The Soil Food Web

The Soil Food Web: The Ecological Basis of Fertility and Soil Food Web

For a long time, we have looked at agricultural soil as a simple container.
A container made of clay, sand, silt, and organic matter.
We have determined its pH and electrical conductivity, fertilized it, and worked it.
For years, we have simplified fertility by speaking almost exclusively of macronutrients and micronutrients.
Yet soil is more than just this.
Soil is not a simple anchoring substrate for plants, but a living system, traversed by a network of living and nonliving components: roots, bacteria, fungi, protozoa, nematodes, microarthropods, earthworms, organic matter, minerals, water, air, and energy.
This network is called the Soil Food Web and represents a key ecological literature for understanding fertility, the carbon cycle, the nitrogen cycle, soil structure, and the functioning of agroecosystems (de Vries et al., 2013; Bardgett & van der Putten, 2014).
Dr. Elaine Ingham was one of the key figures in developing, systematizing, applying, and disseminating this approach, especially from a regenerative and microbiological perspective.
According to this vision, soil fertility does not arise simply from the presence of nutrients, but from the presence of a biological community capable of biotransforming, retaining, recycling, and making them bioavailable to plants.
The soil food web constitutes the underground biodiversity of the agroecosystem and regulates processes crucial to plant productivity and the functioning of terrestrial biological systems (van der Heijden et al., 2008; Bardgett & van der Putten, 2014).
In other words, fertile agricultural soil is not just soil “rich” in nutrients.
It is also ecologically alive and functioning soil.
But let’s start from the beginning.
It all starts with light.
Yes, sunlight.
If the sun hits bare soil, much of that energy is transformed into heat. The soil heats up, loses water, oxidizes, and becomes biologically impoverished.
In uncovered soil, solar energy is not fully intercepted by plants and is not completely transformed into stable biological carbon (Kuzyakov & Domanski, 2000; Jones et al., 2009).
In covered soil, plants absorb almost all solar energy, water, and carbon dioxide and transform it into organic compounds such as sugars, organic acids, amino acids, polysaccharides, and secondary metabolites.
This activity transforms light into biological carbon, transferring it to the roots and then to the soil.
In fact, plants do not produce sugars solely for themselves. A significant portion is transported and released by the roots into the soil in the form of root exudates (Kuzyakov & Domanski, 2000; Jones et al., 2009), feeding microorganisms, mycorrhizae, and rhizospheric processes (Kuzyakov & Domanski, 2000; Jones et al., 2009; Philippot et al., 2013).
Root exudates are composed of sugars, amino acids, organic acids, mucilages, enzymes, phenolic compounds, and other metabolites.
They are biochemical messages, energy sources, and ecological tools through which the plant attracts or repels, nourishes, or deters bacteria and fungi present in the rhizosphere, that is, the portion of the soil most closely linked to the root system (Jones et al., 2009; Philippot et al., 2013; Trivedi et al., 2020).
It is underground, therefore, that biological carbon silently becomes nourishment for the soil food web.
This is the first major concept on which the Soil Food Web is based.
The rhizosphere, in this view, represents one of the most important biological hotspots in the soil: it hosts high microbial densities, intense biochemical interactions, and a continuous transformation of carbon and nutrients (Philippot et al., 2013; Trivedi et al., 2020).
It is a small but powerful area.
It is there that microorganisms multiply.
It is there that roots encounter bacteria, fungi, protozoa, nematodes, and microfauna.
It is there that photosynthetic carbon enters the soil food web.
The plant, through its exudates, does not randomly nourish everything it encounters. It modulates root release based on its phenological phase, nutritional status, water conditions, the presence of pathogens, and the surrounding microbial community (Jones et al., 2009; Berendsen et al., 2012; Philippot et al., 2013).
Research on the plant microbiome shows that plants influence the assembly of root-associated microbial communities and that these communities, in turn, can support nutrition, stress tolerance, and plant health (Berendsen et al., 2012; Trivedi et al., 2020).
The plant, therefore, is not a passive organism.
It doesn’t simply wait for someone to fertilize it.
It interacts with the trophic and ecological system of which it is part.
And the Soil Food Web is the great moderator of this dialogue.
At the base of the soil food web, we find bacteria and fungi.
They are the first great transformers of the organic carbon produced by plants and accumulated in the roots.
They receive sugars and exudates, decompose plant residues, produce enzymes, and release or immobilize nutrients.
These functions are central because soil microorganisms are not simple biological presences, but become the regulators of biogeochemical cycles, plant nutrition, and the productivity of terrestrial ecosystems (van der Heijden et al., 2008; Bardgett & van der Putten, 2014).
Furthermore, the rhizospheric microbiota also contributes to nutrient solubilization, the production of functional metabolites, pathogen competition, and plant health modulation (Berendsen et al., 2012; Philippot et al., 2013; Trivedi et al., 2020).
According to the Soil Food Web, bacteria are essential for the formation of the first biological “glues” in the soil, namely extracellular polymeric substances.
These substances help bacteria adhere to surfaces, form biofilms, remain close to roots, and contribute to the formation of microaggregates (Costa et al., 2018).
Fungi, however, work differently.
They are not only producers of extracellular substances, but above all, they are connection builders.
Fungal hyphae traverse the soil like very thin threads. They connect mineral particles, organic residues, and roots, contributing to the formation of more stable macroaggregates.
Mycorrhizae, in particular, improve the connection between roots, mineral particles, and organic matter (Rillig & Mummey, 2006).
