification of ice-nucleating bacteria and fungi. Combined with miniaturized sampling techniques, we can envisage the development and deployment of microfluidic sample-to-answer platforms for automated, user-friendly sampling and analysis of biological INPs in the field that would enable a greater understanding of their global and seasonal activity. Here, we review the various components that such a platform would incorporate to highlight the feasibility, and the challenges, of such an endeavor, from sampling and droplet freezing assays to separations and bioanalysis.

Integrated environmental and clinical surveillance for the prevention of acute respiratory infections (ARIs) in indoor environments and vulnerable communities (Stell-ARI): Protocol

The epidemiological relevance of viral acute respiratory infections (ARIs) has been dramatically highlighted by COVID-19. However, other viruses cannot be neglected, such as influenza virus, respiratory syncytial virus, human adenovirus. These viruses thrive in closed spaces, influenced by human and environmental factors. High-risk closed communities are the most vulnerable settings, where the real extent of viral ARIs is often difficult to evaluate, due to the natural disease progression and case identification complexities. During the COVID-19 pandemic, wastewater-based epidemiology has demonstrated its great potential for monitoring the circulation and evolution of the virus in the environment. The "Prevention of ARIs in indoor environments and vulnerable communities" study (Stell-ARI) addresses the urgent need for integrated surveillance and early detection of ARIs within enclosed and vulnerable communities such as long-term care facilities, prisons and primary schools. The rapid transmission of ARIs in such environments underscores the importance of comprehensive surveillance strategies to minimise the risk of outbreaks and safeguard community health, enabling proactive prevention and control strategies to protect the health of vulnerable populations. This study consists of designing and validating tools for integrated clinical and environmental-based surveillance for each setting, coupled with analytical methods for environmental matrices. The clinical surveillance involves specialized questionnaires and nasopharyngeal swabs for virus identification, while the environmental surveillance includes air and surface microbiological and chemical monitoring, and virological analysis of wastewater. Integrating this information and the collection of behavioural and environmental risk factors into predictive and risk assessment models will provide a useful tool for early warning, risk assessment and informed decision-making. The study aims to integrate clinical, behavioural, and environmental data to establish and validate a predictive model and risk assessment tool for the early warning and risk management of viral ARIs in closed and vulnerable communities prior to the onset of an outbreak.

Aerosol sources and transport paths co-control the atmospheric bacterial diversity over the coastal East China Sea

Airborne bacteria along with chemical composition of aerosols were investigated during five sampling seasons at an offshore island of the East China Sea. Bacterial diversity was the lowest in spring, the highest in winter, and similar between the autumns of 2019 and 2020, suggesting remarkably seasonal variation but little interannual change. Geodermatophilus (Actinobacteria) was the indicator genus of mineral dust (MD) showed higher proportion in spring than in other seasons. Mastigocladopsis_PCC-10914 (Cyanobacteria) as the indicator of sea salt (SS) demonstrated the highest percentages in both autumns, when the air masses mainly passed over the ocean prior to the sampling site. The higher proportions of soil-derived genera Rubellimicrobium and Craurococcus (both Proteobacteria) and extremophile Chroococcidiopsis_SAG_2023 (Cyanobacteria) were found in summer and winter, respectively. Our study explores the linkage between aerosol source and transport path and bacterial composition, which has implication to understanding of land-sea transmission of bacterial taxa.

On-Site Bioaerosol Sampling and Airborne Microorganism Detection Technologies

Bioaerosols are small airborne particles composed of microbiological fragments, including bacteria, viruses, fungi, pollens, and/or by-products of cells, which may be viable or non-viable wherever applicable. Exposure to these agents can cause a variety of health issues, such as allergic and infectious diseases, neurological disorders, and cancer. Therefore, detecting and identifying bioaerosols is crucial, and bioaerosol sampling is a key step in any bioaerosol investigation. This review provides an overview of the current bioaerosol sampling methods, both passive and active, as well as their applications and limitations for rapid on-site monitoring. The challenges and trends for detecting airborne microorganisms using molecular and immunological methods are also discussed, along with a summary and outlook for the development of prompt monitoring technologies.

