cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/4e36cdfa-0281-423f-99a8-e7c331b2e0d1
title: Plant biodiversity data and environmental and spatial data from Jebel Ichkeul, a limestone mountain in northern Tunisia (1983)

description: Records for herbaceous and woody plants at 78 nested quadrats on a limestone mountain (Jebel Ichkeul) in Le Parc National de L’Ichkeul are presented. Data for plants represent percent cover (Braun-Blanquet scale), to identify environmental gradients and investigate phytosociology of plant communities.  Environmental variables are also presented: altitude, slope, aspect, rock out cropping, index of grazing intensity (78 sites) and olive tree densities by size class (69 sites).  Soil pH was collected for 50 sites.  Plant surveys were done June to August 1983 by Dr. D.A. Kirk as part of his Master’s thesis degree in Conservation at University College London (1983). This work was funded by the Natural Environment Research Council.
description: 78 quadrats were located, stratified using previous data and vegetation maps of the area for guidance. At each site, a thrown quadrat was used to randomly locate the central stake. A nested quadrat design was used. Percent cover was recorded using the Braun Blanquet scale. Plants not identified in the field were collected and compared to specimens at the herbarium in Tunis or the British Museum herbarium. At each quadrat location grazing intensity was ranked on the principal woody plant species. At each quadrat a number of environmental variables were collected: altitude, slope, aspect, rock out cropping, index of grazing intensity (78 sites) and olive tree densities by size class (69 sites).  Soil pH was collected for 50 sites.
Data was recorded on field sheets and then transposed to  Excel spreadsheets. The data were exported to comma separated value files (csv) for deposition into the EIDC.
DOI: 10.5285/921fcc2e-7491-4058-a21b-3d1de0be1507
title: Spatial risk analysis for Phytophthora pluvialis infection of Douglas fir and western hemlock in Scotland

description: This dataset maps the risks of Phytophthora pluvialis infection for 11098 forest fragments in Scotland identified as containing the known hosts Douglas fir or western hemlock. Key risk factors and their scoring were agreed with 15 cross-sectoral stakeholders through a self-completion survey and two workshops. Fragment risk scores integrate climate suitability and proximity to other fragments/infected sites, recent planting of these hosts (forestry grant schemes), inspected premises and water courses. Infections of P. pluvialis have been reported on Douglas fir and Western hemlock in Cornwall, Devon, Cumbria, Wales and Scotland since the outbreak was first detected in 2021. Outside of the UK, pine species (Pinus radiata, P. strobus, P. patula) are also susceptible to the pathogen. The scored fragment data were intersected with the boundaries of conservancies, local authorities and active P. pluvialis demarcated areas to summarise the distribution of risks across regions in Scotland.  
description: We employed an iterative and collaborative co-production process that brought together stakeholders with diverse expertise from across Scotland’s plant health sector including forestry, conservation, horticulture, and government agencies. The distributions of Douglas fir and western hemlock fragments in Scotland were mapped using the National Forest Estate Subcompartments 2019 and the Native Woodland Survey of Scotland. This was supplemented with Scottish Forestry Phytophthora surveillance data and Statutory Plant Health Notices (SPHNs) since 2013 and detections on Douglas fir or western hemlock in a global Phytophthora database. Felled areas since 2013 were removed using the National Forest Inventory. Key risk factors and their scoring were agreed with 15 cross-sectoral stakeholders through a self-completion survey and two workshops. The consensus among workshop participants was for climate suitability to be the primary risk factor. The final report was peer reviewed by the Plant Health Centre. In addition, a knowledge integration and validation workshop (November 13, 2024) examined the adequacy of the outputs for horizon scanning and decision-making across sectors. Validation of the climate suitability models for other Phytophthora species has been attempted using independent UK and European detections.
DOI: 10.5285/61170f63-5ce0-43e3-8b0e-49c5a47bd3d0
title: Riparian vegetation structure data for three intensively studied Wessex chalkstream sites, England, UK

