Spore Samples Research Articles

Nanopore sequencing in surveillance of fungicide resistance

By detecting plant pathogens as early as possible, swift action can be taken to mitigate the spread of disease. Monitoring fungicide is another key part of effective disease control as pathogens can develop resistance to fungicides, rendering them ineffective. The area of plant disease management is advancing apace thanks to innovative research incorporating technical advances in detection and monitoring. For example, Dr Semcheddine Cherrad, Research and Development Manager at Conidia Coniphy, is conducting innovative studies on microbiological assessment and contamination control. The research team at Conidia Coniphy has been working on the detection of plant pathogens and monitoring of fungicide resistance for over 15 years and the teamâ–™s collective efforts in bioassay and molecular analysis, combined with the adoption of new technologies and processes is overcoming challenges in the field. For example, the researchers are utilising new generation sequencing (NGS) with long-read sequencing to generate huge datasets on DNA molecules of genes coding for proteins targeted by fungicides. The team has developed a tool for mould identification called ID-Fungi Plates (IDFP). It is a user-friendly medium that accelerates the identification of fungal pathogens by Maldi-tof. They have also developed a software called FUNGI MESURE, which can quantify fungal spores in samples, providing an accurate overview of fungal measures and facilitating lab routine tasks of methods with fungi. In addition, a database established by the team called FUNGI DNA supports the identification and study of fungal strains through DNA analysis.

Determination of Some Fungal Spores in the Atmosphere of Iğdır and Comparison with Meteorological Factors

In this study, the density of fungal spores belonging to 10 specific taxa with allergenic effects and their relationship with meteorological factors in the atmosphere of Iğdır, Türkiye was investigated. Hirst trap device was used for atmospheric spore sampling during the study. As a result of the study, fungal spores were found more or less in the atmosphere in all months. A total of 156702 spores/m3 were detected in the atmosphere of Iğdır during the study. The densities of the 10 taxa detected in the atmosphere of Iğdır were recorded as Cladosporium (85.00%), Alternaria (6.16%), Aspergillus/Penicillium (5.91%), Fusarium (1.30%), Epicoccum (0.61%), Chaetomium (0.26%), Drechslera (0.24%), Stemphylium/ Ulocladium (0.21%), Pithomyces (0.19%) and Curvularia (0.11%), respectively. It was determined that the density of fungal spores was at a high level between August and October and that this period posed a risk for individuals with an allergic tendency to fungal spores.

Optimizing an integrated biovigilance toolbox to study the spatial distribution and dynamic changes of airborne mycobiota, with a focus on cereal rust fungi in western Canada.

In the face of evolving agricultural practices and climate change, tools towards an integrated biovigilance platform to combat crop diseases, spore sampling, DNA diagnostics and predictive trajectory modelling were optimized. These tools revealed microbial dynamics and were validated by monitoring cereal rust fungal pathogens affecting wheat, oats, barley and rye across four growing seasons (2015-2018) in British Columbia and during the 2018 season in southern Alberta. ITS2 metabarcoding revealed disparity in aeromycobiota diversity and compositional structure across the Canadian Rocky Mountains, suggesting a barrier effect on air flow and pathogen dispersal. A novel bioinformatics classifier and curated cereal rust fungal ITS2 database, corroborated by real-time PCR, enhanced the precision of cereal rust fungal species identification. Random Forest modelling identified crop and land-use diversification as well as atmospheric pressure and moisture as key factors in rust distribution. As a valuable addition to explain observed differences and patterns in rust fungus distribution, trajectory HYSPLIT modelling tracked rust fungal urediniospores' northeastward dispersal from the Pacific Northwest towards southern British Columbia and Alberta, indicating multiple potential origins. Our Canadian case study exemplifies the power of an advanced biovigilance toolbox towards developing an early-warning system for farmers to detect and mitigate impending disease outbreaks.

Global Spore Sampling Project: A global, standardized dataset of airborne fungal DNA

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.

Evaluating Bacterial Spore Preparation Methods for Scanning Electron Microscopy.

