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Biota

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  • Agilent gene expression microarrays (Bham Chlamydomonas reinhardtii Agilent-029192 15k v1) were used to profile transcriptional changes afeter exposure of Chlamydomonas reinardtii algae to cerium dioxide nanoparticles. The data are generated from NERC-funding but not held by EIDC. This data is held by ArrayExpress with accession reference E-MTAB-2454.

  • The data describe: Genome sequencing of desiccating bdelloid rotifers Population genomics of bdelloid rotifers Comparative genomics of bdelloid rotifers: evaluating the effects of asexuality and desiccation tolerance on genome evolution This data is NERC-funded but not held by the EIDC. This data is archived in the Environmental Nucleotide Archive

  • Samples were collected from the slurry tank of a 200-cow dairy farm in the East Midlands once per month between June and October 2017 (n=5). Triplicate extractions were performed on each sample using two extraction kits: PowerFecal Kit (Qiagen) and Isolate II Fecal DNA kit (BioLine) (30 extractions in total). DNA was quantified using a Qubit fluorometer (Invitrogen) while quality was assessed via Nanodrop (ThermoFisher). Extracted DNA was stored at 4˚ C pending sequencing. Metagenomic shotgun sequencing of extracted slurry DNA was performed and demultiplexed by Edinburgh Genomics using the Illumina NovaSeq platform (150bp paired end library). Viral metagenomes were prepared firstly by homogenising cattle slurry in PBS. The homogenate was ultracentrifuged to pellet unwanted solids and bacteria. To further remove bacteria, the supernatant was passed sequentially through 0.45um and 0.22um filters. The filtrate was concentrated on an Amicon column and DNA was extracted using a standard phenol-chloroform extraction. Sequencing was conducted using Illumina Novaseq with a 2x150bp library. This data is NERC-funded but not held by the EIDC. This data is archived in the European Nucletotide Archive.

  • Genotype-by-sequencing and chloroplast genome sequencing were carried out for 192 accessions of wild and landrace wheat accessions. This produced 10 nuclear DNA sequences, each 10-20 kb in length, and one 80 kb chloroplast DNA sequence, from each of 192 accessions of wild or domesticated emmer wheat. NB The data are stored in the European Nucleotide Archive (ENA) with accession number Study PRJEB42105 ena-STUDY-UOM-23-08-2017-14:32:05:787-517 and can be accessed at https://www.ebi.ac.uk/ena/browser/view/PRJEB42105

  • Data comprise plot location (latitude, longitude, elevation), taxonomic family and species names and measurements of trees (diameter, height, health). Presence of lianas (vines) and their measurements were also recorded. Funder: NERC - Brazil (CONFAP) Newton Fund: “Dry forest biomes in Brazil: biodiversity and ecosystem services” (NE/N000587/1) Full details about this dataset can be found at https://doi.org/10.5285/aa3babe9-072c-42ce-9ea5-9dbb921a922d

  • The dataset contains a stratified survey of ecological and soil states at sites where fine scale patterns of covariation between vegetation and edaphic characteristics were recorded. Key data collection included leaf area index, moss and organic matter thickness, surface and deeper soil moisture. Data were collected at sites in the Yukon (2013) and Northwest Territories (2014), Canada. Full details about this dataset can be found at https://doi.org/10.5285/36f4e380-d01d-44a7-8321-7a677e6996b2

  • The data set comprises vegetation species and abundance information, surveyed using a 50 x 50 cm point quadrat, from a selection of the plots within an experimental site at Sourhope, Scotland. The surveys were carried out in the summers of 1998, 1999, 2000, 2001 and 2002. The data were collected as part of the NERC Soil Biodiversity Thematic Programme, established in 1999 and centred upon the intensive study of a large field experiment located at the Macaulay Land Use Research Institute (now the James Hutton Institute) farm at Sourhope in the Scottish Borders (Grid reference: NT8545019630). During the experiment, the site was monitored to assess changes in above-ground biomass production (productivity), species composition and relative abundance (diversity). Full details about this dataset can be found at https://doi.org/10.5285/c730867f-ffd7-4d2d-9dd0-e2f30a7dbbf6

