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Tegart LJ, Schiro G, Dickinson JL, Green BJ, Barberán A, Marthick JR, Bissett A, Johnston FH, Jones PJ. Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis. ENVIRONMENTAL RESEARCH 2024; 243:117808. [PMID: 38043901 DOI: 10.1016/j.envres.2023.117808] [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: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
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.
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Affiliation(s)
- Lachlan J Tegart
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, United States.
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Brett J Green
- Office of the Director, Health Effects Laboratory Division, Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, Morgantown, WV, 26505, United States.
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, 85721, United States.
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
| | - Andrew Bissett
- Commonwealth Scientific and Industrial Research Organisation, Hobart, TAS, Australia.
| | - Fay H Johnston
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia; Public Health Services, Department of Health, Hobart, TAS, 7000, Australia.
| | - Penelope J Jones
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, 7000, Australia.
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Whitley BS, Li Z, Jones L, de Vere N. Mega-Barcoding Projects: Delivering National DNA Barcoding Initiatives for Plants. Methods Mol Biol 2024; 2744:445-473. [PMID: 38683335 DOI: 10.1007/978-1-0716-3581-0_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Plant DNA barcoding has a multitude of applications ranging from species detection and biomonitoring to investigating ecological networks and checking food quality. The ability to accurately identify species, using DNA barcoding, depends on the quality and comprehensiveness of the reference library that is used. This chapter describes how to create plant reference libraries using the rbcL, matK, and ITS2 DNA barcode regions. It covers the creation of species lists, the collection of specimens from the field and herbarium, DNA extraction, PCR amplification, and DNA sequencing. This methodology gives special attention to using samples from herbaria, as they represent important collections of easily accessible, taxonomically verified plant material.
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Affiliation(s)
- Brandon S Whitley
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Zhao Li
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Laura Jones
- National Botanic Garden of Wales, Llanarthne, UK
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
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Bell KL, Turo KJ, Lowe A, Nota K, Keller A, Encinas‐Viso F, Parducci L, Richardson RT, Leggett RM, Brosi BJ, Burgess KS, Suyama Y, de Vere N. Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding. Mol Ecol 2023; 32:6345-6362. [PMID: 36086900 PMCID: PMC10947134 DOI: 10.1111/mec.16689] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
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.
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Affiliation(s)
- Karen L. Bell
- CSIRO Health & Biosecurity and CSIRO Land & WaterFloreatWAAustralia
- School of Biological SciencesUniversity of Western AustraliaCrawleyWAAustralia
| | - Katherine J. Turo
- Department of Ecology, Evolution, and Natural ResourcesRutgers UniversityNew BrunswickNew JerseyUSA
| | | | - Kevin Nota
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
| | - Alexander Keller
- Organismic and Cellular Networks, Faculty of BiologyBiocenter, Ludwig‐Maximilians‐Universität MünchenPlaneggGermany
| | - Francisco Encinas‐Viso
- Centre for Australian National Biodiversity ResearchCSIROBlack MountainAustralian Capital TerritoryAustralia
| | - Laura Parducci
- Department of Ecology and GeneticsEvolutionary Biology Centre, Uppsala UniversityUppsalaSweden
- Department of Environmental BiologySapienza University of RomeRomeItaly
| | - Rodney T. Richardson
- Appalachian LaboratoryUniversity of Maryland Center for Environmental ScienceFrostburgMarylandUSA
| | | | - Berry J. Brosi
- Department of BiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Kevin S. Burgess
- Department of BiologyCollege of Letters and Sciences, Columbus State University, University System of GeorgiaAtlantaGeorgiaUSA
| | - Yoshihisa Suyama
- Field Science CenterGraduate School of Agricultural Science, Tohoku UniversityOsakiMiyagiJapan
| | - Natasha de Vere
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
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4
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Frisk CA, Apangu GP, Petch GM, Creer S, Hanson M, Adams-Groom B, Skjøth CA. Microscale pollen release and dispersal patterns in flowering grass populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163345. [PMID: 37028666 DOI: 10.1016/j.scitotenv.2023.163345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/17/2023] [Accepted: 04/03/2023] [Indexed: 05/27/2023]
Abstract
