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Pogner CE, Antunes C, Apangu GP, Bruffaerts N, Celenk S, Cristofori A, González Roldán N, Grinn-Gofroń A, Lara B, Lika M, Magyar D, Martinez-Bracero M, Muggia L, Muyshondt B, O'Connor D, Pallavicini A, Marchã Penha MA, Pérez-Badia R, Ribeiro H, Rodrigues Costa A, Tischner Z, Xhetani M, Ambelas Skjøth C. Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 957:177439. [PMID: 39549753 DOI: 10.1016/j.scitotenv.2024.177439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2024] [Revised: 10/27/2024] [Accepted: 11/05/2024] [Indexed: 11/18/2024]
Abstract
Bioaerosol is composed of different particles, originating from organisms, or their fragments with different origin, shape, and size. Sampling, analysing, identification and describing this airborne diversity has been carried out for over 100 years, and more recently the use of molecular genetic tools has been implemented. However, up to now there are no established protocols or standards for detecting airborne diversity of bacteria, fungi, viruses, pollen, and plant particles. In this review we evaluated commonalities of methods used in molecular genetic based studies in the last 23 years, to give an overview of applicable methods as well as knowledge gaps in diversity assessment. Various sampling techniques show different levels of effectiveness in detecting airborne particles based on their DNA. The storage and processing of samples, as well as DNA processing, influences the outcome of sampling campaigns. Moreover, the decisions on barcode selection, method of analysis, reference database as well as negative and positive controls may severely impact the results obtained. To date, the chain of decisions, methodological biases and error propagation have hindered DNA based molecular sequencing from offering a holistic picture of the airborne biodiversity. Reviewing the available studies, revealed a great diversity in used methodology and many publications didn't state all used methods in detail, making comparisons with other studies difficult or impossible. To overcome these limitations and ensure genuine comparability across studies, it is crucial to standardize protocols. Publications need to include all necessary information to enable comparison among different studies and to evaluate how methodological choices can impacts the results. Besides standardization, implementing of automatic tools and combining of different analytical techniques, such as real-time evaluation combined with sampling and molecular genetic analysis, could assist in achieving the goal of accurately assessing the actual airborne biodiversity.
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Affiliation(s)
- C-E Pogner
- Unit Bioresources, Center of Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria.
| | - C Antunes
- Department of Medical and Health Sciences, School of Health and Human Development University of Évora and Earth Sciences Institute (ICT), Pole of the University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - G P Apangu
- Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - N Bruffaerts
- Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - S Celenk
- Bursa Uludag University, Arts and Science Faculty, Biology Department, Görükle-Bursa, Turkey
| | - A Cristofori
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Via Mach 1, 38098 San Michele all'Adige, TN, Italy; NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - N González Roldán
- Pollen Laboratory, Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 7B, 41390 Gothenburg, Sweden
| | - A Grinn-Gofroń
- Institute of Biology, University of Szczecin, Wąska 13 Street, 71-415 Szczecin, Poland
| | - B Lara
- Institute of Environmental Sciences, University of Castilla-La Mancha, Avda Carlos III, s/n, 45071 Toledo, Spain
| | - M Lika
- Department of Biology, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
| | - D Magyar
- National Center for Public Health and Pharmacy, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - M Martinez-Bracero
- Department of Botany, Ecology and Plant Physiology, Córdoba University, 14071 Córdoba, Spain
| | - L Muggia
- Department of Life Sciences, University of Trieste, via L. Giorgieri 7, 34127 Trieste, Italy
| | - B Muyshondt
- Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - D O'Connor
- School of Chemical Sciences, Dublin City University, Dublin D09 V209, Ireland
| | - A Pallavicini
- Department of Life Sciences, University of Trieste, via L. Giorgieri 7, 34127 Trieste, Italy
| | - M A Marchã Penha
- Department of Medical and Health Sciences, School of Health and Human Development University of Évora and Earth Sciences Institute (ICT), Pole of the University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - R Pérez-Badia
- Institute of Environmental Sciences, University of Castilla-La Mancha, Avda Carlos III, s/n, 45071 Toledo, Spain
| | - H Ribeiro
- Department of Geosciences, Environment and Spatial Plannings, Faculty of Sciences, Earth Sciences Institute (ICT), Pole of the Faculty of Sciences, University of Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal
| | - A Rodrigues Costa
- Department of Medical and Health Sciences, School of Health and Human Development University of Évora and Earth Sciences Institute (ICT), Pole of the University of Évora, Rua Romão Ramalho, 59, 7000-671 Évora, Portugal
| | - Z Tischner
- National Center for Public Health and Pharmacy, Albert Flórián út 2-6, 1097 Budapest, Hungary
| | - M Xhetani
- Department of Biology, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
| | - C Ambelas Skjøth
