Tracking seasonal changes in diversity of pollen allergen exposure: Targeted metabarcoding of a subtropical aerobiome

Environmental DNA analysis of airborne poaceae (grass) pollen reveals taxonomic diversity across seasons and climate zones

BACKGROUND

Grasses populate most biogeographical zones, and their diversity influences allergic sensitisation to pollen. Previously, the contribution of different Poaceae subfamilies to airborne pollen has mostly been inferred from historical herbarium records. We recently applied environmental (e)DNA metabarcoding at one subtropical site revealing that successive airborne grass pollen peaks were derived from repeated flowering of Chloridoid and Panicoid grasses over a season. This study aimed to compare spatiotemporal patterns in grass pollen exposure across seasons and climate zones.

METHODS

Airborne pollen concentrations across two austral pollen seasons spanning 2017-2019 at subtropical (Mutdapilly and Rocklea, Queensland) and temperate (Macquarie Park and Richmond, New South Wales) sites, were determined with a routine volumetric impaction sampler and counting by light microscopy. Poaceae rbcL metabarcode sequences amplified from daily pollen samples collected once per week were assigned to subfamily and genus using a ribosomal classifier and compared with Atlas of Living Australia sighting records.

RESULTS

eDNA analysis revealed distinct dominance patterns of grass pollen at various sites: Panicoid grasses prevailed in both subtropical Mutdapilly and temperate Macquarie Park, whilst Chloridoid grasses dominated the subtropical Rocklea site. Overall, subtropical sites showed significantly higher proportion of pollen from Chloridoid grasses than temperate sites, whereas the temperate sites showed a significantly higher proportion of pollen from Pooideae grasses than subtropical sites. Timing of airborne Pooid (spring), Panicoid and Chloridoid (late spring to autumn), and Arundinoid (autumn) pollen were significantly related to number of days from mid-winter. Proportions of eDNA for subfamilies correlated with distributions grass sighting records between climate zones.

CONCLUSIONS

eDNA analysis enabled finer taxonomic discernment of Poaceae pollen records across seasons and climate zones with implications for understanding adaptation of grasslands to climate change, and the complexity of pollen exposure for patients with allergic respiratory diseases.

Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis

Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies.

Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding

Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.

Airborne grass pollen and thunderstorms influence emergency department asthma presentations in a subtropical climate

BACKGROUND

Grass pollen is considered a major outdoor aeroallergen source worldwide. It is proposed as a mechanism for thunderstorm asthma that lightning during thunderstorms promotes electrical rupture of pollen grains that leads to allergic airway inflammation. However, most evidence of associations between grass pollen and asthma comes from temperate regions. The objective of this study was to investigate short-term associations between airborne grass pollen exposure and asthma emergency department presentations in a subtropical population.

METHODS

Episode level public hospital presentations for asthma (2016-2020) were extracted for greater Brisbane, Australia, from Queensland Health's Emergency Data Collection. Concentrations of airborne pollen were determined prospectively using a continuous flow volumetric impaction sampler. Daily time series analysis using a generalised additive mixed model were applied to determine associations between airborne grass pollen concentrations, and lightning count data, with asthma presentations.

RESULTS

Airborne grass pollen showed an association with asthma presentations in Brisbane; a significant association was detected from same day exposure to three days lag. Grass pollen exposure increased daily asthma presentations up to 48.5% (95% CI: 12%, 85.9%) in female children. Lightning did not modify the effect of grass pollen on asthma presentations, however a positive association was detected between cloud-to-cloud lightning strikes and asthma presentations (P = 0.048).

CONCLUSION

Airborne grass pollen exposure may exacerbate symptoms of asthma requiring urgent medical care of children and adults in a subtropical climate. This knowledge indicates an opportunity for targeted management of respiratory allergic disease to reduce patient and health system burden. For the first time, an influence of lightning on asthma was detected in this context. The outcomes support a need for continued pollen monitoring and surveillance of thunderstorm asthma risk in subtropical regions.

