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D.L.","Cowan, N.J.","Skiba, U.","Reinsch, S."],"bibtex":"https://catalogue.ceh.ac.uk/documents/59f81d41-a789-4c5c-8ab8-36baa7ac2c55/citation?format=bib","day":24,"doi":"10.5285/59f81d41-a789-4c5c-8ab8-36baa7ac2c55","month":4,"publisher":"NERC Environmental Information Data Centre","resourceTypeGeneral":"dataset","ris":"https://catalogue.ceh.ac.uk/documents/59f81d41-a789-4c5c-8ab8-36baa7ac2c55/citation?format=ris","title":"Soil biological properties from an inorganic fertiliser (grass trial) experiment at North Wyke, Henfaes Farm and Easter Bush, UK (2016)","url":"https://doi.org/10.5285/59f81d41-a789-4c5c-8ab8-36baa7ac2c55","year":2019},"custodians":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"custodian","email":"info@eidc.ac.uk"}],"datasetReferenceDate":{"publicationDate":"2019-04-24","releasedDate":"2020-12-13"},"description":"The data nitrogen gene data, soil biodiversity indices and microbial community composition, for three soil depths (0-15, 15-30 and 30-60 cm) from a three-cut silage plot trial located at three grassland sites within the UK collected between April 2016 and October 2016. The sites were Rothamsted Research at North Wyke in Devon, Bangor University at Henfaes Research Station in North Wales and Easter Bush in Scotland.\n\nAt each site measurements were taken from 16 plots, organised within a randomised complete block design where 4 plots did not receive fertilizers (controls), 4 plots received urea only, 4 plots received urea and urea-inhibitors, and 4 plots received ammonium-nitrate (Nitram). Fertiliser was applied three times and three cuts were performed, all parameters measured were following a fertiliser application. Samples were taken before the fertilizer additions, at peak growth and before the last silage cut.\n\nSoil chemical parameters were: soil nitrate, ammonium, dissolved organic carbon and nitrogen, amino acids and peptides, soil organic matter content as loss-on-ignition, pH, sodium, potassium, calcium, magnesium, permanganate oxdisable carbon citric acid extractable phosphorous, Olsen-P and total carbon, nitrogen and phosphorus. Soil biological measure were: microbial biomass carbon and nitrogen. Soil physico-chemical parameters were measured on the same samples and are available in a related dataset measured on the same soil samples and are presented in a separate dataset in the project data series (https://catalogue.ceh.ac.uk/id/7a87dde4-b54e-49b0-8751-1d59e8aebb90).\n\nMeasurements were undertaken by members of staff from the Centre of Ecology & Hydrology (Bangor, Edinburgh, Lancaster, Wallingford), Bangor University, School of Environment, Natural Resources & Geography and Rothamsted Research, Sustainable Agricultural Sciences, North Wyke.\n\nData was collected for the Newton Fund project \"UK-China Virtual Joint Centre for Improved Nitrogen Agronomy\". Funded by Biotechnology and Biological Sciences Research Council (BBSRC) and NERC -  Ref BB/N013468/1","distributionFormats":[{"name":"Comma-separated values (CSV)","type":"text/csv","version":"unknown"}],"distributorContacts":[{"organisationName":"NERC EDS Environmental Information Data Centre","organisationIdentifier":"https://ror.org/04xw4m193","role":"distributor","email":"info@eidc.ac.uk"}],"funding":[{"funderName":"Biotechnology and Biological Sciences Research Council","funderIdentifier":"https://ror.org/00cwqg982","awardTitle":"Newton Fund project - UK-China Virtual Joint Centre for Improved Nitrogen Agronomy (CINAg)","awardNumber":"BB/N013468/1","awardURI":"https://gtr.ukri.org/projects?ref=BB%2FN013468%2F1","orcid":false,"ror":true}],"id":"59f81d41-a789-4c5c-8ab8-36baa7ac2c55","incomingCitationCount":0,"infoLinks":[{"url":"https://data-package.ceh.ac.uk/sd/59f81d41-a789-4c5c-8ab8-36baa7ac2c55.zip","name":"Supporting information","description":"Supporting information available to assist in re-use of this dataset","function":"information","type":"OTHER"}],"inspireThemes":[{"theme":"Environmental Monitoring Facilities","uri":"http://inspire.ec.europa.eu/theme/ef"},{"theme":"Agricultural and Aquaculture Facilities","uri":"http://inspire.ec.europa.eu/theme/af"}],"keywordsOther":[{"value":"Urease Inhibitor"},{"value":"Soil