Transformation of Organic Matter

What is Soil Organic Matter?

Before discussing transformations, let us agree on terminology. Soil organic matter (SOM) is the sum of all naturally occurring organic materials present in or on the soil, excluding the above‑ground parts of living plants (Baldock et al., 2012). This definition includes:

• Living components – plant roots, microbial biomass, soil fauna
• Dead components – plant residues, microbial cells, products of their decay
• Stabilised forms – organic substances protected from decomposition

It is important to understand that SOM is not a static mass but a dynamic system in which synthesis and decomposition processes occur continuously (Baldock, 2007). A key feature of SOM is its heterogeneity: we are dealing with a mixture of substances that differ greatly in their resistance to decomposition.

The Carbon Cycle as the Basis of Transformations

The transformation cycle of organic matter in soil is part of the global carbon cycle (Eash et al., 2016; White, 2006). Carbon enters the soil through photosynthesis, when plants fix atmospheric CO₂ into organic compounds. Some of this carbon is immediately returned to the atmosphere through plant respiration, but a significant fraction accumulates in biomass.

When plants die, their residues – leaves, stems, roots – become the main source of organic matter for the soil. This is where the transformation cycle we will study begins.

Stage 1: Litter – Input of Organic Matter

The topsoil is constantly replenished with organic residues. The main sources of input are:

1. Above‑ground plant residues – leaves, needles, twigs, fruits

2. Below‑ground organs – dead roots and their fragments

3. Root exudates (rhizodeposits) – organic substances released by living roots during their activity

4. Microbial biomass – microorganisms themselves, their metabolites and cell walls

5. Remains of soil animals and their excreta

The amount and quality of incoming litter vary greatly. In temperate forests, 1.5–4 tonnes of organic carbon per hectare are deposited on the soil surface annually (White, 2006). Below ground, through root death and root exudates, an additional 20–40% of that amount may be added. In tropical forests, these figures are much higher.

Stage 2: Decomposition (Decay)

Once in the soil, organic residues undergo decomposition – a process in which complex organic molecules are broken down into simpler compounds.

Decomposition is not a single process but a chain of sequential reactions involving different groups of organisms (Eash et al., 2016; Weil & Brady, 2017). First, soil animals – earthworms, centipedes, mites, springtails – come into play. They shred plant material, rupture cell walls, and increase the surface area accessible to microorganisms. This is a critical stage of physical preparation of the substrate.

Then microorganisms – bacteria, actinomycetes, and fungi – take over. They release enzymes into the external environment (extracellular enzymes) that hydrolyse complex polymers into monomers: cellulose to glucose, proteins to amino acids, lipids to fatty acids and glycerol (Huang & Hardie, 2012). These monomers can then be taken up by microbial cells.

It is important to note that different groups of microorganisms specialise in different substrates. Fungi and actinomycetes are particularly important for decomposing lignin and cellulose, while bacteria actively consume simple sugars and proteins (Eash et al., 2016).

Stage 3: Mineralisation

Mineralisation is the process of complete decomposition of organic substances to inorganic compounds (Eash et al., 2016; Foth, 1990). This is the final oxidation stage, when organic carbon is converted to carbon dioxide (CO₂), and organically bound nitrogen, phosphorus, and sulfur are released in mineral forms – ammonium, nitrates, phosphates, sulfates.

Mineralisation is a key process for plant nutrition. It is through mineralisation that nitrogen, phosphorus, and other elements from plant residues become available to the next generation of plants. This process closes one biogeochemical cycle and initiates the next.

The rate of mineralisation depends on the same factors that determine microbial activity: temperature, moisture, aeration, and substrate availability.

Stage 4: Microbial Processing and Immobilisation

Here is where it gets really interesting. Microorganisms do not merely decompose organic matter – they actively process it for their own needs. Part of the carbon from plant residues is used by microorganisms to obtain energy (and then we speak of mineralisation), and part is used to build their own cells.

Immobilisation is the reverse of mineralisation: inorganic forms of elements (e.g., ammonium, nitrates) are taken up by microorganisms and incorporated into organic compounds in their cells (Eash et al., 2016; Foth, 1990). At this moment, these elements become unavailable to plants.

Mineralisation and immobilisation occur simultaneously. Their balance is determined by the carbon‑to‑nitrogen ratio (C:N) in the decomposing material.

Think of microorganisms as tiny factories. They need carbon (energy) and nitrogen (for building proteins) to operate. Plant residues may contain too little or too much of these elements.