Scanning electron microscopy (SEM) can reveal the ultrastructure of bacterial spores, including morphology, surface features, texture, spore damage, germination, and appendages. Understanding these features can provide a basis for adherence, how physical and environmental stressors affect spore viability, integrity, and functionality, as well as the distribution and function of surface appendages. However, the spore sample preparation method can significantly impact the SEM images' appearance, resolution, and overall quality. In this study, we compare different spore preparation methods to identify optimal approaches for preparation time, spore appearance and resolved features, including the exosporium and spore pili, for SEM imaging. We use Bacillus paranthracis as model species and evaluate the efficacy of preparation protocols using different fixation and drying methods, as well as imaging under room- and cryogenic temperatures. We compare and assess method complexity to the visibility of the spore exosporium and spore appendages across different methods. Additionally, we use Haralick texture features to quantify the differences in spore surface appearance and determine the most suitable method for preserving spore structures and surface features during SEM evaluation. The findings from this study will help establish protocols for preparing bacterial spores for SEM and facilitating accurate and reliable analysis of spores' characteristics.

Predicting airborne ascospores of Sclerotinia sclerotiorum through machine learning and statistical methods

AbstractA main biological constraint of dry bean (Phaseolus vulgaris) production in Canada is white mould, caused by the fungal pathogen Sclerotinia sclerotiorum. The primary infectious propagules of S. sclerotiorum are airborne ascospores and monitoring the air for inoculum levels could help predict the severity of white mould in bean fields. Daily air samples were collected in commercial dry bean fields in Alberta, Manitoba and Ontario and ascospores were quantified using quantitative PCR. Daily weather data was obtained from in‐field weather stations. The number of ascospores on a given day was modelled using 63 different environmental variables and several modelling methods, both regression and classification approaches, were implemented with machine learning (ML) (random forests, logistic regression and support vector machines) and statistical (generalized linear models) approaches. Across all years and provinces, ascospores were most highly correlated with ascospore release from the previous day (r ranged from 0.15 to 0.6). This variable was also the only variable included in all models and had the greatest weight in all models. Models without this variable had much poorer performance than those with it. Correlations of ascospores with other environmental variables varied by province and sometimes by year. A comparison of ML and statistical models revealed that they both performed similarly, but that the statistical models were easier to interpret. However, the precise relationship between airborne ascospore levels and in‐field disease severity remains unclear, and spore sampling methods will require further development before they can be deployed as a disease management tool.

A UAV-Borne Six-Vessel Negative-Pressure Enrichment Device with Filters Designed to Collect Infectious Fungal Spores in Rice Fields

Fungal spores that cause infectious fungal diseases in rice are mainly transmitted through air. The existing fixed, portable or vehicle-mounted fungal spore collection devices used for rice infectious diseases have several disadvantages, such as low efficiency, large volume, low precision and incomplete information. In this study, a mobile fungal spore collection device is designed, consisting of six filters called “Capture-A”, which can collect spores and other airborne particles onto a filter located on a rotating disc of six filters that can be rotated to a position allowing for the capture of six individual samples. They are captured one at a time and designed and validated by capturing spores above the rice field, and the parameters of the key components of the collector are optimized through fluid simulation and verification experiments. The parameter combination of the “Capturer-A” in the best working state is as follows: sampling vessel filter screen with aperture size of 0.150 mm, bent air duct with inner diameter of 20 mm, negative pressure fan with 1500 Pa and spore sampling of cylindrical shape. In the field test, the self-developed “Capturer-A” was compared with the existing “YFBZ3” (mobile spore collection device made by Yunfei Co., Ltd., Zhengzhou, China). The two devices were experimented on at 15 sampling points in three diseased rice fields, and the samples were examined and counted under a microscope in the laboratory. It was found that the spores of rice blast disease and rice flax spot disease of rice were contained in the samples; the number of samples collected by a single sampling vessel of “Capturer-A” was about twice that of the device “YFBZ3”in the test.