Aerobiological Monitoring and Metabarcoding of Grass Pollen

Grass pollen is one of the leading causes of pollinosis, affecting 10-30% of the world's population. The allergenicity of pollen from different Poaceae species is not the same and is estimated from moderate to high. Aerobiological monitoring is a standard method that allows one to track and predict the dynamics of allergen concentration in the air. Poaceae is a stenopalynous family, and thus grass pollen can usually be identified only at the family level with optical microscopy. Molecular methods, in particular the DNA barcoding technique, can be used to conduct a more accurate analysis of aerobiological samples containing the DNA of various plant species. This study aimed to test the possibility of using the ITS1 and ITS2 nuclear loci for determining the presence of grass pollen from air samples via metabarcoding and to compare the analysis results with the results of phenological observations. Based on the high-throughput sequencing data, we analyzed the changes in the composition of aerobiological samples taken in the Moscow and Ryazan regions for three years during the period of active flowering of grasses. Ten genera of the Poaceae family were detected in airborne pollen samples. The representation for most of them for ITS1 and ITS2 barcodes was similar. At the same time, in some samples, the presence of specific genera was characterized by only one sequence: either ITS1 or ITS2. Based on the analysis of the abundance of both barcode reads in the samples, the following order could describe the change with time in the dominant species in the air: Poa, Alopecurus, and Arrhenatherum in early mid-June, Lolium, Bromus, Dactylis, and Briza in mid-late June, Phleum, Elymus in late June to early July, and Calamagrostis in early mid-July. In most samples, the number of taxa found via metabarcoding analysis was higher compared to that in the phenological observations. The semi-quantitative analysis of high-throughput sequencing data well reflects the abundance of only major grass species at the flowering stage.

Isolating the species element in grass pollen allergy: A review

Grass pollen is a leading cause of allergy in many countries, particularly Europe. Although many elements of grass pollen production and dispersal are quite well researched, gaps still remain around the grass species that are predominant in the air and which of those are most likely to trigger allergy. In this comprehensive review we isolate the species aspect in grass pollen allergy by exploring the interdisciplinary interdependencies between plant ecology, public health, aerobiology, reproductive phenology and molecular ecology. We further identify current research gaps and provide open ended questions and recommendations for future research in an effort to focus the research community to develop novel strategies to combat grass pollen allergy. We emphasise the role of separating temperate and subtropical grasses, identified through divergence in evolutionary history, climate adaptations and flowering times. However, allergen cross-reactivity and the degree of IgE connectivity in sufferers between the two groups remains an area of active research. The importance of future research to identify allergen homology through biomolecular similarity and the connection to species taxonomy and practical implications of this to allergenicity is further emphasised. We also discuss the relevance of eDNA and molecular ecological techniques (DNA metabarcoding, qPCR and ELISA) as important tools in quantifying the connection between the biosphere with the atmosphere. By gaining more understanding of the connection between species-specific atmospheric eDNA and flowering phenology we will further elucidate the importance of species in releasing grass pollen and allergens to the atmosphere and their individual role in grass pollen allergy.

Long-Term Monitoring of Bioaerosols in an Environment without UV and Desiccation Stress, an Example from the Cave Postojnska Jama, Slovenia

A natural cave environment subject to regular human visitation was selected for aerobiological study to minimize the effects of severe temperature fluctuations, UV radiation, and desiccation stress on the aerobiome. The longer sampling period of bioaerosols, up to 22 months, was generally not associated with a proportionally incremental and cumulative increase of microbial biomass. The culture-independent biomass indicator ATP enabled quick and reliable determination of the total microbial biomass. Total airborne microbial biomass was influenced by human visitation to the cave, as confirmed by significantly higher concentrations being observed along tourist footpaths (p < 0.05). Airborne beta-glucans (BG) and lipopolysaccharide (LPS) are present in cave air, but their impact on the cave remains to be evaluated. Staphylococcus spp., as an indicator of human presence, was detected at all sites studied. Their long-term survival decrease is likely due to high relative humidity, low temperature, the material to which they adhere, and potentially natural elevated radon concentration. The most commonly recorded species were: S. saprophyticus, which was identified in 52% of the studied sites, S. equorum in 29%, and S. warneri in 24% of the studied sites. Only a few isolates were assigned to Risk group 2: S. aureus, S. epidermidis, S. haemolyticus, S. pasteuri, and S. saprophyticus.