properties"},{"value":"grassland","uri":"http://www.eionet.europa.eu/gemet/concept/3733"},{"value":"nitrogen","uri":"http://onto.nerc.ac.uk/CAST/273"},{"value":"fertiliser","uri":"http://www.eionet.europa.eu/gemet/concept/3169"},{"value":"soil","uri":"http://www.eionet.europa.eu/gemet/concept/7843"}],"keywordsProject":[{"value":"CINAg"},{"value":"Centre for improved Nitrogen agronomy"}],"keywordsTheme":[{"value":"Soil","uri":"http://onto.nerc.ac.uk/CEHMD/topic/17"}],"licences":[{"value":"This resource is made available under the terms of the Open Government Licence","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"}],"lineage":"Soil samples were taken by members of the sites. At North Wyke and Henfaes farm, staff from CEH Bangor helped taking the samples. Two sets of soil cores were taken. One was sent in cooling boxes on ice to CEH Bangor for measuring soil physicochemical properties. The second set was sent to Rothamsted Research Harpenden for the analysis of nitrogen genes and microbial community composition (related dataset). The topsoil 0-15 cm were taken with the same type of corer across the sites, samples below 15 cm soil depth were sampled with corers available at the sites. Samples were wet sieved to 5 mm by staff from Bangor University and CEH Bangor. Subsamples of these were analysed for physicochemical and biological parameters.\n\nDNA extractions were performed by Rothamsted Research Harpenden. Extracts were analyzed for nitrogen genes at Rothamsted Research in Harpenden. Extracts were also sent to CEH Wallingford for analyses of Operational Taxonomic Units (OTU's).\n\nSoil community DNA was extracted from 0.25 gams soil using the MoBio DNA PowerSoil DNA isolation kit (Mo Bio Laboratories, Inc. Carlsbad, CA), following manufacturer’s protocol. Extracted DNA was quantified by fluorometer Qubit® 2.0 dsDNA BR Assay Kit (Thermo Fisher Scientific) and quality checked by nanodrop (Thermo Fisher Scientific).\n\nQuantitative-polymerase chain reaction (qPCR) protocols were as detailed in De Sosa et al. 2018.\n\nMicrobial nitrogen cycling gene abundance was investigated by qPCR targeting specific genes or genetic regions. Bacterial and archaeal communities were targeted via the 16S rRNA genes, while the fungal community abundance was targeted by the ITS region. The different genes involved in soil nitrogen cycling were investigated: \n•\tNitrogen fixation (nifH gene)\n•\tNitrification by targeting the ammonia oxidising bacteria (AOB) and archaea (AOA) (amoA gene)\n•\tDenitrifiers via the nitrite reductase (nirK and nirS genes) and the nitrous oxide reductase (nosZ genes clade I and II)\n•\tDegradation of urea was also assessed by targeting the ureC gene\n\nqPCR amplifications were performed in 10 μL volumes containing 5 μL of QuantiFast (Qiagen, Manchester, UK), 2.8 μL of nuclease-free water (Severn Biotech, Kidderminster, UK), 0.1 μL of each primer (1 μM) and 2 μL of template DNA at 5 ng μL−1, using a CFX384 Touch® Real-Time PCR Detection System (Bio-Rad, Hemel Hempstead, UK). \n\nStandards for each molecular target were obtained using a 10 fold serial dilution of PCR products amplified from an environmental reference DNA (also used as positive control) and purified by gel extraction using the Wizard® SV Gel and PCR Clean Up System (Promega, Southampton, UK) following the manufacturer's instruction and quantified by fluorometer Qubit® 2.0 dsDNA BR Assay Kit (Thermo FisherScientific). \n\nStandard curve template DNA and the negative/positive controls were amplified in triplicate. Amplification conditions for all qPCR assays consisted in 2 steps: first denaturation at 95 degrees Celsius for 5 minutes followed by 40 cycles at 95 degrees Celsius for 10 seconds and 60 degrees Celsius for 30 seconds that included annealing, elongation and reading. Each amplification was followed by melting curve (increase in temperature from 60 degrees Celsius to 95 degrees Celsius, with a reading every 0.5degrees Celsius) to assess the specificity of each assay.\n\nThe efficiency of the qPCR varied between 85.2 percent and 95.9 percent (except nozII 74.4 percent, amplicon 746 bp long), and R2 between 0.987 and 0.999. The melting curves showed specificity for all the genes, except as expected for the fungal Internal Transcribed Spacer (ITS), that showed the amplification of products of different lengths, due to the variability in length of the ITS region between different fungal taxa (Manter and Vivanco, 2007).