Microbes have their own C:N ratio of about 8:1 (Eash et al., 2016; Weil & Brady, 2017). However, during respiration they lose about two‑thirds of the consumed carbon as CO₂. Therefore, to build 1 gram of their biomass with C:N ≈ 8, they need to consume about 24 grams of carbon for every gram of nitrogen.

If the plant material has C:N > 25:1 (for example, straw, where C:N can reach 80:1), microorganisms are short of nitrogen. They are forced to take it from the soil solution – immobilisation occurs. Plants at this time experience nitrogen starvation – the so‑called period of nitrogen depression (Eash et al., 2016).

If C:N < 20:1 (young legumes, manure), there is more nitrogen than microbes need. The excess is released into the soil – net mineralisation occurs, and plants get available nitrogen.

It is this competition between microorganisms and plants for nitrogen that determines whether added organic matter will “feed” the plants or temporarily “starve” them.

Stage 5: Stabilisation – Why Does Some Organic Matter Persist for Centuries?

Now let us return to our main question: why do some organic residues disappear quickly while others persist for centuries?

The fact is that not all carbon from plant residues is mineralised. Some of it is converted into forms that are resistant to further decomposition. This process is called stabilisation of organic matter (Baldock et al., 2012; Scheffer et al., 2018).

During the first year after entering the soil, about two‑thirds of the carbon from plant residues decomposes (White, 2006; Weil & Brady, 2017). Another 20% decomposes over the next few years. The remaining 10–15% can persist for decades and even centuries. What protects them?

Modern science identifies three main stabilisation mechanisms (Baldock & Skjemstad, 2000; Scheffer et al., 2018):

1. Chemical recalcitrance (resistance)

Some compounds, by their chemical structure, are poorly amenable to enzymatic breakdown. These include lignin (especially its highly condensed forms), cutin and suberin (polymers protecting leaves and roots), and black carbon (pyrolysis products from fires).

Lignin is one of the best‑known examples. It is a complex polymer with many strong carbon‑carbon bonds that require special enzymes to break – enzymes found only in a few specialised fungi (white rot). Under anaerobic conditions, lignin can persist for millennia.

2. Physical protection – inaccessibility to microorganisms

Organic matter can be physically isolated from microorganisms. This happens when fine particles of plant residues become trapped inside soil aggregates, in pores smaller than 2–5 µm – too small for bacteria to enter (Eash et al., 2016; Scheffer et al., 2018). Such organic matter is called occluded or intra‑aggregate.

When soil is ploughed, aggregates are destroyed, protected organic matter is released and rapidly mineralised – which is why ploughing virgin land causes a sharp decline in organic matter content.

3. Organo‑mineral interactions (binding to minerals)

This is perhaps the most important mechanism for long‑term stabilisation. Soluble organic substances are adsorbed onto the surface of mineral particles – especially clay minerals and oxides of iron and aluminium (Baldock & Skjemstad, 2000; Scheffer et al., 2018).

Organic molecules “stick” to mineral surfaces in several ways:

• Ligand exchange – when functional groups of organic acids (carboxyl, phenolic) replace hydroxyl groups on mineral surfaces, forming strong covalent bonds. This mechanism is particularly effective in acidic soils with iron and aluminium oxides.

• Electrostatic attraction – when positively charged groups of organic molecules (amines, amino acids) are attracted to negatively charged surfaces of clay minerals.

• Cation bridges – when polyvalent cations (Ca²⁺, Fe³⁺, Al³⁺) simultaneously bind negative charges of minerals and organic acids.

Adsorbed organic molecules become less accessible to enzymes – their mineralisation is slowed down by tens to hundreds of times. This mechanism explains why clay soils contain more organic carbon than sandy soils (all else being equal).

Modern View: Organic Matter as a Continuum

Previously, it was believed that specific high‑molecular‑weight compounds – “humic substances” – are formed in soil, synthesised by microorganisms from breakdown products of lignin and other components. This theory assumed the formation of certain “ready‑made” macromolecules, like resins, that accumulated in soil as stable end‑products.

However, modern research using spectroscopy and isotopic labelling has shown that the classical picture is incorrect (Lehmann & Kleber, 2015). It turns out that much of what we call “humus” in laboratory extractions may be an artefact – the result of chemical reactions occurring during alkaline extraction. In real soil, organic matter is not a set of well‑defined macromolecules but a continuum of molecules with a gradually increasing degree of transformation.

The modern model proposes viewing soil organic matter as a spectrum, with fresh plant residues rich in easily degradable components at one end, and highly transformed molecules, repeatedly processed by microorganisms and tightly bound to mineral surfaces, at the other.

