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Soils are one of the most biodiverse habitats on Earth, with an estimated 4,000 to 50,000 species of microorganism per gram of soil. The ‘soil microbiome’ refers to communities of microbes within the soil, which include bacteria and fungi, but also archaea (single-celled organisms initially identified in extreme habitats), protists (single-celled organisms that, unlike bacteria, contain a nucleus) and viruses. However, although they constitute a large part of the UK’s biodiversity, many soil organisms remain unknown. The soil microbiome underpins many of the ecosystem services that benefit humans, which include:

  • movement and exchange of key plant growth limiting nutrients such as nitrogen and phosphorus;
  • protection of plants from stress, pests and pathogens;
  • decontamination of soils through bioremediation;
  • helping to maintain the physical structure of soil;
  • decomposition of organic wastes while storing carbon;
  • regulating the flow of greenhouse gases, such as carbon dioxide and methane; and,
  • a repository of undiscovered biochemicals, including antibiotics, that can be used to address antibiotic resistance

Soil health is defined in the academic literature as the capacity of a soil to function as a living ecosystem and support to sustain plants, animals and humans, and maintain environmental quality. The Government’s 25 Year Environment Plan highlight the importance of soil health and stated an ambition to manage England’s soils sustainably by by 2030.

Key points in this POSTnote include:

  • The soil microbiome refers to the diverse communities of bacteria, fungi and other microorganisms in soil habitats.
  • Soil microbes underpin key benefits that soils provide, such as food production, the clean-up of pollutants, and carbon storage in soil organic matter.
  • Conventional agricultural practices and climate change can drive changes in soil microbiomes that result in soils providing fewer benefits.
  • New genomic and chemical analyses can characterise the soil microbiome, increasing understanding of the roles it performs.
  • Protecting and restoring the soil microbiome has both economic and environmental benefits, but there is a lack of studies on measures for achieving this.



POSTnotes are based on literature reviews and interviews with a range of stakeholders and are externally peer reviewed. POST would like to thank interviewees and peer reviewers for kindly giving up their time during the preparation of this briefing, including:

  • Dr Matthew Shepherd, Natural England *
  • Philippa Arnold, National Farmers Union
  • Dr Simon Jeffery, Harper Adams University
  • Dr Katie Field, Leeds University
  • Professor Gary Bending, University of Warwick
  • Dr Roy Neilson, James Hutton Institute*
  • Dr Maddy Giles, James Hutton Institute*
  • Dr Davide Bulgarelli, University of Dundee*
  • Dr Lynsay Blake, Durham University*
  • Dr Clare McCann, Newcastle University*
  • Dr Neil Gray, Newcastle University*
  • Professor Richard Bardgett, University of Manchester*
  • Dr Rachel Marshall, Lancaster University*
  • Dr Tim Mauchline, Rothamsted Research*
  • Ian Clark, Rothamsted Research*
  • Professor Jim Harris, Cranfield University*
  • Dr Anna Krzywoszynska, University of Sheffield*
  • Professor Duncan Cameron, University of Sheffield
  • Professor Jurriaan Ton, University of Sheffield   
  • Dr Stephen Rolfe, University of Sheffield*
  • Professor Jonathan Leake, University of Sheffield*
  • Professor Jack Gilbert, University of California San Diego*
  • Dr Christopher Brown,Society for Applied Microbiology
  • The Grantham Centre for Sustainable Futures 

*Denotes people who acted as external reviewers of the briefing

Documents to download

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