Characterizing pollen release and dispersion processes is fundamental for knowledge advancement in ecological, agricultural and public health disciplines. Understanding pollen dispersion from grass communities is especially relevant due to their high species-specific allergenicity and heterogeneously distributed source areas. Here, we aimed to address questions concerning fine level heterogeneity in grass pollen release and dispersion processes, with a focus on characterizing the taxonomic composition of airborne grass pollen over the grass flowering season using eDNA and molecular ecology methods. High resolution grass pollen concentrations were compared between three microscale sites (<300 m apart) in a rural area in Worcestershire, UK. The grass pollen was modelled with local meteorology in a MANOVA (Multivariate ANOVA) approach to investigate factors relevant to pollen release and dispersion. Simultaneously, airborne pollen was sequenced using Illumina MySeq for metabarcoding, analysed against a reference database with all UK grasses using the R packages DADA2 and phyloseq to calculate Shannon's Diversity Index (α-diversity). The flowering phenology of a local Festuca rubra population was observed. We found that grass pollen concentrations varied on a microscale level, likely attributed to local topography and the dispersion distance of pollen from flowering grasses in local source areas. Six genera (Agrostis, Alopecurus, Arrhenatherum, Holcus, Lolium and Poa) dominated the pollen season, comprising on average 77 % of the relative abundance of grass species reads. Temperature, solar radiation, relative humidity, turbulence and wind speeds were found to be relevant for grass pollen release and dispersion processes. An isolated flowering Festuca rubra population contributed almost 40 % of the relative pollen abundance adjacent to the nearby sampler, but only contributed 1 % to samplers situated 300 m away. This suggests that most emitted grass pollen has limited dispersion distance and our results show substantial variation in airborne grass species composition over short geographical scales.
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Affiliation(s)
- Carl A Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK.
| | - Godfrey P Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Geoffrey M Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Simon Creer
- Molecular Ecology and Evolution Group, School of Natural Sciences, Bangor University, LL57 2UW Bangor, UK
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
| | - Carsten A Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester, UK
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5
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Krinitsina AA, Omelchenko DO, Kasianov AS, Karaseva VS, Selezneva YM, Chesnokova OV, Shirobokov VA, Polevova SV, Severova EE. Aerobiological Monitoring and Metabarcoding of Grass Pollen. PLANTS (BASEL, SWITZERLAND) 2023; 12:2351. [PMID: 37375978 DOI: 10.3390/plants12122351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
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.
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Affiliation(s)
- Anastasia A Krinitsina
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Denis O Omelchenko
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, 127051 Moscow, Russia
| | - Artem S Kasianov
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, 127051 Moscow, Russia
| | - Vera S Karaseva
- Department of Biology, Institute of Natural Science, S.A. Esenin Ryazan State University, 390000 Ryazan, Russia
| | - Yulia M Selezneva
- Department of Biology, Institute of Natural Science, S.A. Esenin Ryazan State University, 390000 Ryazan, Russia
| | - Olga V Chesnokova
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vitaly A Shirobokov
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Svetlana V Polevova
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Elena E Severova
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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6
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Apangu GP, Frisk CA, Adams-Groom B, Petch GM, Hanson M, Skjøth CA. Using qPCR and microscopy to assess the impact of harvesting and weather conditions on the relationship between Alternaria alternata and Alternaria spp. spores in rural and urban atmospheres. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023:10.1007/s00484-023-02480-w. [PMID: 37191729 DOI: 10.1007/s00484-023-02480-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/16/2023] [Indexed: 05/17/2023]
Abstract