Establishment of a Halophilic Bloom in a Sterile and Isolated Hypersaline Mesocosm

Extreme environments, including hypersaline pools, often serve as biogeographical islands. Putative colonizers would need to survive transport across potentially vast distances of inhospitable terrain. Hyperhalophiles, in particular, are often highly sensitive to osmotic pressure. Here, we assessed whether hyperhalophiles are capable of rapidly colonizing an isolated and sterile hypersaline pool and the order of succession of the ensuing colonizers. A sterile and isolated 1 m3 hypersaline mesocosm pool was constructed on a rooftop in Charleston, SC. Within months, numerous halophilic lineages successfully navigated the 20 m elevation and the greater than 1 km distance from the ocean shore, and a vibrant halophilic community was established. All told, in a nine-month period, greater than a dozen halophilic genera colonized the pool. The first to arrive were members of the Haloarchaeal genus Haloarcula. Like a weed, the Haloarcula rapidly colonized and dominated the mesocosm community but were later supplanted by other hyperhalophilic genera. As a possible source of long-distance inoculum, both aerosol and water column samples were obtained from the Great Salt Lake and its immediate vicinity. Members of the same genus, Haloarcula, were preferentially enriched in the aerosol sample relative to the water column samples. Therefore, it appears that a diverse array of hyperhalophiles are capable of surviving aeolian long-distance transport and that some lineages, in particular, have possibly adapted to that strategy.

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.

Perspectives on Sampling and New Generation Sequencing Methods for Low-Biomass Bioaerosols in Atmospheric Environments

Bioaerosols play essential roles in the atmospheric environment and can affect human health. With a few exceptions (e.g., farm or rainforest environments), bioaerosol samples from wide-ranging environments typically have a low biomass, including bioaerosols from indoor environments (e.g., residential homes, offices, or hospitals), outdoor environments (e.g., urban or rural air). Some specialized environments (e.g., clean rooms, the Earth's upper atmosphere, or the international space station) have an ultra-low-biomass. This review discusses the primary sources of bioaerosols and influencing factors, the recent advances in air sampling techniques and the new generation sequencing (NGS) methods used for the characterization of low-biomass bioaerosol communities, and challenges in terms of the bias introduced by different air samplers when samples are subjected to NGS analysis with a focus on ultra-low biomass. High-volume filter-based or liquid-based air samplers compatible with NGS analysis are required to improve the bioaerosol detection limits for microorganisms. A thorough understanding of the performance and outcomes of bioaerosol sampling using NGS methods and a robust protocol for aerosol sample treatment for NGS analysis are needed. Advances in NGS techniques and bioinformatic tools will contribute toward the precise high-throughput identification of the taxonomic profiles of bioaerosol communities and the determination of their functional and ecological attributes in the atmospheric environment. In particular, long-read amplicon sequencing, viability PCR, and meta-transcriptomics are promising techniques for discriminating and detecting pathogenic microorganisms that may be active and infectious in bioaerosols and, therefore, pose a threat to human health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s41745-023-00380-x.

Contribution of soil bacteria to the atmosphere across biomes

The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.

Understanding atmospheric intercontinental dispersal of harmful microorganisms

The atmosphere is a major route for microbial intercontinental dispersal, including harmful microorganisms, antibiotic resistance genes, and allergens, with strong implications in ecosystem functioning and global health. Long-distance dispersal is facilitated by air movement at higher altitudes in the free troposphere and is affected by anthropogenic forcing, climate change, and by the general atmospheric circulation, mainly in the intertropical convergence zone. The survival of microorganisms during atmospheric transport and their remote invasive potential are fundamental questions, but data are scarce. Extreme atmospheric conditions represent a challenge to survival that requires specific adaptive strategies, and recovery of air samples from the high altitudes relevant to study harmful microorganisms can be challenging. In this paper, we highlight the scope of the problem, identify challenges and knowledge gaps, and offer a roadmap for improved understanding of intercontinental microbial dispersal and their outcomes. Greater understanding of long-distance dispersal requires research focus on local factors that affect emissions, coupled with conditions influencing transport and survival at high altitudes, and eventual deposition at sink locations.