This continuum consists of:

1. Free particles – macro‑ and micro‑fragments of plants that have not yet lost their cellular structure

2. Occluded particles – fragments inside aggregates, protected from microorganisms

3. Adsorbed molecules – organic substances adsorbed on mineral surfaces

4. Small molecules in solution (DOC – dissolved organic carbon)

Constant transitions occur between these fractions: particles break down, molecules desorb and re‑adsorb, and microorganisms continuously recycle new portions of carbon.

An important implication of this approach: soil organic matter never reaches a state of “eternal stability”. Even the most protected fractions decompose slowly but continuously. Stability is not a property of a molecule but a property of the system, determined by the balance between input and decomposition processes (Baldock, 2007; Schmidt et al., 2011).

Brief Summary

Thus, the cycle of transformations of organic matter in soil includes five successive stages:

1. Litter – input of plant and animal residues

2. Decomposition – shredding and enzymatic hydrolysis of polymers to monomers

3. Mineralisation – complete oxidation to CO₂ and mineral elements

4. Microbial processing – incorporation of part of the carbon into microbial biomass (immobilisation) or release as mineral forms

5. Stabilisation – conversion of part of the organic matter into forms protected from rapid decomposition

The balance between these processes is determined by:

• Chemical composition of litter (C:N, lignin content, polyphenols)
• Soil conditions (temperature, moisture, aeration, pH)
• Physical structure of the soil (capacity to protect organic matter within aggregates)
• Activity of microbial communities and microfauna

It is the combination of these factors that determines whether carbon will be rapidly returned to the atmosphere or remain in the soil for a long time, shaping its fertility and participating in the global carbon cycle.

In the following sections, we will examine each of these stages in detail, as well as the factors determining process rates. We will discuss what happens at the molecular level, why some plant residues decompose in weeks while others persist for centuries, and how modern models describe these complex processes.

Definition and Essence of Mineralisation

Mineralisation is the process by which organic forms of chemical elements are converted into inorganic (mineral) forms under the action of microorganisms (Eash et al., 2016; Foth, 1990). Essentially, it is the final stage of decomposition, when nothing remains of a complex organic molecule but simple mineral compounds.

When we speak of mineralisation, we most often mean carbon mineralisation:

However, not only carbon and hydrogen are mineralised. In this process, nitrogen, phosphorus, sulfur, and other elements that were bound in complex structures within organic molecules are also released. For example, amino groups of proteins are converted to ammonium (NH₄⁺), organic phosphates to orthophosphates (H₂PO₄⁻), and sulfur‑containing amino acids to sulfates (SO₄²⁻) (Eash et al., 2016).

Key point: mineralisation is not just destruction; it is the release of elements for a new cycle of life. It is through mineralisation that elements “locked” in dead plants and animals become available again to living organisms.

Mineralisation and Immobilisation – Two Poles of One Process

It is important to understand immediately: mineralisation never occurs in isolation. Simultaneously with it, the opposite process – immobilisation – takes place, i.e., the uptake of inorganic elements by microorganisms and their incorporation into organic compounds of their own cells (Eash et al., 2016; White, 2006).

These two processes always go in parallel. The net result – an increase or decrease in the content of available mineral elements in the soil – depends on which process prevails.

Imagine two arrows pointing in opposite directions:

• Mineralisation: organic nitrogen → ammonium/nitrate
• Immobilisation: ammonium/nitrate → organic nitrogen

The balance between them determines whether the soil will “feed” the plants or “starve” them at any given moment (we will examine this balance in more detail in Section 6, when we discuss the factors determining process rates).

Who Carries Out Mineralisation?

Mineralisation is the result of the activity of a complex community of microorganisms and microfauna. The participants include:

1. Heterotrophic bacteria – the main workforce. They release extracellular enzymes that hydrolyse complex polymers to monomers, then absorb them and oxidise them to CO₂ and water (Eash et al., 2016; Weil & Brady, 2017).

2. Fungi – especially important for decomposing lignin and cellulose. Their hyphae penetrate hard‑to‑reach places (e.g., inside plant residues), and they can tolerate more acidic environments than many bacteria (White, 2006).

3. Actinomycetes – a special group of bacteria that form mycelium. They actively decompose lignin and other recalcitrant polymers and are particularly active in alkaline soils (Eash et al., 2016).

4. Soil animals (earthworms, centipedes, mites, springtails) – they do not mineralise much themselves, but they prepare the substrate: they shred plant residues, break cell walls, and increase the surface area for microbial enzymes (White, 2006). They are called “reducers” or “comminutors”, emphasising their role in the mechanical breakdown of organic matter.

