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

PLOS ONE, Aug 2015

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

RESEARCH ARTICLE Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences Jennifer Hawkins1,2☯, Natasha de Vere1,3☯*, Adelaide Griffith1, Col R. Ford1, Joel Allainguillaume4, Matthew J. Hegarty3, Les Baillie2, Beverley Adams-Groom5 1 National Botanic Garden of Wales, Llanarthne, Carmarthenshire, United Kingdom, 2 School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom, 3 Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom, 4 Department of Biological, Biomedical and Analytical Sciences, University of the West of England, Bristol, United Kingdom, 5 National Pollen and Aerobiology Research Unit, University of Worcester, Worcester, United Kingdom ☯ These authors contributed equally to this work. * OPEN ACCESS Citation: Hawkins J, de Vere N, Griffith A, Ford CR, Allainguillaume J, Hegarty MJ, et al. (2015) Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences. PLoS ONE 10(8): e0134735. doi:10.1371/journal.pone.0134735 Editor: Massimo Labra, University of Milano Bicocca, ITALY Received: March 24, 2015 Accepted: July 13, 2015 Published: August 26, 2015 Copyright: © 2015 Hawkins 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. Data Availability Statement: All relevant data are within the paper and its Supporting Information files except the sequence reads which are available through the sequence read archive. SRA accession: SRP055687 (http://www.ncbi.nlm.nih.gov/Traces/sra/ ?study=SRP055687). Funding: This work was supported by the Knowledge Economy Skills Scholarship, European Social Fund, Case ID: 08300 (http://www. higherskillswales.co.uk/kess/) (JH); the Natural Resources Wales, Grant Number: 22694 (http:// naturalresourceswales.gov.uk/) (NdV); and the Abstract 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 PLOS ONE | DOI:10.1371/journal.pone.0134735 August 26, 2015 1 / 20 Floral Composition of Honey National Botanic Garden of Wales (http://www. gardenofwales.org.uk/) (NdV). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. 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. Introduction Insect pollination is a key regulating ecosystem service, vital to the functioning of terrestrial habitats. It is also crucial to crop production systems with 75% of crop species benefiting from insect pollinators [1]. The honey bee (Apis mellifera) is of major importance as a pollinator of both wild and crop plants [2]. It is also the provider of honey, a high-value nutritional product [2, 3]. Numbers of managed honey bee colonies have decreased substantially in Europe and North America, although this has been balanced by increases in countries such as China and Argentina [4]. Overall managed honey bee colonies have increased by around 45% between 1947 and 2005, but in the same time period the proportion of crops requiring insect pollination has increased threefold, meaning food production is more dependent on insect pollinators than ever before [4]. Although the number of managed honey bee colonies has increased, there has been considerable concern worldwide over increased rates of honey bee colony loss due to poor health, in particular due to the syndrome described as Colony Collapse Disorder (CCD) [5]. It is being increasingly recognised that there are a number of interacting drivers causing poor health and colony loss in honey bees. Pests and diseases, exposure to agrochemicals, apicultural mismanagement and lack of genetic diversity all play a part [2, 3]. Alongside this are reductions in habitat suitable for foraging. Honey bee nutritional needs are met by nectar, pollen and water [6]. Intensive farming practices lead to reductions in habitats with diverse floral resources and increases in mass-flowering crops that provide a single floral resource over a limited period of time [1, 2]. Pollen from different plant species varies greatly in its protein content along with the composition of lipids, carbohydrates, vitamins and minerals [7]. Nectar varies in the type and concentration of sugar and also contains a range of other trace elements [6]. Pollen diversity and quantity is known to affect disease tolerance and lo (...truncated)


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Jennifer Hawkins, Natasha de Vere, Adelaide Griffith, Col R. Ford, Joel Allainguillaume, Matthew J. Hegarty, Les Baillie, Beverley Adams-Groom. Using DNA Metabarcoding to Identify the Floral Composition of Honey: A New Tool for Investigating Honey Bee Foraging Preferences, PLOS ONE, 2015, 8, DOI: 10.1371/journal.pone.0134735