DNA analysis of outdoor air reveals a high degree of fungal diversity, temporal variability, and genera not seen by spore morphology

Pashley, Catherine H.; Fairs, Abbie; Free, Robert C; Wardlaw, Andrew J.

doi:10.1016/j.funbio.2011.11.004

Cited by 87 publications

(72 citation statements)

References 42 publications

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“…Comparison with the results from NGS is as yet also hampered because of poor knowledge of the teleomorph and anamorph stages with respect to fungal diversity. Nonetheless, performing visual and DNA sequencing analyses in parallel enriches the information for both approaches, as Pashley and coworkers had also demonstrated (52).…”

Section: Discussionmentioning

confidence: 99%

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

Núñez

Paz

Ferencová

et al. 2017

Appl Environ Microbiol

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Pollen, fungi, and bacteria are the main microscopic biological entities present in outdoor air, causing allergy symptoms and disease transmission and having a significant role in atmosphere dynamics. Despite their relevance, a method for monitoring simultaneously these biological particles in metropolitan environments has not yet been developed. Here, we assessed the use of the Hirst-type spore trap to characterize the global airborne biota by high-throughput DNA sequencing, selecting regions of the 16S rRNA gene and internal transcribed spacer for the taxonomic assignment. We showed that aerobiological communities are well represented by this approach. The operational taxonomic units (OTUs) of two traps working synchronically compiled Ͼ87% of the total relative abundance for bacterial diversity collected in each sampler, Ͼ89% for fungi, and Ͼ97% for pollen. We found a good correspondence between traditional characterization by microscopy and genetic identification, obtaining more-accurate taxonomic assignments and detecting a greater diversity using the latter. We also demonstrated that DNA sequencing accurately detects differences in biodiversity between samples. We concluded that high-throughput DNA sequencing applied to aerobiological samples obtained with Hirst spore traps provides reliable results and can be easily implemented for monitoring prokaryotic and eukaryotic entities present in the air of urban areas.IMPORTANCE Detection, monitoring, and characterization of the wide diversity of biological entities present in the air are difficult tasks that require time and expertise in different disciplines. We have evaluated the use of the Hirst spore trap (an instrument broadly employed in aerobiological studies) to detect and identify these organisms by DNA-based analyses. Our results showed a consistent collection of DNA and a good concordance with traditional methods for identification, suggesting that these devices can be used as a tool for continuous monitoring of the airborne biodiversity, improving taxonomic resolution and characterization together. They are also suitable for acquiring novel DNA amplicon-based information in order to gain a better understanding of the biological particles present in a scarcely known environment such as the air.

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Section: Discussionmentioning

confidence: 99%

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

Núñez

Paz

Ferencová

et al. 2017

Appl Environ Microbiol

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“…We chose the set of samples depending on four criteria: (1) species which had not been analysed concerning their IN activity before, (2) two well-studied Fusarium species in order to be able to compare our results with other published studies, (3) species which are abundant in the atmosphere, such as Agaricomycetes (Fröhlich-Nowoisky et al, 2009;Pashley et al, 2012), Cladosporium (Schüller, 2008;Ariya et al, 2009) and typical food molds (Aspergillus and Penicillium), and (4) species that have been found beyond the tropopause, like Engyodontium album, A. niger and P. chrysogenum (Imshenetsky et al, 1978;Pearce et al, 2009). Strains used in this study and their origin are presented in Table 1.…”

Section: Species Cultivation and Sampling Designmentioning

confidence: 99%

“…Among those are many typical molds, belonging to the Aspergillus, Penicillium, and Trichoderma genus. The Basidiomycota were even less investigated, although their average atmospheric abundance might be higher than that of the Ascomycota (Pashley et al, 2012). Although there are some data about rust and smut fungi (Morris et al, 2013;Haga et al, 2013), no research has been done before on the largest group by far, namely the Agaricomycetes class, to which most of the edible mushrooms belong.…”

