1.1.1 Soil and its ecosystem function
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.
Research at field and microcosm scales further advanced our understanding and knowledge of nutrient cycling, greenhouse gas fluxes and physical structure mediated by interactions between roots and biological communities in Scottish soils. Key research outcomes generated throughout the reporting period included the generation of a dataset that highlighted the response of wheat mutants, with a range of rhizosheath phenotypes, to grow under different stress conditions, and linked to their respective polysaccharide exudate fingerprints. A dataset of soil physical parameters (including water release characteristics, bulk density, and penetrometer resistance) was generated from three Hutton sites (CSC, Glensaugh, and Invergowrie agroforestry) to better understand how land cover type has potential to impact a range of soil physical processes and plant-soil interactions. Finally, experimental data on the mineralisation potential of soils from selected Hutton sites was generated that advanced understanding of the influence of land management and plant species/cultivar selection on carbon and nitrogen cycling processes that underpin sustainable soil functioning. Research outcomes throughout the year have been communicated in high-impact peer-reviewed international journals, policy relevant reports, workshops with farmers/land managers, blogs, Soil Engagement Group, invited (online) conference presentations and SEFARI case studies.
* Presentations to Scottish Policy and International Stakeholders: RESAS-funded soils research was presented at three events during the year: i) A seminar entitled ‘Soil Awareness-Introduction to soils’ (17 November 2021) covering the fundamentals of soil and providing an introduction for future seminars, given to a wide range of staff in Scottish Government’s Environment and Forestry agriculture Policy Divisions amongst others (>50 attending); ii) an invited keynote presentation entitled “Resilient soils for future-proofing sustainable cereal production” at The “Genome enabled biology and contemporary agriculture” session of the Lower Saxony-Scotland Joint Forum (22-23 November 2021); iii) an invited presentation entitled “The value of Scottish soils” to the EU ERRIN Bioeconomy working group session “ The EU Soil Strategy and soil activities in regions” (15 March 2022)
* Report on Soil Health commissioned by CxC, entitled ‘Monitoring soil health in Scotland by land use category – a scoping study’. This new report assesses the efficacy of thirteen potential indicators of soil health identified in a 2020 CxC review. The report considers the relevance and suitability of these indicators across ten land uses (agriculture uncultivated, open upland habitats, environmentally sensitive areas, grassland, arable, peatlands, forestry, urban, amenity, and transport infrastructure), in the context of identifying potential impacts of climate change and biodiversity loss on soil health. While no single indicator was found to be suitable across all land uses, several were identified as being primary indicators for specific land use types, and seven were found to be extremely important indicators of soil health in more than 50% of the land uses.
* Report on reuse of waste-water treatment waste: SEFARI researchers used work funded under the SRP to contribute to a European Environment Agency report on ‘Sewage sludge and the circular economy’. The report focuses on options for recovery of energy and nutrients from sewage sludge in the context of the Green Deal and ambitions for zero-pollution. This multi-national report included contributions from academic, industry and policy experts.
* Research and Innovation Recommendation report published (DOI: 10.5281/zenodo. ) by the European Plant technology platform entitled “Plants for the future’s perspective on sustainable agriculture”. SEFARI researchers contributed to the report and led the chapter on Resilient Production (Eco)Systems.
Building on previous research demonstrating that plant identity (species and variety) impact soil biological functions and the soil physical environment, effects of different grasses on soil greenhouse gas fluxes and soil physical stability were characterised. Grass species and variety were found to be significant controls of soil microbial functional diversity, with differential impacts on carbon dioxide and nitrous oxide emission from soil. This was tested in experimental plots of an established field trial of grass species (monocultures and mixtures) and the data generated highlight potential benefits of grass species selection as a management tool to mitigate greenhouse gas emissions and promote carbon storage in soils. Related work also showed benefits of plant species diversification in field margins and buffer strips, with increased abundance of dicot species being associated with reduced greenhouse gas fluxes. Practical implications of plant-mediated soil stabilisation were further investigated, demonstrating species-specific effects related to rooting patterns, root strength and positive impacts on soil aggregate stability. This research was highlighted in the media coverage of landslips impacting rail and road links during the year and is the focus of new research also involving Transport Scotland and Forest Research.
