McCormack, S.; Ostle, N.; Bardgett, R.D.; Hopkins, D.W.; Pereira, G.M.; Vanbergen, A.J.

Soil biodiversity, carbon cycling and crop plant biomass responses to experimental biochar amendment of agricultural soil (Dundee, UK)

These data describe the results of a three year (2011-2013) factorial experiment using plant-soil mesocosms testing the effects of biochar on soil biodiversity and soil carbon fluxes. The experimental design comprised three treatments:
(1) biochar (absence or presence at 2% w/w);
(2) plant type (barley, perennial ryegrass, or unvegetated); and
(3) soil texture (sandy clay, sandy silt loam, clay loam).

Ecosystem responses measured were net ecosystem exchange of carbon (NEE) & ecosystem respiration (both g CO2 m-2 h-1) and plant biomass (g aboveground and root).

Soil biological responses measured were estimates of microbial community structure (fungal-to-bacterial ratio, total phospho-lipid fatty acid (PFLA) nmol g-1 soil) and densities (g-1 soil) of nematode worms and soil microarthropods (Collembola, Acari).

The experiment was done at the Centre for Ecology & Hydrology in Penicuik, near Edinburgh in Scotland (UK). Soils used in the experiment were taken from the top 20 cm of the soil profile, from the James Hutton Institute’s Balruderry Farm near Dundee, Scotland, UK (56° 27’ N, 3° 4’ W).

This research was funded by a Natural Environment Research Council Open CASE PhD studentship grant (NE/HO18085/1).

Publication date: 2019-08-06

Get the data

This dataset is available under the terms of the Open Government Licence

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

You must cite: McCormack, S.; Ostle, N.; Bardgett, R.D.; Hopkins, D.W.; Pereira, G.M.; Vanbergen, A.J. (2019). Soil biodiversity, carbon cycling and crop plant biomass responses to experimental biochar amendment of agricultural soil (Dundee, UK). NERC Environmental Information Data Centre.


© Natural Environment Research Council


Study area
Temporal extent
2011-06-01    to    2013-08-31

Provenance & quality

72 plant-soil mesocosms were used; they were 38l in volume (380 x 380 x 300 mm).

Soil fauna samples were taken for nematodes on 21–22 June 2011, 28–29 August 2012 and 20 August 2013, and for microarthropods (collembola, mites) on 20 August 2013. On each occasion, each mesocosm was sampled in three random locations with a 3.5 cmØ corer to 10 cm depth. Each soil core was split vertically into two halves, one half designated for nematode extraction and the other for microarthropod extraction. The three replicate halves were pooled into a single sample for each pot, with fresh weight recorded prior to invertebrate extraction. For nematode extraction, soil samples were placed in a Baermann funnel system for 24 h wet extraction. Microarthropods were collected into alcohol-filled vials using Tullgren funnels for 24 h. Following extraction of invertebrates, the soil was oven-dried and weighed to determine soil dry weight. Nematodes and microarthropods (mites and collembola) were counted under a light microscope, and abundance values were converted to standardised densities by calculating individuals per g of dry soil.

To quantify annual aboveground primary production, barley and ryegrass biomass was collected by cutting the vegetation biomass to 1 cm above the soil surface using handheld shears in September of each year, 2011– 2013. Root biomass was determined in August 2013 by taking one soil core from each mesocosm (3.5 cm Ø, 10 cm depth). Only the top 10 cm were analysed so that root data would correspond to the same soil stratum as sampled for invertebrates. Separation of roots from soil was accomplished using washing, sieving (1mm mesh) and handpicking. Once separated, the plant material was oven-dried prior to weighing.

Phospholipid fatty acid (PLFA) analysis was used in order to quantify the dry weight-based mass of markers for microbial biomass and fungal-to-bacterial ratio in the soil in different treatments. One soil sample per mesocosm (3.5 cm Ø core to 10 cm depth) was taken in August 2013 and stored at −20 °C prior to freeze-drying at −20 °C. A subsample (1 g) of the freeze-dried soil was subsequently taken for phospholipid fatty acid (PLFA) analysis. Three measures of microbial community structure were derived. Total PLFA provided a measure of overall microbial biomass; the 16:1ω5 fatty acid marker was used as a proxy measurement for arbuscular mycorrhizal biomass and the fungal-to-bacterial PLFA ratio was calculated by dividing the fungal PLFA marker (18:2ω6,9) by the summed bacterial PLFA markers (i15:0, a15:0, 15:0, i16:0, 16:1ω7, a17:0, i17:0, cy17:0, cis18:1ω7, cy19:0).

Ecosystem respiration and net ecosystem exchange (NEE) of CO2 fluxes from each mesocosm were quantified monthly. An IRGA EGM-4 connected to a gas sampling chamber (45,693 cm3) was used. The chamber was inlaid with Propafilm C on all five sides to allow light transmission so NEE of CO2 could be measured. Ecosystem respiration was measured by using an aluminium cover to exclude light from the chamber. Prior to the onset of the experiment, chamber air-tightness was confirmed by injecting a known concentration of SF6 into a chamber connected to a trial pot, then using a gas chromatograph to monitor SF6 levels over the course of one hour. Net CO2 efflux data were expressed as positive values whereas net CO2 uptake data were expressed as negative values.

Supplemental information

This dataset is a supplement to:

McCormack, S.A.; Ostle, N.; Bardgett, R.D.; Hopkins, D.W.; Pereira, M.G.; Vanbergen, A.J. (2019). Soil biota, carbon cycling and crop plant biomass responses to biochar in a temperate mesocosm experiment. Plant and Soil, 440(1–2), 341–356.

Correspondence/contact details

Dr Adam Vanbergen
Institut national de la recherche agronomique (INRA)


McCormack, S.
Centre for Ecology & Hydrology
Ostle, N.
Lancaster University
Bardgett, R.D.
Manchester University
Hopkins, D.W.
Scotland’s Rural College (SRUC)
Pereira, G.M.
Centre for Ecology & Hydrology
Vanbergen, A.J.
Institut national de la recherche agronomique (INRA)

Other contacts

Environmental Information Data Centre
NERC Environmental Information Data Centre

Additional metadata

Topic categories
biochar,  Biodiversity Climate and climate change Soil
Natural Environment Research Council Award: NE/HO18085/1
Spatial representation type
Tabular (text)
Spatial reference system
WGS 84
Last updated
26 February 2021 12:55