Healthy Soil

Soil biology and the soil food web

Why soil biology matters more than inputs

Healthy soil is not just a mix of sand, silt, clay, nutrients, and water. It is a living system. Biological processes mediate how particles associate, how nutrients are transformed and exchanged, and how water moves and is retained within soil systems, under specific conditions and material constraints.

While fertilisers, conditioners, and amendments can all play a role, none of them work well in isolation. Where biological processes are suppressed or absent, added nutrients are more easily lost and structural degradation risk increases, depending on context and existing material condition. In contrast, biologically active soils can buffer some stresses and modify system behaviour over time, depending on context and constraints.

In short, biological processes help soils behave as soils rather than inert substrates, within physical and chemical constraints.

What is often missed, however, is where the metabolic energy that powers this biology actually comes from.

Plants as active metabolic energy transfer agents in soil

Soil biology does not originate with plants. Microbial life existed on Earth long before land plants evolved, and many soil organisms can derive energy from non-plant sources.

In modern soil systems, however, plants play a central regulatory role in energy transfer. Through photosynthesis, green plants fix atmospheric carbon into organic compounds, some of which are retained in plant tissues and some of which are transferred into soil.

Plants contribute metabolic energy to soil biology in two primary ways:

  • Direct carbon transfer via root exudates and symbioses, including arbuscular mycorrhizal fungi (AMF), where sugars are exchanged for nutrients.
  • Indirect carbon transfer through the decomposition of plant residues (roots, litter, and crop residues), which provide energy sources for microbes and detritivores.

It is also important to note that in managed systems, a substantial proportion of plant-derived metabolic energy is exported from fields as harvested biomass and consumed by livestock or humans. Only the fraction returned to soil contributes to sustaining soil biological processes.

In this sense, plants are not the sole source of energy for soil life, but they are a major conduit through which metabolic energy enters, is partitioned, and is regulated within soil systems.

The plant–soil metabolic energy loop

At the heart of soil biology is a conditional interaction pattern:

  • Sunlight → photosynthesis captures carbon as sugars
  • Sugars → roots and leaves build plant structure and capacity
  • Root exudates release carbon into the soil
  • AMF and soil microbes can trade nutrients for carbon, depending on nutrient availability and relative uptake costs
  • Improved nutrient uptake supports stronger plant growth

The strength of this loop is conditional. Plants allocate carbon to roots and symbionts when the nutrient return justifies the metabolic cost; abundant soluble nutrients can reduce this exchange, while moderate limitation can increase it.

This is why plant performance and soil condition are tightly linked in soil-based systems, even though plants can be grown successfully in non-soil environments.

Scope and boundary clarification

This pillar explains how soil systems function and renew themselves over time. It does not claim that biological activity is required for all forms of plant production. Plants can grow in biologically minimal or biologically absent systems where nutrients, water, oxygen, and energy are supplied directly.

In soils, biological processes contribute to the formation and renewal of structure, nutrient buffering, and functional resilience over long time periods, alongside material properties, management, and time. Materials, engineering, or management can substitute for some of these functions, sometimes very effectively, but only within defined limits and time horizons. Where renewal processes are absent, soil performance depends on what has already been built, until degradation thresholds are reached.

Carbon allocation is not waste — it is investment

Plants do not leak carbon into soil by accident.

A substantial fraction of photosynthetically fixed carbon can be released through roots as exudates: sugars, amino acids, organic acids, and signalling compounds. This is often misunderstood as inefficiency or surplus disposal.

In reality, it is an investment strategy.

By feeding microbes and arbuscular mycorrhizal fungi (AMF), plants extend their functional root system far beyond the physical root surface. Fungal hyphae access phosphorus, nitrogen, and micronutrients that roots alone cannot reach.

Plants invest carbon in these partnerships when the nutrient return outweighs the carbon cost; where nutrients are readily available in soluble form, this investment is often reduced or bypassed.