\n\nMicrobial diversity indices:\nExtracted DNA was supplied from Rothamsted Research in Harpenden (see section 5.4.13 in main supporting document) for amplicon sequencing at the facilities of the Molecular Ecology Group, Centre for Ecology & Hydrology, Wallingford. <50 μL volumes of DNA extract were supplied in 96-well plate format, these were subject to:\n•\t16S rRNA amplicon sequencing as per Kozich 2013 (Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform), utilising V3-V4 region primers\n•\tITS rRNA amplicon sequencing employing the Kozich 2013 strategy, utilizing ITS primers by Ihrmark 2012 (New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities)\n\nAmplicons were sequenced on Illumina MiSeq platform with V3 chemistry. Resulting sequences were demultiplexed using Illumina Basespace. 16S amplicons were processed using in-house developed pipelines for quality filtering, merging and taxonomic assignment (GreenGenes database) of operational taxonomic units (OTUs). ITS amplicons were processed using the R package Dada2 for quality filtering, merging. \nR package Vegan was used to analyse amplicon sequences. Bacterial and fungal Shannon’s Index diversity scores for each sample were produced from rarefied data using diversity function. Species richness for each sample were similarly produced using ‘specnumber’ function.\n\nBacterial phylum level frequencies were produced from taxonomically identified OTU sequences (using Greengenes database), these values are a percentage of the rarefied total.\n\nAll results were entered into CSV spreadsheet.","metadataDate":"2026-06-29T16:59:02","notGEMINI":false,"onlineResources":[{"url":"https://data-package.ceh.ac.uk/data/59f81d41-a789-4c5c-8ab8-36baa7ac2c55","name":"Download the data","description":"Download a copy of this data","function":"download","type":"OTHER"},{"url":"https://data-package.ceh.ac.uk/sd/59f81d41-a789-4c5c-8ab8-36baa7ac2c55.zip","name":"Supporting information","description":"Supporting information available to assist in re-use of this dataset","function":"information","type":"OTHER"}],"pointsOfContact":[{"familyName":"Reinsch","givenName":"S.","organisationName":"UK Centre for Ecology & 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K., & Vivanco, J. M. (2007). Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. Journal of Microbiological Methods, 71(1), 7–14.","url":"https://doi.org/10.1016/j.mimet.2007.06.016","function":"relatedArticle"},{"name":"Kozich 2013 ","description":"Kozich, J.J., Westcott, S.L., Baxter, N.T., Highlander, S.K., & Schloss, P.D. (2013). Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform. Applied and Environmental Microbiology, 79(17), 5112–5120.","url":"https://doi.org/10.1128/aem.01043-13","function":"relatedArticle"},{"name":"GreenGenes database","url":"http://greengenes.lbl.gov/Download/","function":"relatedDataset"},{"name":"The UK-China Virtual Joint Centre for Improved Nitrogen Agronomy (CINAG)","url":"https://www.rothamsted.ac.uk/international/china/cinag","function":"website"},{"description":"de Sosa, L.L., Glanville, H.C., Marshall, M.R., Schnepf, A., Cooper, D.M., Hill, P.W., … Jones, D.L. (2018). Stoichiometric constraints on the microbial processing of carbon with soil depth along a riparian hillslope. Biology and Fertility of Soils, 54(8), 949–963. ","url":"https://doi.org/10.1007/s00374-018-1317-2","function":"relatedArticle"}],"temporalExtents":[{"begin":"2016-04-01","end":"2016-08-31"}],"title":"Soil biological properties from an inorganic fertiliser (grass trial) experiment at North Wyke, Henfaes Farm and Easter Bush, UK (2016)","topicCategories":[{"value":"farming","uri":"http://inspire.ec.europa.eu/metadata-codelist/TopicCategory/farming"},{"value":"environment","uri":"http://inspire.ec.europa.eu/metadata-codelist/TopicCategory/environment"}],"topics":["http://onto.nerc.ac.uk/CEHMD/topic/17"],"type":"dataset","uri":"https://catalogue.ceh.ac.uk/id/59f81d41-a789-4c5c-8ab8-36baa7ac2c55","useConstraints":[{"value":"This resource is made available under the terms of the Open Government Licence","code":"license","uri":"https://eidc.ac.uk/licences/ogl/plain"},{"value":"© Rothamsted Research","code":"copyright"},{"value":"© UK Centre for Ecology & Hydrology","code":"copyright"},{"value":"© Bangor University","code":"copyright"}]}