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Integrated management systems

Work Package Agricultural systems and land management

Research Deliverable 
Integrated management systems


Modern agriculture faces the challenge of simultaneously producing healthy food, adapting to climate change, protecting natural resources and conserving biodiversity. Designing farming systems to achieve these multiple goals, combining both improved productivity and sustainability, is a complex design problem with synergies, trade-offs and conflicts between the different elements of the system. Whole-system effects of management change are rarely studied and so trade-offs and conflicts between different components of the agricultural system are poorly understood. Here, we focus on systems level integrated management options for multiple benefits; designing livestock and cropping systems to maintain productivity whilst protecting the environment and enhancing farmland biodiversity.

Aim of Research

The aim of this research is to develop integrated management systems to enhance economic and environmental sustainability in agriculture, focusing on two production systems: arable and ruminant livestock. First, new technologies and management strategies rom existing research and linked RDs (primarily 2.1.6, 2.1.8, 2.3.4, 2.3.8) will be reviewed to identify state-of-the-art best practice options. These will then be combined into a set of integrated management systems, applied in four case studies: animal mounted sensors for the detection of parturition in beef cattle; targeted selective treatment for management of worm burden in sheep; integrated arable cropping system for sustainability at the Balruddery long-term experimental platform, and; the EU-ENDURE wheat based rotation for integrated management. Once established, these case studies are used to test and develop tools for assessing the impact of new management strategies based on suites of systems-level indicators. Finally, each case study scenario will provide data for the quantification of environmental and economic sustainability and the elements therein. Analysis and multi-attribute decision tools will be developed for future agricultural sustainability assessment by key stakeholders in the policy development, industry and research communities.



Traditional agri-environment incentive schemes, based on application of prescribed management interventions often do not deliver the biodiversity or sustainability outcomes they were intended to achieve. The reasons vary widely, but without reliable systems in place to monitor the direct impact of changes in management for environmental benefit, improvements in agroecosystem biodiversity and environmental impact are unlikely. Work in 2.3.9 via Hutton’s Centre for Sustainable Cropping long-term experimental platform and associated farm networks across Scotland and the UK have been instrumental in delivering a framework for outcomes-based approaches. Multiple benefits are defined in terms of (i) soil health (CSC is a lighthouse for UKSoils with the Soil Association as a key stakeholder), (ii) biodiversity (working closely with NatureScot on Piloting Outcomes Based Approaches in Scotland, and CEH on the UK Pollinator Monitoring Scheme, with 2 associated PhD studentships developing work alongside the Scottish Pollinator Strategy), and (iii) crop quality (with funded projects on variety trials with SSCR, and direct KE input from the Association for Independent Crop Consultants, Soil Essentials and LEAF).

Indicator data gathered at the CSC has been used to identify trade-offs between different elements of sustainability in the transition period towards regenerative, nature-based farming. Cost-benefit analysis has clearly shown an initial financial cost to the farmer of adopting agroecological practices.  Although this cost is predicted to decline over time to a point where the new farming system is both more profitable and environmentally sustainable than the comparable future standard, we have shown how outcomes-based incentive schemes approaches can be used to encourage initial uptake, deliver better results through iterative monitoring, and help realise the potential for an agroecological approach to farming in Scotland.


This work has provided the underpinning for a range of new joint ventures

  • UKRI and CTP proposals with LEAF, NatureScot, Syngenta and University of Dundee to produce a suite of biodiversity, water quality and soil function indicators for use by farmers to directly measure the impact of environmentally friendly farming practices. These will be based on Syngenta’s LivinGroTM project and Hutton’s long-term research platforms (GrievesHouse and CSC) to identify indicators and ground truth the resulting set of user-friendly monitoring tools in commercial farms.
  • Indicator-based tools must be cost effective, easy to use by non-experts and provide rapid, unbiased, accurate and representative data. Automated monitoring and phone-based apps to help achieve this using smartphone imagery and spectral imaging devices and has been demonstrated for soil physical properties at the CSC, Hutton platforms and commercial farms throughout the UK.
  • The NERC funded RETINA project with University of Aberdeen and CEH is also developing smartphone technology to combine remote sensing, ground based sensors and high-performance computing at the CSC platform to monitor changes in soil carbon and GHG emissions under different management systems in near real time.
  • Biodiversity indicators are notoriously difficult to monitor using automated techniques, but BOREALIS, a seedcorn funded pilot study has been funded based on prior collaboration with Syngenta and NatureScot at the CSC to explore deep learning image analysis approaches for on-farm biodiversity monitoring, reporting and verification.

