cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/9d17d85d-eae2-4056-ad77-f1bc1c368b56
title: Nitrogen transformations in riverine sediments, Hampshire Avon, United Kingdom

description: The dataset contains denitrification, anaerobic ammonium oxidation (anammox) and nitrification activity of riverine sediments in the Hampshire Avon catchment (UK). Six rivers within sub-catchments of contrasting geology (clay, sand, chalk) were investigated. Data were obtained via direct, field-based measurements in seasonal campaigns conducted between spring 2013 and winter 2014. Also included are chemical parameters determined in porewaters prior to in situ rate measurements.
description: All data were generated by the authors. As chemical data were generated, checks were made to ensure accuracy (certified reference materials) and precision (repeat measurements) were within accepted tolerance limits. We also ensured measured values fit within those of calibration standards and, if necessary, re-analysed samples diluted to fall within the calibration range. For data generated via mass spectrometry, beam areas of all measured mass-to-charge ratios were corrected for drift offline using control standards. All data were checked to ensure reported values were above the detection limit of the method. All calculations were checked for errors before data was accepted.
DOI: 10.5285/dd2f7d23-6f11-4053-bc18-3cf2431c1963
title: Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) meteorological data from Abbotts Hall, Essex

description: The meteorological data describes the air and soil temperatures, net radiation balance, down-welling photosynthetically active radiation, wind speed, wind direction and the vapour pressure deficit.

Data collection was carried out at Abbotts Hall marsh from the 15th of December 2012 till the 27th of January 2015. The Abbotts Hall site is in Essex, South East England, and the meteorological tower was situated in the middle of the marsh. 

This data was collected as part of Coastal Biodiversity and Ecosystem Service Sustainability (CBESS): NE/J015644/1. The project was funded with support from the Biodiversity and Ecosystem Service Sustainability (BESS) programme. BESS is a six-year programme (2011-2017) funded by the UK Natural Environment Research Council (NERC) and the Biotechnology and Biological Sciences Research Council (BBSRC) as part of the UK's Living with Environmental Change (LWEC) programme.

description: Measurements are recorded on Campbell Scientific (CS) dataloggers. The wind direction and wind speed are measured at 10 Hz by a CS CSAT3A anemometer install at 4.3 m on a lattice tower by a CS CR3000 datalogger. The remaining variables are record at 1/60 Hz (i.e. every minute) by a CS CR1000 with multiplexer. Air temperature and humidity is measured with Vaisala HMP155A and then converted to Vapour Pressure deficit (VPD). Precipitation is record by an Environmental Measurements Limited (EML) ARG100 tipping bucket rain gauge. Net radiation is measured with a Kipp and Zonen NR Lite. 

Photosynthetically active radiation (PAR) is measured with a Skye Instruments SKP215. Soil temperatures are measured with CS 107 thermistors.
Mean half hourly values were calculated in Matlab. The time refers to the middle of the half hourly period. E.g. 00:15 refers to the half hour from (and including) 00:00 up to (but not including) 00:30.
DOI: 10.5285/1766eb32-1878-47e6-8dc8-d434957d1e32
title: Ammonia measurements from passive samplers at four UK Eutrophying and Acidifying Pollutants (UKEAP) network sites, 2020

description: Data comprise monthly ammonia air concentrations from UK CEH ALPHA® (Adapted Low-cost Passive High Absorption) samplers co-located with UKEAP DELTA sites. The UK Eutrophying and Acidifying atmospheric Pollutants (UKEAP) network measures air pollutants at rural sites across the UK. The UK CEH ALPHA® sampler is a passive sampler for measuring NH3 in air. Originally the purpose of these measurements was for a calibrated ALPHA® uptake rate for the UK CEH Edinburgh research laboratory.

Local site operator duties are completed by UK CEH staff and AFBI staff (at Hillsborough) and analysis is completed by UK Centre for Ecology and Hydrology Edinburgh.

