CEFAS26f95f67-6ce8-46d6-8e4a-f5a7879fe28d English dataset Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk pointOfContact 2025-09-11T12:39:33 EPSG Geodetic Parameter Registry 2022-01-07 revision WGS 84 Metabarcoding of pond environmental DNA samples towards development of DNA-based metrics for the assessment of pond condition 2025-09-11 publication 2025-09-11 revision 2025-07-30 creation CEFAS22282 https://data.cefas.co.uk 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. Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk originator Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk custodian Centre for Environment, Fisheries and Aquaculture Science, Lowestoft Laboratory (CEFAS) Cefas Lowestoft Laboratory Pakefield Road Lowestoft Suffolk NR33 0HT UK data.manager@cefas.co.uk distributor Department for Environment, Food and Rural Affairs (DEFRA) defra.helpline@defra.gov.uk owner notPlanned Freshwater ecosystem Molecular biology GEMET, version 1.0 2008-06-01 publication Molecular biology parameters SeaDataNet P02 parameter discovery vocabulary 2011-03-25 revision Species distribution Habitats and biotopes GEMET - INSPIRE themes, version 1.0 2008-06-01 publication Marine Environmental Data and Information Network MEDIN metadata record availability 2012-01-11 publication data.gov.uk MEDIN metadata record availability 2012-01-11 publication otherRestrictions noLimitations otherRestrictions Publicly available data licensed under the Open Government Licence v3.0 ( `https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/`_ ) – Please note the applicable attribution statement is as follows: ‘includes Crown copyright, Cefas 2025' .. _`https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/`: https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/ English biota environment 1.73881 1.74086 52.4581 52.4595 2023-05-01 2023-09-01 Unknown https://data.cefas.co.uk/view/22282 Cefas Data Portal information The Cefas Data Portal contains metadata records and data sets available to download and connect to in support of our commitment to open science. dataset INSPIRE Data Specification on Species Distribution – Technical Guidelines 2013-12-10 publication false See the referenced specification INSPIRE Data Specification on Habitats and Biotopes – Technical Guidelines 2013-12-10 publication false See the referenced specification Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services 2010-12-08 publication true See the referenced specification 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). MEDIN 3.1.1