  • This dataset comprises summary data for a literature search on invasive alien species (IAS) control efficacy and their outcomes. It contains article title, authors, journal, year of publication, taxa investigated, type of control method, and whether the paper evaluated outcomes. Overall, 373 publications were assessed. The literature search on Web of Science and the subsequent screening were conducted between May and July 2020. Full details about this dataset can be found at https://doi.org/10.5285/7b274f84-0d93-416d-a5b3-54f3387cebd5

  • The dataset contains annual soil greenhouse gas emissions following sheep urine (real and artificial) applications to a semi-improved upland grassland in North Wales, UK, across two seasons (spring and autumn) within the year 2016-2017. Soil greenhouse gas data were collected using a combination of automated chambers and manually sampled chambers, both analysed via gas chromatography. Supporting data include meteorological data, soil chemistry and above ground biomass data collected on a time-series throughout the study, following urine application. The data were used to calculate sheep urine patch nitrous oxide emission factors from an upland environment, to improve estimates of greenhouse gas emissions from extensively grazed agroecosystems. Full details about this dataset can be found at https://doi.org/10.5285/0434c74c-4a8e-45b8-a187-13e422c0ed0f

  • KRILLBASE is a data rescue and compilation project which aims to improve the availability of information on two of the Southern Ocean''s most important zooplankton taxa: Antarctic krill (Euphausia superba) and salps (Family Salpidae). In 2016, the project released a database of information from 15,194 scientific net hauls, collected between 1926 and 2016 by scientists from ten countries. These data, on the density of Antarctic krill and salps, provide a resource for analysing the distribution and abundance of these taxa throughout the Southern Ocean, to support ecological and biogeochemical research as well as fisheries management and conservation. The data are available as a downloadable csv files and via a seachable web interface. Each row of the main data table represents either a net haul or a composite of several net hauls. The columns describe searchable and filterable sampling and environmental information as well as the krill and salp density. The krill data are presented as both the observed density (NUMBER_OF_KRILL_UNDER_1M2, no.m-2) and the density standardised to a single, relatively efficient sampling method (STANDARDISED_KRILL_UNDER_1M2, no.m-2). The salp data are presented as observed density for all species combined, where an individual can be either a solitary oozoid or a member of an aggregate chain (NUMBER_OF_SALPS_UNDER_1M2, no.m-2). 12,758 of the net hauls in the database include krill data, 9,726 include salp data. 7,295 of the net hauls include both krill and salp data. For hauls where data for either salps or krill were not available the relevant field is blank. The RECORD_TYPE column distinguishes between four types of record and we emphasise that every analysis of the data should first screen on this field to avoid using the same data twice. Most records are labelled "haul", and these result from a single net sampling the water column at a specific station. Others, labelled "stratified pooled haul", are the combined result of several (typically three) stratified hauls (labelled "stratified haul") sampling different parts of the water column. A small number of records, labelled "survey mean" represent the arithmetic mean densities from multiple stations as this was the only recoverable information from the relevant surveys, which were mainly conducted in the 1980s. The dataset is fully described in the following publication which should be cited in published analyses of these data: Atkinson A, Hill SL, Pakhomov E, Siegel V, Anadon R, Chiba S, Daly KL, Downie R, Fielding S, Fretwell P, Gerrish L, Hosie GW, Jessopp MJ, Kawaguchi S, Krafft BA, Loeb V, Nishikawa J, Peat HJ, Reiss CS, Ross RM, Langdon B Quetin, Schmidt K, Steinberg DK, Subramaniam RC, Tarling GA, Ward P (2017) KRILLBASE: a circumpolar database of Antarctic krill and salp numerical densities, 1926-2016. Earth Syst. Sci. Data, 9: 193-210 (doi:10.5194/essd-9-193-2017)