Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles

C-E Pogner; C Antunes; G P Apangu; N Bruffaerts; S Celenk; A Cristofori; N González Roldán; A Grinn-Gofroń; B Lara; M Lika; D Magyar; M Martinez-Bracero; L Muggia; B Muyshondt; D O'Connor; A Pallavicini; M A Penha; R Pérez-Badia; H Ribeiro; A Rodrigues Costa; Z Tischner; M Xhetani; C Ambelas Skjøth

doi:10.1016/j.scitotenv.2024.177439

Airborne DNA: State of the art - Established methods and missing pieces in the molecular genetic detection of airborne microorganisms, viruses and plant particles

Sci Total Environ. 2024 Nov 14:177439. doi: 10.1016/j.scitotenv.2024.177439. Online ahead of print.

Authors

C-E Pogner¹, C Antunes², G P Apangu³, N Bruffaerts⁴, S Celenk⁵, A Cristofori⁶, N González Roldán⁷, A Grinn-Gofroń⁸, B Lara⁹, M Lika¹⁰, D Magyar¹¹, M Martinez-Bracero¹², L Muggia¹³, B Muyshondt⁴, D O'Connor¹⁴, A Pallavicini¹³, M A Penha², R Pérez-Badia⁹, H Ribeiro¹⁵, A Rodrigues Costa², Z Tischner¹¹, M Xhetani¹⁰, C Ambelas Skjøth¹⁶

Affiliations

¹ Unit Bioresources, Center of Health and Bioresources, AIT Austrian Institute of Technology GmbH, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria. Electronic address: [email protected].
² 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.
³ Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK.
⁴ Mycology and Aerobiology, Sciensano, Rue J. Wytsmanstraat 14, 1050 Brussels, Belgium.
⁵ Bursa Uludag University, Arts and Science Faculty, Biology Department, Görükle-Bursa, Turkey.
⁶ 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.
⁷ Pollen Laboratory, Department of Biological and Environmental Sciences, University of Gothenburg, Medicinaregatan 7B, 41390 Gothenburg, Sweden.
⁸ Institute of Biology, University of Szczecin, Wąska 13 Street, 71-415 Szczecin, Poland.
⁹ Institute of Environmental Sciences, University of Castilla-La Mancha, Avda Carlos III, s/n, 45071 Toledo, Spain.
¹⁰ Department of Biology, Faculty of Natural Sciences, University of Tirana, Tirana, Albania.
¹¹ National Center for Public Health and Pharmacy, Albert Flórián út 2-6, 1097 Budapest, Hungary.
¹² Department of Botany, Ecology and Plant Physiology, Córdoba University, 14071 Córdoba, Spain.
¹³ Department of Life Sciences, University of Trieste, via L. Giorgieri 7, 34127 Trieste, Italy.
¹⁴ School of Chemical Sciences, Dublin City University, Dublin D09 V209, Ireland.
¹⁵ 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.
¹⁶ Department of Environmental Science, iCLIMATE, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark.

PMID: 39549753
DOI: 10.1016/j.scitotenv.2024.177439

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.

Keywords: Aerobiology; Bacteria; Bioaerosols; DNA sequencing; Fungi; Molecular genetic analysis; Pollen; Virus.

Publication types

Review