Bioaerosols on the atmospheric super highway: An example of long distance transport of Alternaria spores from the Pannonian Plain to Poland

From air to insight: the evolution of airborne DNA sequencing technologies

Historically, the analysis of airborne biological organisms relied on microscopy and culture-based techniques. However, technological advances such as PCR and next-generation sequencing now provide researchers with the ability to gather vast amounts of data on airborne environmental DNA (eDNA). Studies typically involve capturing airborne biological material, followed by nucleic acid extraction, library preparation, sequencing and taxonomic identification to characterize the eDNA at a given location. These methods have diverse applications, including pathogen detection in agriculture and human health, air quality monitoring, bioterrorism detection and biodiversity monitoring. A variety of methods are used for airborne eDNA analysis, as no single pipeline meets all needs. This review outlines current methods for sampling, extraction, sequencing and bioinformatic analysis, highlighting how different approaches can influence the resulting data and their suitability for specific use cases. It also explores current applications of airborne eDNA sampling and identifies research gaps in the field.

Environmental drivers of the allergenic load caused by Ambrosia artemisiifolia pollen and its major allergen Amb a 1 in the atmosphere

Understanding the environmental factors influencing the allergenicity of Ambrosia artemisiifolia pollen is crucial for effective allergy prevention. This study, conducted from 2019 to 2022 in Bratislava, Slovakia, utilised a Hirst-type Burkard pollen trap and a Burkard multi-vial cyclone sampler to measure airborne ragweed pollen (by microscopic analysis) and Amb a 1 allergen concentrations (by ELISA), enabling the calculation of pollen allergen potency (PAP). The data analysis showed that annual pollen and allergen levels are affected by meteorological conditions: sunny and dry weather in May accelerated pollen production, while dry conditions in August increased allergenic potency during the main flowering phase. Based on Spearman's correlation analysis, daily allergen levels were significantly associated with pollen concentrations. Regression analysis confirmed the influence of environmental factors on pollen, allergen and PAP levels. Pollen concentration showed a positive association with temperature and wind speed but a negative association with precipitation. Relative humidity was the only meteorological factor negatively linked to allergen levels, while temperature had a negative impact on PAP. The most relevant air pollutants were CO and SO2, which increased allergen levels and PAP, respectively.

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.

Comparative analysis of airborne fungal spore distribution in urban and rural environments of Slovakia

Monitoring airborne fungal spores is crucial for public health and plant production since they belong to important aeroallergens and phytopathogens. Due to different land use, their concentration can differ significantly between urban and rural areas. We monitored their spectrum and quantity on two geographically close sites with a different degree of urbanisation: Bratislava City and Kaplna Village in Slovakia, located 38 km apart. We recorded the spectrum of airborne fungal spores over a year and confirmed the microscopic results by amplicon-based metagenomic analysis. The main spore season of the most frequent genera lasted over a week longer in Kaplna, but its intensity was approximately two-fold higher in Bratislava. This can be possibly connected to the microclimatic conditions of the urban area (especially wind speed and heat island effect) and the lesser use of fungicides. Cladosporium was the dominant genus on both sites, influencing the intensity most significantly. Through statistical analysis of the influence of meteorological parameters on airborne fungal spore levels, we identified a significant relationship with temperature, while the impact of other parameters varied depending on the spore type and release mechanism. Our results show the differences in airborne fungal spore levels between urban and rural areas and highlight the necessity for more monitoring stations in various environments.

Identifying key environmental factors to model Alt a 1 airborne allergen presence and variation