Measuring the Distance and Effects of Weather Conditions on the Dispersal of Nothopassalora personata.

Nothopassalora personata is one of the most economically severe pathogens of peanut in the United States. The fungus primarily relies on wind and rain for dispersal, which has been documented up to 10 m from an inoculum source. Spore traps have been used in a wide variety of pathosystems to study epidemiology, document detection, develop alert systems, and guide management programs. The objective of this study was to use spore traps and N. personata-specific qPCR primers to quantitatively evaluate dispersal of N. personata conidia at distances up to 70 m from an infected peanut field and to examine relationships between quantities captured and weather variables. Impaction spore samplers were placed at 4, 10, 30, 50, and 70 m from peanut fields at the Edisto Research and Education Center (six fields) and commercial peanut fields in Barnwell and Bamberg counties (one field each) from 2020 to 2022. Following initial detection, samples were collected at a 48-, 48-, 72-h interval until harvest. N. personata conidia were detected at all locations and distances, documenting dispersal up to 70 m from an inoculum source. This result is a reminder that volunteer management is crucial when rotating peanut in nearby fields. A model for predicting log spore quantities was developed using temperature and humidity variables. Temperature variables associated with observed sampling periods had a negative correlation with N. personata quantities, whereas parameters of relative humidity and mean windspeed were positively correlated.

A case study on the application of spore sampling for the monitoring of macrofungi.

Fungi play a vital role in ecosystem functioning, yet significant knowledge gaps persist in understanding their diversity and distribution leading to uncertainties about their threat status and extinction risk. This is partly owed to the difficulty of monitoring fungi using traditional fruiting body surveys. The present study evaluates airborne environmental DNA (eDNA) sampling as a monitoring tool with a focus on grassland macrofungi. We applied active and passive air sampling methods, complemented by extensive field surveys of waxcap and clavarioid fungi-species groups of high relevance for conservation. Twenty-nine species were recorded during the field surveys, 19 of which were also detectable by ITS2 metabarcoding of the collected samples. An additional 12 species from the studied genera were identified exclusively in air eDNA. We found that the patterns of species detection and read abundance in air samples reflected the abundance and occurrence of fruiting bodies on the field. Dispersal kernels fitted for the three dominant species predicted rapidly decreasing spore concentrations with increasing distance from fruitbodies. Airborne assemblages were dominated by a high diversity of common species, while rare and threatened red-listed species were under-represented, which underscores the difficulty in detecting rare species, not only in conventional surveys. Considering the benefits and drawbacks of air sampling and fruitbody surveys, we conclude that air sampling serves as a cost- and time-efficient tool to characterize local macrofungal communities, providing the potential to facilitate and improve future fungal monitoring efforts.

Characterization of the Pollen Trapped by Populus L. Seeds during the Dispersion Season

Our study aimed to quantify the pollen trapped by the seeds and relate it with the airborne pollen concentrations. Individual Populus spp. tuft-like seeds were sampled while suspended twice a day in 2017 and 2018 during the seed dispersal season. The seeds were submitted to laboratory treatment for pollen extraction, which was quantified using an optical microscope. Airborne pollen was monitored using a seven-day Hirst-type volumetric spore sampler. A correlation analysis was performed between the airborne pollen, the pollen on the seeds, and the meteorological parameters. A total of 26 pollen grains/mg was counted in the airborne tuft-like seeds, with 26 different taxa being identified, compared with the 18 pollen taxa identified in the airborne samples. Quercus, Poaceae, Urticaceae, Pinus, and Platanus were the most frequent pollen found on the seeds, while in the atmosphere, pollen from Urticaceae, Quercus, and Cupressaceae were the most representative. A tendency of higher pollen concentrations found in the afternoon samples, both airborne and on the seeds, was observed. Correlations between the meteorological parameters and pollen concentration found airborne and in the seeds were overall not significant. Thus, airborne poplar tuft-like seeds can trap and transport pollen, most of which has been recognized to induce respiratory allergies.