It’s as if they stitch the soil together.
Furthermore, mycorrhizae expand the exploratory capacity of roots, improve the absorption of phosphorus and other nutrients, and contribute to the structural stability of the soil through extraradical hyphae and organic compounds.
Among these, glomalin, or more correctly glomalin-related soil proteins, associated primarily with arbuscular mycorrhizal fungi, is often mentioned (Rillig & Mummey, 2006).
Soil structure, therefore, is not just a physical issue.
It is a biological construction.
When the soil has acquired structure, water infiltrates better, air circulates, roots descend deeper, aerobic microorganisms find suitable habitats, and organic matter is protected.
Structure therefore arises from the interaction between mineral particles, organic matter, roots, microorganisms, root exudates, fungal hyphae, and soil fauna (Costa et al., 2018; Rillig & Mummey, 2006).
For this reason, well-aggregated soil is not only “physically good” soil, but also biologically active and organized.
When soil becomes compacted due to over-tillage, water stagnates, oxygen decreases, pores collapse, roots stop, and aerobic life is reduced.
In these conditions, fermentative and reductive processes, or processes that are otherwise unfavorable to plant growth, can increase.
Dr. Ingham emphasizes this point: a soil that loses structure also tends to lose its living quality.
Naturally, in nature, there are anaerobic environments with important ecological and agroecological roles, such as wetlands and rice fields.
But in agricultural soil intended for plants that require healthy, oxygenated roots, widespread and persistent anaerobic conditions are a sign of imbalance.
This is why compaction isn’t just a mechanical problem.
It’s also an agroecological problem.
Compacted soil isn’t simply “hard.”
It’s a soil in which the Soil Food Web works poorly, or not at all.
The literature confirms that the soil food web contributes to key ecosystem services, including carbon cycling, nitrogen cycling, and organic matter regulation (de Vries et al., 2013; Bardgett & van der Putten, 2014).
One of the issues related to soil fertility is not only the presence of nutrients in the soil, but their biological availability.
Take phosphorus, for example.
Many soils contain significant amounts, but they are not always accessible to plants. In alkaline soils, it can be blocked by calcium, while in acidic soils, by iron and aluminum.
According to the Soil Food Web, nutrient availability depends on pH, texture, moisture, redox potential, microbial activity, the presence of root exudates, mycorrhizae, enzymes, and trophic interactions (Jones et al., 2009; Philippot et al., 2013; Rillig & Mummey, 2006).
Solubilizing bacteria, mycorrhizal fungi, organic acids, enzymes, and microbial predators are organisms capable of transforming what’s present in the soil into something truly available to plants.
Interactions between roots and microorganisms profoundly influence nutrient availability and plant nutrition (Jones et al., 2009; Philippot et al., 2013).
At the same time, soil microbial biodiversity is considered a key factor for plant productivity and the stability of terrestrial ecosystems (van der Heijden et al., 2008; Bardgett & van der Putten, 2014).
This means that chemical fertilizers cannot replace the biological function of the soil.
We can add phosphorus, nitrogen, or potassium, but if the soil is depleted of life, compacted, oxidized, or devoid of active roots, we continue to work with an incomplete and inefficient system.
We must view the soil not as a warehouse, but as a complex trophic system.
Bacteria and fungi in the soil are essential, but alone they are not enough.
They absorb nutrients and retain them in their biomass. This prevents them from being easily leached or lost. However, if they remain locked in the microbial or fungal biomass, the plant cannot utilize them.
A next step is needed.
This is where protozoa, bacteriophagous nematodes, fungivorous nematodes, microarthropods, and other small soil organisms come into play.
These organisms feed on bacteria and fungi and, in doing so, release nutrients in forms more available to plants.
Bonkowski (2004) describes this process as part of the soil microbial loop: protozoa, by preying on bacteria, regulate the microbial community and contribute to the release of nutrients into the rhizosphere.
Bacteriophagous nematodes and protists are therefore equally important components of soil biodiversity and can influence nitrogen and phosphorus availability, thus affecting plant growth and the functioning of agroecosystems, just like bacteria and fungi (Bonkowski, 2004; Trap et al., 2016).
We should explain this mechanism much more often to farmers.
Soil fertility depends on many organisms that together are capable of making nutrients bioavailable.
From this perspective, compost takes on a crucial role.
It is not just a soil conditioner rich in organic matter and a source of nutrients. It contains bacteria, fungi, protozoa, beneficial nematodes, enzymes, secondary metabolites, humic substances, and organic matrices capable of nourishing soil life.
For this reason, it should be evaluated not only for its chemical content, but also for its biological quality and its ability to support microbial communities and functional food webs (Bardgett & van der Putten, 2014; de Vries et al., 2013).
Poorly produced, anaerobic, immature, or putrefactive compost can create problems for soils and agricultural crops.
Mature, well-oxygenated, stable, and biologically rich compost can instead help rebuild or support the Soil Food Web, improve soil structure, nourish microbial biomass, and support the transformation of organic matter (Costa et al., 2018; Bardgett & van der Putten, 2014).
This is why we should stop asking ourselves how much organic matter we are contributing.
It would be more useful to ask ourselves:
What kind of life am I restoring to the soil?
Compost, from an agroecological perspective, should primarily serve to reactivate trophic and biological processes.
This differs from conventional fertilization, which often applies linear reasoning to nonlinear systems.
Lack of nitrogen? Add nitrogen.
Lack of phosphorus? Add phosphorus.
But soil is a complex system, and its responses are nonlinear.
