cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5285/d47e78bc-2227-4bc7-90ae-9ec871c52bec
title: Lightning strike locations and characteristics in Nyungwe National Park, Rwanda, surveyed in June 2022 and October 2023

description: The dataset details the locations and attributes of canopy disturbances in Nyungwe National Park, Rwanda, that were suspected to have been caused by lightning strikes. Disturbances were located by surveying 23 km of trails and assessing whether disturbances (clusters of dead or damaged trees) had damage signatures consistent with lighting. Only disturbances that were thought to potentially have been caused by lightning were recorded. As well as providing a qualitative assessment of the confidence that the damage was caused by lightning, the dataset contains the number of dead and damaged trees in different size classes, as well as the taxonomic identity and degree of crown damage experienced by canopy trees within the putative strike. Photographs of a subset of strikes are also provided.

Data were collected as part of the project Lightning in African tropical forests: from tree mortality to carbon dynamics (NE/W003872/1).
description: A total of 23.3 km of trails were surveyed in Nyungwe National Park in June 2022, covering the majority of trails accessible from the Uwinka station. Canopy disturbances (i.e. clusters of dead or damaged trees) encountered along these trails were inspected to assess for flashover damage (visually apparent as the defoliation of the two nearest branches of neighbouring trees in a directionally biased pattern). If a tree exhibited potential flashover damage to two or more neighbours, it was selected for more detailed surveys to assess whether patterns of damage were consistent with lightning.

The presumptive directly struck tree was identified as the canopy tree at the centre of observed flashover damage. Tree-level surveys of lightning damage were conducted for this tree, along with any other tree with a diameter at breast height > 50 cm within the lightning strike area.

A subset of trails was resurveyed in October 2023, revisiting existing strike locations on these trails and surveying new disturbances.
DOI: 10.5285/7991871e-382f-422f-b5b2-91b4f6d8598f
title: Biomass, mycorrhizal colonization, carbon and nitrogen content of Scots pine and birch seedlings grown in soil from mixed and monoculture stands

description: Seedlings were grown in soil collected from an experiment at Hambleton Forest, North Yorkshire. Soils originated from plots containing either Scots pine or birch monocultures, or a mixture of both species.  In the lab, pairs of seedlings of birch and Scots pine were grown as monocultures and mixtures from each of the three plot treatments.  The data represent the biomass, leaf C:N ratio and mycorrhizal status determined after 20 weeks.
description: Soils were collected and transported to the lab and sieved.  Conetainers were filled with sieved soil and non-mycorrhizal seedlings germinated for 2-4 weeks were placed in the containers and transferred to a controlled environment chamber for 20 weeks. Plants were extracted, roots removed and assayed for colonisation under a microscope, and leafs dried, weighed, ground and analysed on a CN analyser.

C and N analysis was using a CUBE elemental analyser and included known standards to check for drift and precision.

Balances are calibrated regularly.

Data were imported into Excel and plotted to check for any outliers.
DOI: 10.5285/aa20f8c4-bbdb-4dfa-82b4-b9b3fd8f34eb
title: GPS tracking data for 32 individual European nightjars in Humberhead Peatlands NNR from 2015-2018

description: This dataset contains GPS data fixes (WGS84 format) from 32 European nightjars (Caprimulgus europaeus) . The data contains additional information on identity of the bird, date, time of fix acquisition, and the associated site and night number (between 6 and 17 nights of data, varying between individuals). These data were collected on the Humberhead peatlands NNR, South Yorkshire, from 2015 until 2018. Birds were caught in mist nets and tail-mounted miniaturised GPS tags (Pathtrack, Otley, UK; <3% bird bodyweight) were fitted by BTO-licensed researchers.