description: A measure of the extent and complexity of riprian vegetation upstream of chalkstream sites derived from Light Detection and Ranging (LiDAR) data for three chalkstream sites within the Wessex chalk area (River Till, River Wylye and Nine Mile River). For each site there is an estimate of the minimum, maximum, mean and standard deviation height of vegetation along the banks for a range of distances upstream from the sampling location. Information on the extent and complexity of riparian vegetation upstream of chalkstream sites were used to better understand the relationships between in-stream biological communities and catchment and riparian land use. Stream sites surveyed represented a sample of chalkstreams across a gradient of catchment land cover intensification from catchments dominated by extensive calcareous grassland and woodland (Nine Mile River) to those dominated by arable and improved grasslands (Wylye). LiDAR data were obtained from the Environment Agency in April 2014. This dataset was created as part of work package 3.2 of the Wessex Biodiversity & Ecosystem Service Sustainability (BESS) project.
description: LiDAR data were split between trees (vegetation >2m from the ground) and low (<2m) vegetation (with buildings masked out). Three areas relative to each stream sampling point were defined; a 10m-wide riparian zone buffer strip on each bank either 100m, 200m or 1km upstream. For each defined area the minimum, maximum, mean and standard deviation of vegetation heights were calculated from the LiDAR data, in addition to the total vegetation area and volume. These statistics were calculated for all vegetation, and separately for trees (>2m) and low vegetation (<2m). LiDAR metadata is available from https://data.gov.uk/dataset/lidar-composite-dsm-1m1. Visual checks were made within ArcGIS to confirm the validity of the buffer strips created upstream of each site, prior to applying them to the LiDAR data. Derived statistics were checked to confirm that the sum of 'Tree' and 'Low' values equalled the relevant 'All' value.
DOI: 10.5285/37e7a1b3-0564-4c6f-84df-a9635edb57b4
title: Suspended organic matter stocks of Welsh upland rivers in response to organic matter addition (2012-2013)

description: These data are suspended organic matter stocks of coarse and fine particulate organic matter 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). To characterise the suspended organic matter of the studied streams, water was filtered to collect monthly samples from December 2012 to January 2013 (before deciduous leaf addition) and from February to April 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 leaf addition in moorland and conifer forested rivers. Dr Isabelle Durance was responsible for organising the surveys, Marian Pye was 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 suspended organic matter were collected by filtering water. Deciduous leaves were added directly to the stream and by fixing 'Onion bags' of leaves the stream bed and bank. Samples were collected on six occasions, December (3-10/12/2012) January (3-16/01/2013), February (4-7/02/2013), March (11-14/03/2013), April (3-8/04/2013) and May (22-26/05/2013) in all the streams in both the upstream reference zones and downstream experimental zones. Upon collection,Suspended Organic Matter (SOM) samples were refrigerated at 4 degrees celsius, returned to the laboratory and frozen within 24 hours. Frozen SOM samples were then freeze-dried at -20 degrees Celsius for 48 to 72 hours and weighed to the nearest 0.0001gramme. Freeze-dried SOM samples were ground, homogenised and subsampled (3mg ±0.3mg) for analysis of elemental (C, N) and stable isotopic (delta-13C, delta-15N) composition on a mass spectrometer (University of California Davis Stable Isotope Facility). All SOM samples were corrected for inorganic content by combusting a subset (%) of samples from each site at 550 degrees Celsius for 5 hours and applying an ash-free conversion factor. Results were recorded in an Excel spreadsheet. Data was exported to a comma separated value files for ingestion into the Environmental Information Data Centre (EIDC).
DOI: 10.5285/9257a999-2844-4be1-80d1-fd29e2ccf9ef
title: Daily rainfall, stream discharge and hydraulic conductivity of soils from catchments dominated by different vegetation types, Western Ghats, India, 2014-2016

description: Data are presented for daily rainfall, stream discharge and hydraulic conductivity of soils from catchments located in the Upper Nilgiris Reserve Forest in the state of Tamil Nadu. The catchments are dominated by four land cover types, shola, grassland, pine and wattle. The data were collected between May 2014 and December 2016. Tipping bucket wired rain gauges were used to measure rainfall. Stream discharge was measured from stilling wells and capacitance probe-based water level recorders. A mini-disk infiltrometer was used to measure the hydraulic conductivity of soils. Dry season data has not been included in this dataset as its focus is on extreme rain events.