* Policy publication: A CxC funded report showed that Scotland has a significant, world-leading soil knowledge base. However, the existing evidence base on soils does not contain tools identified as appropriate for monitoring change in Scottish soils. The report, which was signed off by the cabinet secretary for Environment, Climate Change and Land Reform, has resulted in a follow up study being commissioned.
* Root hairs for improved tolerance to drought and phosphorus deficiency; SEFARI scientists and collaborators have demonstrated the importance of maintaining root hairs on crop plants designed to cope with the impacts of environmental change. In two recently published papers root hairs in barley were found to be critical in maintaining yield in the extremely dry growing season of 2018 (Marin et al. 2020) and modelling work has demonstrated that root hairs are able to allow plants to acquire more of the phosphorus stored in soils following fertilisation (Ruiz et al 2020)
* Covid impact on UK systems: SEFARI researchers co-authored a recently published paper on the impact of covid-19 on UK food and nutrition security. The study provides an opportunity to place the initial lessons being learnt from the on‐going responses to the pandemic in respect of food and nutrition security in the context of other long‐term challenges such as climate change and biodiversity loss.
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.
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.
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.
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.
Outputs from Year 6 work coupled with continued use of several research platforms (including Grieves House and the grass/legume platform) established during the SRP will be the building blocks of aspects of JHI-D3-1, Healthy Soils for a Green Recovery funded through the SRP. This new research and associated data synthesis will identify and validate emerging land management practices to maintain and improve soil health, identify potential indicators of improvement, and quantify trade-offs between soil functions impacting ecosystem service delivery. Linkages between biogeochemical processes, plant genotype, and soil biology (e.g., grass microbiome) that underpin GHG fluxes and plant productivity will be explored (WP1, JHI-D3-1). Through development of sustainable soil management practices implemented across multiple land uses, future research activities will seek to protect soils (WP2, JHI-D3-1). This will be achieved via innovations in soil management techniques (e.g., Grieves House – low/alternative input systems, adapted rotations, novel forages, supplemented grasslands, alternative grazing regimes), or by increasing systems-based understanding of the impact of management combinations, including nature-based solutions (e.g., waste co-products, cover crops, organic amendments, increased legumes) to generate, for example, disease suppressive soils. Impacts of adopting these techniques will be assessed through existing and innovative monitoring methodologies (e.g., soil sensor networks, multispectral soil analysis). Furthermore, the CxC reports published in 2020 and 2021 have formed a key component of WP3 (JHI-D3-1) as identified soil health indicators from these studies will be tested and validated across different management practices for Scottish soils.
2016/ / / / /21
* Is soluble protein mineralisation and protease activity in soil regulated by supply or demand? Soil Biology & Biochemistry, 150, Article Number * Root-soil-microbe interactions mediating nutrient fluxes in the rhizosphere, Gupta WSR & Sharma AK (eds.).
* Rhizosphere Biology: Interactions between Microbes and Plants. Springer, Singapore, pp75-91.
* Zhou, J.; Chai, X.; Zhang, L. George, T.S.; Feng, G.; Different arbuscular mycorrhizal fungi cocolonizing on a single plant root system recruit distinct microbiomes; mSystems, 5, Article No. e .
* Researchers contributed to a report on the vulnerability of Scottish soils to a changing climate (/research/projects/measuring-the-vulnerability-of-scottish-soils-to-a-changing-climate/)
* Article in the Press and Journal on landslides and their impact on transport infrastructure (/fp/news/specials/ /landslip-stonehaven-derailment/).
* Mezeli, M.M., Page, S., George, T.S., Neilson, R., Mead, A., Blackwell, M.S.A. and Haygarth, P.M. (2020). Using a meta-analysis approach to understand complexity in soil biodiversity and phosphorus acquisition in plants. Soil Biology & Biochemistry, 142, e107695.