The integrated management systems developed here are designed to provide improved environmental outcomes from agricultural systems and therefore higher levels of public goods, whilst maintaining productivity and economic viability. Balancing these trade-offs requires a whole systems approach to assessing arable ecosystem sustainability (Hawes et al., 2016), and previous studies based at the Centre for Sustainable Cropping platform have demonstrated improvements to soil properties, biodiversity (Hawes et al., 2018) and overall environmental impact (Hawes et al., 2019). However, at least in the initial stages of transition from standard commercial practice, these benefits traded off against poorer economic outcomes (Abdul-Salam et al., 2019). In Year 5, a cost-benefit analysis of conventional vs integrated cropping systems was used to further explore this economic trade-off for farmers and inform development of incentives to promote public good provision in arable farming. Analysis confirmed that during the initial stages, integrated systems had higher costs, lower income, and consequently lower profits and a poorer cost benefit ratio when compared to conventional practice. Environmental gains are, predominantly, public goods (OECD, 2001) and we have demonstrated that this may come with a private cost to farmers. Promoting integrated cropping to farmers in Scotland for environmental gains will therefore need to overcome financial barriers. Further work is now required to identify appropriate outcomes-based incentive approaches (e.g. POBAS, NatureScot) and the longer-term effects of more environmentally sustainable management where regenerative approaches may help improve efficiency, reduce costs and therefore ameliorate the initial losses in profitability over longer time scales.


  • The integrated management system has proven that regenerative approaches enhance arable diversity and sustainability, resulting better internal regulation of ecosystem processes and less reliance on external inputs (review published by CABI).
  • The DEXi-CSC model is now the basis for collaborative work with INRAE (developing decision support tools) and Qualitix (application of our framework to roll-out their sustainability tool from US to UK and EU).
  • Technical notes have been produced for LEAF, contributing to the new LEAF Innovation Library. Other online resources have been made available through UKSoils Soil Lighthouse, SEFARI reports, podcasts and webinars (TEAGASC, Agrii, BASE and Arable Scotland).
  • A virtual tour of the CSC case study platform has been produced through SEFARI funding and is available via the link from the CSC website ( or at

Improvements in arable production must include multiple co-benefits to the whole cropping system, not just yield. To this end, we have reviewed best practice options and put together a suite of management tools to achieve these multiple goals of productivity, soil health, biodiversity and resilience. These have been applied in two case studies, monitored using indicators of system function and results used to refine the system through iterative consultation with stakeholders. Analysis of case study data highlighted specific areas where performance could be improved. These were primarily in relation to resource use and losses from the arable system which reduced efficiency of production and negatively impacted on economic viability. IPM strategies were also highlighted as opportunities for further development, particularly with respect to biofortification for resilience to disease. Consultation with agronomists, farmer groups and other stakeholders, enabled refinements to the management practice options of the integrated crop system to address these issues.

Cereal -focussed surveys, designed to establish baselines for IPM adoption in the UK, identified factors including farm area, and familiarity with IPM, as drivers to IPM adoption. The source of information on pest control influenced farmer familiarity with IPM with those who were proactive in seeking information from impartial sources being more engaged and reporting higher levels of adoption. Findings were presented at International Plant Protection Congress (IPPC) in November 2019 and a paper was written and presented at the Crop Production in Northern Britain Conference. Investigations into the potential for barley varietal mixtures to be used as part of an Integrated Disease Management strategy continued with early findings showing specific combinations of varieties can outperform monocultures under reduced fungicides programmes. These findings were presented at FAS events in Lanark and Aberdeen. The requirement for an IPM plan was included for the first time in the Scottish Quality Crop quality assurance scheme covering 95% of arable cropping in Scotland and links with the Voluntary Initiative in Scotland established to further enhance uptake and awareness of IPM practices. Joint KE events (such as farm open days, plot tours, podcasts and workshops) linked the systems work to the findings on cropping diversity and alternative management practices.