The data were collected as part of a series of eco-hydrology projects that explored the impact of land cover on rain-runoff response, carbon sequestration and nutrient and sediment discharge.

The dataset presented here was collected by a team of three to five researchers and field assistants who were engaged in the installation of the data loggers and their regular operation and maintenance. Four research agencies have partnered across multiple projects to sustain the data collection efforts that started in June 2013 and continue (June 2020). These are the Foundation for Ecological Research, Advocacy and Learning - Pondicherry, the Ashoka Trust for Research in Ecology and the Environment - Bangalore, the Lancaster Environmental Centre, Lancaster University - UK, and the National Centre for Biological Sciences - Bangalore. Funding was provided by Ministry of Earth Sciences Government of India from the Changing Water Cycle programme (Grant Ref: MoES/NERC/16/02/10 PC-II) and the Hydrologic footprint of Invasive Alien Species project (MOES/PAMC/H&C/85/2016-PC-II). Additional funding was provided by UKRI Natural Environment Research Council grant NE/I022450/1 (Western Ghats-Capacity within the NERC Changing Water Cycle programme) and WWF-India as part of the Noyyal-Bhavani program.This research took place inside protected areas in the Nilgiri Division for which permissions and support were provided continually by the Tamil Nadu Forest Department, particularly the office of the District Forest Officer, Udhagamandalam.
description: Tipping bucket wired rain gauges were used to measure rainfall. Stream discharge was measured from stilling wells and capacitance probe based water level recorders. A mini-disk infiltrometer was used to measure the hydraulic conductivity of soils. Data from loggers on the rain gauges and water level recorder were downloaded fortnightly onto field laptops. Field notes were maintained for the hydraulic conductivity data and for recording metadata during field visits. Data was processed in the field station using R scripts which included routines to plot and visualise data to assure quality. Rainfall and discharge data were aggregated to daily time steps and output as a .csv file for deposit into the EIDC.
DOI: 10.5285/f6cec7d4-edee-44b8-8f44-86d4f12ac72d
title: Parameters for rainfall-runoff modelling in subcatchments of the Citarum basin, Java, Indonesia

description: The dataset contains parameter values that maximize revised Kling Gupta Efficiency (KGE’) between modelled and observed daily mean river flows when running one of 24 different hydrological models with one of 21 different climatic input datasets in one of 33 different catchments across the Citarum basin or 5 catchments across the Ciliwung basin, both in Java island, Indonesia. This dataset was created as part of a study on the advantages and disadvantages of using existing hydrological models, primarily developed for temperate and cold climates, in a tropical volcanic region. The hydrological models were based on those created for MARRMoT v1.2 (10.5194/gmd-12-2463-2019), recoded as sequential models in the R programming language.

This work was supported by the Natural Environment Research Council (Grants NE/S00310X/1 and NE/S002790/1).

description: The parameter set in each row of each file was selected from 100,000 candidate sets – being the one set that maximized KGE’ between modelled and observed river flow.

First, 100,000 candidate parameter sets were generated by sampling the parameter values from uniform distributions with upper and lower limits suggested for each model parameter in the documentation of MARRMoT v1.2 (10.5194/gmd-12-2463-2019). Each model was input with one of 21 combinations of seven precipitation datasets of daily time resolution (AgMERRA, CHIRPS v2, CPC, MSWEP v2, PERSIANN-CDR, SA-OBS, Yanto (10.1038/sdata.2017.72)) and three evapotranspiration datasets of daily time resolution (AgMERRA, SA-OBS, Yanto) as climatic input data – for each catchment separately, catchment-average values were produced by identifying the catchment outline from a hydrologically corrected Digital Elevation Model  (HydroSHEDS v1.1 CON 15-arcsecond) and overlaying this into the gridded precipitation and evapotranspiration products. Daily mean runoff (the model outflow) was obtained for each of the 38 catchments for 2,100,000 cases (100,000 parameter sets with 7 precipitation and 3 evapotranspiration datasets). Then, modified Kling-Gupta Efficency (KGE’) between modelled and observed daily mean flow was found, ignoring the first three years of modelled flow as “spin-up”.

