Soil Biology and Soil Health Partnership


Funded by AHDB and BBRO, the five-year Soil Biology and Soil Health (SBSH) Partnership (2017–2022) was a cross-sector programme of research and knowledge exchange.

It was designed to help farmers and growers maintain and improve the productivity of UK agricultural and horticultural systems, through better understanding of soil biology and soil health.

Soil physics, chemistry and biology are interlinked and play a role in maintaining productive agricultural and horticultural systems.

While physical and chemical properties of soil are relatively well understood, the same was not necessarily true for soil biology at the start of the Partnership.

Interest in soil health has increased and a range of indicators for soil biology had been developed through research. However, these indicators often had not been produced in parallel with the necessary guidance and tools to support management decisions on farm.

The Partnership worked closely with farmers, growers, advisers, and the wider industry, to draw together and build on knowledge and experience to create accessible guidance and tools to help farmers improve soil health.

The work formed part of the AHDB GREATSoils programme.

Reports and protocols overview

Access the reports and protocols from the 'Downloads' section at the bottom of this page.

Integrated final summary report

Projects reports 1–14 are interconnected, with findings from one informing activity in another. This report provides an integrated summary for the full Soil Biology and Soil Health Partnership project. 

Report 1: How management affects soil health

This element reviewed the scientific and grey literature on soil health, with a focus on UK (temperate) cropping systems. The work described how management affects the biological, physical and chemical properties of soil. Based on the findings, the work improved a model and ways to describe soil-health interactions.

Report 2: Development of a soil health scorecard

This project identified 45 biological, physical, and chemical indicators of soil health. Following assessments for relevance and practicality, the list was reduced to 12 indicators, including: pH, routine nutrients, loss-on-ignition, microbial biomass, respiration, nematodes, earthworms, visual evaluation of soil structure (VESS), bulk density, and water infiltration. A provisional scorecard was developed to indicate the status of a soil against the indicators. The work also detailed the threshold values used to delineate the categories.

Report 3: Molecular approaches for soil health assessment

This review summarised and evaluated molecular (DNA) approaches to analyse soil microbial communities, including soilborne pathogens, and other indicators of soil health. It included a review of soil sampling and DNA extraction procedures. It also described the markers used to investigate soil organisms and their functions and identified technical challenges associated with adoption.

Report 4: Quantifying how sites and management affect soil health

This project measured the impact of site and management on soil health scorecard indicators at seven experimental sites (2017–20). The research identified areas of ‘sub-optimal’ soil health and a positive relationship between grain yield and some indicators, particularly organic matter, and nutrient status. Differences between sites were greater than differences between management practices at a single site. Based on management practices, the following observations were made:

  • Optimising pH ( 6.5) maximises nutrient availability, biological activity and crop productivity
  • Organic materials (particularly bulky, high dry matter materials) are a valuable source of organic matter and nutrients, and promote soil biological activity
  • Inclusion of grass leys (2–3 years) improves soil organic matter, nutrient status, biology and structure
  • Intensive cultivations reduce soil penetration resistance, bulk density, and earthworm numbers
  • However, occasional tillage of no-till fields does not necessarily result in a significant decline in soil function

Report 5: Molecular approaches for soilborne disease management

This project optimised and standardised methods for sampling and extraction of DNA from soil samples. Quantitative PCR (qPCR) was used to detect and quantify bacterial and fungal communities, including pathogens and biocontrol agents. DNA sequencing data revealed the diversity of bacteria, fungi and mesofauna present. The molecular approaches were used to assess the impact of various soil management practices in long-term field trials (Projects 4, 6 and 7). This found that soil pH affected general bacterial and fungal activity, and that cropping stage had an interacting role. Total bacterial and fungal populations were also affected by repeat applications of farmyard manure. However, they were not affected by inorganic fertiliser, tillage approach or drainage routines. However, the largest differences were observed between trial locations.

The final report from a linked PhD studentship project is also available

Report 6: Using DNA to assess soil health

Soils contain a large amount of life. Large organisms, such as earthworms (macrofauna), are relatively easy to detect. However, smaller organisms, such springtails (mesofauna), nematodes (microfauna) and bacteria, fungi and viruses (microorganisms) often require specialist skills and equipment to identify them.