Data were collected as part of a NERC ACCE-funded PhD.
description: Data were collected at Thorne (53.636, -0.89682) and Hatfield Moors (53.545, -0.93493), part of Humberhead Peatlands NNR, South Yorkshire. Tags were briefly calibrated to estimate error (between 5 - 25 metres depending on habitat type) and programmed to acquire fixes every 3 or 5 minutes (2015/16 and 2017/18 respectively). 
Nightjars captured by mist net from 21:00 to 01:00 using mist nets, under BTO licence. Birds were measured, ringed and equipped with a nanoFix mini GPS tag (Pathtrack, Otley, UK.) on the two central tail feathers. 
GPS data has been analysed to produce foraging tracks, home ranges and resource selection in ArcMap and R.
DOI: 10.5285/de5ca6cc-02e9-42bc-a39e-80ec8acbffba
title: Loch Leven diatom counts 1968-2007

description: The dataset comprises counts of four planktonic diatom taxa collected from Loch Leven from 1968-2007 by staff at the Centre for Ecology & Hydrology and its predecessor bodies, as part of their long-term monitoring programme of the lake. Count units are the density of cells per millilitre of water for four species; Asterionella formosa, Aulacoseira spp, Diatoma spp, Unicellular centric diatoms. Counts are of weekly to monthly frequency and from a single sampling station
description: Validation of data was in line with protocols referenced in the supporting documents. The dataset was quality controlled by all three authors who have worked on the Loch Leven long-term monitoring project since 1968. Dr Tony Bailey-Watts counted all the pre-2001 data and this was checked and collated by Alex Kirika.  Dr Laurence Carvalho counted and checked all the data from 2001-2007.
DOI: 10.5285/b2d17962-3c7f-4193-a180-cde885d1a83e
title: Unmanned aerial vehicle images of drought-stressed European beech forests in the Rhӧn Biosphere Reserve, Germany, 2020

description: This dataset comprises four RGB unmanned aerial vehicle (UAV) images collected in September 2020 of European beech (Fagus sylvatica) forest within core protected areas of the UNESCO Rhӧn Biosphere Reserve, Germany. The study forests were subject to the extreme drought event that impacted central Europe in 2018/2019 and this project sought to collect data to enable the analysis of individual tree and stand level response (canopy damage and defoliation) of European beech trees to extreme drought events. The RGB images available in this dataset have approx. 3cm pixel size with an associated 10cm pixel digital elevation model (DEM) and are suitable for identifying individual trees and the degree of canopy damage (defoliation, discolouration, and mortality) sustained by individuals/stands within the forest. 

The work was supported by the Natural Environment Research Council (Grant NE/V00929X/1).
description: The RGB UAV data and associated Digital Elevation Model were collected using a DJI Phantom 4 UAV. Individual images were processed by the NERC Field Spectroscopy Facility with the orthorectified mosaics made available.
DOI: 10.5285/bc4d0325-b67b-4fff-a14b-6e06edf397bd
title: Visible leaf injury of Trifolium repens versus Lolium perenne after ozone exposure in solardomes

description: The dataset consists of proportions of ozone injured or senesced leaves from a study which investigated how the presence of competing species in a community affects these two common responses to ozone. Monocultures and mixtures of Trifolium repens and Lolium perenne were grown in large containers and were exposed in solardomes to either a rural episodic ozone profile (AOT40 (Accumulated Ozone Threshold exposure of 40 parts per billion) of 12.86 ppm h) or control conditions (AOT40 of 0.02 ppm h) for 12 weeks. The proportion of ozone-injured or senesced leaves was determined in different regions of the canopy, the upper canopy (>14cm high), the canopy edge and the inner canopy, by separating injured/senesced leaves from healthy leaves. The experiment was carried out at the CEH Bangor Air Pollution Facility. This work was funded by the Centre for Ecology & Hydrology Integrating Fund Initiative
description: This study has investigated how the presence of competing species in a community affects two common responses to ozone: visible injury and senescence. Monocultures and mixtures of Trifolium repens and Lolium perenne were grown in large containers and were exposed in solardomes to either a rural episodic ozone profile (AOT40 of 12.86 ppm h) or control conditions (AOT40 of 0.02 ppm h) for 12 weeks. The proportion of ozone-injured or senesced leaves was different in the different regions of the canopy. The highest proportions of injured/senesced leaves were in the plant material growing at the edge of the canopy and the upper canopy, with a significantly lower proportion of injured leaves in the inner canopy. The presence of L. perenne increased the proportion of ozone-injured leaves in T. repens at the final harvest, whilst the presence of T. repens decreased the proportion of senesced leaves in L. perenne. In L. perenne, the proportion of injured leaves at the edge and inner canopy decreased significantly when grown in competition, whilst for T. repens the reverse effect occurred in the inner canopy only. Different mechanisms appeared to influence the interaction between response to ozone and competitors in these two species. In L. perenne the response to ozone may have been related to nitrogen supply, whereas in T. repens canopy structure was more important.
DOI: 10.5285/b28c13f2-7355-4c4b-8c34-10470e1772d1
title: Parasitoid abundance, aphid population mass and glucosinolate concentration from experimental ozone and diesel exhaust fumigation of Brassica napus