Section: Introductionmentioning

confidence: 99%

Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments

et al. 2013

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Abstract. Fungal spores are ubiquitous biological aerosols, which are considered to act as ice nuclei. In this study the ice nucleation (IN) activity of spores harvested from 29 fungal strains belonging to 21 different species was tested in the immersion freezing mode by microscopic observation of waterin-oil emulsions. Spores of 8 of these strains were also investigated in a microdroplet freezing array instrument. The focus was laid on species of economical, ecological or sanitary significance. Besides common molds (Ascomycota), some representatives of the widespread group of mushrooms (Basidiomycota) were also investigated.Fusarium avenaceum was the only sample showing IN activity at relatively high temperatures (about 264 K), while the other investigated fungal spores showed no freezing above 248 K. Many of the samples indeed froze at homogeneous ice nucleation temperatures (about 237 K). In combination with other studies, this suggests that only a limited number of species may act as atmospheric ice nuclei. This would be analogous to what is already known for the bacterial ice nuclei.Apart from that, we selected a set of fungal strains from different sites and exposed them to occasional freezing stress during their cultivation. This was in order to test if the exposure to a cold environment encourages the expression of ice nuclei during growth as a way of adaptation. Although the total protein expression was altered by this treatment, it had no significant impact on the IN activity.

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“…Everybody inhales a complex mixture of hyphal fragments, fungal spores, and yeasts daily [14]. The species' composition varies depending on the day and season, with the highest concentrations in late summer and early autumn, when >50 000 fungal spores per cubic meter of air per day can be present [14]. Spores frequently exceed the concentration of pollen grains by 100 to 1000-fold [9].…”

Section: Introductionmentioning

confidence: 99%

Allergic Fungal Airway Disease

Rick¹,

Woolnough²,

Pashley³

et al. 2016

J Investig Allergol Clin Immunol

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Fungi are ubiquitous and form their own kingdom. Up to 80 genera of fungi have been linked to type I allergic disease, and yet, commercial reagents to test for sensitization are available for relatively few species. In terms of asthma, it is important to distinguish between species unable to grow at body temperature and those that can (thermotolerant) and thereby have the potential to colonize the respiratory tract. The former, which include the commonly studied Alternaria and Cladosporium genera, can act as aeroallergens whose clinical effects are predictably related to exposure levels. In contrast, thermotolerant species, which include fungi from the Candida, Aspergillus, and Penicillium genera, can cause a persistent allergenic stimulus independent of their airborne concentrations. Moreover, their ability to germinate in the airways provides a more diverse allergenic stimulus, and may result in noninvasive infection, which enhances inflammation. The close association between IgE sensitization to thermotolerant filamentous fungi and fixed airflow obstruction, bronchiectasis, and lung fibrosis suggests a much more tissue-damaging process than that seen with aeroallergens. This review provides an overview of fungal allergens and the patterns of clinical disease associated with exposure. It clarifies the various terminologies associated with fungal allergy in asthma and makes the case for a new term (allergic fungal airway disease) to include all people with asthma at risk of developing lung damage as a result of their fungal allergy. Lastly, it discusses the management of fungirelated asthma. Key words: Thermotolerant fungi. Allergic fungal airway disease (AFAD). ABPA. SAFS. Asthma. Allergic fungal rhinosinusitis (AFRS). Immune responses. Diagnosis. Treatment. ResumenLos hongos son obicuos y forman su propio reino. Hasta 80 géneros de hongos han sido asociados con la enfermedad alérgica tipo I; sin embargo, los reactivos comerciales para testar las sensibilizaciones a los mismos, se encuentran disponibles para un número relativamente pequeño de especies. En cuanto al asma, es importante distinguir entre especies incapaces de crecer en temperatura ambiente y aquellas que son termotolerantes y que, por lo tanto, tienen una capacidad potencial para colonizar el tracto respiratorio. Los primeros, que incluyen los géneros comúnmente estudiados Alternaria y Cladosporium, pueden actuar como aeroalérgenos y sus efectos clínicos están relacionados con los niveles de exposición. En contraste, las especies termotolerantes, que incluyen hongos del género Candida, Aspergillus y Penicillium, pueden causar un estímulo alergénico persistente independiente de su concentración en el aire. Además, su capacidad para germinar en las vías aéreas da lugar a estímulos alergénicos más diversos y puede dar como resultado infecciones no invasivas que facilitan la inflamación. La estrecha asociación entre sensibilización dependiente de IgE a hongos filamentosos termotolerantes y la obstrucción del flujo aéreo, bronquiectasias y fib...

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DNA analysis of outdoor air reveals a high degree of fungal diversity, temporal variability, and genera not seen by spore morphology

Cited by 87 publications

References 42 publications

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

Validation of the Hirst-Type Spore Trap for Simultaneous Monitoring of Prokaryotic and Eukaryotic Biodiversities in Urban Air Samples by Next-Generation Sequencing

Spores of many common airborne fungi reveal no ice nucleation activity in oil immersion freezing experiments

Allergic Fungal Airway Disease

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