cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/9d0a6437-f01e-4cf3-9f83-86d2f4ead869
title: Concentrations and antibiotic resistance of faecal indicator organisms and human pathogens associated with sewage waste on Scottish beaches, 2021

description: The data includes concentrations of faecal indicator organisms isolated from the plastic waste and natural substrates found on Scottish beaches, as well as the antibiotic resistance of selected strains of these organisms.
Sewage-associated plastic waste, and naturally occurring substrates (seaweed and sand), were collected in 2021 from ten beaches along the Firth of Forth estuary (Scotland, UK). The concentrations of faecal indicator organisms (FIOs), E. coli and intestinal enterococci (IE), and potential human pathogens (Vibrio spp.) on the plastic waste and natural substrates were  analysed using selective media. Minimum inhibitory concentration (MIC) analysis was used to determine antibiotic resistance in selected strains.

description: Sewage-associated plastic waste (wipes, cotton bud sticks and sanitary products) was collected from ten beaches. All samples were stored at 4 °C and processed within 48 h.
Replicate composite samples of wipes, cotton bud sticks and seaweed from each site were pre-enriched in non-selective media Luria-Bertani (LB) broth or Vibrio selective Bile Peptone broth at 37 °C in a shaking incubator for 18 h. Following pre-enrichment, serial dilutions were carried out in phosphate buffered saline (PBS) and dilutions were plated onto selective media. All plates were inverted and incubated. The presence or absence of target bacteria on all sewage-associated plastic waste samples was determined by enumerating colony forming units (CFUs).
Minimum inhibitory concentration (MIC): Representative individual colonies of E. coli, IE and Vibrio spp. isolated from seaweed, wet wipe, and cotton bud stick samples, were picked off agar plates, grown further overnight in LB broth, and subjected to MIC analysis to determine antibiotic resistance to  amoxicillin, ampicillin, streptomycin, cephalexin, and tetracycline at varying concentrations. Two-fold serial dilutions of each antibiotic were made in LB broth in 96-well plates. Bacterial cultures were adjusted to an optical density at a wavelength of 600nm (OD600nm) of 0.1, and 10 μL added to each well of a 96-well plate. Samples were incubated overnight at 37 °C.
DOI: 10.5285/fc219733-a8e8-4ec0-a34e-e0e8115f0d68
title: Yield of winter-sown oilseed rape plants in relation to insect pollination

description: Yield data on winter sown oilseed rape plants, in relation to pollination by insects and in relation to the ecosystem services provided by beneficial insects. Data includes yield assessed for entire field, whole plant and within different parts of the plant (per raceme and per pod). These data can be linked to the related natural enemy data set and the pollinator data set collected as part of the Wessex BESS project, funded by the NERC Biodiversity and Ecosystem Service Sustainability research program.
description: All people carrying out laboratory analysis were trained by and followed a set protocol in raceme and pod collection. A specific form was used for recording data in the lab and data were entered in MS Access database to prevent duplicates. The data were checked for anomalous entries.
DOI: 10.5285/00601260-285e-4ffa-b381-340b51a7ec50
title: Seasonal streambed carbon and nitrogen cycling (including greenhouse gases) in an agriculturally-impacted stream. Measured at Wood Brook UK, 2016-2017