- Department of Environmental Science, iCLIMATE, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark
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Apangu GP, Frisk CA, Petch GM, Hanson M, Skjøth CA. Unmanaged grasslands are a reservoir of Alternaria and other important fungal species with differing emission patterns. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2024; 370:122416. [PMID: 39255575 DOI: 10.1016/j.jenvman.2024.122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/12/2024]
Abstract
Alternaria is a ubiquitous fungal genus with many allergenic and pathogenic species inhabiting grasslands. We hypothesise that grasslands (natural/man-made) host a diversity of fungal species whose spores have varying emission patterns. Therefore, the purpose of this study was to examine the potential of grasslands for emission, diversity and composition of Alternaria and other fungal species. To test the hypothesis, Hirst-type and multi-vial Cyclone samplers collected air samples from two grassland sites (unmanaged and managed) and a non-grassland site at Lakeside campus of the University of Worcester, United Kingdom for the period May to September 2019. The unmanaged grassland was originally planted with grasses and left uncut for three years. The managed grassland was a roadside verge that was cut once every year, typically after most grasses have flowered. We used optical microscopy and Illumina MiSeq sequencing to investigate the emission, abundance, diversity and composition of the fungal spores from each site alongside meteorological variables. Kruskal-Wallis and Wilcoxon tests examined differences in the bi-hourly Alternaria concentrations between the sites. Shannon's and Simpson's Index determined the diversity of the fungal spores between the unmanaged and non-grassland sites. The results showed that grasslands are a strong source of Alternaria spores with considerably higher numbers of clinically important days compared with the non-grassland site. The managed grassland varied in Alternaria spore emission pattern from the unmanaged, probably due to differences in environmental variables and cutting frequency. The unmanaged grassland and non-grassland sites showed a high diversity of fungi including Alternaria, Cladosporium, Ascochyta, Botrytis and Aureobasidium. Overall, the study shows that grasslands are a strong source of fungal spores with allergenic and pathogenic potential and have varying emission patterns, compared with nearby urban areas where monitoring stations are located. This information is useful for atmospheric modelling of airborne fungal spore sources and has implications for allergy sufferers in particular.
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Affiliation(s)
- Godfrey Philliam Apangu
- University of Worcester, School of Science and the Environment, Henwick Grove, WR2 6AJ, Worcester, United Kingdom.
| | - Carl Alexander Frisk
- University of Worcester, School of Science and the Environment, Henwick Grove, WR2 6AJ, Worcester, United Kingdom
| | - Geoffrey M Petch
- University of Worcester, School of Science and the Environment, Henwick Grove, WR2 6AJ, Worcester, United Kingdom
| | - Mary Hanson
- University of Worcester, School of Science and the Environment, Henwick Grove, WR2 6AJ, Worcester, United Kingdom
| | - Carsten Ambelas Skjøth
- University of Worcester, School of Science and the Environment, Henwick Grove, WR2 6AJ, Worcester, United Kingdom
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Liu B, Han J, Zhang H, Li Y, An Y, Ji S, Liu Z. The regulatory pathway of transcription factor MYB36 from Trichoderma asperellum Tas653 resistant to poplar leaf blight pathogen Alternaria alternata Aal004. Microbiol Res 2024; 282:127637. [PMID: 38382286 DOI: 10.1016/j.micres.2024.127637] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 02/23/2024]
Abstract
In fungi, MYB transcription factors (TFs) mainly regulate growth, development, and resistance to stress. However, as major disease-resistance TFs, they have rarely been studied in biocontrol fungi. In this study, MYB36 of Trichoderma asperellum Tas653 (Ta) was shown to respond strongly to the stress caused by Alternaria alternata Aa1004. Compared with wild-type Ta (Ta-Wt), the inhibition rate of the MYB36 knockout strain (Ta-Kn) on Aa1004 decreased by 11.06%; the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities decreased by 82.15 U/g, 0.19 OD470/min/g, and 1631.2 μmol/min/g, respectively. The MYB36 overexpression strain (Ta-Oe) not only enhanced hyperparasitism on Aa1004, caused its hyphae to swell, deform, or even rupture, but also reduced the incidence rate of poplar leaf blight. MYB36 regulates downstream (TFs, detoxification genes, defense genes, and other antifungal-related genes by binding to the cis-acting elements "ACAT" and "ATCG". Zinc finger TFs, as the main antifungal TFs, account for 90% of the total TFs, and Zn37.5 (23.24-) and Zn83.7 (23.18-fold) showed the greatest expression difference when regulated directly by MYB36. The detoxification genes mainly comprised 11 major major facilitator superfamily (MFS) genes, among which MYB36 directly increased the expression levels of three genes by more than 2-3.44-fold. The defense genes mainly encoded cytochrome P450 (P450) and hydrolases. e.g., P45061.3 (2-10.95-), P45060.2 (2-7.07-), and Hyd44.6 (2-2.30-fold). This study revealed the molecular mechanism of MYB36 regulation of the resistance of T. asperellum to A. alternata and provides theoretical guidance for the biocontrol of poplar leaf blight and the anti-disease mechanism of biocontrol fungi.