The sites were set up on 1st March 2020 and measurements are ongoing.
description: Samplers were prepared/ analysed by UK CEH Edinburgh and the samplers exposed by local site operators. Data processing was performed using the UK CEH AAGA data handling tool.
DOI: 10.5285/4062e6d9-2e90-4775-87f1-179dea283ef1
title: Groundwater microbiology and chemistry of shallow wells, boreholes and springs in Kisumu, Kenya in 2014

description: This dataset contains free residual chlorine, turbidity, nitrate, chloride, sulphate, fluoride, phosphate and thermatolerant coliform concentrations in groundwater from a variety of sources within two neighbourhoods of Kisumu, Kenya. A total of 73 groundwater sources were tested between February and March 2014. The data were collected as part of the Groundwater2030 project, which aims to reduce the health problems that result from consumption of contaminated groundwater in urban areas of Africa. The project was co-ordinated by the University of Southampton, with partners at the University of Surrey, the Victoria Institute of Research on Environment and Development (VIRED) International, and the Jaramogi Oginga Odinga University of Science and Technology. The project was funded by the Natural Environment Research Council and the Department for International Development as part of the Unlocking the Potential of Groundwater for the Poor (UPGro) programme.
description: Samples were collected using a standardised protocol and analysed within seven hours of collection. Laboratory analyses were conducted by the same individual using calibrated instrumentation. Blanks were run for each analytical method and, where the number of samples allowed, duplicate analyses were carried out on the first and last sample of each batch to measure analytical repeatability.
DOI: 10.5285/9d7810c7-92af-47b2-81ec-365aafc39691
title: Morphological and morphometric data on the axial skeleton of the little skate, Leucoraja erinacea

description: CT scans of adult little skates (Leucoraja erinacea). These scans consist of series of tiff images that can be imported into CT segmenting software to reconstruct their shape in three dimensions. Supplemental files include CT scanning parameters, landmark coordinates for each vertebra in each skate, up to vertebra 70, as well as an R script with code for analysing vertebral shape using morphometrics and segmented linear regression tests.

Computed tomography scans of three adult little skates were obtained in order to quantitatively study vertebral column morphology and regionalization. The skate fins were removed to facilitate shipping to our scanning facility, and so the scans include only the head, gill basket, and axial column. The specimens are now housed in the University of Cambridge Museum of Zoology (specimen identification numbers 2021.50.1, 20201.50.2, and 2021.50.3). 
description: The skates were collected by the Marine Biological Laboratory in Woods Hole, MA, USA, in the waters off the Massachusetts coast in the summer of 2019. The specimens were fixed in 4% paraformaldehyde for one week, rinsed in water, and stored in 70% ethanol. Computed tomography scans were obtained at the Cambridge Biotomography Centre by Keturah Smithson, a trained CT technician, using a Nikon  XTEK H 225 ST MicroCT scanner. Post-processing to optimise CT reconstructions and minimise scan artefacts was performed in Nikon’s CT-Pro program, and scan reslicing was performed using VG STUDIOMAX (Volume Graphics).
DOI: 10.5285/bf0d7332-4cfe-4277-bd99-3caf35332a7b
title: Eddy covariance measurements of carbon dioxide, energy and water fluxes at a short rotation coppice plantation, Lincolnshire, UK, 2014-2017

description: This dataset contains time series observations of surface-atmosphere exchanges of net ecosystem carbon dioxide exchange (NEE), sensible heat (H) and latent heat (LE), and momentum (τ) measured at a short rotation coppice willow plantation in Lincolnshire, UK. Turbulent flux densities were monitored using the micrometeorological eddy covariance (EC) technique between 9 January 2014 and 26 November 2017. The dataset includes ancillary weather and soil physics observations, as well as variables describing atmospheric turbulence and the quality of the turbulent flux observations. 

This work was supported by the Natural Environment Research Council award number NE/R016429/1 as part of the UK-SCAPE programme delivering National Capability.
description: Eddy covariance (EC) and micrometeorological observations were made above the willow canopy using an open-path eddy covariance system.  Ancillary meteorological and soil physics observations were made from a scaffold tower at the northern end of the plantation.  

Turbulent flux densities were calculated from the raw EC data using the EddyPRO® Flux Calculation Software Version 6.1. 

Quality Control of EC data involved removal of statistical outliers and tests that theoretical requirements for the successful application of the EC technique were not violated significantly.  Data gaps in EC data (NEE, LE, H) were filled using the Marginal Distribution Sampling approach.  Gaps in key meteorological variables (SWin, LWin, Ta, RH) were filled using linear relationships derived from weather stations located in adjacent fields. 