This project evaluated DNA extracted from soil samples – ‘environmental DNA’ – to help identify organisms (dead and alive). The researchers examined three DNA extraction methods (and helped standardise them). The extraction method used affected the organisms detected. The best approaches accounted for intracellular and extracellular DNA.

The project also helped measure soil biological communities in the Soil Biology and Soil Health Partnership’s long-term trials. Nematodes and springtails were mainly influenced by site factors, such as soil type and land use. Microbial community composition was affected by geographical location and relatively small changes in soil pH.

With no robust UK benchmarks for biological communities (and DNA-based testing costly), the research did not recommend using such approaches for the routine monitoring of soil health. However, the project did significantly advance the use of such approaches.

Report 7: Organic and biological amendments in horticulture

This project focused on the effects of organic and biological amendments (incorporated pre-planting) on soilborne pathogens associated with three horticultural crops – a vegetable (onions), an ornamental (narcissus) and a fruit (raspberry) crop.

7a onions

This trial incorporated cover crops and/or green compost into a field with a recent history of onion fusarium basal rot, prior to planting onions. Molecular diagnostics quantified the presence of Fusarium oxysporum, with results compared to an unamended control. Although disease levels were high (with only 9.5% of onions deemed marketable) no significant crop-performance differences were recorded between treatments.

7b narcissus

This trial incorporated pig farmyard manure (FYM) and/or green compost into a field, prior to cultivation and planting narcissus. A granular mycorrhiza product was also applied to bulbs during planting. Although molecular diagnostics detected no Fusarium oxysporum in the field, it was present in 38% of the planted bulbs. The single application of FYM and/or green compost had little effect on topsoil health, and no impact on fusarium infection or crop performance. Although the mycorrhizal product appeared to be associated with reduced disease levels (fusarium and Verticillium dahliae) and improved crop growth, the trials could not rule out a plot position effect.

7c raspberry

This trial incorporated anaerobic digestate solids (PAS 110 vegetable waste) at a commercial fruit farm field infested with Verticillium dahliae (the cause of verticillium wilt), prior to growing a susceptible raspberry variety for three years. The work also tested three annual applications of a biofungicide (Prestop, Gliocladium catenulatum) to the planting holes. Overall, no benefit to crop vigour, fruit yield or expression of Verticillium wilt symptoms in raspberries was recorded and no significant change in V. dahliae soil inoculum levels was observed.

Report 8: Benchmarking of soil health understanding

This project used an online questionnaire and two industry workshops (2017), which involved farmers, growers, advisors and industry partners, to shape soil health research and knowledge exchange. In parallel, the researchers consulted with academics and other technical experts. The process identified a wide variety of on-farm soil health innovation and the need for soil health guidance at various levels, from basic background to in-depth technical information. The information informed the development of subsequent projects and activities.

Report 9: Evaluating the soil health scorecard approach

This report describes the evaluation of the soil health scorecard approach on UK commercial farms, with diverse climate, soil types and systems represented. Around 100 farmers worked together across eight innovation-research groups. Collectively, the farmers had a range of experience, from those unsure to those confident about soil-improving management practices. The work confirmed that the field sampling protocol was relatively easy to follow, with most farmers (80%) completing field data and submitting field samples. Overall, farmers liked the approach and its ability to provide an integrated snapshot of soil heath, promote discussion and identify ways to improve soil management. The project also led to refinements to some soil health indicators.

Report 10: Knowledge transfer elements

This element of the project covered knowledge transfer. As such, no specific report is due. Delivery of this component was assessed via the various outputs from the project, such as guidance and events.

Report 11: Indicators of soil microbial activity

The size and activity of soil microbial biomass can be used to help indicate soil-health status. The standard assessment method uses hazardous reagents (chloroform extraction) and is not offered by the main commercial laboratories in the UK. This project explored two potential alternatives:

  1. Potentially mineralisable nitrogen (PMN), which measures of the quantity of nitrogen readily decomposed under controlled (anaerobic) conditions
  2. Solvita respiration burst, which measures the quantity of carbon (C) released (as CO2) when a dried soil is rewetted

This project analysed UK agricultural soils establish ‘typical’ guideline values for all mineral soil textures (<20% soil organic matter). It involved the analysis of many soils: PMN (625 arable soils) and respiration burst (1,803 arable and 310 grassland soils).