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.

Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland

Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey’s air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site’s nature and location.

Antimicrobial Resistance in the Environment: Towards Elucidating the Roles of Bioaerosols in Transmission and Detection of Antibacterial Resistance Genes

Antimicrobial resistance (AMR) is continuing to grow across the world. Though often thought of as a mostly public health issue, AMR is also a major agricultural and environmental problem. As such, many researchers refer to it as the preeminent One Health issue. Aerial transport of antimicrobial-resistant bacteria via bioaerosols is still poorly understood. Recent work has highlighted the presence of antibiotic resistance genes in bioaerosols. Emissions of AMR bacteria and genes have been detected from various sources, including wastewater treatment plants, hospitals, and agricultural practices; however, their impacts on the broader environment are poorly understood. Contextualizing the roles of bioaerosols in the dissemination of AMR necessitates a multidisciplinary approach. Environmental factors, industrial and medical practices, as well as ecological principles influence the aerial dissemination of resistant bacteria. This article introduces an ongoing project assessing the presence and fate of AMR in bioaerosols across Canada. Its various sub-studies include the assessment of the emissions of antibiotic resistance genes from many agricultural practices, their long-distance transport, new integrative methods of assessment, and the creation of dissemination models over short and long distances. Results from sub-studies are beginning to be published. Consequently, this paper explains the background behind the development of the various sub-studies and highlight their shared aspects.

Seasonal Variation of the Atmospheric Bacterial Community in the Greenlandic High Arctic Is Influenced by Weather Events and Local and Distant Sources

The Arctic is a hot spot for climate change with potentially large consequences on a global scale. Aerosols, including bioaerosols, are important players in regulating the heat balance through direct interaction with sunlight and indirectly, through inducing cloud formation. Airborne bacteria are the major bioaerosols with some species producing the most potent ice nucleating compounds known, which are implicated in the formation of ice in clouds. Little is known about the numbers and dynamics of airborne bacteria in the Arctic and even less about their seasonal variability. We collected aerosol samples and wet deposition samples in spring 2015 and summer 2016, at the Villum Research Station in Northeast Greenland. We used amplicon sequencing and qPCR targeting the 16S rRNA genes to assess the quantities and composition of the DNA and cDNA-level bacterial community. We found a clear seasonal variation in the atmospheric bacterial community, which is likely due to variable sources and meteorology. In early spring, the atmospheric bacterial community was dominated by taxa originating from temperate and Subarctic regions and arriving at the sampling site through long-range transport. We observed an efficient washout of the aerosolized bacterial cells during a snowstorm, which was followed by very low concentrations of bacteria in the atmosphere during the consecutive 4 weeks. We suggest that this is because in late spring, the long-range transport ceased, and the local sources which comprised only of ice and snow surfaces were weak resulting in low bacterial concentrations. This was supported by observed changes in the chemical composition of aerosols. In summer, the air bacterial community was confined to local sources such as soil, plant material and melting sea-ice. Aerosolized and deposited Cyanobacteria in spring had a high activity potential, implying their activity in the atmosphere or in surface snow. Overall, we show how the composition of bacterial aerosols in the high Arctic varies on a seasonal scale, identify their potential sources, demonstrate how their community sizes varies in time, investigate their diversity and determine their activity potential during and post Arctic haze.

Analysis of Environmental and Pathogenic Bacteria Attached to Aerosol Particles Size-Separated with a Metal Mesh Device

Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by size. Structurally, MMDs consist of a periodic arrangement of square apertures of characteristic shapes and sizes on a thin nickel membrane. The present study describes the separation of aerosol particles using palm-top-size collection devices equipped with three types of MMDs differing in pore size. Aerosols were collected at a farm located in the suburbs of Nairobi, Kenya; aerosol particles were isolated, and pathogenic bacteria were identified in this microflora by next-generation sequencing analysis. The composition of the microflora in aerosol particles was found to depend on particle size. Gene fragments were obtained from the collected aerosols by PCR using primers specific for the genus Mycobacterium. This analysis showed that Mycobacterium obuense, a non-tuberculous species of mycobacteria that causes lung diseases, was present in these aerosols. These findings showed that application of this MMD analytical protocol to aerosol particles can facilitate the investigation of airborne pathogenic bacteria.