description: The dataset contains chemistry data from streambed porewater (10 and 20 cm) and surface water, as well as nitrogen chemistry data at 2.5 cm resolution within the upper 15 cm of the streambed. The dataset includes concentrations of dissolved organic carbon (DOC), carbon dioxide, methane, ammonium, nitrate, nitrite and nitrous oxide, and isotopic ratios of δ13CCO2, δ15NNO3+NO2 and δ18ONO3+NO2. Also included are measurements of dissolved oxygen and temperature. Samples were collected from three reaches within the stream, an upstream sandy reach, a mid-stream sandy reach and a downstream gravel reach. The work was carried out with Natural Environment Research Council (NERC) funding through a PhD (NERC award number 1602135), grant (NE/L004437/1) and Life Sciences Mass Spectrometry Facility grant (CEH_L102_05_2016).
description: Water samples were collected from the streambed (10 and 20 cm from multilevel piezometers) and the surface water in July 2016, October 2016, January 2017 and March 2017. Dissolved oxygen concentration and temperature was measured in-situ using a YSI ProODO or EcoSense ODO200 meter, water samples were filtered (0.45 then 0.22 um) and frozen until analysis. Gas samples were produced in-situ from porewaters with ultrapure helium using a headspace equilibrium method. Gas samples were stored dark, at room temperature, until analysis. Diffusive equilibrium in thin-film (DET) gels were deployed 72 hours prior to sampling, and were removed at the same time as porewater sampling, sliced within 25 minutes and stored cold (4 °C) until processing. DET gel slices were processed in the laboratory by weighing them, adding 5 ml ultrapure water and shaking for 24 hours. DOC concentrations were measured on a Shimadzu TOC analyser (TOC-L CPH with ASI-L autosampler), ammonium, nitrate and nitrite concentrations were measured on a Skalar San++ continuous flow analyser, greenhouse gas concentrations were measured on Agilent 7890A Gas Chromatographs fitted with thermal conductivity detector for carbon dioxide, flame ionization detector for methane and micro electron capture detector or electron capture detector for nitrous oxide. Headspace greenhouse gas concentrations were converted to porewater concentrations using Henry’s constant. Nitrate isotopes were determined by converting nitrate+nitrite to nitrous oxide using denitrifying bacteria, which was subsequently measured on a GEO 20:20 gas chromatograph isotope ratio mass spectrometer, carbon dioxide isotopes were determined on a Isoprime Tracegas Preconcentrator coupled to an isotope ratio mass spectrometer. Results from the experiments were entered into an Excel spreadsheet and exported as a comma separated value file (.csv) for ingestion into the EIDC.
DOI: 10.5285/d895fadb-d762-441a-9f3f-1ebe1cbabfa7
title: Extreme river discharge and associated tide gauge co-occurrences from UK estuaries 1984-2013 

description: This dataset  contains the dates and magnitudes of extreme river discharge and associated skew surge peaks for UK estuaries between 1984 and 2013. The lag time between the drivers is also provided. 

Thirty years of river discharge and sea level data for 126 estuaries around the UK were analysed. The river discharge and tide gauge data were used at a 15-minute temporal resolution. A peaks over threshold analysis was completed to identify peaks in the river discharge record which exceeded the 95th percentile. The largest skew surge associated with each extreme discharge event was identified, and saved if this value also exceeded the 95th percentile. 

description: Observed total water level (TWL, mODN) data were obtained from 27 class-A tide gauges, which form part of the UK National A-Class Tide Gauge Network, from the British Oceanographic Data Centre (BODC). Skew surge (S, m) was calculated from the detrended TWL. It is the difference between the maximum observed TWL and the maximum predicted TWL based on astronomical tidal constituents for every 12.42-h tidal cycle, and the time of maximum TWL  was assigned to each S value. 

River discharge measurements were obtained from the Environmental Agency, Natural Resources Wales, and the Scottish Environment Protection Agency for 265 rivers across Britain. Discharge (Q) measurements were taken from the most downstream, non-tidal gauges on each river. River gauges were then selected based on two criteria; 1) they recorded 30 years of discharge from 01 January 1984 to 31 December 2013 (with no data gaps), and 2) they recorded a maximum discharge during this period that exceeded 50 m3 /s to identify rivers that could potentially contribute to flooding.  This set 30-year period (1984−2013) was selected to ensure consistency between gauges and to maximise the number of gauges with full data included in the analysis. These criteria isolated 126 gauges, located in 126 distinct estuaries. 

A peaks over threshold analysis was then carried out on these data to identify co-occurrences between extreme river discharge and skew surge peaks. The dates and magnitudes of these co-occurrences were recorded in Microsoft Excel spreadsheets (one for each catchment), and these were converted to .csv files.
DOI: 10.5285/03e74f94-88a5-4f09-b9ea-1447dd3e2b85
title: Simulated winter wheat and maize above-ground dry matter, soil organic matter and soil water, Changwu, China 1983-2015 and future climate scenarios to 2049

description: The model-generated dataset includes simulated daily dry matter accumulation of above-ground organs (leaves, stems and grains) of winter wheat and maize, soil water content in different soil layers and organic matter stocks in the topsoil and subsoil layers, and final crop dry matter from 1983 to 2004 (wheat) or 2015 (maize). A prediction of the variables under various future climatic scenarios is also included.