5. Microfauna – protozoa and nematodes that feed on bacteria and fungi. They not only regulate microbial population numbers but also actively participate in nitrogen mineralisation: by consuming microbial biomass, they excrete excess nitrogen as ammonium, making it available to plants (Weil & Brady, 2017).

Biochemistry of Mineralisation: What and How Decomposes

Different components of plant residues mineralise at different rates. This is determined by their chemical structure and availability to microorganisms. Below we consider the main classes of compounds in order of decreasing mineralisation rate.

Enzymes – The Main Actors

Microorganisms cannot absorb large polymers – they are too large to pass through the cell membrane. Instead, they release extracellular enzymes into the external environment, which “cut” long molecules into shorter fragments (Eash et al., 2016; Huang & Hardie, 2012).

The most important groups of enzymes involved in mineralisation:

• Hydrolases – cleave bonds with the participation of water. These include cellulases, amylases (starch), proteases (proteins), lipases (fats), phosphatases (organic phosphates), and sulfatases (organic sulfates).
• Oxidoreductases – catalyse redox reactions. Particularly important for lignin degradation: peroxidases, laccases, phenol oxidases.

Enzymes can remain active in soil even after the microorganisms that released them have died. They can adsorb onto clay particles and retain partial activity for a long time (Huang & Hardie, 2012; Scheffer et al., 2018). This is yet another example of the complexity of the soil system: enzymes outlive their creators.

Energetics of Mineralisation

Mineralisation is an energetically favourable process for microorganisms. During the oxidation of organic compounds, chemical energy is released, stored as ATP, and used by cells for vital activities.

Recall the basic equation of aerobic respiration:

On average, about 40 kJ of energy is released per gram of oxidised organic carbon, available to microorganisms (Weil & Brady, 2017). This allows them not only to survive but also to multiply. However, microorganisms use only part of this energy – about 40–60% – for synthesis of new biomass. The rest is dissipated as heat. This is why the temperature of composting materials can reach 60–70 °C – it is the result of heat release during active mineralisation.

Mineralisation as a Source of CO₂

The global significance of mineralisation cannot be overstated. Soils annually return about 60 petagrams (Pg = 10¹⁵ g) of carbon to the atmosphere as CO₂ (Weil & Brady, 2017). For comparison: burning fossil fuels releases about 7–8 Pg of carbon per year. Soil respiration is one of the largest carbon fluxes in the biosphere.

By measuring the rate of CO₂ release from the soil, scientists estimate the intensity of mineralisation. This indicator is called soil respiration and is used as an integral indicator of biological activity (Eash et al., 2016; Scheffer et al., 2018).

However, it is important to distinguish:

• Heterotrophic respiration – CO₂ released by microorganisms during decomposition of organic residues (this is mineralisation proper)
• Autotrophic respiration – CO₂ released by the plants themselves (root respiration)

Both processes contribute to total soil respiration, but heterotrophic respiration is the mineralisation of organic matter that we are studying.

Mineralisation and Plant Nutrition

For plants, mineralisation is the main source of nitrogen, phosphorus, sulfur, and many trace elements. Without this process, nutrients would remain forever locked in dead plant residues. However, the rate of mineralisation must be balanced: too slow – plants starve; too fast – nutrients may be leached from the soil before they can be used.

In natural ecosystems, the balance is established automatically: mineralisation occurs at about the same rate as plants take up elements. In agroecosystems, this balance is often disrupted: ploughing accelerates mineralisation, while crop removal reduces organic matter input. The result is fertility degradation, which we face in many regions of the world.

Rate of Mineralisation: Quantitative Assessment

In laboratory and field experiments, mineralisation is most often measured by the rate of CO₂ release or by the increase in mineral nitrogen (NH₄⁺ + NO₃⁻) over a given period (White, 2006; Weil & Brady, 2017).

The mineralisation rate is described by first‑order kinetics:

where:

• C – amount of organic carbon
• k – decomposition rate constant (time⁻¹)
• t – time

This formula means that the decomposition rate is proportional to the amount of remaining organic matter. The more carbon, the faster it decomposes – but as it decreases, the process slows down.

However, the real picture is much more complex. In soil, many fractions of organic matter with different rate constants (k) coexist simultaneously. Therefore, the first‑order model describes well only the initial stages of decomposition (first months‑years), while for longer periods more complex multi‑component models are required (White, 2006; Scheffer et al., 2018). We will return to this in Section 7 “Modern Models of SOM Formation”.

What Determines the Rate of Mineralisation?