Airborne environmental DNA for terrestrial vertebrate community monitoring

Biodiversity monitoring at the community scale is a critical element of assessing and studying species distributions, ecology, diversity, and movements, and it is key to understanding and tracking environmental and anthropogenic effects on natural ecosystems.1, 2, 3, 4 Vertebrates in terrestrial ecosystems are experiencing extinctions and declines in both population numbers and sizes due to increasing threats from human activities and environmental change.5, 6, 7, 8 Terrestrial vertebrate monitoring using existing methods is generally costly and laborious, and although environmental DNA (eDNA) is becoming the tool of choice to assess biodiversity, few sample types effectively capture terrestrial vertebrate diversity. We hypothesized that eDNA captured from air could allow straightforward collection and characterization of terrestrial vertebrate communities. We filtered air at three localities in the Copenhagen Zoo: a stable, outside between the outdoor enclosures, and in the Rainforest House. Through metabarcoding of airborne eDNA, we detected 49 vertebrate species spanning 26 orders and 37 families: 30 mammal, 13 bird, 4 fish, 1 amphibian, and 1 reptile species. These spanned animals kept at the zoo, species occurring in the zoo surroundings, and species used as feed in the zoo. The detected species comprise a range of taxonomic orders and families, sizes, behaviors, and abundances. We found shorter distance to the air sampling device and higher animal biomass to increase the probability of detection. We hereby show that airborne eDNA can offer a fundamentally new way of studying and monitoring terrestrial communities.

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49 vertebrate species detected through metabarcoding of airborne eDNA from the zoo

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Detections included 30 mammal, 13 bird, 4 fish, 1 amphibian, and 1 reptile species

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6 to 21 vertebrate species were detected per air filtering sample

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Shorter geographical distance and higher biomass increased probability of detection

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.

Challenges and Perspectives for Biosensing of Bioaerosol Containing Pathogenic Microorganisms

As an important route for disease transmission, bioaerosols have received increasing attention. In the past decades, many efforts were made to facilitate the development of bioaerosol monitoring; however, there are still some important challenges in bioaerosol collection and detection. Thus, recent advances in bioaerosol collection (such as sedimentation, filtration, centrifugation, impaction, impingement, and microfluidics) and detection methods (such as culture, molecular biological assay, and immunological assay) were summarized in this review. Besides, the important challenges and perspectives for bioaerosol biosensing were also discussed.

Airborne Spread of Methicillin Resistant Staphylococcus aureus From a Swine Farm

Spread of livestock-associated methicillin resistant Staphylococcus aureus (LA-MRSA) to farmworkers has been recognized as a risk when working in LA-MRSA positive stables, due to LA-MRSA being present on airborne dust particles. Based on this, airborne spread of LA-MRSA through stable vents is a concern that is addressed in this study. The aim of the investigation was to quantify the airborne spread of LA-MRSA from a MRSA positive swine farm. In order to achieve this, a method for sampling large volumes of air was applied. The results were compared to meteorological data and bacteriological investigation of samples from the air inside the swine barn, soil outside the farm, and nasal samples from the individuals participating in the sampling process. MRSA was detected up to 300 m (the maximal measuring distance) from the swine farm in the air but only at low levels at distances above 50 meters (0.085 CFU/m3 at a distance of 50 m in the wind plume). MRSA was detected in sock samples obtained at the soil surfaces up to 400 m (the maximal measuring distance) from the farm building. The proportion of MRSA positive soil samples decreased from ~80 to 30% with increasing distance from the farm. A total of 25 human nasal samples were sampled after the farm visits after the participants had stayed in the surroundings of the farm for an average of 10.5 h. When leaving the farm, only two of the samples (8%) were LA-MRSA-positive both obtained from one individual who was the one who had sampled the ventilation shafts. In conclusion, airborne spread of MRSA from swine farms does not seem to be an important route for human contamination for individuals staying a whole working day outside a swine farm.