Fungal spores, commonly found in the atmosphere, can trigger important respiratory disorders. The glycoprotein Alt a 1 is the major allergen present in conidia of the genus Alternaria and has a high clinical relevance for people sensitized to fungi. Exposure to this allergen has been traditionally assessed by aerobiological spore counts, although this does not always offer an accurate estimate of airborne allergen load. This study aims to pinpoint the key factors that explain the presence and variation of Alt a 1 concentration in the atmosphere in order to establish exposure risk periods and improve forecasting models. Alternaria spores were sampled using a Hirst-type volumetric sampler over a five-year period. The allergenic fraction from the bioaerosol was collected using a low-volume cyclone sampler and Alt a 1 quantified by Enzyme-Linked ImmunoSorbent Assay. A cluster analysis was executed in order to group days with similar environmental features and then analyze days with the presence of the allergen in each of them. Subsequently, a quadratic discriminant analysis was performed to evaluate if the selected variables can predict days with high Alt a 1 load. The results indicate that higher temperatures and absolute humidity favor the presence of Alt a 1 in the atmosphere, while time of precipitation is related to days without allergen. Moreover, using the selected parameters, the quadratic discriminant analysis to predict days with allergen showed an accuracy rate between 67 % and 85 %. The mismatch between daily airborne concentration of Alternaria spores and allergen load can be explained by the greater contribution of medium-to-long distance transport of the allergen from the major emission sources as compared with spores. Results highlight the importance of conducting aeroallergen quantification studies together with spore counts to improve the forecasting models of allergy risk, especially for fungal spores.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Seasonality and intensity of airborne Boletus-type spores in relation to land use and weather pattern

Forests are a natural source of airborne bolete spores. The timing of sporulation and its intensity as well as the dispersal of airborne spores and in consequence their concentrations depend in particular on the type of land use determining the availability of matter on which they develop and on meteorological factors. The aim of this study was to perform a spatial and temporal analysis of the occurrence of Boletus-type spores in the warm temperate climate of the Northern Hemisphere. An assumption was made that the spore concentrations depend on the type of land cover and weather conditions. The volumetric method was applied to investigate differences in spore concentrations and using spore traps installed at different heights and at locations with different land cover types. Boletus-type spores occurred in the air at high concentrations in late summer and in the autumn. The season start dates and maximum concentrations did not differ significantly between sites and seasons, but the season intensity varied. Higher spore concentrations were usually found in the region with a larger proportion of green areas, including forests. An analysis of the diurnal cycles showed that within 24 h spore concentration reached high levels twice, which was especially noticeable in ground level monitoring. Air temperature and air humidity were the main weather factors affecting the occurrence of airborne spores. This research indicates that when studying the effects of different factors on the concentration of airborne basidiospores, many environmental elements should be analyzed, including the characteristics of habitats in which basidiomycetes grow. Climate, weather, geobotany, and land use type should be taken into account in analysis and interpretation of aeromycological phenomena.

Pollen long-distance transport associated with symptoms in pollen allergics on the German Alps: An old story with a new ending?

Pollen grains are among the main causes of respiratory allergies worldwide and hence they are routinely monitored in urban environments. However, their sources can be located farther, outside cities' borders. So, the fundamental question remains as to how frequent longer-range pollen transport incidents are and if they may actually comprise high-risk allergy cases. The aim was to study the pollen exposure on a high-altitude location where only scarce vegetation exists, by biomonitoring airborne pollen and symptoms of grass pollen allergic individuals, locally. The research was carried out in 2016 in the alpine research station UFS, located at 2650 m height, on the Zugspitze Mountain in Bavaria, Germany. Airborne pollen was monitored by use of portable Hirst-type volumetric traps. As a case study, grass pollen-allergic human volunteers were registering their symptoms daily during the peak of the grass pollen season in 2016, during a 2-week stay on Zugspitze, 13-24 June. The possible origin of some pollen types was identified using back trajectory model HYSPLIT for 27 air mass backward trajectories up to 24 h. We found that episodes of high aeroallergen concentrations may occur even at such a high-altitude location. More than 1000 pollen grains m^-3 of air were measured on the UFS within only 4 days. It was confirmed that the locally detected bioaerosols originated from at least Switzerland, and up to northwest France, even eastern American Continent, because of frequent long-distance transport. Such far-transported pollen may explain the observed allergic symptoms in sensitized individuals at a remarkable rate of 87 % during the study period. Long-distance transport of aeroallergens can cause allergic symptoms in sensitized individuals, as evidenced in a sparse-vegetation, low-exposure, 'low-risk' alpine environment. We strongly suggest that we need cross-border pollen monitoring to investigate long-distance pollen transport, as its occurrence seems both frequent and clinically relevant.