The intensity of mineralisation depends on many factors, all of which are closely interrelated. We will briefly list them here – a detailed analysis will be given in Section 6 “What Determines the Rate of Processes”:

1. Temperature – with increasing temperature, the rate of mineralisation increases (roughly 2–3 times per 10 °C in the range 5–35 °C), but only up to a certain limit (Weil & Brady, 2017; White, 2006).

2. Moisture – optimum moisture is about 60% of water‑holding capacity (Eash et al., 2016).

3. Aeration – most mineralisation processes require oxygen (aerobic conditions).

4. pH – most bacteria are active at pH 6–7.5, fungi at lower values.

5. Substrate composition – the more readily decomposable compounds (sugars, proteins) and the less lignin and polyphenols in plant residues, the faster the mineralisation.

6. C:N ratio – a critical parameter determining whether net mineralisation or immobilisation will occur (Eash et al., 2016; Weil & Brady, 2017; White, 2006).

These factors do not act in isolation but in complex interaction, creating unique mineralisation conditions in each specific soil.

Mineralisation under Anaerobic Conditions

When soil is waterlogged and oxygen supply is limited, aerobic mineralisation slows down and is replaced by anaerobic processes. Under these conditions, organic matter does not decompose completely – organic acids, alcohols, methane (CH₄), and other reduced compounds are formed (Eash et al., 2016; Weil & Brady, 2017). This process is energetically less favourable for microorganisms and significantly slower.

This is why organic matter accumulates for millennia in wetlands and peatlands: mineralisation under anaerobic conditions is tens to hundreds of times slower than under aerobic conditions.

Brief Summary

Thus, mineralisation is:

• A biological process carried out by microorganisms and microfauna
• An oxidative process in which organic carbon is converted to CO₂, and organically bound nitrogen, phosphorus, and sulfur are converted to mineral ions available to plants
• An energy‑yielding process – microorganisms gain energy for their life activities
• The main source of plant nutrition in natural ecosystems and a vital reservoir of available elements in agroecosystems
• A process in dynamic equilibrium with immobilisation – the balance between them determines the availability of nutrients
• A process whose rate depends on many factors – temperature, moisture, aeration, composition, and quality of the substrate

Mineralisation is not uniform: some compounds mineralise in hours, others in decades. This heterogeneity is the key to understanding why organic matter in soil does not disappear completely but is partly preserved, forming a reservoir of carbon and nutrients for many years.

In the next section, we will examine in more detail the process opposite to mineralisation – immobilisation – and understand why microorganisms “take away” nitrogen and other elements from plants and how this affects soil fertility.

Definition and Essence of Immobilisation

Immobilisation is the process by which inorganic (mineral) forms of elements are converted into organic forms when they are incorporated into the cells of microorganisms (Eash et al., 2016; Foth, 1990). Simply put, it is the “capture” of mineral nutrients from the soil solution by microorganisms and their binding into organic compounds.

When we speak of immobilisation, we most often mean nitrogen immobilisation – the uptake of ammonium (NH₄⁺) or nitrate (NO₃⁻) nitrogen by microorganisms and its incorporation into organic compounds – proteins, nucleic acids, amino acids (Eash et al., 2016). But analogous processes occur with phosphorus, sulfur, potassium, and other elements.

It is important to emphasise: immobilisation is not a loss of elements from the soil. The elements remain in the soil but shift from mineral (plant‑available) form to organic (temporarily unavailable) form, being locked inside microbial cells. This is fundamentally different from, for example, nitrate leaching or denitrification, where nitrogen actually leaves the soil.

Who Carries Out Immobilisation?

Immobilisation is a process inherent in almost all heterotrophic microorganisms and, to a lesser extent, plants themselves. However, in the context of soil dynamics, we mainly refer to microbial immobilisation. The key participants are:

1. Bacteria – the most active immobilisers. They have a low C:N ratio (about 4–5:1), meaning they are relatively rich in nitrogen and therefore need a lot of nitrogen to build their biomass (White, 2006). Bacteria multiply rapidly and respond quickly to the input of available organic substances.

2. Fungi – immobilise nitrogen more slowly, but their biomass is often larger than bacterial biomass. Fungi have a broader C:N ratio (about 10–15:1) (White, 2006; Weil & Brady, 2017). They are especially important for immobilisation in acidic soils and forest litter.

3. Actinomycetes – occupy an intermediate position between bacteria and fungi in their properties.

Immobilisation is especially intense during periods of active microbial population growth, when a large amount of readily available organic matter (fresh plant residues, root exudates) enters the soil. This leads to rapid increases in microbial biomass and, consequently, temporary binding of mineral nitrogen.