DNA metabarcoding of fungal diversity in air and snow of Livingston Island, South Shetland Islands, Antarctica

We assessed fungal diversity present in air and freshly deposited snow samples obtained from Livingston Island, Antarctica, using DNA metabarcoding through high throughput sequencing (HTS). A total of 740 m3 of air were pumped through a 0.22 µm membrane. Snow obtained shortly after deposition was kept at room temperature and yielded 3.760 L of water, which was filtered using Sterivex membranes of 0.22 µm mesh size. The total DNA present was extracted and sequenced. We detected 171 fungal amplicon sequence variants (ASVs), 70 from the air and 142 from the snow. They were dominated by the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Pseudogymnoascus, Cladosporium, Mortierella and Penicillium sp. were the most dominant ASVs detected in the air in rank order. In snow, Cladosporium, Pseudogymnoascus, Penicillium, Meyerozyma, Lecidea, Malassezia, Hanseniaspora, Austroplaca, Mortierella, Rhodotorula, Penicillium, Thelebolus, Aspergillus, Poaceicola, Glarea and Lecanora were the dominant ASVs present. In general, the two fungal assemblages displayed high diversity, richness, and dominance indices, with the assemblage found in snow having the highest diversity indices. Of the total fungal ASVs detected, 29 were only present in the air sample and 101 in the snow sample, with only 41 present in both samples; however, when only the dominant taxa from both samples were compared none occurred only in the air and, among the rare portion, 26 taxa occurred in both air and snow. Application of HTS revealed the presence of a more diverse fungal community in the air and snow of Livingston Island in comparison with studies using traditional isolation methods. The assemblages were dominated by cold-adapted and cosmopolitan fungal taxa, including members of the genera Pseudogymnoascus, Malassezia and Rhodotorula, which include some taxa reported as opportunistic. Our results support the hypothesis that the presence of microbiota in the airspora indicates the possibility of dispersal around Antarctica in the air column. However, further aeromycology studies are required to understand the dynamics of fungal dispersal within and beyond Antarctica.

Aerosolization and recovery of viable murine norovirus in an experimental setup

Noroviruses are the major cause for viral acute gastroenteritis in the world. Despite the existing infection prevention strategies in hospitals, the disease continues to spread and causes extensive and numerous outbreaks. Hence, there is a need to investigate the possibility of airborne transmission of norovirus. In this study, we developed an experimental setup for studies on the infectivity of aerosolized murine norovirus (MNV), a model for the human norovirus. Two aerosol generation principles were evaluated: bubble bursting, a common natural aerosolization mechanism, and nebulization, a common aerosolization technique in laboratory studies. The aerosolization setup was characterized by physical and viral dilution factors, generated aerosol particle size distributions, and the viral infectivity after aerosolization. We found a lower physical dilution factor when using the nebulization generator than with the bubble bursting generator. The viral dilution factor of the system was higher than the physical dilution; however, when comparing the physical and viral dilution factors, bubble bursting generation was more efficient. The infectivity per virus was similar using either generation principle, suggesting that the generation itself had a minor impact on MNV infectivity and that instead, the effect of drying in air could be a major reason for infectivity losses.

Recent Advances in Monitoring, Sampling, and Sensing Techniques for Bioaerosols in the Atmosphere

Bioaerosols in the form of microscopic airborne particles pose pervasive risks to humans and livestock. As either fully active components (e.g., viruses, bacteria, and fungi) or as whole or part of inactive fragments, they are among the least investigated pollutants in nature. Their identification and quantification are essential to addressing related dangers and to establishing proper exposure thresholds. However, difficulties in the development (and selection) of detection techniques and an associated lack of standardized procedures make the sensing of bioaerosols challenging. Through a comprehensive literature search, this review examines the mechanisms of conventional and advanced bioaerosol detection methods. It also provides a roadmap for future research and development in the selection of suitable methodologies for bioaerosol detection. The development of sample collection and sensing technology make it possible for continuous and automated operation. However, intensive efforts should be put to overcome the limitations of current technology as most of the currently available options tend to suffer from lengthy sample acquisition times and/or nonspecificity of probe material.

