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Soil and its ecosystem function

Work Package 1.1 - Soil

Research Deliverable 
1.1.1 Soil and its ecosystem function
Leading Ideas 
Climate and the Environment


Soils in good condition mediate processes that underpin essential ecosystem services including plant growth, water quality and greenhouse gas mitigation. These functions are affected by complex interactions between biological, physical and chemical components of the soil. Understanding these interactions and their consequences for soil functions provides insights into the health of soils and soil’s ability to provide ecosystem services and allows us to identify indicators that can be used to support development of management practices to protect and enhance beneficial soil functions.

Aim of Research

To combine physical, chemical and biological approaches to characterise soil functions delivering essential ecosystem services. This will be done in the context of identifying the potential to promote beneficial functions of soils (e.g. water-holding capacity, resistance to erosion, storage of carbon, nutrient cycling) and to mitigate impacts on the environment (e.g. nutrient leaching and greenhouse gas emissions). The applied context that this research is directed toward is to identify management options (e.g. grass cultivar selection and tillage practice) that foster sustainable soil functioning and mitigate impacts on the wider environment.

The research builds of previous work within the RESAS Strategic Research Programme and on collaborations with UK and International partners.


2018 / 2019
2018 / 2019

The previous Year 2 laboratory work focussing on interactions between grass roots and soil biological/ physical functions was transferred into a field context with a research platform established that provided an opportunity to study both individual species (and varieties) of grass as well as mixtures of species. The importance of this research came into sharp focus with the publication of an IPCC report (October 2018) highlighting agriculture as a sector with highest recalcitrant GHG emissions, and it is noteworthy that grass seed companies have proactively engaged with the research. Extensive biotic and abiotic measurements were taken throughout the growing season. Initial analysis of data gathered confirmed Year 2 laboratory findings that variations in soil CO2 flux rates amongst grass species were not explained by differences in plant growth rates, providing evidence of species-specific impacts on soil microbiological processes. Compared to the Year 2 laboratory data, measured differences in CO2 emissions amongst grass species from the field platform were less well defined, although CO2 emissions would have been affected by the atypical hot dry spring/summer experienced during Year 3.

Parallel fundamental research to unpick microbial-root interactions was also initiated. Laboratory research coupling novel transparent soils and microscopy determined that the root systems of different cultivars were significantly different, with Phleum pratense (Timothy grass) producing smaller roots and fewer laterals than Lolium perenne (Perennial ryegrass). Furthermore, a small-scale proof-of-concept study highlighted that microbial colonisation of roots of both grasses was highly variable.

Finally, in work investigating the functional consequences of soil physics on GHG emissions from different grass species, methods (pin vane, corkscrew and laboratory based direct shear testing) developed in RD 1.1.2 indicated  an increase in soil strength (irrespective of sampling device used ) under the grass plots of the research platform when compared to adjacent bare areas of soil, although no differences between grass varieties were found at this early stage.


  • Policy interaction: Using digital mapping resources for soil hydrological data (developed in the SRP through interaction with CREW and Underpinning Capacity), SEFARI researchers were able to respond to a request from SG Policy (Climate Change and Business Support) to provide evidence in support of a derogation request to the European Commission. The evidence on the impact of the wet spring (2018) and potential damage that would result from farmers being forced to cultivate saturated soils (Crop Diversification under EU CAP Greening), supported a successful approach by SG to the European Commission that prevented thousands of farmers across Scotland facing penalties for breaching an EU regulation.
  • Knowledge exchange: Research from WP1.1 was presented to a range of science audiences (e.g. EGU Vienna, ESSC Showcase Imola, BSSS Soils and Sustainable Development Goals, and World Congress of Soil Science), industry (e.g. Continental Farming Group, Soil Essentials Ltd, Anglian Water, Beeswax Dyson Farming Ltd, Glenside Group Ltd, Potatoes in Practice), stakeholders (Farmers Journal, MSPs visiting James Hutton Institute on 28th May, Glensaugh Open Farm Sunday) and at a SEFARI Showcase event at the Scottish Parliament (highlighted in a SEFARI blog).
  • Agency and policy interaction: Prior to publication of a consultation on their Crop Production Sector plan, SEPA approached the SEFARI Sector Lead for Soils and Crops and funding was obtained via a SEFARI Spark (stakeholder priority-need targeted Think Tank) call to hold a workshop of stakeholders and policy makers (Centre for Carbon Innovation, Edinburgh, 4th March 2019) to further discuss content and implementation of the SEPA Crop Production Sector Plan.
2017 / 2018
2017 / 2018

A tool to assess soil strength (developed in Year 1) has now been used to assess impacts of soil restoration in semi-natural habitats (RD1.1.2) and applied in Theme 2 research (WP2.3) to quantify impacts of tillage management on soil structural stability. Uptake of the research is illustrated by additional stakeholder funding (Forest Research and UK Transport Research Laboratory) to investigate soil conditions in relation to landslides adjacent to a key Scottish transport corridor, Rest and Be Thankful. Further, collaborative links have been established with the University of Dundee for modelling soil reinforcement as part of an EPSRC funded project.