* Orr, J.N., Cock, P.J.A., Freitag, T.E., Neilson, R., Roberts, D.M., Davies, K.G. and Blok, V.C. (2020). Parallel microbial ecology of Pasteuria and nematode species in Scottish soils. Frontiers in Plant Science, 10, e1763
* Vink, S.N., Bienkowski, D., Roberts, D.M., Daniell, T.J. and Neilson, R. (2020). Impact of land management on nematode communities of Machair, a low-input calcareous ecosystem of conservation importance. Science of the Total Environment, 738, e .
* Neilson, R., Caul, S., Fraser, F., King, D., Mitchell, S., Roberts, D.M. and Giles, M.E. (2020). Microbial community size is a potential predictor of nematode functional group in limed grasslands. Applied Soil Ecology, 156, e103702.
* Pozzebon, Alberto; Nanda, Amrit; Schubert, Andrea; Leyva, Antonio; Miles, Branwen; Gonzalez, Cesar; Grondal, Christoph; Azevedo, Daniel; Marushchak, Denys; Maggioni, Filippo; Nelissen, Hilde; Riechmann, José Luis; José Vogelezang; Van De Velde, Karel; Ivarsson, Kjell; Bruynseels, Koen; Cornelissen, Marc; Agena, Marcel; Aguilar, Maria Boluda; Des Roseaux, Marion; Bodin, Paulin; Vamerali, Teofilo; Tilvikienė, Vita; Neilson, Roy. Plants for the future’s perspective on sustainable agriculture, doi: 10.5281/zenodo. * Neilson, R., Aitkenhead, M., Lilly, A. and Loades, K.E. (2021). Monitoring soil health in Scotland by land use sector – a scoping study, CxC, December 2021, pp. 1-8, doi:
* Xiang, Q., Qiao, M., Zhu, D., Giles, M.E., Neilson, R., Yang, X.-R., Zhu, Y.-G., Chen, Q.-L. (2021). Seasonal change is a major driver of soil resistomes at a watershed scale. Isme Communications, 1, 17.
* Holland, J., Brown, J.L., MacKenzie, K., Neilson, R., Piras, S., and McKenzie, B.M. (2021). Over winter cover crops provide yield benefits for spring barley and maintain soil health in northern Europe. European Journal of Agronomy, 130, .
* Yang, L.-Y., Zhou, S.-Y., Lin, C., Huang, X.-R., Neilson, R. (2022). Effects of biofertilizer on soil microbial diversity and antibiotic resistance genes. Science of the Total Environment, 820, * Homulle, Z, George, TS, Karley, AJ. (2022). Root traits with team benefits: understanding belowground interactions in intercropping systems. Plant and Soil, 471, 1-26.
* Lu, YQ, Wang, EZ, Tang, ZY, Rui, JP, Li, YL, Tang, ZX, Dong, WL, Liu, XD, George, TS, Song, A, Fan, FL. (2022). Roots and microbiome jointly drive the distributions of 17 phytohormones in the plant soil continuum in a phytohormone-specific manner. Plant and Soil, 470, .
* Ekeoma, EC, Boldrin, D, Loades, KW, Bengough, AG. (2021). Drying of fibrous roots strengthens the negative power relation between biomechanical properties and diameter. Plant and Soil, 469, 321–334.
* Jiang, FY, Zhang, L, Zhou, JC, George, TS, Feng, G. (2021). Arbuscular mycorrhizal fungi enhance mineralisation of organic phosphorus by carrying bacteria along their extraradical hyphae. New Phytologist, 230, .
* Mwafulirwa, L, Baggs, EM, Russell, J, Hackett, CA, Morley, N, Canto, CD, Paterson, E. (2021). Identification of barley genetic regions influencing plant-microbe interactions and carbon cycling in soil. Plant and Soil, 468, .