Culturability, metabolic activity and composition of ambient bacterial aerosols in a surrogate lung fluid

Interactions of particulate matter (PM) and respiratory tract play a crucial role in PM-related respiratory diseases. The majority of the work focuses on the oxidative stress induced by reactions between PM-borne redox-active components and lung lining fluid (LLF). The effects of PM-borne biological components are largely unknown. Of all PM-borne biologicals, bacteria, as living microorganisms, are closely related with inflammatory immune responses. However, its inhalation risk is usually determined without considering the respiratory physiological conditions. In this study, a surrogate lung fluid (SLF) with four typical antioxidants was applied to characterize the ambient bacteria, including concentrations of total bacteria/viable bacteria/culturable bacteria, metabolic activity, bacteria-derived endotoxin, as well as the community structure. Comparing to those determined by SLF, we find that use of PBS leads to an underestimation of the bacterial culturability and metabolic activity. No effect was seen regarding the number of total bacteria and viable bacteria (with intact membrane). Population structure change was seen for bacteria cultured from SLF-collected samples, when compared to that from PBS. Spore-forming bacteria, e.g., genus Bacillus, were found to be easily recovered with SLF. This implies that use of PBS could underestimate the bacteria inhalation risk, especially those bacterial endospores. Our work highlights the necessity to consider the respiratory airway environment when evaluating microbial inhalation risk.

Bioaerosol Sampling: Classical Approaches, Advances, and Perspectives

Bioaerosol sampling is an essential and integral part of any bioaerosol investigation. Since bioaerosols are very diverse in terms of their sizes, species, biological properties, and requirements for their detection and quantification, bioaerosol sampling is an active, yet challenging research area. This paper was inspired by the discussions during the 2018 International Aerosol Conference (IAC) (St. Louis, MO) regarding the need to summarize the current state of the art in bioaerosol research, including bioaerosol sampling, and the need to develop a more standardized set of guidelines for protocols used in bioaerosol research. The manuscript is a combination of literature review and perspectives: it discusses the main bioaerosol sampling techniques and then overviews the latest technical developments in each area; the overview is followed by the discussion of the emerging trends and developments in the field, including personal sampling, application of passive samplers, and advances toward improving bioaerosol detection limits as well as the emerging challenges such as collection of viruses and collection of unbiased samples for bioaerosol sequencing. The paper also discusses some of the practical aspects of bioaerosol sampling with particular focus on sampling aspects that could lead to bioaerosol determination bias. The manuscript concludes by suggesting several goals for bioaerosol sampling and development community to work towards and describes some of the grand bioaerosol challenges discussed at the IAC 2018.

Biogenic Sources of Ice Nucleating Particles at the High Arctic Site Villum Research Station

The radiative balance in the Arctic region is sensitive to in-cloud processes, which principally depend on atmospheric aerosols, including ice nucleating particles (INPs). High temperature INPs (active at ≥-15 °C) are common in the Arctic. While laboratory and limited in situ studies show that the high-temperature active INPs are associated with bioaerosols and biogenic compounds, there is still little quantitative insight into the Arctic biogenic INPs and bioaerosols. We measured concentrations of bioaerosols, bacteria, and biogenic INPs at the Villum Research Station (VRS, Station Nord) in a large number of snow (15) and air (51) samples. We found that INPs active at high subzero temperatures were present both in spring and summer. Air INP concentrations were higher in summer (18 INP m^-3 at ≥-10 °C) than in spring (<4 INP m^-3 at ≥-10 °C), when abundant INPs were found in snowfall (1.4 INP mL^-1 at ≥-10 °C). Also, in summer, a significantly higher number of microbial and bacterial cells were present compared to the spring. A large proportion (60%-100%) of INPs that were active between -6 °C and -20 °C could be deactivated by heating to 100 °C, which was indicative of their predominantly proteinaceous origin. In addition, there was a significant linear regression between the summer air concentrations of INPs active at ≥-10 °C and air concentrations of bacterial-marker-genes (p < 0.0001, R² = 0.999, n = 6), pointing at bacterial cells as the source of high-temperature active INPs. In conclusion, the majority of INPs was of proteinaceous, and possibly of bacterial, origin and was found in air during summer and in snowfall during springtime.