Mechanisms of Immobilisation

How do microorganisms capture inorganic elements? Let us consider this process using nitrogen as an example – the most studied element in the context of immobilisation.

Mineralisation and Immobilisation: Dynamic Equilibrium

Immobilisation never occurs in isolation from mineralisation. These two processes always occur simultaneously, like two sides of the same coin. The net result – an increase or decrease in the content of available mineral elements in the soil – depends on the balance between them.

Mineralisation: organic N (in plant residues, microbial cells) → inorganic N (NH₄⁺, NO₃⁻)

Immobilisation: inorganic N (NH₄⁺, NO₃⁻) → organic N (in microbial cells)

At any moment, these two arrows point in opposite directions. When mineralisation exceeds immobilisation, we observe net mineralisation – the content of available nitrogen in the soil increases. When immobilisation prevails, we observe net immobilisation – available nitrogen decreases (Eash et al., 2016; Weil & Brady, 2017).

The intensity of both processes depends on microbial activity, which in turn is determined by:

• availability of readily available organic carbon;
• availability of nitrogen and other elements;
• environmental conditions (temperature, moisture, aeration, pH);
• composition of the microbial community.

The Role of C:N Ratio in Governing Immobilisation

The key factor determining whether mineralisation or immobilisation will dominate is the carbon‑to‑nitrogen ratio (C:N) of the decomposing material (Eash et al., 2016; Foth, 1990; Weil & Brady, 2017; White, 2006).

Imagine a microbial cell as a “building block” with an average C:N ratio of about 8:1. However, microorganisms, by oxidising organic matter to obtain energy, lose about 60–75% of consumed carbon as CO₂ (White, 2006). Therefore, to build 1 gram of microbial biomass with C:N = 8, they need to consume 3–4 grams of carbon, i.e., about 24–32 grams of carbon per gram of nitrogen.

This yields a critical ratio – about 25–30:1 (depending on carbon use efficiency). If plant residues have C:N above this threshold, microorganisms are short of nitrogen and must take it from the soil solution – net immobilisation occurs and available nitrogen in the soil decreases. If C:N is below the threshold – there is more nitrogen than microbes need, and the excess is released into the soil – net mineralisation occurs (Eash et al., 2016).

Consider specific examples (Table 2.1).

Table 2.1. Typical C:N ratios of various organic materials (data from Eash et al., 2016; Weil & Brady, 2017; White, 2006).

When straw (C:N ≈ 80:1) is added to soil, microorganisms experience acute nitrogen deficiency. They actively absorb NH₄⁺ and NO₃⁻ from the soil solution, incorporating them into their biomass. The content of mineral nitrogen in the soil drops sharply – plants begin to suffer nitrogen starvation. This period is called the period of nitrogen depression (Eash et al., 2016; Weil & Brady, 2017). It can last from several weeks to several months, depending on the quantity and quality of added organic matter, soil temperature, and moisture.

Conversely, when alfalfa (C:N ≈ 13:1) is added, microorganisms receive more nitrogen than they need. The excess is released into the soil as ammonium, and plants get additional nutrition.

Immobilisation Is Not Loss, but Delayed Release

It is important to understand: immobilisation is not permanently lost nitrogen. It is temporarily bound nitrogen, locked in living microbial cells. When these cells die (the average lifespan of bacteria in soil is from a few days to several weeks), their contents become available to other microorganisms or to plants.

The process of microbial biomass death and decomposition is continuous. Part of the nitrogen is mineralised and becomes available; part is again immobilised by a new generation of microorganisms. This endless cycling of nitrogen through microbial biomass is called microbial turnover or mineralisation‑immobilisation turnover (MIT) (Foth, 1990; Weil & Brady, 2017).

This turnover is extremely important for soil fertility. It is precisely because of it that nitrogen and other elements are retained in the soil and not leached, while gradually becoming available to plants.

Immobilisation in Different Soil Types and Ecosystems

The intensity of immobilisation varies greatly among different soils and ecosystems.

• In forest soils with mor humus type (coniferous forests, acidic litter rich in polyphenols), immobilisation often dominates over mineralisation. The slowly decomposing organic matter is poor in nitrogen, microorganisms constantly lack it, and they compete with plants. Therefore, nitrogen deficiency is often observed in such forests (White, 2006).

• In meadow and steppe soils with mull humus type (herbaceous vegetation, nitrogen‑rich litter, high calcium content), mineralisation and immobilisation are often balanced. Microbial turnover is intense, nitrogen cycles rapidly, and plants receive it in adequate amounts (Weil & Brady, 2017).