Alternaria is a plant pathogen and human allergen. Alternaria alternata is one of the most abundant fungal spores in the air. The purpose of this study was to examine whether Alternaria spp. spore concentrations can be used to predict the abundance and spatio-temporal pattern of A. alternata spores in the air. This was investigated by testing the hypothesis that A. alternata dominates airborne Alternaria spp. spores and varies spatio-temporally. Secondarily, we aimed at investigating the relationship between airborne Alternaria spp. spores and the DNA profile of A. alternata spores between two proximate (~ 7 km apart) sites. These were examined by sampling Alternaria spp. spores using Burkard 7-day and cyclone samplers for the period 2016-2018 at Worcester and Lakeside campuses of the University of Worcester, UK. Daily Alternaria spp. spores from the Burkard traps were identified using optical microscopy whilst A. alternata from the cyclone samples was detected and quantified using quantitative polymerase chain reaction (qPCR). The results showed that either A. alternata or other Alternaria species spores dominate the airborne Alternaria spore concentrations, generally depending on weather conditions. Furthermore, although Alternaria spp. spore concentrations were similar for the two proximate sites, A. alternata spore concentrations significantly varied for those sites and it is highly likely that the airborne samples contained large amounts of small fragments of A. alternata. Overall, the study shows that there is a higher abundance of airborne Alternaria allergen than reported by aerobiological networks and the majority is likely to be from spore and hyphal fragments.
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Affiliation(s)
- Godfrey Philliam Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK.
- Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Carl Alexander Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
- Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
| | - Geoffrey M Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
- Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
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7
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Frisk CA, Adams-Groom B, Smith M. Isolating the species element in grass pollen allergy: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 883:163661. [PMID: 37094678 DOI: 10.1016/j.scitotenv.2023.163661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/03/2023]
Abstract
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.
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Affiliation(s)
- Carl A Frisk
- Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway.
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Worcester, United Kingdom
| | - Matt Smith
- School of Science and the Environment, University of Worcester, Worcester, United Kingdom
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8
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Métris KL, Métris J. Aircraft surveys for air eDNA: probing biodiversity in the sky. PeerJ 2023; 11:e15171. [PMID: 37077310 PMCID: PMC10108859 DOI: 10.7717/peerj.15171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/13/2023] [Indexed: 04/21/2023] Open
Abstract
Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.
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Affiliation(s)
- Kimberly L. Métris
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
- Airborne Science LLC, Clemson, SC, United States
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Maya-Manzano JM, Oteros J, Rojo J, Traidl-Hoffmann C, Schmidt-Weber C, Buters J. Drivers of the release of the allergens Bet v 1 and Phl p 5 from birch and grass pollen. ENVIRONMENTAL RESEARCH 2022; 214:113987. [PMID: 35961547 DOI: 10.1016/j.envres.2022.113987] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/12/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
The drivers affecting the Pollen Allergen Potency (PAP, amount of allergen released per pollen) are sparsely known. Betula and Poaceae airborne pollen are the two main allergenic pollen in the World. Airborne pollen and their allergens Bet v 1 and Phl p 5 were simultaneously measured from 2010 to 2015 in Davos (Switzerland) and Munich (Germany) by using volumetric traps and ChemVol cascade impactors. Daily variations in PAP were analysed in PM>10 and PM2.5-10 air fractions and generalized additive models were created to explain which factors determine PAP, including meteorological parameters and inorganic pollutants. 87.1 ± 13.9% of Bet v 1 and 88.8 ± 15.5% of Phl p 5 was detected in the fraction PM>10 where most pollen grains were collected. Significantly higher PAP for grasses (3.5 ± 1.9 pg Phl p 5/pollen grain) were observed in Munich than in Davos (2.4 ± 1.5 pg/pollen grain, p < 0.001), but not for Betula (2.5 ± 1.6 pg Bet v 1/pollen grain in Munich and 2.3 ± 1.7 in Davos, N.S.). PAP varied between days, years and location, and increased along the pollen season for Poaceae, but remaining constant for Betula. Free allergens (allergens observed in the fraction with limited pollen, PM2.5- 10) were recorded mostly at the beginning or at the end of the pollen season, being linked to higher humidity and rainy days. Also, PAP was higher when the airborne pollen concentrations increased rapidly after one day of low/moderate levels. Our findings show that pollen exposure explains allergen exposure only to a limited extend, and that day in the season, geographic location and some weather conditions need to be considered also to explain symptoms of allergic individuals.