The SPACSYS model was applied to a historic experimental site on the Loess Plateau in China. Observed crop yields of winter wheat from 1993 to 2004 and maize from 1983 to 2015 were used to validate the model. The validated model was run again under different climate scenarios from 2015 to 2049 to predict daily dry matter accumulation of above-ground organs including leaves, stems and grains, daily soil water content in different layers and soil organic carbon stocks in the topsoil and subsoil layers. 
description: The dataset was generated by simulations with the process-based SPACSYS model. Parameters were calibrated with the published crop dry matter at the site
For management in simulations, ploughing before the wheat growing season occurred in September and for maize in April each year. A fertiliser application rate for winter wheat and maize is 20.7g N/m2 and 14.7g N/m2. The form of fertiliser was assumed as urea. Simulation results for the variables are complete.
DOI: 10.5285/110199cf-245e-4fa8-a9ca-386657b5fe20
title: Habitat data from grassland, moorland and woodland restoration sites in South West England in 2014

description: This dataset contains vegetation abundance data and sward height data from a number of plots across a restoration gradient within South West England. The restoration gradient covered intensive land use (referred to in the data as reference or control), restoring and pristine habitats. Data were collected between April and July in 2014. Vegetation abundance was recorded as percentage cover of species within a 1m x 1m quadrat. Five quadrats were recorded per plot. Sward height was recorded using two methods: drop disc or direct measure. Five height measurements were taken using both methods at each site.

To protect the anonymity of private landholders, details of sampling plot location is not provided with this dataset. 

The data were collected by the Centre for Ecology & Hydrology as part of the Tellus South West project.
description: Experienced botanical surveyors were used to collect the data to ensure accurate values in percentage covers and species identification. Data were checked for anomalous values (e.g. percentage cover above 100), checked with original recording sheets and corrected.
DOI: 10.5285/2ce71612-df48-40f2-9402-03d93104c623
title: Model output for soil carbon and nitrogen turnover in agricultural sites in the Red Soil region of China

description: Summary output data (including soil organic carbon concentration, nitrogen, available water and carbon dioxide) from simulations of soil in a small agricultural catchment (Sunjia) in Southeast China (Jianxi province). The simulations were performed using the ECOSSE model; a pool-based carbon and nitrogen turnover model. The simulations were performed using soil and climate input data from the research farm. Input data for the simulations were provided by the soil science department of the Chinese Academy of Sciences. Simulations were conducted in 2017. 
description: The data presented is the output of model simulations. These were performed to simulate carbon and nitrogen turnover in the soil for comparison with carbon dioxide flux measurements being made at the site (these are still being made). Simulations were carried out by Dr Joseph Oyesiku-Blakemore in the Environmental modelling group at the University of Aberdeen. The work was part of the UK China Critical Zone Observatory project (the Red Soil project within this group of projects), funded by NERC and NSFC.
DOI: 10.5285/55118e26-cf5c-41d6-9157-738fce6bdddf
title: Single nucleotide polymorphism (SNP) genotypes and phenotypes for marker-trait association analysis of three pine species grown in a glasshouse

description: This dataset contains details of the phenotypes (height, bud set and budburst) and genotypes (via SNP array) of trees from a common garden multi-species pine (Pinus sylvestris, Pinus mugo and Pinus uncinata) glasshouse trial between 2010 and 2013.
description: A common garden glasshouse trial was established in 2010 using seed from natural populations from three species of pine: Pinus sylvestris (SY), Pinus mugo (MU), Pinus uncinata (UN). Open-pollinated seeds were collected from three to five trees per population from twenty-eight natural populations in Europe covering the geographic range of each species. The collection consisted of thirteen populations of SY, nine MU, and six UN. The trial was divided into 25 randomized blocks with up to five families per population, of which the first 18 blocks were analysed by Wachowiak et al. (2018a).

Phenotypes (height, bud set and budburst) were assessed in the glasshouse during spring (budburst), autumn (bud set) and winter (height) between 2010 and 2013. 