Rare Virulences and Great Pathotype Diversity of a Central European Blumeria hordei Population.

Barley is an important crop grown on almost 49 Mha worldwide in 2021 and is particularly significant in Europe where powdery mildew is the most frequent disease on susceptible varieties. The most suitable way to protect crops is by exploiting genetic resistance. However, the causal agent Blumeria hordei is an extremely adaptable pathogen. The aims of this research were to increase our knowledge of the rapidly changing pathogen population and detect rare virulences. Random samples of the pathogen were obtained from the air by means of a mobile spore sampler. Spores were collected by driving across the Czech Republic in 2019, 2021 and 2023, and 299 isolates were analyzed on 121 host varieties. No infection occurred on 35 differentials, rare virulence was recorded on 31 varieties and a higher virulence frequency was found on 55 differentials. A core set of differentials along with four additional varieties distinguishes 295 pathotypes (Simple Index = 0.987) and the virulence complexity of isolates varied from 4 to 19 with an average of 10.39. The detection of new virulences, the increasing frequency of previously rare virulences and high pathotype diversity as well as high virulence complexity confirm that using nonspecific durable resistance is crucial for successfully breeding commercial varieties.

Seasonal Periodicity of the Airborne Spores of Fungi Causing Grapevine Trunk Diseases: An Analysis of 247 Studies Published Worldwide.

Grapevine trunk diseases (GTDs) are among the most devastating grapevine diseases globally. GTDs are caused by numerous fungi belonging to different taxa, which release spores into the vineyard and infect wood tissue, mainly through wounds caused by viticultural operations. The timing of operations to avoid infection is critical concerning the periodicity of GTD spores in vineyards, and many studies have been conducted in different grape-growing areas worldwide. However, these studies provide conflicting and fragmented information. To synthesize current knowledge, we conducted a systematic literature review, extracted quantitative data from published papers, and used these data to identify trends and knowledge gaps that need to be addressed in future studies. Our database included 26 papers covering 247 studies and 3,529 spore sampling records concerning a total of 29 fungal taxa responsible for Botryosphaeria dieback (BD), Esca complex (EC), and Eutypa dieback (ED). We found a clear seasonality in the presence and abundance of BD spores, with a peak from fall to spring, more in the northern hemisphere than in the southern hemisphere, but not for EC and ED. Spores of these fungi were present throughout the growing season in both hemispheres, possibly because of higher variability in spore types, sporulation conditions, and spore release mechanisms in EC and ED fungi than in BD. Our analysis has limitations because of knowledge gaps and data availability for some fungi (e.g., basidiomycetes, which cause EC). These limitations are discussed to facilitate further research.

A rapid glove-based inoculum sampling technique to monitor Erysiphe necator in commercial vineyards.

Information on the presence and severity of grape powdery mildew (GPM), caused by Erysiphe necator, has long been used to guide management decisions. While recent advances in the available molecular diagnostic assays and particle samplers have made monitoring easier, there is still need for more efficient field collection of E. necator. The use of vineyard worker gloves worn during canopy manipulation as a sampler (glove swab) of E. necator was compared with samples identified by visual assessment with subsequent molecular confirmation (leaf swabs) and airborne spore samples collected by rotating-arm impaction traps (impaction traps). Samples from U.S. commercial vineyards in Oregon, Washington, and California were analyzed using two TaqMan qPCR assays targeting the internal transcribed spacer regions or cytochrome b gene of E. necator. Based on qPCR assays, visual disease assessments misidentified GPM up to 59% of the time with a higher frequency of misidentification occurring earlier in the growing season. Comparison of the aggregated leaf swab results for a row (n=915) to the row's corresponding glove swab had 60% agreement. The latent class analysis (LCA) indicated that glove swabs were more sensitive than leaf swabs in detecting E. necator presence. The impaction trap results had 77% agreement to glove swabs (n=206) taken from the same blocks. The LCAs estimated that the glove swabs and impaction trap samplers varied each year in which was more sensitive for detection. This likely indicates that these methods have similar levels of uncertainty and provide equivalent information. Additionally, all samplers, once E. necator was detected, were similarly sensitive and specific for detection of the A-143 resistance allele. Together, these results suggest that glove swabs are a viable sampling method for monitoring the presence of E. necator and, subsequently, the G143A amino acid substitution associated with resistance to quinone outside inhibitor fungicides in vineyards. Glove swabs could significantly reduce sampling costs due to the lack of need for specialized equipment, and time required for swab collection and processing.