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Affiliation(s)
- José M Maya-Manzano
- Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center Munich, Munich, Germany
| | - Jose Oteros
- Department of Botany, Ecology and Plant Physiology, Agrifood Campus of International Excellence CeiA3, Andalusian Inter-University Institute for Earth System IISTA, University of Cordoba, Spain.
| | - Jesús Rojo
- Department of Pharmacology, Pharmacognosy and Botany, Complutense University, Madrid, Spain
| | - Claudia Traidl-Hoffmann
- Department of Environmental Medicine, Faculty of Medicine, University of Augsburg, Augsburg, Germany; Institute of Environmental Medicine, Helmholtz Center Munich - German Research Center for Environmental Health, Augsburg, Germany; Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
| | - Carsten Schmidt-Weber
- Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center Munich, Munich, Germany
| | - Jeroen Buters
- Center of Allergy & Environment (ZAUM), Member of the German Center for Lung Research (DZL), Technical University and Helmholtz Center Munich, Munich, Germany
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Banerjee P, Stewart KA, Dey G, Antognazza CM, Sharma RK, Maity JP, Saha S, Doi H, de Vere N, Chan MWY, Lin PY, Chao HC, Chen CY. Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review. AOB PLANTS 2022; 14:plac031. [PMID: 35990516 PMCID: PMC9389569 DOI: 10.1093/aobpla/plac031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.
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Affiliation(s)
- Pritam Banerjee
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Kathryn A Stewart
- Institute of Environmental Science, Leiden University, 2333 CC Leiden, The Netherlands
| | - Gobinda Dey
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Caterina M Antognazza
- Department of Theoretical and Applied Science, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Raju Kumar Sharma
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Jyoti Prakash Maity
- Department of Chemistry, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar, Odisha 751024, India
| | - Santanu Saha
- Post Graduate Department of Botany, Bidhannagar College, Salt Lake City, Kolkata 700064, India
| | - Hideyuki Doi
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Natasha de Vere
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K
| | - Michael W Y Chan
- Department of Biomedical Sciences, Graduate Institute of Molecular Biology, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Pin-Yun Lin
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
| | - Hung-Chun Chao
- Department of Earth and Environmental Sciences, National Chung Cheng University, 168 University Road, Min-Hsiung, Chiayi County 62102, Taiwan
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11
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Polling M, Sin M, de Weger LA, Speksnijder AGCL, Koenders MJF, de Boer H, Gravendeel B. DNA metabarcoding using nrITS2 provides highly qualitative and quantitative results for airborne pollen monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150468. [PMID: 34583071 PMCID: PMC8651626 DOI: 10.1016/j.scitotenv.2021.150468] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/28/2021] [Accepted: 09/16/2021] [Indexed: 05/30/2023]
Abstract
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.
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Affiliation(s)
- Marcel Polling
- Naturalis Biodiversity Center, Leiden, the Netherlands; Natural History Museum, University of Oslo, Norway.
| | - Melati Sin
- Naturalis Biodiversity Center, Leiden, the Netherlands
| | - Letty A de Weger
- Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Arjen G C L Speksnijder
- Naturalis Biodiversity Center, Leiden, the Netherlands; Leiden University of Applied Sciences, Leiden, the Netherlands
| | | | - Hugo de Boer
- Naturalis Biodiversity Center, Leiden, the Netherlands; Natural History Museum, University of Oslo, Norway
| | - Barbara Gravendeel
- Naturalis Biodiversity Center, Leiden, the Netherlands; Radboud Institute for Biological and Environmental Sciences, Nijmegen, the Netherlands
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12
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Apangu GP, Frisk CA, Petch GM, Muggia L, Pallavicini A, Hanson M, Skjøth CA. Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK. AEROBIOLOGIA 2022; 38:457-481. [PMID: 36471880 PMCID: PMC9715499 DOI: 10.1007/s10453-022-09760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/28/2022] [Indexed: 05/05/2023]
Abstract
UNLABELLED Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09760-9.