Further details are available in the supporting documentation.
DOI: 10.5285/d61b6033-be45-4682-b4dc-a2f95feefa7d
title: Global positioning system (GPS) locations and elevations of soil sampling sites across UK saltmarshes 2018 to 2021

description: The dataset details global positioning system (GPS) locations and elevations recorded for 1323 sampling sites across UK saltmarshes. Between 2018 and 2021, soil was sampled at 1323 locations as part of the Carbon Storage in Intertidal Environments (C-SIDE) project to facilitate the calculation of saltmarsh soil organic carbon stocks and burial rates. Sites were chosen to represent contrasting habitat types in the UK, in particular sediment types, vegetation and sea level history. 

The work was carried out under the NERC programme - Carbon Storage in Intertidal Environment (C-SIDE), NERC grant reference NE/R010846/1.

description: GPS locations were recorded using a Juniper Systems, Leica and Trimble Differential Global Positioning System (DGPS), systems. Data were recorded in WGS84 (decimal degrees) and Northings, Eastings and elevation relative to Ordnance Datum Newlyn. No subsequent processing has been undertaken. Data were exported as comma separated value (.csv) files for ingestion into the EIDC.
DOI: 10.5285/732f6134-bb94-44af-99b1-8f2732532bf9
title: Surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a data from Windermere South Basin, UK, 2021-2022

description: This is part of an ongoing long-term monitoring dataset of surface temperature, surface oxygen, water clarity, water chemistry and phytoplankton chlorophyll a from fortnightly sampling at the South Basin of Windermere in Cumbria, England that began in 1945 for some variables. The data have been collected by the UK Centre for Ecology & Hydrology (UKCEH). The data available to download comprise surface temperature (TEMP) in degree Celsius, surface oxygen saturation (OXYG) in % air-saturation, Secchi depth (SECC) in metres, alkalinity (ALKA) in µg per litre as CaCO3 and pH. Ammonium (NH4N), nitrate (NO3N), soluble reactive phosphate (PO4P), total phosphorus (TOTP), dissolved reactive silicon expressed as SiO2 (SIO2) and phytoplankton chlorophyll a (TOCA) are all given in µg per litre. Water samples are based on a sample integrated from 0 to 7m. All data are from January 2021 until the end of 2022.
description: Please note that the data presented here are raw data that have not yet been quality controlled and calibrated. However, data has been double entered and checked visually. Missing data are due to weather conditions, covid-19 restrictions or staff shortages.
Measurements are made from a boat at a marked location (buoy) at the deepest part of the lake.
DOI: 10.5285/e5f361b3-b434-4d11-9407-e5f48fe442b0
title: Soil respiration in human-modified forests of Eastern Amazonia

description: This dataset includes measurements of soil respiration in 20 plots (250 x 10 m each) in the Brazilian Amazon. Study plots were distributed across a gradient of forest disturbance, including: undisturbed primary forests , logged primary forests, logged-and-burned primary forests, and secondary forests. Data were collected from January 2015 until November 2017. In December 2015, during the El Niño-mediated drought, eight of our study plots were affected by understory fires.
description: We measured total soil respiration in 20 study plots (0.25ha) distributed along a gradient of forest disturbance in Eastern Amazonia: undisturbed primary forests (n = 5), logged primary forests (n = 5), logged-and-burned primary forests (n = 5), and secondary forests (n = 5). Forest disturbance classes were based on both an analysis of canopy disturbance in a chronosequence of satellite images (1988 to 2010) and on field assessments of fire scars, charcoal, and logging debris.
 