Biological and isotopic methods developed and validated in the previous year were applied with a strong focus on interactions between grass roots and soil biological/ physical functions. This was in the context of use of grass in grazing systems (Theme 1) and crop rotations and winter cover crops (Theme 2). Using barley as a model system, research in Year 1 demonstrated significant cultivar-specific impacts on soil functions. In Year 2 this concept was extended to consideration of impacts of different grass species and varieties on soil nutrient cycling and greenhouse gas fluxes. Screening of 10 grasses from current national recommended lists, planted in a single soil type, demonstrated significant variation (up to 3-fold differences) in carbon dioxide fluxes to the atmosphere. Stable isotope approaches resolved that impacts of the grasses on soil organic matter decomposition were not directly related to plant growth, suggesting that productivity and fostering beneficial soil functions could each be independently selected for. Design of a new field trial of grass species and mixtures to run through the remainder of the programme has been agreed. This will provide a focus for co-ordinated soil biological, physical and chemical analyses to assess impacts of grass cultivar selection on soil health and resilience.


  • Disseminating research on root-soil interactions: A presentation on mediating nutrient cycling and carbon storage was delivered at an international conference on soil organic matter and soil functions. This resulted in discussions with members of the international 4 Pour 1000 initiative, which aims to increase global soil carbon content by 0.4% annually to offset carbon emissions, and has led to new collaborations with the National University of Ireland and TEAGASC (PhD). Future funding opportunities through UK/Canada partnerships for research on soil health are being explored.
  • Soil functions: The research on impacts of grass varieties and mixtures on soil greenhouse gas (GHG) emissions is supported by two commercial seed companies, providing material for the experiments and field trial. The methods developed are also being applied to research on arable cropping systems (Theme 2) and findings from grass variety work have supported new cross-theme research on GHG mitigation potential of field margins for 2019/20. The results to date were presented at a SEFARI Gateway Event at the Scottish Parliament.
2016 / 2017
2016 / 2017

The first year of this research, methods to assess soil biological and physical functions have been developed and tested in range of Scottish soils and land uses. This has allowed improved understanding of how soils function and practical information on how management can influence delivery of ecosystem services. For example, characterisation of microbial communities in peatland soils following restoration (deforestation and drain-blocking to raise the water-table) has identified that recovery of peatland function to sequester carbon from the atmosphere is associated with changes in fungal community composition and abundance. This was assessed across peatland sites where restoration practices have been in place for different durations (i.e. a restoration chronosequence following deforestation). This is important in the context of the large contribution that healthy peat soils make to carbon storage, and the potential for degraded soils to be a source of greenhouse gases to the atmosphere. The approach can now be used to provide an index of peatland functioning, potentially providing an early indicator of the trajectory of recovery of carbon sequestration.

Soil processes that support plant productivity, mediate greenhouse gas fluxes, stabilise structure and regulate pollutant leaching have been studied, applying a range of established and novel methodologies. Stable isotope approaches have been applied to quantify plant-soil interactions influencing the greenhouse gas balances of soils, and as affected by management practices. The results highlight potential of cultivar selection to promote beneficial soil functions (nutrient cycling and soil greenhouse gas mitigation). Molecular assessment of nematode community structure has been developed as an indicator of soil functions and was used to identify that unlike other low input systems studied in Scotland, Machair soils are dominated by microbial communities that promote rapid cycling of carbon and nutrients. Novel transparent soil systems and imaging techniques have been developed to study plant-microbe-nematode interactions in detail and provide a powerful approach to characterise the mechanistic basis of processes at the root-soil interface.

Physical condition strongly affects the susceptibility of soils to erosion and landslips following heavy rainfall. A portable and practical tool to quantify soil strength in being developed and has been applied to establish the importance of root-soil interactions in maintaining soil integrity. This has potential to be applied in the practical contexts of roadside embankment stabilisation and use of cover crops to mitigate winter soil erosion losses from cultivated land.



  • A tool to measure soil shear strength has been developed to assess root-mediated stabilisation of soils, for a wide range of conditions including for embankments along transport networks. This will aid the assessment of how roots and root penetration can reduce landslips.
  • Several papers detailing novel isotopic approaches (using isotope ratios to understand organic and inorganic C partitioning) have been published with work also presented at an international workshop in Germany.
  • Five practitioner workshops were held on the importance of soil function for soil health, with around 300 stakeholders attending these events.

Future Activities

The grass field trial will provide a focus for research and knowledge exchange activities in the final two years of the programme. Monitoring of change in biological properties (microbial and faunal communities), processes (nutrient cycling and greenhouse gas fluxes) and physical stability (soil strength) will quantify impacts of grass cover on soil over time. In parallel, key plant traits (e.g. rooting structure and transfer of carbon from plants to soil) will be assessed with respect to field-measured impacts on soil processes. This will be done for grasses grown in monoculture and mixtures, aiming to identify optimal grass cover to promote beneficial soil functions. Data will be synthesised to provide a basis for communication with scientific and stakeholder audiences on best practices for use of grasses in arable systems. With the most recent IPCC report (2018) highlighting that the agriculture sector is a major contributor to climate change, this work places Scotland in a leading position globally to tackle reductions in agricultural GHG emissions and move towards a C neutral agricultural sector.

Selected Outputs