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Affiliation(s)
- Godfrey Philliam Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, AL5 2JQ Hertfordshire UK
| | - Carl Alexander Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Geoffrey M. Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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13
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Wang H, Peng H, Zhang L, Gao W, Ye J. Novel Insight into the Relationship Between Muscle-Fat and Bone in Type 2 Diabetes Ranging from Normal Weight to Obesity. Diabetes Metab Syndr Obes 2022; 15:1473-1484. [PMID: 35586203 PMCID: PMC9109979 DOI: 10.2147/dmso.s364112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/30/2022] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE Decreased bone mineral density (BMD) is a common complication in individuals with type 2 diabetes mellitus (T2DM). Body weight, mainly consisting of muscle and fat, is the main determinant of BMD and fracture risks but does not accurately describe nutritional status. Most studies suggest that skeletal muscle mass (SMM) promotes BMD, while body fat mass (BFM) decreases BMD. However, the combined effect of SMM and BFM on BMD is elusive. Thus, the study aims to explore the combined effect of fat and muscle by the ratio index SMM/BFM on BMD in T2DM. METHODS BFM and SMM were measured by the bioelectrical impedance analysis (BIA) method among 593 T2DM individuals ranging from normal weight and obesity. BMD was analyzed by DXA. Novel non-linear generalized additive models (GAMs) were used as the statistical analysis method. RESULTS The results demonstrated that BMD T score/Z score of both femur and lumbar vertebrae were significantly higher and waist-hip ratio (WHR) was significantly lower in the high SMM/BFM group of both normal weight and overweight groups in T2DM individuals. Hence, SMM/BFM might be a good factor indicating BMD in different weight ranges. Additionally, the relationship between muscle fat and BMD was not linear. Notably, this correlation was not influenced by hyperglycemia in T2DM since different analytic models adjusted with the age, gender, BMI and HbA1c were adopted in this study. Furthermore, the impact of trunk fat (central, visceral fat most) and non-trunk fat (peripheral, the sum of subcutaneous limb fat most) on BMD was inconsistent. BMD presented unlimited reduction with trunk BFM increasing, while sustaining minimal diminishment with non-trunk BFM accumulation. CONCLUSION Our study provided a novel viewpoint relationship between muscle-fat and bone, and SMM/BFM might be a potential biomarker for bone health and clinical treatments of diabetes and related metabolic syndromes.
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Affiliation(s)
- Hui Wang
- Department of Endocrinology, Yancheng City No.6 People’s Hospital, Yancheng, Jiangsu Province, People’s Republic of China
| | - Huaiming Peng
- Department of Endocrinology, Yancheng City No.6 People’s Hospital, Yancheng, Jiangsu Province, People’s Republic of China
| | - Linlin Zhang
- Department of Endocrinology, Yancheng City No.6 People’s Hospital, Yancheng, Jiangsu Province, People’s Republic of China
| | - Wei Gao
- Department of Endocrinology, Yancheng City No.6 People’s Hospital, Yancheng, Jiangsu Province, People’s Republic of China
| | - Jingya Ye
- Department of Endocrinology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Department of Endocrinology, The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, Jiangsu, People’s Republic of China
- Correspondence: Jingya Ye, Department of Endocrinology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310000, People’s Republic of China, Tel +011-86-571-87783882, Fax +011-86-571-87022776, Email
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14
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Monitoring respiratory effects of allergenic pollen. Nat Rev Genet 2021; 22:267. [PMID: 33758380 DOI: 10.1038/s41576-021-00353-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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