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The interplay between microbial communities and soil properties

Nature Reviews Microbiology volume 22, pages 226–239 (2024)Cite this article

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Abstract

In recent years, there has been considerable progress in determining the soil properties that influence the structure of the soil microbiome. By contrast, the effects of microorganisms on their soil habitat have received less attention with most previous studies focusing on microbial contributions to soil carbon and nitrogen dynamics. However, soil microorganisms are not only involved in nutrient cycling and organic matter transformations but also alter the soil habitat through various biochemical and biophysical mechanisms. Such microbially mediated modifications of soil properties can have local impacts on microbiome assembly with pronounced ecological ramifications. In this Review, we describe the processes by which microorganisms modify the soil environment, considering soil physics, hydrology and chemistry. We explore how microorganism–soil interactions can generate feedback loops and discuss how microbially mediated modifications of soil properties can serve as an alternative avenue for the management and manipulation of microbiomes to combat soil threats and global change.

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Fig. 1: The interplay between soil environmental conditions and the soil microbiome.
Fig. 2: Microorganisms break down minerals and build mineral structures.
Fig. 3: Microbial processes that affect soil aggregation.
Fig. 4: Microbial processes with varying impacts on water-related soil properties.
Fig. 5: Harnessing microbial communities to combat soil threats and global change.

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Authors and Affiliations

  1. Université de Bourgogne Franche-Comté, INRAE, Institut Agro Dijon, Department of Agroecology, Dijon, France

    Laurent Philippot

  2. University of Paris-Saclay, INRAE, AgroParisTech, Palaiseau, France

    Claire Chenu

  3. Center for Applied Geosciences, University of Tübingen, Tübingen, Germany

    Andreas Kappler

  4. Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tübingen, Germany

    Andreas Kappler

  5. Freie Universität Berlin, Institute of Biology, Berlin, Germany

    Matthias C. Rillig

  6. Berlin-Brandenburg Institute of Advanced Biodiversity Research, Berlin, Germany

    Matthias C. Rillig

  7. Department of Ecology and Evolutionary Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, USA

    Noah Fierer

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Glossary

Adaptative radiation

The rapid diversification of species as a consequence of adaption to different environmental conditions.

Ammonification

The respiratory reduction of nitrate to ammonium when oxygen is limiting.

Arbuscular mycorrhizal fungi

Fungi that form a symbiosis with plants by penetrating the cortical cells of the roots of a vascular plant.

Denitrification

The respiratory reduction of nitrogen oxides to N2O and N2 when oxygen is limiting.

Extracellular polymeric substances

(EPSs). Polymeric organic compounds (mainly polysaccharides, proteins and nucleic acids) that are produced and released by microorganisms.

Hydrophobins

Small proteins produced by filamentous fungi that can spontaneously self-assemble and change the polarity of a surface.

Niche construction theory

The concept that organisms can modify their environment and that, in turn, these changes influence the organisms.

Nitrification

Aerobic oxidation of ammonium to nitrite and then to nitrate to generate energy.

Photosynthetic autotrophs

An organism that uses light energy to fix CO2.

Siderophores

Organic compounds that are produced and released by microorganisms to make otherwise poorly soluble Fe(III) ions bioavailable for the cells and to facilitate their uptake.

Soil micropores

Pores in which water is essentially held by capillary forces (≤0.08 mm), nearly immobile and in which solute movement is limited to diffusion.

Weathering

The process of breaking down or dissolving solids (minerals and rocks) by biological, chemical or physical processes.

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Philippot, L., Chenu, C., Kappler, A. et al. The interplay between microbial communities and soil properties. Nat Rev Microbiol 22, 226–239 (2024). https://doi.org/10.1038/s41579-023-00980-5

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