Metabarcoding airborne pollen from subtropical and temperate eastern Australia over multiple years reveals pollen aerobiome diversity and complexity

eDNA metabarcoding is an emergent tool to inform aerobiome complexity, but few studies have applied this technology with real-world environmental pollen monitoring samples. Here we apply eDNA metabarcoding to assess seasonal and regional differences in the composition of airborne pollen from routine samples collected across successive years. Airborne pollen concentrations over two sampling periods were determined using a continuous flow volumetric impaction air sampler in sub-tropical (Mutdapilly and Rocklea) and temperate (Macquarie Park and Richmond), sites of Australia. eDNA metabarcoding was applied to daily pollen samples collected once per week using the rbcL amplicon. Composition and redundancy analysis of the sequence read counts were examined. The dominant pollen families were mostly consistent between consecutive years but there was some heterogeneity between sites and years for month of peak pollen release. Many more families were detected by eDNA than counted by light microscopy with 211 to 399 operational taxonomic units assigned to family per site from October to May. There were 216 unique and 119 taxa shared between subtropics (27°S) and temperate (33°S) latitudes, with, for example, Poaceae, Myrtaceae and Causurinaceae being shared, and Manihot, Vigna and Aristida being in subtropical, and Ceratodon and Cerastium being in temperate sites. Certain genera were observed within the same location and season over the two years; Chloris at Rocklea in autumn of 2017-18 (0.625, p ≤ 0.004) and 2018-19 (0.55, p ≤ 0.001), and Pinus and Plantago at Macquarie Park in summer of 2017-18 (0.58, p ≤ 0.001 and 0.53, p ≤ 0.003, respectively), and 2018-19 (0.8, p ≤ 0.003 and 0.8, p ≤ 0.003, respectively). eDNA metabarcoding is a powerful tool to survey the complexity of pollen aerobiology and distinguish spatial and temporal profiles of local pollen to a far deeper level than traditional counting methods. However, further research is required to optimise the metabarcode target to enable reliable detection of pollen to genus and species level.

Monitoring nature's calendar from space: Emerging topics in land surface phenology and associated opportunities for science applications

Vegetation phenology has been viewed as the nature's calendar and an integrative indicator of plant-climate interactions. The correct representation of vegetation phenology is important for models to accurately simulate the exchange of carbon, water, and energy between the vegetated land surface and the atmosphere. Remote sensing has advanced the monitoring of vegetation phenology by providing spatially and temporally continuous data that together with conventional ground observations offers a unique contribution to our knowledge about the environmental impact on ecosystems as well as the ecological adaptations and feedback to global climate change. Land surface phenology (LSP) is defined as the use of satellites to monitor seasonal dynamics in vegetated land surfaces and to estimate phenological transition dates. LSP, as an interdisciplinary subject among remote sensing, ecology, and biometeorology, has undergone rapid development over the past few decades. Recent advances in sensor technologies, as well as data fusion techniques, have enabled novel phenology retrieval algorithms that refine phenology details at even higher spatiotemporal resolutions, providing new insights into ecosystem dynamics. As such, here we summarize the recent advances in LSP and the associated opportunities for science applications. We focus on the remaining challenges, promising techniques, and emerging topics that together we believe will truly form the very frontier of the global LSP research field.

The AusPollen partnership project: Allergenic airborne grass pollen seasonality and magnitude across temperate and subtropical eastern Australia, 2016-2020

BACKGROUND

Allergic rhinitis affects half a billion people globally, including a fifth of the Australian population. As the foremost outdoor allergen source, ambient grass pollen exposure is likely to be altered by climate change. The AusPollen Partnership aimed to standardize pollen monitoring and examine broad-scale biogeographical and meteorological factors influencing interannual variation in seasonality of grass pollen aerobiology in Australia.

METHODS

Daily airborne grass and other pollen concentrations in four eastern Australian cities separated by over 1700 km, were simultaneously monitored using Hirst-style samplers following the Australian Interim Pollen and Spore Monitoring Standard and Protocols over four seasons from 2016 to 2020. The grass seasonal pollen integral was determined. Gridded rainfall, temperature, and satellite-derived grassland sources up to 100 km from the monitoring site were analysed.