Finally, the parameter set resulting in the highest KGE’ was saved for each catchment with each combination of input climatic data (38 catchments × 7 precipitation datasets × 3 evapotranspiration datasets = 798 parameter sets), for each model, resulting in the 24 files of 798 rows each that comprise this dataset.
DOI: 10.5285/eb9f4320-3c8e-4bfe-bb58-9a6df63f3f37
title: Phenotypic measurements of Howea belmoreana and Howea forsteriana from a common garden experiment on Lord Howe Island

description: The dataset describes the effect of soil type, soil sterilisation and drought treatment on survival rate and growth of Howea belmoreana and Howea forsteriana, grown from seed in an experiment on Lord Howe Island for 30 months. The data describe the number of surviving plants per replicate, as well as height and number of leaves of individual plants at two timepoints. The work was carried out by Dr Owen Osborne and Prof. Vincent Savolainen, Imperial College London, and was funded by the NERC grant NE/M015742/1.
description: The dataset describes the results of a long-term common garden experiment. Seeds of Howea belmoreana and Howea forsteriana were planted in 140 boxes (50 seeds per box; 7000 seeds in total) and grown outdoors under shade canopies at the Lord Howe Island Nursery, Lord Howe Island, New South Wales, Australia. Seeds were collected wild from six locations on Lord Howe Island. They were then planted in two native soil types from the island: calcareous and volcanic soil. For half of the replicates for each soil type-species combination, the soil was sterilised with an industrial soil steamer. Boxes were then sealed and left to germinate and establish. After 14 months, survival rate was recorded for each replicate box and plant height and leaf number was recorded for all surviving seedlings. At this point all seedlings were re-potted into individual pots and their order was randomised. After another 16 months, seedling survival, leaf number and height were again recorded. Half of the seedlings for each soil type-species-sterilisation treatment combination were then subjected to drought conditions for two weeks. Final survival rates were recoded two months after this. The data package contains two datasets. The first records the survival rate of each replicate (50 seed box) at each time point. The second records height, number of leaves and survival for each surviving seedling. Full materials and methods are included in the supplementary information.
DOI: 10.5285/355c1ba5-ced8-4b42-b769-01b51797a647
title: Soil respired radiocarbon as CO2 and CH4 from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada

description: This dataset contains measures of soil respired radiocarbon as CO2 and CH4 from peatland plateaus and thawing peatland plateaus and from burnt and unburnt forests from permafrost in subarctic Canada. The radiocarbon content of soil respired CO2 and CH4 was measured during summer in 2013 and 2014 in Yukon and Northwest Territories. Monitored sites included peatland plateaus, thawing features of peatland plateaus and unburnt and burnt black spruce forests.
description: Soil respired CO2 and CH4 was collected from chambers and probes in zeolite molecular sieve cartridges (Type 13X). The cartridges were sent to the NERC Radiocarbon Facility in East Kilbride, UK for 14C analysis and were assigned a publication code. 

Values of radiocarbon enrichment are expressed in percent modern carbon. Ages are reported as conventional radiocarbon age with years BP (before present, where present is defined as AD 1950).
DOI: 10.5285/5fe25b28-f10b-467b-8812-0b1ee6fd7491
title: Quantitative and qualitative data relating to the inhibition of a phosphatase reaction by microcystin on a paper-based analytical device (PAD)

description: This dataset contains information about the development of a paper analytical device for the detection of the microcystin toxin. Water samples were collected weekly from Rostherne Mere and Tatton Park Lake, Cheshire between 20/07/2022 and 12/10/2022. Samples were analysed for the presence of microcystin-producing genes and released microcystin. A paper analytical device incorporating a protein phosphatase inhibition assay was also used to monitor microcystin levels. Preliminary user evaluation of the paper analytical devices and associated mobile photo applications is also provided. 