• In agroecosystems, immobilisation becomes a serious problem when large amounts of straw residues (maize, wheat) are incorporated after harvest. Adding nitrogen fertilisers can “feed” the microorganisms and shorten the period of nitrogen depression.

Managing Immobilisation in Agriculture

Agronomists and soil scientists have developed several strategies to manage immobilisation and minimise its negative effects:

1. Composting – pre‑decomposition of high‑carbon materials (straw, sawdust) with addition of nitrogen‑rich materials (manure, green mass). During composting, the C:N ratio narrows, and incorporation of such compost into soil does not cause nitrogen depression (Weil & Brady, 2017; Scheffer et al., 2018).

2. Co‑application of high‑carbon and nitrogen‑rich materials – for example, ploughing straw together with green manure (catch crop) from legumes, or applying mineral nitrogen fertiliser simultaneously with straw (Eash et al., 2016).

3. Timing of application – if high‑carbon materials are applied in autumn, the period of nitrogen depression occurs in winter when plants are not growing, and by spring the nitrogen is already released (Weil & Brady, 2017).

4. Selection of crops with low C:N residues – legumes, buckwheat, rape leave behind more nitrogen‑rich organic matter.

5. Minimum tillage – reduces the rate of mineralisation, making immobilisation less rapid and more spread out over time (Weil & Brady, 2017).

Immobilisation in the Context of Cycles of Other Elements

Although we focus mainly on nitrogen, analogous processes occur with phosphorus, sulfur, and micronutrients. For example:

• Phosphorus – immobilisation of phosphorus by microorganisms is particularly important in tropical soils, where phosphorus is strongly fixed by minerals. Microbial biomass becomes a reservoir of available phosphorus (Weil & Brady, 2017).
• Sulfur – immobilisation of sulfate sulfur into organic compounds occurs similarly to nitrogen. The C:S ratio plays a role analogous to C:N (Eash et al., 2016).
• Micronutrients (Zn, Cu, Mn, Fe) – microorganisms actively absorb and retain these elements, reducing their toxicity when in excess and preventing losses when deficient.

Thus, immobilisation is a universal mechanism regulating the availability of all nutrients in soil.

Modern View: Immobilisation as a Survival Strategy

Modern microbial ecology considers immobilisation not as an inconvenient obstacle for plants but as an important survival strategy for the microorganisms themselves. In natural soils, carbon is the main limiting factor for heterotrophs. When fresh organic matter arrives, microorganisms must use it as quickly as possible, otherwise competitors will outpace them. For this they need nitrogen. So they “invest” available nitrogen into building new cells, even if they have to “take” it from plants.

Moreover, immobilisation is a way to retain nutrients in the biologically active layer of the soil. Without immobilisation, most of the mineral nitrogen produced during mineralisation would simply be leached from the soil by rainwater. Microorganisms act as a “filter” that binds elements and prevents them from leaving the root zone (White, 2006; Weil & Brady, 2017).

This is why ecosystems with high microbial biomass (old pastures, forests) retain nutrients better than ploughed fields with low microbial activity (Weil & Brady, 2017).

Brief Summary

Thus, immobilisation is:

• A biological process in which mineral (inorganic) elements are taken up by microorganisms and incorporated into organic compounds of their cells
• The reverse process of mineralisation – instead of releasing elements, they are bound
• Temporary binding – elements are not lost from the soil, only become unavailable to plants for the lifetime of microbial cells
• Dependent on C:N ratio – the higher the C:N of added organic matter, the stronger the immobilisation
• The cause of nitrogen depression – a period of temporary plant starvation after addition of high‑carbon residues
• An important mechanism for retaining elements in soil – prevents leaching of nitrates and other mobile forms
• An integral part of microbial turnover – the endless cycle of binding and release of nutrients

In natural ecosystems, immobilisation and mineralisation are in dynamic equilibrium, ensuring a sustainable cycle of elements. In agroecosystems, this equilibrium is often disrupted, and the agronomist’s task is to manage it by combining organic residue inputs, mineral fertilisers, and tillage so as to minimise periods of nitrogen deficit and maximise nutrient retention and use.

In the next section, we will move on to humification – a process which, unlike mineralisation and immobilisation, does not simply redistribute elements between organic and inorganic forms but leads to the formation of complex organic compounds that can persist in soil for centuries.

Introduction

We have already discussed two key processes of organic matter transformation in soil: mineralisation (conversion of organic compounds into inorganic ones) and immobilisation (incorporation of inorganic elements into microbial biomass). But the fate of plant residues is not limited to these two pathways. A significant part of organic carbon does not fully mineralise and return to the atmosphere, but remains in the soil in the form of complex, decomposition‑resistant compounds. This process is called humification.