description: These datasets contain aphid/parasitoid abundances and glucosinolate concentrations associated with Brassica napus plants within eight field-based diesel exhaust and ozone fumigation rings located at the University of Reading’s Sonning farm.
description: The experiment was conducted within field fumigation rings over two summer seasons (2018 and 2019). Brassica napus plants were separated into four groups of plants: 1) inoculated with 10 Brevicoryne brassicae aphids and netted until harvest, 2) inoculated with 50 B. brassicae aphids and netted until harvest, 3) inoculated with no aphids, and 4) inoculated with 10 B. brassicae aphids then exposed to free-living parasitoids. Aphid populations were collected from plants with pooters and weighed. Parasitoids were counted from sticky traps that were surrounded by aphid-infested and non-infested plants (groups 1-3). Parasitoids were taxonomically classified into two groups (Diaeretiella rapae and other parasitoids). Brassica napus plants were harvested (from groups 2 and 3) and analysed for glucosinolate concentrations. The number of D. rapae parasitoids that emerged from parasitised aphids were counted from sticky traps inside the nets surrounding plants that were previously exposed to free-living parasitoids.
DOI: 10.5285/40a80d95-5a8a-4586-aa24-d6c87f9968b6
title: Groundwater monitoring data following 2016-2017 extreme rainfall and floods in the Gaborone catchment, Upper Limpopo basin, Botswana

description: The dataset contains borehole groundwater levels and physico-chemical parameters for the period May 2017 to June 2018 including; (1) near-monthly measurements of water table depth, groundwater temperature, pH, electrical conductivity and total dissolved solids obtained from manual sampling of 22 boreholes; and (2) higher temporal resolution (5-min time-step) timeseries of water table depth, groundwater temperature and electrical conductivity obtained from automatic dataloggers in 3 of the abovementioned boreholes.
description: Manual water table depth measurements during the near-monthly campaigns were done in situ using a standard groundwater dipmeter. Manual groundwater pH, temperature, electrical conductivity and total dissolved solids measurements (Strategy 1) were obtained on pumped grab groundwater samples from borehole taps.
Automatic loggers immersed in a selection of three boreholes provided high-temporal resolution (5-min) groundwater level, temperature, electrical conductivity data (Strategy 2). Raw groundwater levels were provided in meter equivalent freshwater head above the logger, later converted in depth in Excel through two sequential processing steps: (1) barometric compensation, from a barometric sensor installed; (2) depth correction using the manual depth measurements (Strategy 1) and applying linear interpolation between measurement dates.
Datasets were post-process through removal of obvious measurement errors, including human errors when writing up values on field notebook and anomalous datalogger records associated to sensor extraction from the well.
DOI: 10.5285/6529004d-b6e8-429d-ac68-0f5324d7e5d0
title: Fine root phosphatase enzyme activity in fertilised plots in Central Amazon, 2018

description: The data consists of potential phosphatase activity released by fine roots in old growth forests in Central Amazon. Fine roots younger than three months were sampled using the ingrowth core technique in a large-scale nutrient fertilisation experiment. Phosphatase activity is given as a mean of the plant community per plot, where five points inside each plot were sampled and separated in two different soil layers (0-10 and 10-30cm). 