In each plot, we installed five PVC collars 50 m apart. Each collar was approximately 7 cm in size and were installed so approximately 2 cm stayed belowground and 5 cm aboveground. Collars had a 10 cm diameter. After installation, all collars were left to ‘settle’ for at least a week before the first measurement.  The collar was connected to an infrared gas analyser (EGM5®) to measure the soil CO2 efflux (i.e. soil respiration). Immediately after every soil respiration measurement, both the soil temperature and humidity were measured inside and outside the collar. We also took note on the collar height. Measures were taken every month. After measuring the soil respiration, we also measured the temperature inside and outside the collar, as well as the soil moisture, the latter with the aid of a HydroSense II.
DOI: 10.5285/45f5c9eb-7bd3-435f-97f3-ce149f3b381c
title: Bird survey data from the Atlantic Forest of Brazil, 2015-2017

description: The data contains bird species records from the Vale do Paraíba and Serra do Mar regions in the state of São Paulo, Brazil. Bird species were surveyed using point counts between December 2015 and February 2017, with four temporal replicates per point for which the number of replicates in which each bird species was detected is recorded. A total of thirty-four fragmented and fifteen near continuous land-use landscapes were surveyed using a nine-point grid system with each point separated by 75m. For fragmented landscapes three of the points were situated within a native forest fragment, three at the fragment edge and three in the surrounding matrix habitat. Fifteen fragments had a Eucalyptus plantation matrix and nineteen had a pasture matrix. Continuous land-use landscapes were split equally between native forest, plantation forest and pasture. A total of 267 bird species were detected across the different land-use types.
description: Three sampling points were conducted along a 150 m transect with each having four temporal replicates, split equally between wet and dry seasons. Sampling was conducted between December 2015 and February 2017. Each sampling point used a 15-minute point count with a 25 m radius. The data was then checked and the temporal replicates aggregated. The sampling forms part of the ECOFOR (Biodiversity and Ecosystem Functioning in Degraded and Recovering Amazonian and Atlantic Forests) project.
DOI: 10.5285/63d4b774-4e03-4db2-95ad-dcca18f0d681
title: Tree diameter census data in intact forest permanent plots across the Amazon Basin, 2017-2019

description: The dataset contains information of Diameter at Breast Height (DBH) of 8,729 trees. These trees are distributed in 29 RAINFOR network forest plots across the Brazilian Amazon, comprising the states of Acre, Mato Grosso and Pará. All the plot censuses are located in terra-firme non-flooded lowland forests. The measurements were collected between 2017 and 2019. 

The Amazon Forest Inventory Network is a long-term, international collaboration to understand the dynamics of Amazon ecosystems. Since 2000 they have developed a framework for systematic monitoring of forests from the ground-up, centred on plots that track the fate of trees and species, and includes soil and plant biogeochemical records, as well as intensive monitoring of carbon cycle processes at some sites. RAINFOR works with partners across the nations of Amazonia to support and sustain forest monitoring and help develop new generations of Amazon ecologists. The work of RAINFOR is currently supported by funding agencies in Brazil, the UK, and the EU.
description: We re-censused 29 plots in the Brazilian Amazon, located in the states of Acre, Pará and Mato Grosso. In total, 8,729 trees and new recruited trees >=10 cm diameter at breast height (DBH) had diameter measured following the RAINFOR protocol. We also collected data on state of the alive trees and dead trees. 
After the field campaigns, we uploaded the date to the forestplot.net platform. 
The field campaigns were conducted between 2017 and 2019.
DOI: 10.5285/29726cda-09f5-4661-8fd4-ddaa5555466a
title: Risk of Phytophthora infection in woodland and larch fragments across Scotland

description: These spatial layers contain risk factors and overall risk scores, representing relative risk of Phytophthora infection (Phytophthora ramorum and P. kernoviae), for Core Native Woodland and known larch fragments across Scotland. Risk factors include climate suitability, proximity to road and river networks and suitability of habitat for key hosts of Phytophthora and were broadly concurrent with the period between 2007 and 2013. This research was funded by the Scottish Government under research contract CR/2008/55, 'Study of the epidemiology of Phytophthora ramorum and Phytophthora kernoviae in managed gardens and heathlands in Scotland' and involved collaborators from St Andrews University, Science and Advice for Scottish Agriculture (SASA), Scottish Natural Heritage (SNH), Forestry Commission, the Food and Environment Research Agency (FERA) and the Centre for Ecology & Hydrology (CEH).
description: Risk factors were extracted and summarised for Core Native Woodland and Larch fragments, and included habitat suitability for the principal sporulation host, Rhododendron ponticum, and predicted abundance for the additional host, Vaccinium myrtillus, climatic suitability for growth and sporulation, proximity to inspected garden or trade premises, proximity to infected premises, and proximity to larch and infected larch. Final weighting for risk factors were agreed with partners for the final calculation of risk scores. Newly developed methods for modelling habitat suitability of invasive species were used to predict habitat suitability for the invasive shrub Rhododendron ponticum.A suite of climate, soil, biotic and abiotic factors were used to predict percent cover for Vaccinium myrtillus. Data on outbreaks in 2011, 2012 and up to May 2013 were provided by SASA and locations of larch infections up to April 2013 were provided by the Forestry Commission. A small proportion of core native woodland fragments were missing data for climate and Vaccinium myrtillus habitat suitability. Adam Butler from Biomathematics and Statistics Scotland (BioSS) provided statistical advice for habitat suitability modelling.
DOI: 10.5285/4b27e5d5-2ec4-4b72-9939-ab66c2818612
title: Growth and physiological responses of grassland soil bacteria (Bacillus and Pseudomonas) to drought treatment in experimental microcosms

