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Woodcock, B.A. ; Oliver, A.E.; Newbold, L.K.; Gweon, H.S.; Roy, D.B.; Pywell, R.F.

Data describing pollen identified from honey samples originating from the UKCEH National Honey Monitoring Scheme for 2019

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This dataset is available under the terms of the Open Government Licence

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https://doi.org/10.5285/e9ec63be-3f2b-4d1b-b9bf-77ca2b96c7f5
The following data set describes regional and temporal occurrence of plants foraged upon by managed honey bees (Apis mellifera). This data was derived from DNA meta-barcoding of pollen extracted from honey samples provided by bee keepers archived as part of the UK National Honey Monitoring Scheme (https://honey-monitoring.ac.uk/). All data provided is from the first full year of the scheme in 2019.

Working in partnership with UK beekeepers, the National Honey Monitoring Scheme aims to use honeybees to monitor long-term changes in the condition and health of the UK countryside. Data associated with subsequent years will be made available as samples are processed.

The Honey Monitoring Scheme is supported by national capability funding from UK Centre for Ecology & Hydrology under the ASSIST programme.
Publication date: 2022-01-18
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View numbers valid from 01 June 2023 Download numbers valid from 20 June 2024 (information prior to this was not collected)

Format

Comma-separated values (CSV)

Spatial information

Study area
Spatial representation type
Tabular (text)
Spatial reference system
UK regions

Temporal information

Temporal extent
2019-01-01    to    2019-12-31

Provenance & quality

All honey samples were submitted following an application though the National Honey Monitoring Scheme online portal which required minimum meta-data on site location and sample date which was verified. This included in some cases additional data on hive health metrics. DNA meta-barcoding to rapidly process samples to identify plant species. Quality assurance of the DNA metabarcoding was delivered through operational deployment of sophisticated protocols for barcoding and interpreting large volumes of honey samples. To do this we developed the HONEYPI pipeline implemented in python 2.7 and is open access (https://github.com/hsgweon/honeypi). The HONEYPI pipeline is divided into several parts as follows: 1) the raw amplicon sequences are quality filtered and adapters removed; 2) DADA2 pipeline is subsequently used to generate an Amplicon Sequence Variant (ASV) abundance table containing chimera-removed, high-quality error-corrected sequences. 3). For each ASV, conserved regions flanking ITS2 are removed; and (4) resulting sequences taxonomically classified using the naive Bayesian classifier against in-house ITS2 database. Since HONEYPI uses ASVs rather than clusters of sequences for classification, it allows combining of ASV tables, i.e. data from two or more separate sequencing runs can be merged without re-clustering sequences.

A full open access methodological paper describing this approach is given in Oliver et al (2021) MethodsX, 8, 101303 (https://doi.org/10.1016/j.mex.2021.101303)

Licensing and constraints

This dataset is available under the terms of the Open Government Licence

Cite this dataset as:
Woodcock, B.A. ; Oliver, A.E.; Newbold, L.K.; Gweon, H.S.; Roy, D.B.; Pywell, R.F. (2022). Data describing pollen identified from honey samples originating from the UKCEH National Honey Monitoring Scheme for 2019. NERC EDS Environmental Information Data Centre. https://doi.org/10.5285/e9ec63be-3f2b-4d1b-b9bf-77ca2b96c7f5

Supplemental information

Oliver, A. E., Newbold, L. K., Gweon, H. S., Read, D. S., Woodcock, B. A., & Pywell, R. F. (2021). Integration of DNA extraction, metabarcoding and an informatics pipeline to underpin a national citizen science honey monitoring scheme. In MethodsX (Vol. 8, p. 101303). Elsevier BV

Correspondence/contact details

Woodcock, B.A.
UK Centre for Ecology & Hydrology
 enquiries@ceh.ac.uk

Authors

Woodcock, B.A.
UK Centre for Ecology & Hydrology
Oliver, A.E.
UK Centre for Ecology & Hydrology
Newbold, L.K.
UK Centre for Ecology & Hydrology
Gweon, H.S.
University of Reading
Roy, D.B.
UK Centre for Ecology & Hydrology
Pywell, R.F.
UK Centre for Ecology & Hydrology

Other contacts

Rights holder
UK Centre for Ecology & Hydrology
Custodian
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC EDS Environmental Information Data Centre
 info@eidc.ac.uk

Additional metadata

Topic categories
biota
INSPIRE theme
Environmental Monitoring Facilities
Keywords
Agriculture , Apis mellifera , Assist , Biodiversity , DNA Metabarcoding , forage crop , Forage plants , Honey , Honeybee , National Honey Monitoring Scheme , pollen , Pollinators , United Kingdom
Funding
Natural Environment Research Council Award: NE/N018125/1
Last updated
08 February 2024 17:27