You are here

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.


2019 / 2020
2019 / 2020

Year 4 research combined controlled-environment and field experiments and built on work conducted in years 1-3. A microcosm experiment, run under controlled conditions, was used to identify the effects of grass ley species composition on the production of greenhouse gases (GHG) from soil and identify opportunities to balance grass productivity and mitigation of GHG losses through cultivar selection.

Synthesis of Years 2-4 data sought to identify the extent of variation in GHG emissions across species mixtures, the degree to which this can be predicted from the established contributions of individuals, and the extent to which this is correlated (or not) with aboveground biomass production (productivity). Data analysis is  ongoing, with initial results suggesting that CO2 emissions varied between grass mixtures, and was correlated with root growth;  above ground diversity; and presence of clover in the grass mixture.

Previous work demonstrated variation in plant-mediated impacts on microbial community structures; providing a potential means of manipulating soil functions for benefits such as enhanced nutrient supply and mitigation of GHG fluxes. Using the previously established grass platform, baseline data was collected throughout Year 4 to be used as a comparator and conditioned soil obtained for use in future (Year 5) experiments. Complementary studies on physical aspects of soil are key to understand plant-soil interactions. Thus, measurements of soil stability using the previously developed field measurement tool were applied to the replicated grass plots to investigate temporal changes in soil stability resulting from grass sowing. In addition, the temporal dynamics following revegetation (grass plots), were investigated to understand the time required to deliver similar levels of reinforcement by established roots as observed in previous studies. Data collation and analysis have been completed with interpretation of results to follow.

Utilising approaches developed to visualise microbial community development in the rhizosphere of grasses (Year 3), grass species were screened to identify their impacts on soil microbial community structure, nutrient cycling and GHG emissions. This work sought to identify phenotypic root traits that could be used as predictors of impacts on soil functions. Detailed study of root interactions with soil bacteria (Pseudomonas fluorescens and Bacillus subtilis) demonstrated dynamic processes surrounding root meristems, and these explained subsequent colonisation and formation of biofilms on or surrounding plant roots. The dataset provided quantitative information on variation in root morphological traits and their impacts on microbial populations around roots. Furthermore, using similar approaches on Bere barley supported work that identified candidate genes involved in rhizosheath traits.



  • Global distribution and functionality of soil nematode communities. SEFARI research contributed to a paper published in Nature detailing the global distribution of soil nematode communities. This international collaboration utilised data generated from 6,759 georeferenced samples from across the globe to quantify distribution of nematode functional groups. The paper closely aligns with SRP research utilising nematode functional group abundances to infer soil health and biogeochemical cycling. The paper highlights how the global dataset can be used to improve representation of biological processes in global climate change models.
  • Invited presentations to academia and industry. SEFARI scientists have been invited to present work from the SRP at a range of key international meetings (e.g. Slope Processes and Vegetation Effects, Soil Organic Matter in a Stressed World, BES Annual Meeting), to industry stakeholders (e.g. CHAP Soil Forum, Finding Fertile Fields for the Future) and for industry publications (e.g. Farmers Journal Scotland) emphasising the work’s sectoral and international interest in and impact  of SRP-soils research.
  • Translational science in Africa: In Jan 2020 a SEFARI researcher secured funding (GCRF NERC/BBSRC Translation Award) to continue work on optimising agronomic and crop variety selection for sustainable maize cultivation systems in southern Africa. The research project (AfricaSOIL) will apply approaches originally developed within the RESAS SRP and has a focus on trial sites and small holder farmer communities in Malawi and Zimbabwe.
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 platform will continue to provide a focus for research and knowledge exchange activities but expanded with the introduction of replicated plots of mixed grass and legume species and supported by further controlled environment studies. Controlled environment experimental results with respect to impacts on soil processes, and to investigate potential trade-offs between productivity and beneficial soil functions (i.e. to inform management strategies for ley rotations) will be validated using the grass platform. The forthcoming research will include exploring and identifying the impact of plant and management legacy effects on soil microbial community functioning. This will be achieved under controlled conditions using soils conditioned during Year 4 and will test the long-term interaction of crop and management on soil function. Approaches used in the grass work will be translated to work on buffer strips where those dominated with grass species generate more nitrous oxide emissions than those dominated by dicots. We will test whether dicots release fewer GHG emissions than monocot species under controlled conditions. This will generate objective evidence on the potential advantage, with respect to GHG mitigation, of plant species diversification in buffer strips. Underpinning the soil biological data, the dataset generated on the changes in root mechanical properties, and changes in soil stability as different grass varieties become established, will be analysed to look for significant effects over time and between species. The overarching aim is to support farmers in development of strategies to promote soil nutrient cycling functions and mitigate GHG emissions. This work will place Scotland in a leading position globally to tackle reductions in agricultural GHG emissions and move towards a C neutral agricultural sector. Thus, helping to address concerns that the agricultural sector is a major contributor to climate change.

Selected Outputs