From the livestock perspective, technology integration and data management strategies have been deployed in collaboration with industry partners to improve production efficiency and traceability of cattle. Compulsory electronic tagging of cattle using ultra-high frequency (UHF) technology will be coming into force in 2021. UHF offers many benefits over low-frequency technology (speed, accuracy, cost, read-distance, multiple simultaneous reads). The work carried out in collaboration with ScotEID, has focussed on using UHF technology and GPS in commercially applicable situations by retrofitting this technology to create a state-of-the-art livestock transportation box. A batch of cattle were UHF tagged and had exceptionally high read rates over multiple loadings. This represents a huge leap forward in terms of livestock traceability.

In terms of animal health, analysis of minerals and DCAD (dietary cation anion difference) from 28 silages were used to provide recommendations to farmers for improved dietary related health issues and a resulting improvement in animal health was noted. Health events from all cows during this time period were collated to examine the effects of silage fed in the dry period on health. Pneumonia is also a significant economic and welfare problem for both pre-weaned dairy calves and weaned suckler beef calves. Previous work has shown that activity and feeding behaviours are good indicators of respiratory disease, often 2-3 days before clinical symptoms. State-of-the-art heart rate sensors were therefore adapted for calves and a pilot dataset captured to understand the effects of disease status on heart rate variability.



  • New best practice management strategies have improved the input use efficiency, soil quality and biodiversity of the integrated arable production system at the Centre for Sustainable Cropping and trials at Balruddery Farm. These formed the basis of discussions with stakeholders at the IPM/CSC stakeholders workshop (October 2019) and results were presented at the Hutton symposium (October 2019) and Barley and Potato Away days (February 2020).
  • Legacy effects of legume- and oat-based biomass crops have proven to increase subsequent winter wheat yields by 30%, representing a significant gain in production efficiency with minimal environmental impact as part of an integrated cropping system.
  • We have developed and integrated technologies and automated data transfer (ultra-high frequency EID, GPS, temperature) to optimise traceability of cattle in the UK during transport.
  • Refinements based on novel on-farm nutritional data have been used to optimise health and productivity in dairy cattle; a GPU powered system and Deep Learning software was deployed to extend our analysis power further.

Measurements of systems performance indicators for environmental and economic sustainability have demonstrated significant impact of integrated management on system properties including biodiversity, pollution and resource use, soil health, productivity and gross margins. Integrated systems improve soil health, enhance farmland biodiversity and reduce losses of agrochemicals which cause pollution of water courses, air and soil. However, economic performance, viability and yield stability tend to be lower, particularly in more intensively managed crops such as potato and winter cereals. In collaboration with key stakeholders, iterative improvement to the integrated management systems are being made to further build on the positive outcomes and mitigate the costs of more sustainable farming practices. This work has been reported and demonstrated to industry and policy stakeholders through 24 KE activities over the course of the year including farm tours, site visits, presentations and regular annual institute events.

Data from the two arable case studies where integrated management options have been applied were used to parameterise MADM DEXi models for testing overall sustainability, broken down hierarchically into Environmental and Economic components and a suite of aggregated indicators. Results are used to assess "success" of the management options with respect to the overall sustainability goals and provide a targeted means by which improvements in the management systems can be made.

The integrated cropping system improved environmental sustainability at the field scale relative to standard practice through enhanced biodiversity, reduced losses and more efficient resource use. However, economic sustainability was lower relative to conventional practice due to lower yields for some crops, although varieties with deeper rooting structures tended to perform better under integrated management, particularly during dry years. Lower scores for economic sustainability offset the benefit in terms of environmental indicators, resulting in no difference in overall sustainability.

The MADM can now be used for sensitivity testing to identify key drivers of system sustainability and trade-offs between components of arable ecosystems. Specific areas of research were identified that require further testing and investigation in years 4 and 5. These focus on uptake of IPDM strategies and include testing barley varietal mixtures as part of an Integrated Disease Management Strategy and establishing a baseline for IPM uptake for cereal crops in Scotland.

Findings were reported at Syngenta Cereals winter meeting, SRUC annual potato conference, SSCR winter meeting and the IPM@Hutton stakeholders’ workshop.