Report 12: How cultivation affects soil microbiology

This field experiment investigated how cultivation affects soil microbiology. Three strips were ploughed in a long-term (>7 years) direct drilled field. After three years (in 2020), soil samples were analysed for functional microbial activity and diversity. No increase in nitrous oxide was observed in any plot. Generally, carbon dioxide (an indicator of greater microbial activity) and soil organic matter were relatively high in direct drilled plots. Results also suggested that microbial community in these plots had a greater functional diversity, as they metabolised a wider range of substrates compared to the ploughed plots. In general, DNA-based measures failed to detect significant differences between treatments. Several challenges with DNA testing were identified, including high soil sample variability.

Report 13: Data analysis and statistical modelling

This project used data analysis and statistical modelling. In particular, the work explored the associations between soil health indicators and crop yield. It also investigated the relationships with environmental and management variables.

The work used 78 farmer-completed and 169 research/agronomist-completed soil health scorecards. Management data for 336 crops/intervals was also collated.

The analysis established that soil organic matter (SOM), soil structure, pH and nutrient (P, K, Mg) availability were the most important measures.

The research suggested that rotational land use explained some of the differences in scorecard data. Grassland sites could be distinguished from rotational cropping systems, mainly due to higher SOM content and earthworm numbers, and, conversely, lower pH, P and K. The cropping sites were more similar, although sites with rotations including-late harvested crops generally had lower SOM and earthworm numbers. When the scorecard results were considered by soil texture group, there was weak evidence of separation between soils with light and heavy textures.

Simple segmentation can support benchmarking, but it cannot explain soil health variation fully. Additionally, the importance of site-specific factors makes the production of robust benchmarks, at a regional or national scale, challenging.

Project 14: Rectifying soil structural damage

This project summarised current guidance on how to rectify soil structural damage, with findings presented across three sections:

  1. Effect of vigorous rooting green crops (cover crops, catch crops, green manures and short-term herbal leys)
  2. Guidance on rectifying soil structure
  3. Evaluation of the soil health scorecard in situations with evident soil structural damage

The results highlighted a lack of a clear and consistent effect of vigorous rooting crops on soil structure. Some results suggest that such crops may benefit topsoil structure in reduced or no-till cropping systems after multiple years. Tap-rooted species may also be most suited to improving soil structure in compacted soils.

Soil Health Scorecard sampling protocol and benchmarking tables

The protocols provide guidance on taking soil samples and making field records. They also include detailed information about benchmarks for physical, chemical, and biological indicators of soil health. Due to variations in the approaches required across GB regions, protocols for England and Wales, and Scotland are available.

Beef & Lamb,Cereals & Oilseeds,Dairy,Pork
Project code:
01 January 2017 - 28 February 2022
AHDB sector cost:
Total project value:
Project leader:
NIAB (Scientific partners: ADAS, FERA, GWCT, ORC, SRUC, Natural England, University of Lincoln. Industry partners: BASF, Frontier Ltd, Innovation for Agriculture, LEAF, NRM, Wye & Usk Foundation)


91140002 integrated final summary report for the SBSH Final Report 1: Translating knowledge of management effects on soil biology and soil health for practitioners Final Report 1b: Translating knowledge of management effects on soil biology and soil health for practitioners (supplementary information) Final Report 2: Selecting methods to measure soil health and soil biology and the development of a soil health scorecard Final Report 3: Molecular approaches for routine soil-borne disease and soil health assessment – establishing scope Final Report 4: Quantifying the effects of management on soil health Final Report 5: Molecular approaches for soilborne disease management Final Report 6: Using DNA to assess soil health Final Report 7a: Organic and biological amendments in horticulture – onions Final Report 7b: Organic and biological amendments in horticulture – narcissus Final Report 7c: Organic and biological amendments in horticulture – raspberries Final Report 8: Industry benchmarking – Identifying current understanding, knowledge gaps and confirming the key priority issues in understanding and management of soil biology and health Final Report 9: Evaluating the soil health scorecard approach Final Report 9 (Annex 1): soil health scorecard data Final Report 11: Developing UK-relevant benchmarks for soil health indicators: Potentially Mineralisable Nitrogen and Solvita respiration burst Final Report 12: How cultivation affects soil microbiology Final Report 13: Data analysis and statistical modelling Final Report 14: Rectifying soil structure damage using vigorous rooting green crops AHDB Soil health scorecard protocol and benchmarking - England and Wales (v1.0) AHDB Soil health scorecard protocol and benchmarking - Scotland (v1.0)