description: This dataset contains information on the performance of soil eubacteria inoculated into soil microcosms and exposed to a series of experimental droughts (or control conditions) in an experimental evolution study. Isolates of Bacillus and Pseudomonas included in the experimental evolution study had been sampled from the roots of Festuca ovina in the control treatment at the Buxton Climate Change Impacts Lab (BCCIL). 

Variables measured included estimates of microbial population size (via qPCR), microcosm soil respiration in response to substrate addition (in a substrate utilisation profiling assay) and water loss from the soil in response to the experimental drought/control treatments. 
description: Bacterial isolates from BCCIL (twelve from each of genera Bacillus and Pseudomonas) were raised in liquid media and used to inoculate sterilised soil in kilner jars (approx 100 ml soil in 500 ml jars). Each isolate of each bacterial taxon was inoculated into five replicate microcosms per moisture treatment (drought and control) and microcosms were assigned random positions within four experimental blocks. Microcosms in the control treatment were topped up weekly to a volumetric water content of 40%. Those in the drought treatment were subjected to a series of four simulated droughts lasting six weeks, where watering was not carried out. Soil moisture content determination and watering was carried out by assessing the mass of each kilner jar and the dried soil it initially contained, allowing controlled watering to the target soil water content. Substrate utilisation profiling was carried out by taking soil samples from the microcosms at the end of the final drought cycle, which were amended with different substrates (water, glucose, cellulose, artificial root exudate)in MicroResp(TM) colourimetric microplates, before CO2 efflux detection on a FLUOstar Omega spectrophotometer (BMG Labtech, Ortenberg, Germany). q-PCR was carried out by taking soil samples from the microcosms in the experimental evolution. RNA was extracted from the soil samples and amplified using qPCR primers specific to the isolates which had been used to inoculate the microcosms.
DOI: 10.5285/c42b0e3b-69e4-4941-addf-20c2e0612c58
title: Substrate utilisation profiles and moisture content data from soil sampled in an upland grassland experiment at Sourhope, Scotland [NERC Soil Biodiversity Programme]

description: These data comprise substrate utilisation profiles (using the BIOLOG gram-negative method) and moisture content data from soil sampled in an upland grassland experiment at Sourhope, Scotland.  BIOLOG-GN (gram-negative) substrate utilisation analyses were used to give an indication of the ability of a subset of the bacterial community to utilise various carbon sources. These data include both temporal and spatial diversity in different depths of semi-natural grassland soil cores collected at different sample dates.  Samples were collected in July 1999, October 1999, April 2000 and August 2000.

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)'s farm at Sourhope in the Scottish Borders (Grid reference: NT 8545 1963).  During this time, the site was monitored to assess changes in aboveground biomass production (productivity), species composition and relative abundance (diversity). 
description: Data were collected as part of the NERC Soil Biodiversity Thematic Programme, which was established in 1999 and was centred upon the intensive study of a large field experiment located at the Macaulay Land Use Research Institute (MLURI) (now the James Hutton Institute)'s farm at Sourhope in the Scottish Borders (Grid reference: NT8545019630). 

Data were collected by scientists employed by Centre for Ecology & Hydrology, University of Newcastle-upon-Tyne and MLURI, and were managed by the Centre for Ecology & Hydrology.