First Report of the Physiological Race (XXIV) of Hemileia vastatrix (Coffee Leaf Rust) in Hawaii.

Hawaii's coffee industry, produced commercially on six islands by over 1,470 growers on ~10,000 acres, is conservatively valued at $100M per year (USDA NASS 2023). Until late October 2020, Hawaii was the only major coffee producing region of the world that was free of Coffee Leaf Rust (CLR). Growers are currently facing their most formidable production challenge with the arrival of Hemileia vastatrix Berk. & Broome, the most economically devastating pathogen of coffee worldwide. Since its introduction (Keith et al. 2022), CLR has rapidly spread throughout the state and can be found on coffee farms and feral coffee throughout the six islands. Implementation of CLR control measures will be difficult in Hawaii, given the extreme environmental heterogeneity, differences in management practices, high production costs, and labor shortages. Compounding these challenges is that all coffee genotypes grown on a large scale in the state are susceptible to CLR. More than 55 different rust races from coffee growing countries worldwide have been identified (Silva et al. 2022). Since key control measures include developing and establishing resistant coffee cultivars, determining the rust race(s) present in Hawaii was imperative. In June 2021, nine spore samples from symptomatic cultivated and feral plants ('Typica') growing on three islands (Hawaii Island: 3, Maui: 5, Molokai: 1) were collected in gelatin capsules using a G-R Electric Manufacturing portable vacuum pump with a mini cyclone spore adapter. The samples were sent to the Coffee Rust Research Center (CIFC) in Portugal. At CIFC, the urediniospores were bulked on susceptible genotype 849/1 Matari and inoculated on a set of coffee differentials following a standard race-typing procedure (Várzea and Marques 2005). The genotype of virulence of rust samples was inferred according to Flor's gene-for-gene theory (Silva et al. 2022). The genes of virulence v2, v4, and v5 (Race XXIV) were identified in all rust samples from all islands in Hawaii, supporting the theory of a single introduction to the state, which subsequently spread (Ramírez-Camejo et al. 2022). Race XXIV was previously characterized at CIFC and is commonly found in the majority of coffee-growing countries in South and Central America, Africa and Asia (CIFC's data base). According to Figueiredo & Arruda (1974), race XXIV is considered highly aggressive with a high spore germination rate, medium germ tube length, and short incubation period required for infection. Race XXIV is pathogenic to all coffee Arabica genotypes with the resistance genes SH5 or SH2,5 like varieties Blue Mountain, Bourbon, Catuaí, Caturra, Kent's, Kona, K7, Mundo Novo, SL 28, SL 39, as well as Accession "Agaro" with resistance genes SH4,5 (CIFC's records). On the other hand, this race is not virulent to some other Arabica genotypes, such as Geisha (SH1,5), S.288 (SH3,5), and Dilla & Alghe (SH1). Race XXIV is unable to infect derivatives of interspecific tetraploid hybrids like the groups Catimor and Sarchimor (Bettencourt and Rodrigues 1988). This is the first report of race XXIV on Coffea arabica in Hawaii. This finding is essential to evaluate the potential resistance of coffee germplasm existing in Hawaii or to be introduced in this region to develop new varieties. Since the emergence of new H. vastatrix races occur preferentially at germplasm collections (Li et al. 2021), proper management is imperative where multiple genotypes/varieties are planted.

