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      The detection of a non-anemophilous plant species using airborne eDNA

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          Abstract

          Genetic analysis of airborne plant material has historically focused (generally implicitly rather than as a stated goal) on pollen from anemophilous (wind-pollinated) species, such as in multiple studies examining the relationship of allergens to human health. Inspired by the recent influx of literature applying environmental DNA (eDNA) approaches to targeted-species and whole-ecosystem study, we conducted a proof-of-concept experiment to determine whether airborne samples reliably detect genetic material from non-anemophilous species that may not be releasing large plumes of pollen. We collected airborne eDNA using Big Spring Number Eight dust traps and quantified the amount of eDNA present for a flowering wind-pollinated genus ( Bouteloua) and insect-pollinated honey mesquite ( Prosopis glandulosa) that was not flowering at the time of the study. We were able to detect airborne eDNA from both species. Since honey mesquite is insect-pollinated and was not flowering during the time of this study, our results confirm that airborne eDNA consists of and can detect species through more than just pollen. Additionally, we were able to detect temporal patterns reflecting Bouteloua reproductive ecology and suggest that airborne honey mesquite eDNA responded to weather conditions during our study. These findings suggest a need for more study of the ecology of airborne eDNA to uncover its potential for single-species and whole-community research and management in terrestrial ecosystems.

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          Most cited references26

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          “Sight-unseen” detection of rare aquatic species using environmental DNA

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            Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences

            Identifying the floral composition of honey provides a method for investigating the plants that honey bees visit. We compared melissopalynology, where pollen grains retrieved from honey are identified morphologically, with a DNA metabarcoding approach using the rbcL DNA barcode marker and 454-pyrosequencing. We compared nine honeys supplied by beekeepers in the UK. DNA metabarcoding and melissopalynology were able to detect the most abundant floral components of honey. There was 92% correspondence for the plant taxa that had an abundance of over 20%. However, the level of similarity when all taxa were compared was lower, ranging from 22–45%, and there was little correspondence between the relative abundance of taxa found using the two techniques. DNA metabarcoding provided much greater repeatability, with a 64% taxa match compared to 28% with melissopalynology. DNA metabarcoding has the advantage over melissopalynology in that it does not require a high level of taxonomic expertise, a greater sample size can be screened and it provides greater resolution for some plant families. However, it does not provide a quantitative approach and pollen present in low levels are less likely to be detected. We investigated the plants that were frequently used by honey bees by examining the results obtained from both techniques. Plants with a broad taxonomic range were detected, covering 46 families and 25 orders, but a relatively small number of plants were consistently seen across multiple honey samples. Frequently found herbaceous species were Rubus fruticosus, Filipendula ulmaria, Taraxacum officinale, Trifolium spp., Brassica spp. and the non-native, invasive, Impatiens glandulifera. Tree pollen was frequently seen belonging to Castanea sativa, Crataegus monogyna and species of Malus, Salix and Quercus. We conclude that although honey bees are considered to be supergeneralists in their foraging choices, there are certain key species or plant groups that are particularly important in the honey bees environment. The reasons for this require further investigation in order to better understand honey bee nutritional requirements. DNA metabarcoding can be easily and widely used to investigate floral visitation in honey bees and can be adapted for use with other insects. It provides a starting point for investigating how we can better provide for the insects that we rely upon for pollination.
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              Efficient and sensitive identification and quantification of airborne pollen using next-generation DNA sequencing.

              Pollen monitoring is an important and widely used tool in allergy research and creation of awareness in pollen-allergic patients. Current pollen monitoring methods are microscope-based, labour intensive and cannot identify pollen to the genus level in some relevant allergenic plant groups. Therefore, a more efficient, cost-effective and sensitive method is needed. Here, we present a method for identification and quantification of airborne pollen using DNA sequencing. Pollen is collected from ambient air using standard techniques. DNA is extracted from the collected pollen, and a fragment of the chloroplast gene trnL is amplified using PCR. The PCR product is subsequently sequenced on a next-generation sequencing platform (Ion Torrent). Amplicon molecules are sequenced individually, allowing identification of different sequences from a mixed sample. We show that this method provides an accurate qualitative and quantitative view of the species composition of samples of airborne pollen grains. We also show that it correctly identifies the individual grass genera present in a mixed sample of grass pollen, which cannot be achieved using microscopic pollen identification. We conclude that our method is more efficient and sensitive than current pollen monitoring techniques and therefore has the potential to increase the throughput of pollen monitoring. © 2014 John Wiley & Sons Ltd.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                20 November 2019
                2019
                : 14
                : 11
                : e0225262
                Affiliations
                [001]Department of Natural Resources Management, Texas Tech University, Lubbock, TX, United States of America
                University of Hyogo, JAPAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-0460-945X
                Article
                PONE-D-19-19722
                10.1371/journal.pone.0225262
                6867632
                31747439
                28b83dcc-c0d3-4804-ae87-66a2ff80edf9
                © 2019 Johnson et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 12 July 2019
                : 31 October 2019
                Page count
                Figures: 5, Tables: 0, Pages: 13
                Funding
                This work was funded by Texas Tech University as startup funding to Matthew A. Barnes.
                Categories
                Research Article
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Pollen
                Biology and Life Sciences
                Agriculture
                Animal Products
                Honey
                Biology and Life Sciences
                Nutrition
                Diet
                Food
                Honey
                Medicine and Health Sciences
                Nutrition
                Diet
                Food
                Honey
                Research and analysis methods
                Extraction techniques
                DNA extraction
                Biology and Life Sciences
                Genetics
                Plant Genetics
                Biology and Life Sciences
                Plant Science
                Plant Genetics
                Physical Sciences
                Materials Science
                Materials
                Dust
                Ecology and Environmental Sciences
                Species Colonization
                Invasive Species
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Research and Analysis Methods
                Molecular Biology Techniques
                Artificial Gene Amplification and Extension
                Polymerase Chain Reaction
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Flowering Plants
                Custom metadata
                All relevant data are within the paper and its Supporting Information files.

                Uncategorized
                Uncategorized

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