RESULTS

The complexity of grass pollen seasons was related to latitude with multiple major summer-autumn peaks in Brisbane, major spring and minor summer peaks in Sydney and Canberra, and single major spring peaks occurring in Melbourne. The subtropical site of Brisbane showed a higher proportion of grass out of total pollen than more temperate sites. The magnitude of the grass seasonal pollen integral was correlated with pasture greenness, rainfall and number of days over 30 °C, preceding and within the season, up to 100 km radii from monitoring sites.

CONCLUSIONS

Interannual fluctuations in Australian grass pollen season magnitude are strongly influenced by regional biogeography and both pre- and in-season weather. This first continental scale, Southern Hemisphere standardized aerobiology dataset forms the basis to track shifts in pollen seasonality, biodiversity and impacts on allergic respiratory diseases.

Medium-Term Increases in Ambient Grass Pollen Between 1994-1999 and 2016-2020 in a Subtropical Climate Zone

Grass pollen is the major outdoor trigger of allergic respiratory diseases. Climate change is influencing pollen seasonality in Northern Hemisphere temperate regions, but many aspects of the effects on grass pollen remain unclear. Carbon dioxide and temperature rises could increase the distribution of subtropical grasses, however, medium term shifts in grass pollen in subtropical climates have not yet been analysed. This study investigates changes in grass pollen aerobiology in a subtropical city of Brisbane, Australia, between the two available monitoring periods, 1994-1999 and 2016-2020. Potential drivers of pollen change were examined including weather and satellite-derived vegetation indicators. The magnitude of the seasonal pollen index for grass showed almost a three-fold increase for 2016-2020 over 1994-1999. The number and proportion of high and extreme grass pollen days in the recent period increased compared to earlier monitoring. Statistically significant changes were also identified for distributions of CO₂, satellite-derived seasonal vegetation health indices, and daily maximum temperatures, but not for minimum temperatures, daily rainfall, or seasonal fraction of green groundcover. Quarterly grass pollen levels were correlated with corresponding vegetation health indices, and with green groundcover fraction, suggesting that seasonal-scale plant health was higher in the latter period. The magnitude of grass pollen exposure in the subtropical region of Brisbane has increased markedly in the recent past, posing an increased environmental health threat. This study suggests the need for continuous pollen monitoring to track and respond to the possible effects of climate change on grass pollen loads.

Pollen Monitoring by Optical Microscopy and DNA Metabarcoding: Comparative Study and New Insights

Environmental samples collected in Brindisi (Italy) by a Hirst-type trap and in Lecce (Italy) by a PM10 sampler were analysed by optical microscopy and DNA-metabarcoding, respectively, to identify airborne pollen and perform an exploratory study, highlighting the benefits and limits of both sampling/detection systems. The Hirst-type trap/optical-microscopy system allowed detecting pollen on average over the full bloom season, since whole pollen grains, whose diameter vary within 10–100 μm, are required for morphological detection with optical microscopy. Conversely, pollen fragments with an aerodynamic diameter ≤10 μm were collected in Lecce by the PM10 sampler. Pollen grains and fragments are spread worldwide by wind/atmospheric turbulences and can age in the atmosphere, but aerial dispersal, aging, and long-range transport of pollen fragments are favoured over those of whole pollen grains because of their smaller size. Twenty-four Streptophyta families were detected in Lecce throughout the sampling year, but only nine out of them were in common with the 21 pollen families identified in Brindisi. Meteorological parameters and advection patterns were rather similar at both study sites, being only 37 km apart in a beeline, but their impact on the sample taxonomic structure was different, likely for the different pollen sampling/detection systems used in the two monitoring areas.

DNA metabarcoding using nrITS2 provides highly qualitative and quantitative results for airborne pollen monitoring