Companion planting and mixtures trials at the ENDURE rotation demonstrated a positive response of rye and legumes to low rate nitrogen inputs in terms of biomass production, relative to barley and oats monocultures which had considerably reduced yield with no nitrogen. Protein and digestibility were both increased with legume composition, but dry matter was highest in barley and lowest in legume monoculture. Overall dry matter production was highest for rye, but pea-rye and bean-rye were also high with better digestibility and protein at both nitrogen inputs. Legume mixtures can therefore significantly reduce the reliance on mineral fertiliser inputs in arable production and options for inclusion of this management strategy into the Integrated Management System and the long-term platform will be reviewed.


  • We have constructed and parameterised a multi-attribute decision support model that allows a field scale assessment of environmental and economic sustainability. This model is available for sensitivity testing and identification of key sustainability indicators in arable ecosystems and can be used to predict likely impacts of a change in management strategy or cropping system.
  • We have demonstrated that an integrated management system can provide multiple benefits including improved soil health, enhanced biodiversity and reduced pollution whilst maintaining crop yield. Developments formed the basis for Scottish Parliament Citizen’s Jury on land management and the natural environment.
  • A stakeholder group has been convened to provide input to sustainability research directions at the institute and Hutton colleagues gave talks at the inaugural meeting, which was attended by six stakeholders from farming, land use and industry organisations. Future meetings will focus on specific areas of research that are considered of particular importance to sustainable farming in the future.

Frameworks, indicators and monitoring apps developed in the first year of this RD have been applied to a range of different systems. Case studies have been established where the goal of management has been to improve the overall sustainability of the arable and livestock food production systems. Monitoring of key system indicators and assessment of system performance was carried out throughout the year, generating a large number of datasets for quantification of progress towards sustainability goals.

Consultation with independent agronomists and industry bodies, together with information on IPM, soil management and novel cropping from linked RDs, have generated new developments to the management system. These include more cover cropping, intercropping and IPM strategies to be tested and incorporated as part of the iterative development of the IMS in future years.

A survey was carried out with colleagues from N and S Ireland and England, to elicit data on awareness and uptake on integrated management practices and determine the base line awareness in each country to inform future work and KE needs.  Awareness of IPM was strongly linked to uptake of IPM measures. Field trials testing key interventions were also run to inform and support publication and KE. A paper was written and presented at the Crop Protection in Northern Britain Conference.

Using smartphone imagery and the original visible-wavelength low-cost sensor, we have generated a dataset of soil sample data and spectral/colour information. This data is from a number of locations across Scotland and is being used to produce national-scale and local-scale spectral and colour estimation of soil properties. One paper has been published and three more are being written. We can now use smartphone imagery of topsoil to estimate a number of soil properties including carbon, pH, texture, major nutrients and a number of elements. This will enable us to improve our estimation of soil properties in the field.

Data gathered on soil, plants, invertebrates, crop productivity and economic indicators at the CSC long-term platform were collected throughout the growing season. A database was built with a web front end and will be made available via the CSC website to help promote open access use of the information and samples collected. Datasets on selected indicators were extracted from the database for analysis to compare conventional versus IMS management impacts. This work has resulted in 1 published article, 3 further papers under review and 4 in preparation for publication. Results were presented at the SSCR annual winter meeting.

The final season of three different rotations was completed at the ENDURE case study, comparing Current - winter wheat, winter wheat, oilseed rape; Intermediate - winter wheat, spring barley, oilseed rape; and Advanced - winter wheat, peas, oilseed rape rotations where the intermediate and advanced treatments also included reduced dose and more effectively targeted fungicides, resistance elicitors, cultivar choice and mixtures, reduced herbicides and fertiliser. The outcome emphasised the potential for the intermediate treatment to improve sustainability. These findings have been reported to the ENDURE network integrating them with coordinated trials to derive knowledge for improved IPM in cereal-based rotations in north-west Europe in particular.