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EcologyVolume 104, Issue 6 e4102 COVER IMAGEFree Access Cover Image First published: 01 June 2023 https://doi.org/10.1002/ecy.4102AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Graphical Abstract COVER PHOTO: Oyster mushrooms (Pleurotus ostreatus) fruit from a hardwood log in New Hampshire, USA. In their study in this issue, Borgmann-Winter et al. (Article e4039; doi:10.1002/ecy.4039) compared fungal spores in rodent scat to windborne spores and found that these two dispersal pathways support complementary fungal communities. Wood saprotrophs (such as the oyster mushroom) were among those fungal functional types most common in windborne spore samples, whereas mycorrhizal fungi and soil saprotrophs were among those common in rodent scat. These findings demonstrate the importance of vertebrates in supporting fungal communities, which in turn facilitate nutrient cycling, decomposition, and plant community composition through mycorrhizal symbiosis. Photo credit: Benjamin Borgmann-Winter. Volume104, Issue6June 2023e4102 RelatedInformation

Spore dispersal patterns of the ascomycete fungus Ramularia collo-cygni and their influence on disease epidemics

Ramularia leaf spot is a major economic disease of barley caused by the dothidiomycete fungus Ramularia collo-cygni. The fungus has a complex life cycle which includes extensive late season spore release events and a seed-borne phase. Predicting disease epidemics during the growing season remains a difficult challenge. To better understand the interaction between spore movement and disease epidemics, spore samplers were set up in Germany (2 sites over 4 years), Poland (7 sites over 2 years) and the UK (2 sites over 9 years), where the disease has been observed. Spore concentrations were determined using a real-time PCR assay, and meteorological data were obtained from co-located automatic stations. Spore release events were seen to peak in June on mainland Europe and July in the UK. The pattern of spore release was broadly similar across countries with earlier peaks in mainland Europe. A relationship was observed in the UK between July spore levels and disease in following winter barley crops. Rainfall and temperature were proposed as significant drivers of spore release in these months. The major environmental parameter associated with spore release across the two UK sites was crop surface wetness, although some site-specific interactions were noted for rainfall and wind movement. Regression analysis of spore patterns and disease epidemics indicates a relationship between spore levels 75 and 105 days pre-harvest and final disease levels in UK winter barley crops. This relationship was not observed in spring barley. The implications on risk forecasts are discussed.

The effect of different feeding strategies on honey bee gut microbiota and the presence of Nosema

Colony development in honey bees depends on both the environmental conditions and their genetic structure. Nutrition is the one of the most important factors in the honey bee’s health. This study was carried out in 48 colonies and included six groups (a control and five feeding groups). In the experiment, the effect of different feeding strategies on intestinal flora and the presence of Nosema was investigated. Pantoea agglomerans, Pseudomonas luteola, Burkholderia cepacia, Brevibacillus nitrificans, Sphingomonas paucimobilis, Aeromonas hydrophila, and P. alcalidimonas were detected in the intestinal microflora of the bee samples by morphological and phenotypic identification. The results of phenotypic identification were confirmed using 16S rRNA sequence analysis for P. agglomerans and B. nitrificans strains. The presence of Nosema was simultaneously investigated in all groups. Only Nosema cerenae was detected using DNA analysis in the positive Nosema spore samples.

Seasonal and Site-Specific Patterns of Airborne Fungal Diversity Revealed Using Passive Spore Traps and High-Throughput DNA Sequencing

The aim of the present work was to study seasonal and site-specific patterns of airborne fungal diversity, focusing on plant pathogens. The sampling of fungal spores was carried out for twelve months, i.e., between September 2017 and August 2018, using passive spore traps that were placed at three different sites in western (Lenkimai), central (Dubrava), and eastern (Labanoras) Lithuania. Samples were collected every 7–10 days, resulting in 146 samples altogether. Following DNA isolation, samples were individually amplified using ITS2 rRNA as a marker and subjected to high-throughput sequencing. Clustering and taxonomic classification of 283,006 high-quality reads showed the presence of 805 non-singleton fungal taxa. The detected fungi were 53.4% Ascomycota, 46.5% Basidiomycota, and 0.1% Mucoromycota. The most common fungal taxon at Labanoras and Lenkimai was Hannaella coprosmae (23.2% and 24.3% of all high-quality fungal sequences, respectively), while at Dubrava it was Cladosporium macrocarpum (16.0%). In different sites, plant pathogenic fungi constituted between 1.6% and 14.6% of all fungal taxa and among these the most common were Protomyces inouyei (4.6%) and Sydowia polyspora (1.9%). The results demonstrated that the diversity of airborne fungi was mainly determined by the surrounding vegetation and climatic factors, while the occurrence of pathogenic fungi was affected by the availability of their hosts.