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Affiliation(s)
- Bin Liu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Jing Han
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Huifang Zhang
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China; Modern Agricultural Industry Research Institute of Henan Zhoukou National Agricultural High-tech Industry Demonstration Zone, Zhoukou Normal University, Henan 466000, China
| | - Yuxiao Li
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China
| | - Yibo An
- National Forestry and Grassland National Reserve Forest Engineering Technology Research Center, Chongqing Forestry Investment and Development Co., Ltd., Chongqing 401120, China
| | - Shida Ji
- Horticultural College of Shenyang Agricultural University, Shenyang 110866, China
| | - Zhihua Liu
- College of Forestry, Shenyang Agricultural University, Shenyang 110866, China.
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Grewling Ł, Ribeiro H, Antunes C, Apangu GP, Çelenk S, Costa A, Eguiluz-Gracia I, Galveias A, Gonzalez Roldan N, Lika M, Magyar D, Martinez-Bracero M, Ørby P, O'Connor D, Penha AM, Pereira S, Pérez-Badia R, Rodinkova V, Xhetani M, Šauliene I, Skjøth CA. Outdoor airborne allergens: Characterization, behavior and monitoring in Europe. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:167042. [PMID: 37709071 DOI: 10.1016/j.scitotenv.2023.167042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Aeroallergens or inhalant allergens, are proteins dispersed through the air and have the potential to induce allergic conditions such as rhinitis, conjunctivitis, and asthma. Outdoor aeroallergens are found predominantly in pollen grains and fungal spores, which are allergen carriers. Aeroallergens from pollen and fungi have seasonal emission patterns that correlate with plant pollination and fungal sporulation and are strongly associated with atmospheric weather conditions. They are released when allergen carriers come in contact with the respiratory system, e.g. the nasal mucosa. In addition, due to the rupture of allergen carriers, airborne allergen molecules may be released directly into the air in the form of micronic and submicronic particles (cytoplasmic debris, cell wall fragments, droplets etc.) or adhered onto other airborne particulate matter. Therefore, aeroallergen detection strategies must consider, in addition to the allergen carriers, the allergen molecules themselves. This review article aims to present the current knowledge on inhalant allergens in the outdoor environment, their structure, localization, and factors affecting their production, transformation, release or degradation. In addition, methods for collecting and quantifying aeroallergens are listed and thoroughly discussed. Finally, the knowledge gaps, challenges and implications associated with aeroallergen analysis are described.
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Affiliation(s)
- Łukasz Grewling
- Laboratory of Aerobiology, Department of Systematic and Environmental Botany, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
| | - Helena Ribeiro
- Department of Geosciences, Environment and Spatial Plannings of the Faculty of Sciences, University of Porto and Earth Sciences Institute (ICT), Portugal
| | - Celia Antunes
- Department of Medical and Health Sciences, School of Health and Human Development & ICT-Institute of Earth Sciences, IIFA, University of Évora, 7000-671 Évora, Portugal
| | | | - Sevcan Çelenk
- Department of Biology, Faculty of Arts and Sciences, Bursa Uludag University, Bursa, Turkey
| | - Ana Costa
- Department of Medical and Health Sciences, School of Health and Human Development & ICT-Institute of Earth Sciences, IIFA, University of Évora, 7000-671 Évora, Portugal
| | - Ibon Eguiluz-Gracia
- Allergy Unit, Hospital Regional Universitario de Malaga, Malaga 29010, Spain
| | - Ana Galveias
- Department of Medical and Health Sciences, School of Health and Human Development & ICT-Institute of Earth Sciences, IIFA, University of Évora, 7000-671 Évora, Portugal
| | - Nestor Gonzalez Roldan
- Group of Biofunctional Metabolites and Structures, Priority Research Area Chronic Lung Diseases, Research Center Borstel, Leibniz Lung Center, Member of the German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany; Pollen Laboratory, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Mirela Lika
- Department of Biology, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
| | - Donát Magyar
- National Center for Public Health and Pharmacy, Budapest, Hungary
| | | | - Pia Ørby
- Department of Environmental Science, Danish Big Data Centre for Environment and Health (BERTHA) Aarhus University, Aarhus, Denmark
| | - David O'Connor
- School of Chemical Sciences, Dublin City University, Dublin D09 E432, Ireland
| | - Alexandra Marchã Penha
- Water Laboratory, School of Sciences and Technology, ICT-Institute of Earth Sciences, IIFA, University of Évora. 7000-671 Évora, Portugal
| | - Sónia Pereira
- Department of Geosciences, Environment and Spatial Plannings of the Faculty of Sciences, University of Porto and Earth Sciences Institute (ICT), Portugal
| | - Rosa Pérez-Badia
- Institute of Environmental Sciences, University of Castilla-La Mancha, 45071 Toledo, Spain
| | | | - Merita Xhetani
- Department of Biology, Faculty of Natural Sciences, University of Tirana, Tirana, Albania
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