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Cambridge, 14 Feb 2024 

DEFRA’s Farming Innovation Programme has awarded Eagle Genomics, leveraging science from Rothamsted Research and CABI, a £391k award to explore the vital role of soil microbiomes by analysing data signatures between different agricultural practises and linking these to develop a soil health barometer.

The award – to be delivered in partnership with Innovate UK’s Transforming Food Production (TFP) Challenge – aims to give farmers and growers solutions for improved arable productivity with less impact on the environment.

As well as novel data analysis and insights using Eagle Genomics’ innovative e[datascientist] platform,  this two-year feasibility study will utilise soil from sites in the ASSIST farm network, which are also included in the BBSRC funded UK Crop Microbiome Cryobank project, as well as Rothamsted long term experimental fields. It also builds on Rothamsted’s past research in understanding biological, physical, and chemical elements of soil health. 

Dr Yvonne Pinto, Director of Strategy, Innovation, Sustainability and Bioeconomy, Ag Bio at Eagle Genomics, said, “Eagle Genomics will analyse data signatures between different agricultural practises and link these to develop a barometer for soil health, while CABI will biobank these samples for provenance.” 

“This will increase understanding of the effect of different agricultural practices on the functionalities of healthy and poor soil indicators.”

These outputs will directly benefit farmers in the UK, providing indicators of soil health status and guide the transition to more sustainable and restorative agriculture. 

Dr Tim Mauchline, Plant and Soil Microbiologist at Rothamsted Research, said, “Soil Health testing laboratories have the appetite to use these signatures to provide more detailed analysis to guide farmers decision making. This will enable the provision of specific practical advice to farmers to improve their resilience, to increase soil carbon, increase biodiversity and water retention and potentially with additional revenue streams.” 

In the UK roughly 84% of fertile topsoil has been lost since 1850 due to highly mechanised farming systems causing compaction, erosion, and sub optimal plantings. Soil microbiomes drive critical functions in agro- ecosystems, including soil fertility, crop productivity and stress tolerance. 

Soil degradation was calculated to cost £1.2B a year in 2010. System-level agricultural management practices can induce structural alterations, thereby changing the microbial processes at the micro-scale.

These changes have large-scale consequences, such as soil erosion, reduced soil fertility and increased greenhouse gas emissions. Currently, the major soil health indicators are categorised into three groups: physical, chemical, and biological. 

Professor Martin Broadley, Science Director, Sustainable Soils and Crops at Rothamsted highlights, “Rothamsted Research is delighted to be partnering with Eagle Genomics and CABI, to support this exciting project to develop practical indicators of soil health status. Applying recent advances in our understanding of soil biology, to enable the development of ‘next generation’ soil tests, will help farmers and the wider agriculture sector in delivering profitable and healthy agricultural systems.”

The important work, as part of this collaboration, will significantly advance soil microbiology as an important component of the soil health continuum and enable practical strategies for farmers to conserve and regenerate their soils.

Dr Matt Ryan, Research Lead, Biological Resources at CABI, said, “These valuable crop microbial samples are a vital resource for scientific researchers investigating how to ensure food security amid a range of challenges to crop production that also includes the threats posed by pests and diseases.

“Advancing research on solutions to mitigate these stressors is also imperative to help ensure the UK’s food security at a time when chemical fertilizers and pesticides are in the spotlight amid the growing concerns of climate change.”


Dr Tim Mauchline

Plant and Soil Microbiologist


Rothamsted Research is the longest-running agricultural research institute in the world. We work from gene to field with a proud history of ground-breaking discoveries in areas as diverse as crop management, statistical interpretation and soil health. Our founders, in 1843, were the pioneers of modern agriculture, and we are known for our imaginative science and our collaborative approach to developing innovative farm practice.
Through independent research, we make significant contributions to improving agri-food systems in the UK and internationally, with economic impact estimated to exceed £3 bn in annual contribution to the UK economy. Our strength lies in our systems approach, which combines strategic research, interdisciplinary teams and multiple partnerships.
Rothamsted is home to three unique National Bioscience Research Infrastructures which are open to researchers from all over the world: The Long-Term Experiments, Rothamsted Insect Survey and the North Wyke Farm Platform.
We are strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC), with additional support from other national and international funding streams, and from industry. We are also supported by the Lawes Agricultural Trust (LAT).


The Biotechnology and Biological Sciences Research Council is part of UK Research and Innovation, a non-departmental public body funded by a grant-in-aid from the UK government.
BBSRC invests to push back the frontiers of biology and deliver a healthy, prosperous and sustainable future. Through our investments, we build and support a vibrant, dynamic and inclusive community which delivers ground-breaking discoveries and develops bio-based solutions that contribute to tackling global challenges, such as sustainable food production, climate change, and healthy ageing.
As part of UK Research and Innovation (UKRI), we not only play a pivotal role in fostering connections that enable the UK’s world-class research and innovation system to flourish – we also have a responsibility to enable the creation of a research culture that is diverse, resilient, and engaged.
BBSRC proudly forges interdisciplinary collaborations where excellent bioscience has a fundamental role. We pioneer approaches that enhance the equality, diversity, and inclusion of talent by investing in people, infrastructure, technologies, and partnerships on a global scale.


The Lawes Agricultural Trust, established in 1889 by Sir John Bennet Lawes, supports Rothamsted Research’s national and international agricultural science through the provision of land, facilities and funding. LAT, a charitable trust, owns the estates at Harpenden and Broom's Barn, including many of the buildings used by Rothamsted Research. LAT provides an annual research grant to the Director, accommodation for nearly 200 people, and support for fellowships for young scientists from developing countries. LAT also makes capital grants to help modernise facilities at Rothamsted, or invests in new buildings.