d432d96c-7aff-45a5-9d4b-37e4065afdd7 English ISO/IEC 8859-1 (also known as Latin 1) dataset dataset NERC EDS Environmental Information Data Centre Lancaster Environment Centre, Library Avenue, Bailrigg Lancaster LA1 4AP UK info@eidc.ac.uk https://eidc.ac.uk/ EIDC website The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences. information pointOfContact 2025-11-13T16:25:16 UK GEMINI 2.3 WGS 84 Porewater and microbial community properties of permeable riverbed sediments across the south of England, 2018 2022-02-08 publication https://catalogue.ceh.ac.uk/id/d432d96c-7aff-45a5-9d4b-37e4065afdd7 10.5285/d432d96c-7aff-45a5-9d4b-37e4065afdd7 doi: Clark, D.R., Greenwood, B.N., Ma, C., Si, Y., Thomas, G.E., Laissue, P., Whitby, C., McKew, B.A., Trimmer, M. (2022). Porewater and microbial community properties of permeable riverbed sediments across the south of England, 2018. NERC EDS Environmental Information Data Centre 10.5285/d432d96c-7aff-45a5-9d4b-37e4065afdd7 This dataset contains in-stream measurements of sediment porewater nutrients, nitrification rates (and the fraction which is either fully oxidised to nitrate or reduced to N2 gas), and the abundance of microbial 16S rRNA and specific N-cycling genes and transcripts. Sediments were sampled in winter (February 2018) and summer (July 2018), from 12 UK rivers with permeable beds (sand or chalk geology) and a gradient of P concentrations, in the Hampshire Avon catchment, Kent, and Essex. Methods included measurements of porewater nutrients using Skalar SAN++AutoAnalyser, nitrification rates from in-situ ‘push-pull’ injections of 15N-labelled ammonia and -nitrite, and sediment microbial gene and transcript abundance by DNA extraction and qPCR. The work was supported by the Natural Environment Research Council (Grants NE/P01142X/1, NE/P011624/1; A new dynamic for Phosphorus in RIverbed Nitrogen Cycling - PRINCe Full details about this dataset can be found at https://doi.org/10.5285/d432d96c-7aff-45a5-9d4b-37e4065afdd7 Clark, D.R. University of Essex david.clark@essex.ac.uk https://orcid.org/0000-0002-2306-0220 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Greenwood, B.N. University of Essex bgreenc@essex.ac.uk https://orcid.org/0000-0003-4586-1616 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Ma, C. Queen Mary University of London chun.ma@agro.au.dk https://orcid.org/0000-0003-1117-3313 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Si, Y. Queen Mary University of London y.si@qmul.ac.uk https://orcid.org/0000-0001-6016-0530 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Thomas, G.E. University of Essex gthomab@essex.ac.uk https://orcid.org/0000-0002-3883-177X ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Laissue, P. University of Essex plaissue@essex.ac.uk https://orcid.org/0000-0002-0165-5354 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Whitby, C. University of Essex cwhitby@essex.ac.uk https://orcid.org/0000-0003-1998-2748 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author McKew, B.A. University of Essex boyd.mckew@essex.ac.uk https://orcid.org/0000-0001-5607-6619 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author Trimmer, M. Queen Mary University of London m.trimmer@qmul.ac.uk https://orcid.org/0000-0002-9859-5537 ORCID record ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers. information author McKew, B. University of Essex boyd.mckew@essex.ac.uk pointOfContact NERC EDS Environmental Information Data Centre info@eidc.ac.uk custodian NERC EDS Environmental Information Data Centre info@eidc.ac.uk publisher University of Essex boyd.mckew@essex.ac.uk owner Queen Mary University of London m.trimmer@qmul.ac.uk owner Environmental Monitoring Facilities theme GEMET - INSPIRE themes, version 1.0 2008-06-01 publication river bacterium nitrogen cycle ammonia nitrate nitrite ammonium phosphate nitrogen nitrification chalk GEMET - Concepts, version 4.1.3 2019-01-28 creation Water quality 15N Comammox Anammox NirS nosZ amoA hzo hzs nirK nirS nrxB ureC ammonia oxidising AOA AOB Lambourn Cray Ash Darent Wylye Rib Plant Stour Ebble Marden Medway Broadstone Nadder 16S rRNA Archaea Greensand otherRestrictions no limitations otherRestrictions This resource is available under the terms of the Open Government Licence otherRestrictions If you reuse this data, you should cite: Clark, D.R., Greenwood, B.N., Ma, C., Si, Y., Thomas, G.E., Laissue, P., Whitby, C., McKew, B.A., Trimmer, M. (2022). Porewater and microbial community properties of permeable riverbed sediments across the south of England, 2018. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/d432d96c-7aff-45a5-9d4b-37e4065afdd7 textTable 1000 English utf8 inlandWaters 2018-02-01 2018-07-31 -2.2 0.96 51.02 52 Comma-separated values (CSV) NERC EDS Environmental Information Data Centre info@eidc.ac.uk distributor https://data-package.ceh.ac.uk/data/d432d96c-7aff-45a5-9d4b-37e4065afdd7 Download the data Download a copy of this data download https://data-package.ceh.ac.uk/sd/d432d96c-7aff-45a5-9d4b-37e4065afdd7.zip Supporting information Supporting information available to assist in re-use of this dataset information dataset dataset Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services 2010-12-08 Two field campaigns were conducted in 2018 in winter [February] and summer [2018] seasons) to measure in situ rates of nitrogen transformations, porewater chemistry and microbial gene abundance and transcripts in 12 rivers with permeable beds and varying concentrations of phosphorous in the Hampshire Avon catchment, Kent, and Essex. Nitrogen transformations were measured and porewater samples collected with a "push-pull" technique. Briefly, 15 bespoke stainless steel probes were installed in the riverbed at two depths (7 at 5cm and 8 at 10 cm) to cover three unvegetated sediment patches. Porewater samples were obtained by a syringe connected to the porewater probe and applying a slight vacuum (by hand). From each probe, the O2 and pH content of the porewater was first determined and a newly collected porewater sample was preserved for gas analysis. Porewater Temperature and pH were measured with a Hach multi-meter and O2 concentrations were measured with a fast response microelectrode. Finally, another freshly collected porewater sample was passed through a 0.45 micron polypropylene filter and frozen for later nutrient (ammonium, nitrite, nitrate phosphate) analysis on a Skalar SAN++ auto analyser. To measure rates of nitrogen transformations, 15N-labelled ammonium or nitrate was injected into riverbed and porewater samples for gas and nutrient/chloride analysis were recovered from the same probe over time. The tracer was 300 microM, 98 atom % 15N-ammonium or nitrate in a synthetic river water matrix with additional KCl (approx. 150 mg per L). Each experiment used 25 mL of tracer, consisted of 4-time points (immediately following the injection plus three others) and lasted for no more than 60 minutes in total. For each sediment patch, a single 2cm sediment core was taken (before push-pull analyses) and subsampled at 5 and 10 cm depths for molecular analyses. The core was positioned no less than 20cm from a push-pull probe to avoid surface water intrusion into the porespace. Subsamples were then cryopreserved in liquid N2. 16S rRNA and N-cycle functional genes and transcripts were quantified by qPCR and RT-qPCR on a on a BioRad CFX384 following extraction of RNA and DNA with PowerSoil DNA or RNA Isolation kits (Qiagen). Genes were also amplified via PCR, indexed using Nextera XT indices (Illumina) and sequenced using MiSeq Reagent Kits v3 (600-cycle)on an Illumina MiSeq sequencer in foursequencing runs.