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Metadata: Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition
Abstract:
Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition. This project processed and sequenced water samples (c. 1 L volume) from 61 freshwater ponds of varying habitat condition surveyed by Natural England as part of their England Ecosystem Survey. Additional, equivalent samples (48) from high quality freshwater pond habitats were provided by the Freshwater Habitats Trust. All samples were collected between May and September 2023, and sequenced in March 2024. All pond water samples were processed to extract environmental DNA (eDNA), which was sequenced using five metabarcoding markers. This produced species lists for each sampled pond for five taxonomic groups: vertebrates, invertebrates, plants and fungi, microbial eukaryotes, and prokaryotes (bacteria and archaea). Alongside water samples, physicochemical and plant observation data were collected for all ponds surveyed, as presented in separate Natural England-commissioned reports. The analysis of pond sequence data alongside these data is subject to ongoing metric development.
Data holder:
Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS)
| Other details | ||
| Internal code | Internally assigned metadata identifier | 9304 |
| Title | The title is used to provide a brief and precise description of the dataset such as 'Date', 'Originating organisation/programme', 'Location' and 'Type of survey'. All acronyms and abbreviations should be reproduced in full. | Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition |
| File Identifier | The File Identifier is a code, preferably a GUID, that is globally unique and remains with the same metadata record even if the record is edited or transferred between portals or tools. | CEFAS26f95f67-6ce8-46d6-8e4a-f5a7879fe28d |
| Resource Identifier | This is the code assigned by the data owner. | CEFAS22282 |
| Resource type | The resource type will likely be a dataset but could also be a series (collection of datasets with a common specification) or a service. | dataset |
| Start date | This describes the date the resource starts. This may only be the year if month and day are not known | 2023-05-01 |
| End date | This describes the date the resource ends. This may only be the year if month and day are not known | 2023-09-01 |
| Frequency of updates | This describes the frequency with which the resource is modified or updated i.e. a monitoring programme that samples once per year has a frequency that is described as 'annually'. | notPlanned |
| Abstract | The abstract provides a clear and brief statement of the content of the resource. | Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition. This project processed and sequenced water samples (c. 1 L volume) from 61 freshwater ponds of varying habitat condition surveyed by Natural England as part of their England Ecosystem Survey. Additional, equivalent samples (48) from high quality freshwater pond habitats were provided by the Freshwater Habitats Trust. All samples were collected between May and September 2023, and sequenced in March 2024. All pond water samples were processed to extract environmental DNA (eDNA), which was sequenced using five metabarcoding markers. This produced species lists for each sampled pond for five taxonomic groups: vertebrates, invertebrates, plants and fungi, microbial eukaryotes, and prokaryotes (bacteria and archaea). Alongside water samples, physicochemical and plant observation data were collected for all ponds surveyed, as presented in separate Natural England-commissioned reports. The analysis of pond sequence data alongside these data is subject to ongoing metric development. |
| Lineage | Lineage includes the background information, history of the sources of data, data quality statements and methods. | Sample collection and processing: 61 freshwater ponds of varying habitat condition sampled as part of the England Ecosystem Survey, and 13 field negatives. 48 additional high quality pond samples collected by the Freshwater Habitats Trust, plus five field negatives. All pond samples were collected between May and September 2023. For each pond, a volume of between 1000 and 1200 ml pond water was filtered through a 0.8 uM polyethersulfone (PES) membrane, and the membrane preserved from DNA extraction. DNA was extracted from lysate using a phase separation-based protocol, before Illumina amplicon sequencing using five separate primer sets was performed. The primer sets used targeted vertebrates (mitochondrial 12S), invertebrates (mitochondrial COI), plants and fungi (ribosomal ITS2), microbial eukaryotes (ribosomal V4) and prokaryotes (ribosomal V4). Resultant sequence data was processed separately for each metabarcoding primer set to produce tables of taxonomically-annotated actual sequence variants (ASVs). |
| Related keywords | ||
| Keyword | General subject area(s) associated with the resource, uses multiple controlled vocabularies | Freshwater ecosystem |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Molecular biology | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Molecular biology parameters | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Species distribution | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Habitats and biotopes | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | Marine Environmental Data and Information Network | |
| General subject area(s) associated with the resource, uses multiple controlled vocabularies | data.gov.uk | |
| Geographical coverage | ||
| North | The northern-most limit of the data resource in decimal degrees | 52.4595 |
| East | The eastern-most limit of the data resource in decimal degrees | 1.74086 |
| South | The southern-most limit of the data resource in decimal degrees | 52.4581 |
| West | The western-most limit of the data resource in decimal degrees | 1.73881 |
| Responsible organisations | ||
| Role | The point of contact is person or organisation with responsibility for the creation and maintenance of the metadata for the resource. | pointOfContact |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The originator is the person or organisation who created, collected or produced the resource. | originator |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The custodian is the person or organisation that accepts responsibility for the resource and ensures appropriate care and maintenance. If a dataset has been lodged with a Data Archive Centre for maintenance then this organisation is be entered here. | custodian |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The distributor is the person or organisation that distributes the resource. | distributor |
| Organisation name | Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) | |
| Delivery point | Cefas Lowestoft Laboratory, Pakefield Road | |
| Postal code | NR33 0HT | |
| City | Lowestoft | |
| Administrative area | Suffolk | |
| Country | UK | |
| data.manager@cefas.co.uk | ||
| Role | The owner is the person or organisation that owns the resource. | owner |
| Organisation name | Department for Environment, Food and Rural Affairs (DEFRA) | |
| defra.helpline@defra.gov.uk | ||
| Resource locators | ||
| Locator URL | Web address (URL) that links to the resource | https://data.cefas.co.uk/view/22282 |
| Locator name | Name of the web resource | Cefas Data Portal |
| Dataset constraints | ||
| 20.1 Limitations on Public Access - Access constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 20.2 Limitations on Public Access - Other constraints | noLimitations | |
| 21.1 Conditions for Access and Use - Use constraints | This states `otherRestrictions` from ISO vocabulary RestrictionCode and is an INSPIRE/GEMINI requirement. | otherRestrictions |
| 21.2 Conditions for Access and Use - Other constraints | https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/ | |
| Version info | ||
| Date of publication | The publication date of the resource or if previously unpublished the date that the resource was made publicly available via the MEDIN network. | 2025-09-11 |
| Date of last revision | The most recent date that the resource was revised. | 2025-09-11 |
| Date of creation | The date that the resource was created. | 2025-07-30 |
| Harvest date | The date which this record has been (re)harvested from the provider. | 2026-04-19 |
| Metadata date | The date when the content of this metadata record was last updated. | 2025-09-11 |
| Metadata standard name | The name of the metadata standard used to create this metadata | MEDIN |
| Metadata standard version | The version of the MEDIN Discovery Metadata Standard used to create the metadata record | 3.1.1 |