Effect of prevailing winds and land use on Alternaria airborne spore load

Alternaria spores are a common component of the bioaerosol. Many Alternaria species are plant pathogens, and their conidia are catalogued as important aeroallergens. Several aerobiological studies showing a strong relationship between concentrations of airborne spore and meteorological parameters have consequently been developed. However, the Alternaria airborne load variation has not been thoroughly investigated because it is difficult to assess their sources, as they are a very common and widely established phytopathogen. The objective of this study is to estimate the impact of vegetation and land uses as potential sources on airborne spore load and to know their influence, particularly, in cases of long-medium distance transport. The daily airborne spore concentration was studied over a 5-year period in León and Valladolid, two localities of Castilla y León (Spain), with differences in their bioclimatic and land use aspects. Moreover, the land use analysis carried out within a 30 km radius of each monitoring station was combined with air mass data in order to search for potential emission sources. The results showed a great spatial variation between the two areas, which are relatively close to each other. The fact that the spore concentrations recorded in Valladolid were higher than those in León was owing to prevailing winds originating from large areas covered by cereal crops, especially during the harvest period. However, the prevailing winds in León came from areas dominated by forest and shrubland, which explains the low airborne spore load, since the main Alternaria sources were the grasslands located next to the trap. Furthermore, the risk days in this location presented an unusual wind direction. This study reveals the importance of land cover and wind speed and direction data for establishing potential airborne routes of spore transport in order to improve the Alternaria forecasting models. The importance of conducting Alternaria aerobiological studies at a local level is also highlighted.

A Method for Capture and Detection of Crop Airborne Disease Spores Based on Microfluidic Chips and Micro Raman Spectroscopy

Airborne crop diseases cause great losses to agricultural production and can affect people's physical health. Timely monitoring of the situation of airborne disease spores and effective prevention and control measures are particularly important. In this study, a two-stage separation and enrichment microfluidic chip with arcuate pretreatment channel was designed for the separation and enrichment of crop disease spores, which was combined with micro Raman for Raman fingerprinting of disease conidia and quasi identification. The chip was mainly composed of arc preprocessing and two separated enriched structures, and the designed chip was numerically simulated using COMSOL multiphysics5.5, with the best enrichment effect at W2/W1 = 1.6 and W4/W3 = 1.1. The spectra were preprocessed with standard normal variables (SNVs) to improve the signal-to-noise ratio, which was baseline corrected using an iterative polynomial fitting method to further improve spectral features. Raman spectra were dimensionally reduced using principal component analysis (PCA) and stability competitive adaptive weighting (SCARS), support vector machine (SVM) and back-propagation artificial neural network (BPANN) were employed to identify fungal spore species, and the best discrimination effect was achieved using the SCARS-SVM model with 94.31% discrimination accuracy. Thus, the microfluidic-chip- and micro-Raman-based methods for spore capture and identification of crop diseases have the potential to be precise, convenient, and low-cost methods for fungal spore detection.

Climate change impact on fungi in the atmospheric microbiome

The atmospheric microbiome is one of the least studied microbiomes of our planet. One of the most abundant, diverse and impactful parts of this microbiome is arguably fungal spores. They can be very potent outdoor aeroallergens and pathogens, causing an enormous socio-economic burden on health services and annual damages to crops costing billions of Euros. We find through hypothesis testing that an expected warmer and drier climate has a dramatic impact on the atmospheric microbiome, conceivably through alteration of the hydrological cycle impacting agricultural systems, with significant differences in leaf wetness between years (p-value <0.05). The data were measured via high-throughput sequencing analysis using the DNA barcode marker, ITS2. This was complemented by remote sensing analysis of land cover and dry matter productivity based on the Sentinel satellites, on-site detection of atmospheric and vegetation variables, GIS analysis, harvesting analysis and footprint modelling on trajectory clusters using the atmospheric transport model HYSPLIT. We find the seasonal spore composition varies between rural and urban zones reflecting both human activities (e.g. harvest), type and status of the vegetation and the prevailing climate rather than mesoscale atmospheric transport. We find that crop harvesting governs the composition of the atmospheric microbiome through a clear distinction between harvest and post-harvest beta-diversity by PERMANOVA on Bray-Curtis dissimilarity (p-value <0.05). Land cover impacted significantly by two-way ANOVA (p-value <0.05), while there was minimal impact from air mass transport over the 3 years. The hypothesis suggests that the fungal spore composition will change dramatically due to climate change, an until now unforeseen effect affecting both food security, human health and the atmospheric hydrological cycle. Consequently the management of crop diseases and impact on human health through aeroallergen exposure need to consider the timing of crop treatments and land management, including post harvest, to minimize exposure of aeroallergens and pathogens.