Clark, D.R. et al

Porewater and microbial community properties of permeable riverbed sediments across the south of England, 2018

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

Publication date: 2022-02-08

Get the data

This dataset will be available under the terms of the Open Government Licence

Format of the data: Comma-separated values (CSV)

You must 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.



Study area
Temporal extent
2018-02-01    to    2018-07-31

Provenance & quality

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 10cm) 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 25mL of tracer, consisted of 4-time points (immediately following the injection plus 3 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 10cm 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 4 sequencing runs.

Correspondence/contact details

Dr Boyd McKew
University of Essex


Clark, D.R.
University of Essex
Greenwood, B.N.
University of Essex
Ma, C.
Queen Mary University of London
Si, Y.
Queen Mary University of London
Thomas, G.E.
University of Essex
Laissue, P.
University of Essex
Whitby, C.
University of Essex
McKew, B.A.
University of Essex
Trimmer, M.
Queen Mary University of London

Other contacts

NERC EDS Environmental Information Data Centre
NERC EDS Environmental Information Data Centre
Rights Holder
University of Essex
Rights Holder
Queen Mary University of London

Additional metadata

Topic categories
Inland Waters
15N,  16S rRNA,  ammonia oxidising,  ammonium,  amoA,  Anammox,  AOA,  AOB,  Archaea,  Ash,  Bacteria,  Broadstone,  Chalk,  Comammox,  Cray,  Darent,  Ebble,  Greensand,  hzo,  hzs,  Lambourn,  Marden,  Medway,  Nadder,  nirK,  nirS,  NirS,  nitrate,  nitrification,  nitrite,  nitrogen,  Nitrogen cycle,  nosZ,  nrxB,  phosphate,  Plant,  Rib,  Rivers,  Stour,  ureC,  Water quality Wylye
Environmental Monitoring Facilities
Natural Environment Research Council Award: NE/P01142X/1, NE/P011624/1
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
09 February 2022 10:37