A subset of trees were selected to be genotyped using a multi-species SNP array. Trees were genotyped using a multi-species SNP array (Perry et al., 2020). DNA was extracted from needles using a Qiagen DNeasy 96 kit following the manufacturer’s instructions. Needles were dried on silica gel prior to extraction and DNA was quantified using a Qubit spectrophotometer to ensure a minimum standardized concentration of 35ng/µl. The quality of genomic DNA was also checked visually for fragmentation on 1 % agarose gel.

Genotyping was done at Edinburgh Genomics following DNA amplification, fragmentation, chip hybridisation, single-base extension through DNA ligation and signal amplification performed according to the Affymetrix Axiom® Assay protocol. Genotyping was performed in 384-well format on a GeneTitan according to the manufacturer’s procedure. Genotype calls were performed using Axiom Analysis Suite software as recommended by the manufacturer (ThermoFisher). Samples were assigned to an analysis group based on their call rate (CR) and dish QC (DQC: a metric provided by ThermoFisher which is generated by measuring signals at multiple sites in the genome known not to vary among individuals), using the following thresholds: DQC ‘high’ ≥ 0.82; DQC ‘low’ < 0.82; CR ‘high’ ≥ 96; CR ‘low’ < 96. Analyses: 1) DQC high + CR high; 2) DQC high + CR low; 3) DQC low + CR low. High quality samples (N=529), with high CR and DQC, were used to set thresholds for allele calls. Posteriors for allele calls were subsequently used as priors for analyses 2 (N = 753) and 3 (N = 251).
DOI: 10.5285/c8c3f4ef-889b-457a-a05b-1b2214d5802c
title: Coccinellidae competition

description: This dataset contains count data for the number of each aphid life stage (nymphal stages 1-4 and adult) consumed by coccinellids in two lab-based experiments. The unit of observation (row) in the dataset is aphid life stage, therefore five rows correspond to one focal coccinellid. We experimentally assessed changes in feeding behaviour (prey preference and consumption rate) of native UK coccinellid species (Adalia bipunctata and Coccinella septempunctata), whose populations are, respectively, declining and stable, when exposed to the invasive intraguild predator, Harmonia axyridis. Experiment 1 determined the number of aphids consumed by each coccinellid larval stage in the absence of competition for each of the three coccinellid species. Experiment 2 then assessed the impact of competition on the number of aphids consumed by each coccinellid species.
description: This dataset was produced from counting the number of aphids consumed by coccinellids in lab-based arena experiments.
DOI: 10.5285/f13b0975-6af4-4315-9e4f-63a1cb4bd796
title: Algal primary production of Welsh upland rivers in response to organic matter addition (2013)

description: These data are algal production values in eight Welsh upland rivers with contrasting land-use, moorland and exotic conifer, in response to riparian deciduous leaf addition. Eight sampling reaches were chosen at two sites, Llyn Brianne (4 reaches) and Plynlimon (4 reaches). The experiment consisted of adding deciduous leaves to half of the reaches whilst the other half were maintained as a control (no addition of deciduous leaves). In order to characterise the algal production of the studied streams, algal biofilm samples were collected from tiles previously placed, during January 2013 (before deciduous leaf addition) and March 2013 (after deciduous leaf addition) in each sampling reach. The main goal of this survey was to examine how aquatic biodiversity and organic matter stocks respond to deciduous leaf addition in moorland and conifer forested rivers. Dr Isabelle Durance was responsible for organising the surveys, Dr Hugh Feeley, Dr Anne-Laure Sauvadet and Marian Pye were in charge of collecting, processing and sorting the samples. The work was carried out under Diversity in Upland Rivers for Ecosystem Service Sustainability (DURESS) project (Grant reference NERC NE/J014818/1). DURESS was a project funded by the Natural Environment Research Council (NERC) Biodiversity and Ecosystem Service Sustainability (BESS) programme.
description: Each stream was divided into an upstream control zone and a downstream experimental zone. Samples of algal biofilm were collected from tiles previously placed on each sampling site. Deciduous leaves were added directly to the stream and by fixing 'Onion bags' of leaves the stream bed and bank. Algal samples were collected two occasions, January (3-16/01/2013), and March (11-14/03/2013) in all the streams in both the upstream reference zones and downstream experimental zones. Six experimental units (algal tiles) were placed randomly in each reach of the experimental sites before and after the manipulation. Chlorophyll a accrual on tiles was used as a proxy measure of algal production and herbivory rates measured over the sampling periods (after Hladyz et al. 2011). Unglazed ceramic tiles (100 millimetres x 100 millimetres) were glued in pairs to house bricks, which were fixed to the benthos with a rebar stake placed through a hole in the brick centre. The vertical edges of one tile on each brick were coated with a layer of petroleum jelly to deter crawling gazers, and the other tile was left as a control, to assess the strength of grazing pressure. Chlorophyll was extracted using acetone, and the concentration subsequently measured spectrophotometrically (after Layer et al. 2010). Data was entered into an Excel spreadsheet and then exported as a comma separated value file for ingestion into the Environmental Information Data Centre.
DOI: 10.5285/5e944db2-305f-4f15-87b4-5110224ac90d
title: Soil extracellular enzyme activity under controlled CO2 concentrations, Sheffield