Status and Trend of the Main Allergenic Pollen Grains and Alternaria Spores in the City of Rome (2003–2019)

Today a large part of the European population is exposed to levels of air pollution exceeding the standards recommended by the World Health Organization. Moreover, air pollution and the seasonal emission of allergenic pollen are progressively affecting human health and can cause severe allergic reactions, particularly when air pollution combines with pollen allergen peaks. Unlike atmospheric pollutants of anthropogenic origin, pollen sources have a pulsating trend that leads to high values in the flowering period and values close to, or equal to, zero in the rest of the year. This aspect makes essential the definition of data coverage standards for the main allergenic taxa. For air quality assessment detailed classification criteria for monitoring stations are defined by international standards, not the same from the European Standards for the Sampling and analysis of airborne pollen grains and fungal spores. This paper describes the status and the air concentration trends of the main allergenic pollen and the Alternaria spore measured in Rome from 2003 to 2019 by the Aerobiological Monitoring Center of Tor Vergata (Rome) and calculated by the Seasonal Kendall test with the open-source OpenAir R package. The analysis was carried out on the daily concentrations of the most widespread allergenic taxa in Italy: Asteraceae, Betulaceae, Corylaceae, Cupressaceae/Taxaceae, Poaceae, Oleaceae, Urticaceae and the Alternaria spores.

Influence of common palynological extraction treatments on ultraviolet absorbing compounds (UACs) in sub-fossil pollen and spores observed in FTIR spectra

IntroductionBiological life, atmospheric circulation and the Earth’s climate may be influenced by UV-B radiation. In plants, Ultraviolet Absorbing Compounds (UACs) are an indicator of UV-B exposure, and the abundance of UACs in pollen and spores of embryophytes is measurable using Fourier Transform Infrared (FTIR) micro-Spectroscopy. However, understanding the influence of common chemical pre-treatments on sub-fossil pollen and spores with a view to UV-B reconstruction still requires investigation.MethodsHere, peat samples collected from a Late Holocene raised bog were treated with different chemicals (HCl, KOH, and acetolysis) for varying treatment times (up to 210 min). Pollen or spores of three common taxa (Alnus, Calluna and Sphagnum) were isolated and FTIR spectra obtained on individual grains. The spectra were compared to modern pollen and spore samples collected nearby.ResultsSpectra of modern and sub-fossil samples show several visible differences related to lipid and protoplast contents. The results of chemical treatments on sub-fossil pollen and spores reveal that HCl produced limited changes, while KOH and acetolysis altered several peaks, including the UAC-related aromatic peak at 1516 cm−1. We observe that all treatments modify the FTIR spectra to some degree, from weakest (HCl) to strongest (acetolysis). With respect to reduction of UAC peak area and treatment time, we observe in some cases a significant log-decay relationship, notably for KOH treatment on Calluna pollen and acetolysis on Sphagnum spores. Compared to untreated control samples, UAC peak area in Alnus, Calluna and Sphagnum reduced by 68%, 69% and 60% respectively, after only 3 min of acetolysis treatment. After 60 minutes of acetolysis treatment UAC peaks were reduced by 77%, 84% and 88%.DiscussionDue to the potential for taxon-specific effects and significant reductions in UAC peak area even within short treatment times, our recommendation for future applications in palaeoecological studies on palynomorph chemistry is to avoid chemical digestions in the pollen extraction process in favour of separation methods including micro-sieving and density separation.