Adding too much nitrogen can stimulate vegetative growth, but it can also unbalance the relationship between plants and microbes, increase susceptibility to biotic stress, promote losses through leaching or gaseous emissions, and reduce some beneficial symbioses.
Nutrient availability and plant response in balanced agroecological systems depend on the interactions between plant physiology, microbiota, organic matter, and soil food webs (Jones et al., 2009; Philippot et al., 2013; de Vries et al., 2013).
Fertility management should therefore integrate soil chemistry, physics, and biology (Bardgett & van der Putten, 2014; Trivedi et al., 2020).
Agroecological approaches to fertility do not support external inputs for the sole purpose of directly nourishing plants. Instead, they propose the use of compost, preferably produced on the farm, to enrich the biological life of the soil and reactivate ecological processes.
This is the difference between fertilizing and regenerating.
Fertilizing means providing something immediately available to the plant.
Regenerating means restoring the conditions so that the plant can nourish itself through the soil food web.
Regeneration can also involve the use of organic matrices within the farm, provided they are capable of supporting functional microbial and trophic networks (de Vries et al., 2013; Bardgett & van der Putten, 2014).
Another central aspect of the Soil Food Web concerns plant health.
A living, biologically rich, and complex soil does not magically eliminate all plant diseases, but it controls them much more easily.
It creates a balanced and dynamic environment, where roots are surrounded by beneficial bacteria, fungi, protozoa, nematodes, microarthropods, mycorrhizae, biofilms, exudates, and metabolites.
The rhizosphere microbiota can contribute to plant protection through competition, antagonism, stimulation of plant defenses, and modulation of the root environment (Berendsen et al., 2012; Philippot et al., 2013; Trivedi et al., 2020).
In living soil and a complex soil community, a pathogen has a harder time finding a free space to express its pathogenicity.
It must compete, confront antagonistic organisms, stay alive, and only then attempt to attack the plant.
The suppressive nature of soils also arises from this complexity: biodiversity, competition, predation, antagonism, stimulation of plant defenses, and the stability of biological networks (Berendsen et al., 2012; Bardgett & van der Putten, 2014; de Vries et al., 2013).
Research on the plant microbiome shows that interactions between plants, microbial communities, and the environment are crucial for the assembly of the microbiota and the expression of its beneficial functions related to plant health (Trivedi et al., 2020).
Therefore, plant defense should also be thought of as building a stronger and more complex root environment. The Soil Food Web tells us yet another important thing: inoculating a single organism is not enough.
We need to create a network and its associated ecological context.
We need to create the conditions for that life to feed, reproduce, and perform a function.
Microbial communities do not operate in isolation from the plant and the environment.
The root microbiota assembles through complex interactions between plant genotype, soil, climate, agronomic management, carbon availability, and biotic pressures (Philippot et al., 2013; Trivedi et al., 2020).
Similarly, ecosystem functions depend on the overall properties of soil food webs, not the simple presence of a single functional group (de Vries et al., 2013).
If we place bacteria in soil without carbon, without living roots, without porosity, without moisture, and perhaps with excess salts, those bacteria will not be able to perform miracles.
If we inoculate fungi into continuously tilled, poorly covered, and continually disturbed soil, it will be difficult to build a stable fungal network.
Fungal hyphae and mycorrhizae require physical continuity and minimal disturbance to truly contribute to soil structure (Rillig & Mummey, 2006).
Soil biology must be created and cultivated.
Working with the Soil Food Web means changing our perspective.
It means keeping the soil covered for as long as possible, thus activating the flow of carbon into the soil and supporting the rhizosphere through living roots and exudates (Kuzyakov & Domanski, 2000; Jones et al., 2009).
One of the main pathways through which plant carbon enters the soil and supports microorganisms, root microbiota, and trophic processes is rhizodeposition (Kuzyakov & Domanski, 2000; Philippot et al., 2013).
This process requires reducing tillage.
Every process breaks down aggregates, damages fungal hyphae, destabilizes the structure, and accelerates the oxidation of organic matter (Rillig & Mummey, 2006).
Plant biodiversity must also be increased.
Different plants produce different exudates and nourish different microbial communities.
Above- and below-soil biodiversity is closely interconnected, contributing to the productivity, stability, and functioning of terrestrial ecosystems (van der Heijden et al., 2008; Bardgett & van der Putten, 2014).
Plant nutrition should therefore be viewed as the result of interactions between roots, microbiota, nutrient availability, and the soil food web (Jones et al., 2009; Philippot et al., 2013; Trivedi et al., 2020).
Fertility thus becomes the result of life-sustaining agricultural practices, and the
Soil Food Web represents the ecological basis of fertility.
From this perspective, fertility does not derive from a soil rich in mineral elements.
It derives from a soil in which carbon, roots, microbiota, structure, predation, decomposition, and nutrient availability function as parts of a dynamic food web (de Vries et al., 2013; Bardgett & van der Putten, 2014; Trivedi et al., 2020).
A fertile soil is one capable of transforming carbon into life, microbial biomass into available nutrients, and organic matter into a reserve capable of nourishing the system.
From light to carbon.
From carbon to microorganisms.
From microorganisms to nutrients.
From nutrients to plants.
And from plants, back to the soil.
Because there, in the darkness of the soil, one of the most important transformations on the planet takes place.
Light becomes carbon.
Carbon becomes life.
And life becomes fertility.