description: This dataset contains potential activities of soil extra cellular enzyme measured from soil samples from the Phosphorus Limitation And ecosystem responses to Carbon dioxide Enrichment (PLACE). The enzyme activities measured are 1,4-β-glucosidase, cellobiohydrolase, N-acetyl β-D-glucosaminidase, leucine aminopeptidase, and acid phosphatase.

Soil samples were collected in Autumn 2018 and analysed in the laboratory at Wageningen University.

The experimental design uses 35 cm x 35 cm turf mesocosms from a long term nutrient manipulation experiment. The original experiment is based at Wardlow Hay Cop in the Peak District, UK. Two adjacent P-limited grass lands on a limestone/ calcareous soil and an acidic soil have had nutrient manipulated for more than 20 years. In 2018 these mesocosms were exposed to either ambient CO2 (ca. 410 ppm) or 600 ppm.
description: All data were generated by the authors. Enzyme analyses were conducted in triplicate (technical replication) and activities of unknown samples were calculated in reference to known substrate standards. All calculations were checked for errors prior to acceptance.
DOI: 10.5285/b75b40f6-cdb1-4bfd-a599-bd2e171512e7
title: Population responses of wild bees to oilseed rape neonicotinoid seed treatments in Hungary, Germany and the UK

description: This dataset describes the effects of three neonicotinoid seed treatments (clothianidin, thiamethoxam and a control) applied to winter sown oilseed rape in Hungary, Germany and the UK on wild pollinators.  This dataset focuses on two wild pollinator model systems, specifically the solitary bee Osmia bicornis and bumblebee Bombus terrestris.  The data describes population responses in terms of reproductive cell production (O. bicornis), numbers of different developmental stages in colonies (B. terrestris) as well as the presence of neonicotinoid residues in pollen and nectar collected by both species.  This research was undertaken in 2015 using funding from the Natural Environmental Research Council on an experimental platform funded by Syngenta Ltd. and Bayer CropScience.
description: The same experimental design and field protocols were used at all sites. Details of the field protocol have been published on the CEH website (see online resources for link). Concentrations of the neonicotinoids within samples were quantified within the CEH analytical chemistry laboratories, accredited by UKAS to the British Standard ISO/IEC 17025: 2005. Details of the methodology have been published on the CEH website (see online resources for link).
DOI: 10.5285/c1813d0d-193f-4f23-82c6-333d5d099b42
title: Tropical forest seedling census data from Danum Valley, Sabah, Malaysia, 2019-2021

description: This dataset includes records of counts at four censuses between September 2019 and February 2021 of the number of seedlings of woody plants identified to species (or morphospecies) on a total of 207 plots located in either logged forest in the Ulu Segama Forest Reserve or unlogged forest in the Danum Valley Conservation Area, Malaysia.

These data were collected as part of NERC project “Seeing the fruit for the trees in Borneo: responding to an unpredictable community-level fruiting event” (NE/T006560/1).
description: Seedling count data were collected on plots of size 1 m2 established in primary unlogged forest in the Danum Valley Conservation Area and logged forest in the Ulu Segama Forest Reserve in September to October 2019 during a mast fruiting event. These plots were re-censused in November-December 2019, January-May 2020 and February-March 2021. Taxonomic identifications were conducted by comparison with a seedling reference collection and local knowledge.