Seasonal Changes of Airborne Bacterial Communities Over Tokyo and Influence of Local Meteorology

In order to study airborne bacterial community dynamics over Tokyo, including fine-scale correlations between airborne microorganisms and meteorological conditions, and the influence of local versus long-range transport of microbes, air samples were collected on filters for periods ranging from 48 to 72 h. The diversity of the microbial community was assessed by next generation sequencing. Predicted source regions of airborne particles, from back trajectory analyses, changed abruptly from the Pacific Ocean to the Eurasian Continent in the beginning of October. However, the microbial community composition and the alpha and beta diversities were not affected by this shift in meteorological regime, suggesting that long-range transport from oceanic or continental sources was not the principal determinant controlling the local airborne microbiome. By contrast, we found a significant correlation between the local meteorology, especially relative humidity and wind speed, and both alpha diversity and beta diversity. Among four potential local source categories (soil, bay seawater, river, and pond), bay seawater and soil were identified as constant and predominant sources. Statistical analyses point toward humidity as the most influential meteorological factor, most likely because it is correlated with soil moisture and hence negatively correlated with the dispersal of particles from the land surface. In this study, we have demonstrated the benefits of fine-scale temporal analyses for understanding the sources and relationships with the meteorology of Tokyo's "aerobiome."

Seasonal Changes of Airborne Bacterial Communities Over Tokyo and Influence of Local Meteorology

In order to study airborne bacterial community dynamics over Tokyo, including fine-scale correlations between airborne microorganisms and meteorological conditions, and the influence of local versus long-range transport of microbes, air samples were collected on filters for periods ranging from 48 to 72 h. The diversity of the microbial community was assessed by next generation sequencing. Predicted source regions of airborne particles, from back trajectory analyses, changed abruptly from the Pacific Ocean to the Eurasian Continent in the beginning of October. However, the microbial community composition and the alpha and beta diversities were not affected by this shift in meteorological regime, suggesting that long-range transport from oceanic or continental sources was not the principal determinant controlling the local airborne microbiome. By contrast, we found a significant correlation between the local meteorology, especially relative humidity and wind speed, and both alpha diversity and beta diversity. Among four potential local source categories (soil, bay seawater, river, and pond), bay seawater and soil were identified as constant and predominant sources. Statistical analyses point toward humidity as the most influential meteorological factor, most likely because it is correlated with soil moisture and hence negatively correlated with the dispersal of particles from the land surface. In this study, we have demonstrated the benefits of fine-scale temporal analyses for understanding the sources and relationships with the meteorology of Tokyo’s “aerobiome.”

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states

The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×103 ± 1.0×103 cells m-3, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell-1), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.

Application of Cytosense flow cytometer for the analysis of airborne bacteria collected by a high volume impingement sampler

Characterization of airborne bacterial cells requires efficient collection, concentration, and analysis techniques, particularly to overcome the challenge of their dilute nature in outdoor environments. This study aims to establish a rapid and reliable approach for quantification of bacteria in air samples. To do this, a high volume impingement sampler was applied to collect airborne bacteria from a wastewater treatment plant (WWTP). The bacterial cell density was estimated by a Cytosense flow cytometer (Cytobouy) and compared to quantitative PCR (qPCR) data based on 16S rRNA genes. The average bacterial cell density measured by Cytosense ranged from 1.1 to 2.5 × 10⁴ cells m^-3 of air and that estimated by qPCR ranged from 0.08 to 3.8 × 10⁴ cells m^-3 of air. Regression analysis showed no systematic difference in bacterial cell densities between two methods applied when the cells were analyzed in vivo, and statistical tests confirmed that Cytosense counts of unfixed samples provided realistic values. Bacterial cell densities and the amount of DNA extracted from the sample were significantly correlated with relative humidity on a sampling day. The results showed that the present method was reliable to estimate bacteria densities from the outdoor environment, and the analysis given by Cytosense was faster and more sensitive than qPCR method. In addition, the Cytosense gave valuable information about cell characteristics at different sampling conditions.