Strong plants build strong soil biology

The loop works in both directions:

  • Strong photosynthesis supports robust roots
  • Robust roots support microbial partnerships
  • Microbial partnerships improve nutrient efficiency
  • Improved nutrition feeds back into photosynthesis

Conversely, stress breaks the loop. Compaction, poor structure, low oxygen, or disrupted biology reduce photosynthesis and exudation. Microbial populations often respond earlier to stress than visible plant symptoms.

In many systems, early signs of soil degradation are often biological or structural before they are chemical, depending on context and stress history.

Why this matters for soil management

This model reframes soil care:

  • Fertilisers may supply nutrients, but they do not replace carbon flow
  • Organic matter supports symbiotic and rhizosphere-associated biology primarily when plants are active; decomposer communities can persist and function independently of current plant growth
  • Persistent organic–mineral complexes (including humus and mineral-associated organic matter) underpin soil aggregation, nutrient buffering, and resilience over long time periods; renewal and maintenance occur primarily through the decomposition and transformation of plant-derived organic matter (including roots and residues) into these persistent forms, rather than through living roots themselves

Healthy soil is not something applied to land. It emerges from interactions between materials, organisms, and energy inputs over time.

The soil food web explained

In this document, the soil food web is used as a descriptive ecological concept referring to interactions among soil organisms involved in energy and nutrient redistribution. It is not presented as a prescriptive management framework, nor as a substitute for material structure, nutrient supply, or engineered interventions.

The soil food web describes how biological processes operate within soils that already possess, or are being supplied with, appropriate physical and chemical capacity. It does not imply that biological optimisation is required for soil productivity or that biology alone determines soil function.

With the plant–soil metabolic energy loop established, the soil food web can now be understood not as a list of organisms, but as a metabolic-energy and nutrient-distribution system.

The soil food web describes the network of organisms that live in soil and exchange energy, nutrients, and signals. Carbon enters the system primarily through plants, via roots and residues. From there, it flows through microbes and larger organisms before returning to plants in usable forms.

Rather than a simple chain, the soil food web is a dynamic network. Diversity matters more than sheer population size, because different organisms perform different functions at different times and under different conditions.

Under certain conditions, soil food web interactions can:

  • influence the timing and form of nutrient release,
  • contribute to aggregate formation and protection,
  • influence disease dynamics, and
  • affect root–soil interactions.

The key players in living soil

Bacteria and archaea

Bacteria are the primary decomposers of simple organic compounds. They respond quickly to fresh inputs and are central to nutrient cycling, especially nitrogen transformations.

Many soil bacteria live within biofilms—thin, sticky matrices of extracellular polymers that bind cells together and attach them to soil particles. These biofilms act as living infrastructure, helping stabilise aggregates and protect microbes from drying, predation, and chemical shocks.

Archaea, while less visible, play important roles in nitrogen cycling and can dominate in low-nutrient or extreme soil environments.

Fungi and mycorrhizal networks

Fungi differ from bacteria in both form and function. Their long, thread-like hyphae physically bind soil particles together, acting like biological reinforcement within aggregates.

Mycorrhizal fungi form partnerships with plant roots, trading nutrients and water for carbon where soil conditions and nutrient gradients make this exchange advantageous. Through these networks, plants can access phosphorus, micronutrients, and moisture beyond the immediate root zone.

Fungal-dominated soils are typically:

  • more structurally stable,
  • often associated with slower carbon turnover at the aggregate scale, and
  • more resilient to drought and disturbance.

Protozoa and nematodes

Protozoa and nematodes are microbial grazers. By feeding on bacteria and fungi, they release nutrients that would otherwise remain locked inside microbial cells.

This predation is not harmful. It is essential. Nutrient release through grazing is one of the main ways plants access nitrogen and other elements in biologically active soils.

Earthworms and soil fauna

Earthworms, arthropods, and other soil animals are ecosystem engineers. They mix organic matter with mineral soil, create pores, and produce casts rich in microbial life.

Their activity improves aeration, infiltration, and root penetration, while also accelerating the formation of stable aggregates.

Biofilms, aggregates, and soil structure

Soil structure is not simply a function of texture. It reflects interactions among mineral particles, organic matter, and biological processes.