Francesco Di Lorenzo
Agronomist

Essential Bibliography
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Bonkowski, M. (2004). Protozoa and plant growth: The microbial loop in soil revisited. New Phytologist, 162(3), 617–631. https://doi.org/10.1111/j.1469-8137.2004.01066.x

Costa, O. Y. A., Raaijmakers, J. M., & Kuramae, E. E. (2018). Microbial extracellular polymeric substances: Ecological function and impact on soil aggregation. Frontiers in Microbiology, 9, Article 1636. https://doi.org/10.3389/fmicb.2018.01636

de Vries, F. T., Thébault, E., Liiri, M., Birkhofer, K., Tsiafouli, M. A., Bjørnlund, L., Bracht Jørgensen, H., Brady, M. V., Christensen, S., de Ruiter, P. C., d’Hertefeldt, T., Frouz, J., Hedlund, K., Hemerik, L., Hol, W. H. G., Hotes, S., Mortimer, S. R., Setälä, H., Sgardelis, S. P., … Bardgett, R. D. (2013). Soil food web properties explain ecosystem services across European land use systems. Proceedings of the National Academy of Sciences, 110(35), 14296–14301. https://doi.org/10.1073/pnas.1305198110

Jones, D. L., Nguyen, C., & Finlay, R. D. (2009). Carbon flow in the rhizosphere: Carbon trading at the soil-root interface. Plant and Soil, 321, 5–33. https://doi.org/10.1007/s11104-009-9925-0

Kuzyakov, Y., & Domanski, G. (2000). Carbon input by plants into the soil: Review. Journal of Plant Nutrition and Soil Science, 163(4), 421–431. https://doi.org/10.1002/1522-2624(200008)163:4%3C421::AID-JPLN421%3E3.0.CO;2-R

Philippot, L., Raaijmakers, J. M., Lemanceau, P., & van der Putten, W. H. (2013). Going back to the roots: The microbial ecology of the rhizosphere. Nature Reviews Microbiology, 11(11), 789–799. https://doi.org/10.1038/nrmicro3109

Rillig, M. C., & Mummey, D. L. (2006). Mycorrhizas and soil structure. New Phytologist, 171(1), 41–53. https://doi.org/10.1111/j.1469-8137.2006.01750.x

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Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T., & Singh, B. K. (2020). Plant-microbiome interactions: From community assembly to plant health. Nature Reviews Microbiology, 18, 607–621. https://doi.org/10.1038/s41579-020-0412-1

van der Heijden, M. G. A., Bardgett, R. D., & van Straalen, N. M. (2008). The unseen majority: Soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems. Ecology Letters, 11(3), 296–310. https://doi.org/10.1111/j.1461-0248.2007.01139.x