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  • Review Article
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Soil microbiomes and one health

Nature Reviews Microbiology volume 21, pages 6–20 (2023)Cite this article

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Abstract

The concept of one health highlights that human health is not isolated but connected to the health of animals, plants and environments. In this Review, we demonstrate that soils are a cornerstone of one health and serve as a source and reservoir of pathogens, beneficial microorganisms and the overall microbial diversity in a wide range of organisms and ecosystems. We list more than 40 soil microbiome functions that either directly or indirectly contribute to soil, plant, animal and human health. We identify microorganisms that are shared between different one health compartments and show that soil, plant and human microbiomes are perhaps more interconnected than previously thought. Our Review further evaluates soil microbial contributions to one health in the light of dysbiosis and global change and demonstrates that microbial diversity is generally positively associated with one health. Finally, we present future challenges in one health research and formulate recommendations for practice and evaluation.

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Fig. 1: The link between soil, plant, animal and human microbiomes.
Fig. 2: How the soil microbiome influences one health.
Fig. 3: Factors governing the soil microbial contributions to one health.

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Data availability

The data for microbiome composition in Fig. 1 are available in Dryad: https://datadryad.org/stash/share/CPLkD5krQ1-MgaaiI3T0eIyGCTolnsN6tgK0sJ5GlQg.

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Authors and Affiliations

  1. Department of Microbiological Sciences, North Dakota State University, Fargo, ND, USA

    Samiran Banerjee

  2. Plant–Soil Interactions Group, Agroscope, Zurich, Switzerland

    Marcel G. A. van der Heijden

  3. Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland

    Marcel G. A. van der Heijden

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  1. Samiran Banerjee
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The authors contributed equally to all aspects of the article.

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Correspondence to Samiran Banerjee or Marcel G. A. van der Heijden.

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FAO One Health: https://www.fao.org/one-health/

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Glossary

Microbiome

A characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. Thus, the microbiome is holistically defined as the microorganisms and their structural elements including nucleic acids, proteins, lipids, polysaccharides as well as various metabolites. Microbiomes also encompass microorganisms and their activities, including their spatiotemporal dynamics, which results in the formation of specific ecological niches.

Dysbiosis

An imbalance of microbiome structure and composition that is caused by host/environmental perturbations. It is usually associated with loss of taxonomic and/or functional diversity.

Microbial diversity

The number, relative abundance and composition of different microbial taxa present at a particular location. Thus, microbial diversity is a measure of microbial variation at the taxonomic, genetic, phylogenetic, functional and ecosystem levels. An optimal index should incorporate both richness and evenness.

Resistance

The ability of a microbiome to withstand a perturbation and remain unchanged in terms of community structure and composition.

Edaphic factors

Factors related to soil properties.

Global change factors

Natural or anthropogenic factors that are affecting environments globally.

Homogenization

A decline in the differences between ecosystems owing to external factors often resulting in reduced diversity and dominance of certain microbial groups.

Tipping points

Critical points that may occur owing to a single or a series of environmental perturbations and may either lead to dysbiosis or an alternative stable or healthy state.

Eubiosis

A healthy and stable state of microbiota with high diversity and abundance of commensals.

Redundancy

An important trait of microbiome stability whereby some taxa are functionally replaceable as other groups can continue their functions.

Resilience

The ability of a microbiome to endure a perturbation and return to a healthy state despite encountering initial changes in structure and composition.

Insurance

In this hypothesis, biodiversity insures ecosystems against perturbations and decline in functioning, as a diverse community guarantees that some groups will maintain functioning in the event that other groups fail.

Alternative stable state

A ‘healthy’ state that may occur owing to resilience in which the structure and composition of a microbiome are different from that of the original healthy state and yet the microbiome may continue to perform the same functions.

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Banerjee, S., van der Heijden, M.G.A. Soil microbiomes and one health. Nat Rev Microbiol 21, 6–20 (2023). https://doi.org/10.1038/s41579-022-00779-w

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