Samples were collected in February 2018, eight months after the nutrient fertilisation started at the AFEX project area in Manaus, Brazil at the Biological Dynamics of Forest Fragments Project (BDFFP/ INPA). 

The study was funded by NERC, BDFFP (logistical support) and Brazilian government (student scholarship)
description: Root tips, that usually to refer absorptive fine roots directly responsible for nutrient acquisition, were cut from root sampled using ingrowth cores and potential root acid phosphomonoesterase activity was measured within 3 days of root sampling using a fluorimetric microplate assay. Roots were incubated with Methylumbelliferyl-phosphate (MUF) for 30 minutes at ~ 25 ˚C while gently shaking, and after the termination of the reaction  fluorescence was read on a fluorometer (Tecan Infinite® 200 PRO, Grödig, Austria), at 365 nm excitation and 450 nm emission. Root phosphatase activity per plot was expressed in μmol MUF  g−1 dry mass h
DOI: 10.5285/0d5c7e45-2c43-4276-af0d-8d941db2e124
title: Spot gauged flows on the lower River Frome, Dorset, April-November 2022

description: This is a dataset of spot gauged river flows (m3 s-1) at multiple sites along the River Frome, Dorset, UK, conducted during the year 2022. All sites are contained within the stretch of river between the Environment Agency gauging stations located at Dorchester and East Stoke, i.e. the lower part of the River Frome. The monitoring sites included the major tributaries along this river reach, which are: the South Winterbourne, Tadnoll Brook, and the River Win. In total, 19 river channels were spot gauged at 11 river cross-sectional locations. Due to the braided nature of the river, some locations required multiple channels to be measured to produce a total cross-sectional flow for that part of the river. The river cross-sectional locations were evenly spaced, approximately every 3 km along the river reach. Measurements were taken on multiple flow accretion survey days between 12/04/2022 and 05/11/2022. On each day, as many of the sites were spot gauged as possible, working upstream to downstream.

description: Measurements were taken by dividing the river channel into at least 10 equally spaced transects, with the depth and flow velocity recorded at each vertical transect. For small streams (< 3 m width), 5-10 transects were used. The flow velocity was recorded at a depth of 40% above the riverbed. The cross-sectional area for each transect was determined by multiplying the width of the transect by the average depth of the two adjacent vertical transects. This was then multiplied by the average velocity of the two adjacent vertical transects to get discharge for each transect. The sum of all transects provided total stream discharge. To conduct the measurements, a Valeport mechanical flow meter was used. Flows are reported as m3 s-1. Due to time constraints only one flow recording could be taken at each site, on each survey date, i.e. no replicates.
DOI: 10.5285/c9bc537a-d1c5-43a0-b146-42c25d4e8160
title: Farm management and longitudinal data on antibiotic use and antibiotic resistant E. coli for 53 dairy farms, South West England, 2017-2019

description: This dataset contains over 4000 faecally-contaminated environmental samples collected over 2 years across 53 dairy farms in England. The samples were analysed for E. coli resistance to amoxicillin, streptomycin, cefalexin, tetracycline and ciprofloxacin and detection of resistant strains is presented in the dataset as a binary result, along with mechanisms of resistance to third generation cephalosporins where relevant. In addition there is comprehensive farm management data including antibiotic usage data.
description: 1. Records of samples taken from 53 farms including date, type and descriptive location of sample. 2. Records of microbiological analyses of the samples to identify E. coli resistant to amoxicillin, cephalexin, tetracycline, ciprofloxacin and/or streptomycin). 3. For samples where E. coli resistant to cephalexin were detected, results of laboratory testing for resistance mechanism. 4. Questionnaires administered to farmers between Jan 2017 and Jan 2019. These collected demographic and farm management data at the start and end of the data collection periods for each farm, as well as questionnaires around choices of antibiotic administered during the data collection period at the convenience of the participants. 5. Prescription medication records acquired from veterinary practices and farm records. All calculations and data entry were checked for errors before data was accepted.
DOI: 10.5285/d6c787ec-146c-461b-b8a2-e0251259036c
title: Soil fungi gene copy numbers and community composition under birch and willow vegetation in girdled and non-girdled plots, subarctic Sweden, 2017-2019