Microbial biofilms, fungal hyphae, root exudates, and decomposed organic residues all contribute to the formation of aggregates—clusters of particles that behave as a single unit.

Stable aggregates:

  • resist compaction,
  • can physically occlude some organic compounds from rapid microbial access,
  • improve water infiltration and storage, and
  • create a balance of air- and water-filled pores.

Where biological processes are reduced or absent, aggregate stability may decline over time, increasing the risk of compaction or surface crusting, depending on soil type and management.

Plant–microbe signalling and cooperation

Plants participate in soil biological interactions primarily through root-derived compounds and residue inputs. Through their roots, they release a complex mix of sugars, amino acids, organic acids, and signalling compounds.

These root exudates:

  • influence microbial activity near roots,
  • affect nutrient mobilisation pathways, and
  • shape microbial community composition around the root zone.

Mycorrhizal fungi and other microbes respond to these signals, forming cooperative relationships that directly support plant growth. In effect, plants influence the composition and activity of soil organisms in their immediate root environment.

“Inert” amendments and biological response

Some soil amendments appear biologically inert because they contain little or no nutrient value. However, many of these materials still trigger strong biological responses.

Examples include mineral amendments, sands, and some forms of biochar, depending on suitability for soil use. Their influence often comes from:

  • surface area and pore structure,
  • habitat creation for microbes,
  • changes to moisture retention and aeration, and
  • interaction with organic compounds and nutrients.

The biological outcome depends heavily on context. Particle size, pre-loading with nutrients, microbial inoculation, and existing soil condition all affect whether an amendment supports or disrupts the soil food web.

What damages soil biology

Soil biology is robust but not indestructible. Common stressors include:

  • compaction and loss of oxygen,
  • excessive soluble salts and nutrient shocks,
  • repeated disturbance and inversion,
  • prolonged carbon starvation.

These pressures simplify the soil food web, favouring short-term responses over long-term stability.

How management influences soil biological processes (non-prescriptive)

This section describes how common management factors influence biological processes in soil. It does not prescribe actions, targets, or systems, and it does not imply that maximising biological activity is always desirable or necessary.

Biological processes respond to physical conditions, carbon availability, disturbance regimes, moisture and oxygen status, and nutrient form and concentration. Management therefore influences how biological processes operate without determining outcomes in isolation.

Common influencing factors include:

  • the presence and form of carbon inputs,
  • the degree and frequency of physical disturbance,
  • moisture and aeration regimes,
  • nutrient gradients and solubility,
  • compatibility of added materials with existing soil structure.

These factors shape biological activity and its effects on aggregation, nutrient transformations, and resilience, but outcomes remain conditional and context-dependent.

Alignment with the Soil Transition Model (STM)

This pillar describes biological processes in soil. Within the STM, these are treated as dynamic modifiers, not state determinants.

In STM terms:

  • Material condition (structure, persistent organic–mineral complexes, texture) defines baseline soil behaviour.
  • Biological processes influence rates of nutrient transformation, redistribution, and short-term aggregation.
  • Current biological activity may be high or low across multiple STM states.

Key implications:

  • Biological activity does not define STM position.
  • Changes in biological indicators do not imply improved persistence or resilience.
  • Transitions between STM states may occur via biological pathways, material additions, engineering interventions, nutrient substitution, or combinations thereof, over different time horizons.

Within the STM, soil biology functions as an interpretive process lens, not a universal driver or solution.

Summary

This pillar is grounded in a clear separation between stored soil capital and biological process flows:

  • Persistent organic–mineral complexes (humus / MAOM) underpin long-term aggregation, buffering, and resilience.
  • Dead plant-derived organic matter, transformed by decomposer communities, is the primary route by which this capital is renewed.
  • Living roots and symbiotic organisms regulate short-term energy allocation, signalling, and nutrient efficiency, but do not determine baseline soil function.
  • Biological pathways can be substituted or bypassed through materials, engineering, or nutrient supply over limited time horizons.

Within this framework, the soil food web is a mechanism for redistribution and renewal, not a universal solution or requirement.