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Soil structure and microbiome functions in agroecosystems

Nature Reviews Earth & Environment volume 4, pages 4–18 (2023)Cite this article

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Abstract

Soil microbiomes drive key functions in agroecosystems, determining soil fertility, crop productivity and stress tolerance. The microbiome is intricately linked with soil structure, such as aggregation and pore connectivity, because this structure regulates the flow of water, oxygen and nutrients through the system. In this Review, we summarize the key functions of soil microbiomes in agroecosystems, highlight the dependence of these functions on the structural integrity of the soil, and discuss how agricultural practices influence the link between soil structure and microbiome functioning. System-level agricultural management practices can induce structural alterations to the soil, thereby changing the microbial processes occurring at the microscale. These changes have large-scale consequences, such as soil erosion, reduced soil fertility and increased greenhouse gas emissions. Sustainable approaches such as integrated soil fertility management and integrated pest management seek to improve soil structure and enhance microbial biodiversity, but we lack a mechanistic understanding of how multifaceted decisions at the farm level shape these context-dependent small-scale processes in the long term. Future research needs to bridge the microscale and field scale to inform agricultural management decisions for building climate-smart, resource-efficient and stress-resilient agroecosystems, and to harness the soil microbiome as a nature-based solution for sustainable agriculture.

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Fig. 1: Microbial key functions in the plant–soil system.
Fig. 2: Abiotic and biotic interactions at the soil aggregate scale.
Fig. 3: Differences in soil properties between structurally intact versus degraded soils.
Fig. 4: Differences in management practices between industrial and conservation agriculture.

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Acknowledgements

We acknowledge J. Binswanger (Fig. 1) and N. Ohannessian (Figs. 3 and 4) for scientific illustration.

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    Martin Hartmann & Johan Six

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Glossary

Agroecosystems

Sites or integrated regions that support food production while conserving biotic and abiotic resources and providing a balanced supply of ecosystem services.

Antibiosis

A biological interaction between two or more organisms that is detrimental to at least one of them.

Biochar

The product of thermal degradation of organic matter at high temperature in the absence of air (pyrolysis).

Biologicals

Products consisting of either a living organism or a substance derived from it, providing protection against pests and diseases or promoting plant growth and stress tolerance.

Coalescence

The mixing of different biological communities (for example through inoculation) that results in new metacommunities with potential novel functional attributes.

Copiotrophs

Organisms that preferentially consume labile organic C pools, have high nutritional requirements and can exhibit high growth rates when resource conditions are abundant.

Cover cropping

The planting of crops between periods of regular production of the main crop, with the goal of covering and protecting the soil rather than being harvested as cash crop.

Endosphere

Internal environment of the host that can be colonized by microorganisms called endophytes.

Host-mediated indirect selection

Using the host to select for beneficial microbes that improve host performance by selecting and propagating microbial communities associated with specific host-traits of interest (such as plant growth).

Hyperparasitism

A relationship between two parasites in which one acts as parasite on the other.

Integrated soil fertility management

A set of practices related to cropping, fertilizers, organic resources and other amendments on smallholder farms to increase crop production and input use efficiency.

Integrated pest management

A set of best practices that focuses on long-term prevention or suppression of pests and diseases.

Microbiome

A characteristic microbial community occupying a well-defined habitat with distinct physio-chemical properties, and its associated theatre of activity.

Mycorrhizal fungi

Fungi that form mutualistic symbiotic relationships with roots of certain vascular plant species in which the fungus receives carbohydrates from the plant in exchange for mineral nutrients.

Oligotrophs

Organisms that exhibit slow growth, low metabolic rates and generally low population density, but feature high substrate affinity under low nutrient availability.

Phytohormones

Chemicals produced by plants that regulate their growth, development and reproduction, but are also used as signalling molecules to interact with microbes.

Plant-growth-promoting microorganisms

Microorganisms that colonize various plant compartments such as the rhizosphere or endosphere and have positive effects on plant growth and stress tolerance.

Rhizodeposition

Active and passive release of organic compounds from plant roots into the surrounding soil.

Rhizosphere

Zone surrounding plant roots in which the chemistry and microbiology are influenced by root activity.

Root exudates

A suite of substances that are secreted by the roots of living plants into the surrounding compartment.

Secondary metabolites

Organic compounds produced by organisms that are not directly involved in normal growth, development or reproduction of the organism.

Soil aggregates

A group of primary soil particles that are more cohesive than other surrounding particles and are classified by size into macroaggregates (>250 μm) and microaggregates (<250 μm).

Soil organic matter

The organic component of soil derived from plant and animal detritus at various stages of decomposition as well as soil microorganisms and the organic substances synthesized by these organisms.

Soil structure

The arrangement of soil particles and aggregates into a porous structure that regulates the flow of resources.

Systemic resistance

Resistance mechanism in plants induced by microorganisms or abiotic inducers that present a long-lasting defence function against a broad spectrum of pests and pathogens.

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Hartmann, M., Six, J. Soil structure and microbiome functions in agroecosystems. Nat Rev Earth Environ 4, 4–18 (2023). https://doi.org/10.1038/s43017-022-00366-w

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