description: Fungal community DNA was sequenced from soils in northern, subarctic Sweden. Soils were sampled from treeline mountain birch forest and stands of tundra willow that were wither ‘girdled’ (connection between leaves and roots cut by disrupting the phloem transport) or ‘control’ (no treatment), 0, 1 and 2 years after the treatment was applied.
description: The organic soil horizon (O horizon) was sampled on 3rd August 2017, 1st August 2018 and 5th August 2019. For each plot (22 in total), nine 3.8 cm diameter soil cores were collected; in the birch plots, cores were taken in a grid across a 3 x 3 m central area (corresponding to the central area in which soil CO2 efflux, root and mycelium production and soil fauna measurements were taken; (Parker et al., 2020). In the willow plots, the nine cores were distributed evenly across the plot area within the trenched perimeter. The uppermost litter layer, as well as the mineral horizons underlying the organic horizon (clearly identifiable at these sites), were removed from cores immediately after coring. The nine cores from each plot were homogenised and pooled within 6 hours of sampling.
DNA was extracted from a 50 mg sub-sample and ITS2 markers were amplified by PCR. We used a community metabarcoding approach on the pooled DNA samples to identify distinct taxonomic groups at species level where possible. Copy numbers of the fungal ITS2 region were estimated by quantitative PCR (qPCR)
DOI: 10.5285/08bfe302-d33f-490d-97be-27bb83a0f38d
title: Soil microbial communities, soil, environmental and forest structural properties across old-growth forest and naturally regenerating or actively restored selectively logged tropical forest in Sabah, Borneo, March 2018 v2

description: This dataset contains information on soil microbial communities, soil physicochemical properties, forest structural and environmental characteristics across a contiguous area of forest that has undergone contrasting logging disturbance and restoration in Sabah, northern Malaysian Borneo. Sampling was conducted as part of a study investigating soil microbial community responses to either active restoration (enrichment planting) or passive restoration (natural regeneration) of selectively logged forest, relative to old-growth soil microbial communities.

This work was supported through the UK Natural Environment Research Council (NERC) Human Modified Tropical Forests Programme (Biodiversity and Land-use Impacts on Tropical Ecosystem Function (BALI) consortium [NE/K016253/1]), ENVISION Doctoral Training Scheme [NE/L002604/1] and NC International Programme [NE/X006247/1].
description: Soil samples and forest structural and environmental data were collected at nine sites during one campaign in March 2018 . Three sampling sites were chosen in each of three forest types of old-growth, naturally regenerating and actively restored logged forest. Old-growth forest was located in the Danum Valley Conservation Area, and logged forest sites were situated within the adjacent Innoprise Face Foundation Rainforest Rehabilitation Project (INFAPRO) area. A geospatial transect design was employed for soil sampling and measurement of microclimate variables at each site to assess variation in microbial communities over cm to m scales. This comprised three transects radiating out from one centre point positioned at 120 ° to one another. Sampling points were located at the centre point, then at increasing distances of 10 cm, 30 cm, 90 cm, 2.7 m, 8.4 m and 24.3 m along each transect relative to the centre. The circumferences of all tree stems with diameter at breast height (DBH) >5 cm within a 2.5 m buffer of all transects were recorded at each site for site-level calculation of stem density and basal area. Soil physicochemical properties were analysed at the Sabah Forest Research Centre, Sepilok. Organic layer soil microbial community data were generated by 16S and ITS amplicon sequencing at UKCEH Wallingford, and Phospholipid Fatty Acid (PLFA) analysis at Lancaster University in the UK. Fungal functional guild classifications were assigned to fungal sequences using the FUNGuild annotation tool. Alpha diversity indices for microbial groups and relative abundances of fungal guilds were generated after rarefying by minimum read counts for each group . Rates of spatial turnover in soil microbial taxa for different microbial groups were calculated using the distance decay approach via linear modelling.