  • We have produced a fully relational, SQL database with a web based front end to allow open access to systems indicator datasets collected from the Hutton’s long-term sustainability platforms. This has been populated with extensive data on key systems indicators which can be made publicly available on request. The front end will be developed as a part of a website on sustainability research with materials including field mapping for precision agriculture, decision support models, meterological data and agronomic information.
  • A blog post was produced for SEFARI ( along with an article for Crop Production Magazine (  and Global Farming magazine 2017. (, promoting and communicating our RESAS funded research on agricultural sustainability
  • Work on improving measurement of greenhouse gas emissions, particularly methane, from individual cattle and sheep and their systems continues.    In addition to providing new information about the effects of feed components on methane emissions, as well as insights into the pathways for methane production, these studies provided samples for ongoing analysis of the feasibility of using rumen metabolites and/or rumen gene abundances as proxies for methane emissions. Further measurements will be made in year 3 to expand the range of diets in these predictions.
  • Working with a commercial pattern we have extended the amount of individual cow milk mid infrared spectral analyses we have recorded across UK herds. During the reporting year the system was updated to predict 5 traits related to individual animal feed efficiency and metabolic status for over 1,000,000 animals and over 10,000,000 milk test days records. This a rich resources that will be mined through the rest of the programme. If successful this system will help farmers by routinely flagging fertility and/or health status of animals in (near) real time and remotely such that a management intervention can be undertaken.

Significant progress has been made towards the overall aim to develop integrated management systems for improved economic and environmental sustainability. Indicators and monitoring apps have been identified, a framework for assessment has been established and management systems have been put in place in several case studies.

Building on the past 15 years of work on biodiversity and sustainability indicators and monitoring frameworks, we have developed a whole systems framework for designing and testing new sustainable cropping systems. Development of sustainable, integrated management systems is an on-going, iterative process of review, implementation, monitoring and testing. This process has been initiated during the first year and will continue to run throughout the five year work programme.  The initial review has identified four main areas for development: conservation strategies for ecosystem services; soil cultivations to improve structure; sustainable management of plant nutrients, and; integrated pest management strategies to complement reductions in crop protection inputs. A suite of management options has been identified, with input from external agronomic advisors for each of these areas, integrated into a single cropping system and implemented at the Centre for Sustainable Cropping long-term platform. Finally, a suite of indicators for assessing impact were selected to represent environmental, ecological and economic components of the cropping system. The impact of this management system will be monitored and assessed in the coming years. This work has set in place a framework within which future monitoring at the Balruddery platform case study will be carried out through the remainder of the work programme. A peer reviewed publication and book chapter have been produced and the framework is described on the new CSC website, to go live in June 2017.

A portable low-cost hyperspectral sensor has been developed and is currently being tested using field experiments at Balruddery and the Invergowrie site. We have been able to link sensor readings to soil nitrogen levels and can distinguish between individual crops. The sensor can also be used to estimate soil carbon, pH and nitrogen content. Additional work has shown that smartphone imagery of soil can be used to provide estimates of soil characteristics, including soil carbon content. One paper and one book chapter have been published from this work.

Three different rotations were compared at the ENDURE long-term platform: Current - winter wheat, winter wheat, oilseed rape; Intermediate - winter wheat, spring barley, oilseed rape; and Advanced - winter wheat, peas, oilseed rape. The intermediate and advanced treatments also included reduced dose and more effectively targeted fungicides, resistance elicitors, cultivar choice and mixtures, reduced herbicides and fertiliser, and all treatments had minimum tillage. The penultimate trial season was completed, and all the pesticide inputs and assessments recorded in the main data files, and the categorical assessments made for DEXiPM analysis.

The DEXiPM tool proved very useful for defining sustainability hypotheses then testing them. Ex-ante assessment showed whether economic, environmental or social dimensions should be affected by changes in cropping practice and to what degree. Ex-post assessment was used to validate the hypotheses and identified where judgements proved inaccurate and what the consequences were. Two publications have been produced from this work.