Airborne pollen monitoring is of global socio-economic importance as it provides information on presence and prevalence of allergenic pollen in ambient air. Traditionally, this task has been performed by microscopic investigation, but novel techniques are being developed to automate this process. Among these, DNA metabarcoding has the highest potential of increasing the taxonomic resolution, but uncertainty exists about whether the results can be used to quantify pollen abundance. In this study, it is shown that DNA metabarcoding using trnL and nrITS2 provides highly improved taxonomic resolution for pollen from aerobiological samples from the Netherlands. A total of 168 species from 143 genera and 56 plant families were detected, while using a microscope only 23 genera and 22 plant families were identified. NrITS2 produced almost double the number of OTUs and a much higher percentage of identifications to species level (80.1%) than trnL (27.6%). Furthermore, regressing relative read abundances against the relative abundances of microscopically obtained pollen concentrations showed a better correlation for nrITS2 (R2 = 0.821) than for trnL (R2 = 0.620). Using three target taxa commonly encountered in early spring and fall in the Netherlands (Alnus sp., Cupressaceae/Taxaceae and Urticaceae) the nrITS2 results showed that all three taxa were dominated by one or two species (Alnus glutinosa/incana, Taxus baccata and Urtica dioica). Highly allergenic as well as artificial hybrid species were found using nrITS2 that could not be identified using trnL or microscopic investigation (Alnus × spaethii, Cupressus arizonica, Parietaria spp.). Furthermore, perMANOVA analysis indicated spatiotemporal patterns in airborne pollen trends that could be more clearly distinguished for all taxa using nrITS2 rather than trnL. All results indicate that nrITS2 should be the preferred marker of choice for molecular airborne pollen monitoring.

Monitoring techniques for pollen allergy risk assessment

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

Characteristics of emergency patients admitted to hospital with asthma: A population-based cohort study in Queensland, Australia

OBJECTIVE

Patient characteristics with exacerbation of asthma accessing care in the ED who are at risk of hospital admission have not been determined in subtropical climates. The objective of the study was to investigate the spatiotemporal burden of asthma hospital admissions across Queensland (QLD) and model risk factors for asthma hospital admission following an ED visit.

METHODS

Six years of routinely collected data (2012-2017) from 28 QLD public hospitals were extracted from Queensland Health's Emergency Data Collection. The dataset contained individual, episode-level ED presentations having asthma-like diagnoses, and an indicator of hospital admission, including to short-stay unit (SSU). A generalised additive model was used to examine the risk of asthma hospital admission.

RESULTS

Asthma hospital admissions increased from a weekly median of 79 (interquartile range [IQR] 66-99) in 2012 to 104 (IQR 81-135) in 2017. A higher incidence of asthma hospital admission was observed among males (median age 9, IQR 5-32) in childhood and females in adulthood (median age 32, IQR 11-51). Compared to the state capital Brisbane, the odds of asthma hospital admission ranged from 0.48 (95% CI 0.42-0.54) to 1.34 (95%CI 1.21-1.48) in other regions of QLD.

CONCLUSION

Asthma hospital admissions appear to be increasing in QLD, largely driven by utilisation of the SSU admissions for asthma. With large variation in both incidence and proportion admitted across different regions, routinely collected data can in part be used to understand risk factors for asthma-related hospital admission following an ED presentation and further inform public health policy development.

Environmental DNA reveals links between abundance and composition of airborne grass pollen and respiratory health

Grass (Poaceae) pollen is the most important outdoor aeroallergen,¹ exacerbating a range of respiratory conditions, including allergic asthma and rhinitis ("hay fever").^2-5 Understanding the relationships between respiratory diseases and airborne grass pollen with a view to improving forecasting has broad public health and socioeconomic relevance. It is estimated that there are over 400 million people with allergic rhinitis⁶ and over 300 million with asthma, globally,⁷ often comorbidly.⁸ In the UK, allergic asthma has an annual cost of around US$ 2.8 billion (2017).⁹ The relative contributions of the >11,000 (worldwide) grass species (C. Osborne et al., 2011, Botany Conference, abstract) to respiratory health have been unresolved,¹⁰ as grass pollen cannot be readily discriminated using standard microscopy.¹¹ Instead, here we used novel environmental DNA (eDNA) sampling and qPCR^12-15 to measure the relative abundances of airborne pollen from common grass species during two grass pollen seasons (2016 and 2017) across the UK. We quantitatively demonstrate discrete spatiotemporal patterns in airborne grass pollen assemblages. Using a series of generalized additive models (GAMs), we explore the relationship between the incidences of airborne pollen and severe asthma exacerbations (sub-weekly) and prescribing rates of drugs for respiratory allergies (monthly). Our results indicate that a subset of grass species may have disproportionate influence on these population-scale respiratory health responses during peak grass pollen concentrations. The work demonstrates the need for sensitive and detailed biomonitoring of harmful aeroallergens in order to investigate and mitigate their impacts on human health.