The work was supported by the Natural Environment Research Council (Grant NE/X011607/1).

description: Water samples were taken on a weekly basis from three sampling locations at each site. Samples were filtered through a 0.45 µm filter and DNA was extracted from the filter paper using a Qiagen PowerWater kit before being analysed using real-time PCR for detection of the mycE gene, alongside no template controls. Water samples were analysed using an ENZO Life Sciences Microcystins (Adda specific) ELISA kit, alongside microcystin reference standards and controls. 

For the development of the paper analytical device, protein phosphatase 1a was produced using protein expression and confirmed using spectrophotometry. Efficiency was evaluated by comparison to commercially available products and comparing absorbance values for the conversion of pNPP. 

The paper analytical device incorporating the protein phosphatase inhibition assay was then used to detect microcystin. Colourimetric change was recorded for samples and controls using Image J. Preliminary user evaluation of the paper analytical device was obtained using qualitative feedback.
DOI: 10.5285/799db965-3ce7-4e9b-8590-de6a8624d652
title: Dung beetle abundance data from a before-and-after El Niño experiment in the Brazilian Amazon

description: This data set includes longitudinal abundance of dung beetles at dung-baited pitfall traps, recorded in 2010, 2016 and 2017 (around six years before, six months after and 18 months after the 2015-16 El Niño event, respectively) in the Brazilian Amazon region.

Dung beetles were collected during the collaborative projects AFIRE (Assessing ENSO-induced Fire Impacts in tropical Rainforest Ecosystems) and ECOFOR (Biodiversity and Ecosystem Functioning in degraded and recovering Amazonian and Atlantic Forests), which are part of the NERC Human-Modified Tropical Forest (HTMF) programme.
description: Between April and June 2010, dung beetles were sampled across all 381 study plots (total of 3429 pitfall traps set across all study plots). Post-El Niño beetle surveys happened in July 2016 and between March and April 2017 within a subset of 36 forest plots (from those 381 previously established) in the Santarém region (333 pitfall traps for each year). These plots were distributed along a gradient of previous forest degradation, including undisturbed forests (n = 10), logged-forests (n = 10), logged-and-burned forests (n = 10) and secondary forests (n = 6). Half of these forest plots were fire-affected during the 2015-16 El Niño, while the other plots suffered only with the drought effects. Forest disturbance classes were based on analysis of canopy disturbance in time series satellite images (1988 to 2010) and previous field assessments of fire scars, and logging/charcoal debris. Dung beetles were sampled using pitfall traps baited with 50 g of dung (80% pig and 20% human) and half filled with a killing solution (5% detergent and 2% salt). Traps were distributed at the corners of a 3-m equilateral triangle, at three sampling points (0, 150 and 300 m) of a 300-m transect; and were left in the field for 48 h before inspection. Beetle surveys in 2016 and 2017 happened following exactly the same methods established in 2010.
DOI: 10.5285/ebee8bd9-3e68-4f88-a400-7bf72db02714
title: Movement of songbirds between supplementary feeders in urban neighbourhoods in Southern England, UK

description: This dataset contains the time, date and location of when songbirds fitted with a Passive Integrated Transponder (PIT tag) visited a bird feeder fitted with Radio Frequency Identification (RFID) technology. We tagged seven species (n = 348), with Blue tits and Great tits being the most abundantly caught. RFID bird feeders were set up in networks of 20 feeders each in urban gardens at three sites in Southern England.
description: Data set was created from the raw data generated from the rfid readers, merged with ringing data and accompanied by a network plan indicating the relative positions of the bird feeders.