  • We have identified a suite of indicators for monitoring agri-ecosystem sustainability. These represent the key components of agricultural systems and are generic enough to be widely applicable across a range of systems and studies, including two EU funded research projects (EU-AMIGA and EU-PURE).
  • Integrated management systems case studies were presented to a wide range of audiences at the LEAF Open Farm Sunday, the Royal Highland Show, Cereals in Practice , potatoes in practice and were the basis for contributions to LEAF technical articles.
  • In 2014 only 52% of UK beef carcasses met the target fat and confirmation classes. Both over and under specification results in a loss of value to the supply chain (at producer and processor levels). Continuing work from the last programme, with industry, we continue to make advances in the precision and/or automatic recording and monitoring on beef animals, including developments in weighing platforms, motion/positioning systems and 3D camera imaging systems. The technology is available commercially, building on RESAS support activity, and will result in potential production cost savings of over £35 per animal over an average finishing period.
  • Work on the use of milk mid infrared analysis to predict animal production, fertility and health continued from the last programme. During the first year of the programme fed into farm based tools that became available for commercially that allowed farmers to examine the energy turnover in their herd and in animals within their herd.

Future Activities

Agriculture research has contributed to the rapid intensification of crop production and has helped generate a significant increase in yields. Subsequent concerns about the impact of intensification on agroecosystem sustainability have raised the need for an inter-disciplinary approach to understand the functioning of the whole system. Despite an increasing recognition that single issues (crop nutrition or pest control, etc.) are influenced by many other and interrelated factors in the system, very few studies have attempted a truly holistic analysis, incorporating multiple ecosystem services or the functional links between them.

Here, we have established, through a set of case studies, a multi-attribute framework to aid the design of new integrated management practices and assessment of their impact on sustainability. The integrated management systems will be refined through an iterative process of review and testing over the remainder of the research program, bringing in new best practice options from linked RDs on IPM, soil management, biodiversity and sustainable systems research.

In parallel, a suite of practical tools for sustainability assessment of integrated management practices will be developed. These will be made publicly available via a website which will provide information on best practice management options, protocols for indicator monitoring, mapping and GIS information for precision agriculture, access to existing data via the database front end and to the DEXi-CSC multi-attribute model. These resources will be available for scientists, policy makers and industry stakeholders for identifying integrated management options, predicting the effect of new management of system sustainability and monitoring the impact on key economic and environmental elements of agro-ecosystems.

The work carried out as part of RD2.3.9 will be taken forward in the new RESAS program (2022-2026) through development of a framework  developed with NatureScot in D4 “Scotland’s Biodiversity: People, Data and Monitoring and through D2 “Nature Based Solutions for flood risk management”.




Selected Outputs


Whole systems approaches for designing sustainable cropping

Economic versus environmental impacts of integrated management

The capacity and willingness of farmers to monitor biodiversity benefits

Defining targets for reversing declines in soil carbon

Impact of integrated cropping on soil borne potato pathogens

Soil borne pathogens – a SEFARI report

The costs of monitoring pollinators – does monitoring pay for itself?

A review of agroecological practices for sustainable farming

Winter barley cultivars and their response to cultivation

A Living Lighthouse - UKSoils

Maximising rotations – a TEAGASC podcast

A virtual tour of the Centre for Sustainable Cropping platform

Utilising diversity for sustainable agriculture

Facilitation and sustainable agriculture

Improving arable ecosystem sustainability

Food production and nature conservation

Integrated management in arable cropping systems:

IPM research into practice; a long time coming

The role of sustainable intensification in future farming systems

A comparison of methane emissions from beef cattle measured using methane hoods with those measured using respiration chambers

Automated monitoring of urination events from grazing cattle

Thermophysiological, haematological, biochemical and behavioural stress responses of sheep transported on road

EXPRESS: Exploring the impact of different input data types on soil variable estimation

PHYLIS: A low-cost portable visible range spectrometer

Environmental risk assessment of blight-resistant potato

Diversity of methodologies to experiment Integrated Pest Management in arable cropping systems:

A functional overview of conservation biological control

Indicators of sustainability

The agronomic performance and nutritional content of oat and barley

Impact of management systems on product quality.

Plant responses to an integrated cropping system

Photography and spectroscopy for soil composition analysis

The economics of alternative crop production systems

Re-thinking Buffer Strips in Three Dimensions

Using 3D Imaging and Machine Learning to Predict Liveweight and Carcass Characteristics of Live Finishing Beef Cattle

A parsimonious software sensor for estimating the individual dynamic pattern of methane emissions from cattle

The relationship between MIR-predicted energy balance and fertility

Transitioning towards regenerative, nature-based farming

 Potential for an agroecological approach to farming in Scotland

 Outcomes-based incentive schemes


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