For a long time, it was believed that humification is the synthesis of special high‑molecular‑weight compounds – humic substances – formed by polymerisation of breakdown products of lignin and other plant components. It was assumed that these substances have a unique structure, different from all known biomolecules, and that their complexity and “non‑biological” origin provide the stability of organic matter in soil.

However, in recent decades this classical picture has been seriously challenged. Modern analytical methods have allowed us to peer into the “black box” of humification and show that the concept of humus as a set of specific macromolecules is largely an artefact of laboratory procedures. In this section, we will examine what humification is from the perspective of modern science, how it differs from classical concepts, and how soil organic matter is actually organised.

The Classical Model of Humification (Historical Background)

For over a hundred years, the prevailing view was that humus consists of three main fractions, which can be extracted from soil by alkaline extraction (Weil & Brady, 2017; White, 2006):

1. Fulvic acids – soluble in both alkalis and acids; have low molecular weight, light colour.

2. Humic acids – soluble in alkalis but precipitated upon acidification; have medium molecular weight, dark colour.

3. Humin – insoluble in both acids and alkalis; has the highest molecular weight, darkest colour.

It was thought that these substances are formed during humification – a process involving several stages:

• Breakdown of lignin and polyphenols into smaller aromatic fragments;
• Oxidation of these fragments to form quinones;
• Condensation of quinones with amino acids and peptides to form complex nitrogen‑containing polymers;
• Further polymerisation and condensation to form high‑molecular‑weight humic acids.

This model was proposed in the mid‑20th century and seemed logical: plant residues contain lignin – the only known natural aromatic polymer. Its breakdown yields aromatic monomers, which can then polymerise anew with the participation of nitrogen. The resulting compounds, by their properties (colour, solubility, spectral characteristics), indeed resembled what was extracted from soil (Foth, 1990; Scheffer et al., 2018).

Problems with the Classical Model and the Emergence of a New Approach

In the 1990s and 2000s, data accumulated that contradicted the classical views.

First. Using direct in situ analysis methods – especially solid‑state ¹³C‑NMR spectroscopy – it was shown that the chemical composition of organic matter in soil does not match what is extracted by alkaline solutions (Baldock et al., 2012; Lehmann & Kleber, 2015). Alkali does not simply extract existing molecules but creates them – hydrolyses esters, breaks hydrogen bonds, induces polymerisation of monomers that never occur together in real soil.

Second. Isotopic studies (using ¹⁴C and ¹³C) showed that the age of different organic matter fractions does not correlate with their extractability. Some “humic acids” turned out to be younger than “non‑extractable” humin, and some older. If humic acids were products of synthesis, they should have a certain age, but this was not observed (Baldock, 2007; Schmidt et al., 2011).

Third. In soils where humification was supposed to be intense (e.g., Chernozems), the content of “humic acids” often did not correlate with the stability of organic matter. Instead, it turned out that stability is related not to molecular complexity but to their position in the soil matrix – protection by minerals and aggregates (Baldock & Skjemstad, 2000; Scheffer et al., 2018).

Fourth. In forest litters, where lignin and polyphenols are abundant, humification according to the classical scheme should proceed very actively. However, in mor litters, what accumulates is not newly synthesised polymers but modified but unpolymerised lignin and its fragments linked to carbohydrates and proteins through weak bonds (White, 2006; Weil & Brady, 2017).

These contradictions led to a revision of the theory of humification.

Modern View: The Organic Matter Continuum

In 2015, a paper was published that became a manifesto of the new approach (Lehmann & Kleber, 2015). Its key idea: soil organic matter is not a set of discrete classes of compounds (humic acids, fulvic acids, etc.) but a continuum of molecules continuously transformed from easily degradable plant residues to highly modified and protected organo‑mineral complexes.

Instead of “synthesis of new macromolecules”, the modern model proposes viewing humification as sequential transformation:

1. Fresh plant residues (lignocellulose complex, proteins, carbohydrates).

2. Microbial processing: some components are mineralised, others are modified (oxidised, hydrolysed, partially depolymerised).

3. Degradation products and partially decomposed biopolymers interact with the mineral phase.

4. These associations (sorption on clays and oxides, inclusion in micropores) make organic matter inaccessible to enzymes.

5. Gradual “ageing” – further oxidation, formation of new functional groups, but without formation of fundamentally new types of bonds.

Thus, humification is not synthesis but selective preservation and modification of original and microbial compounds, which become stable through interaction with the soil matrix (Baldock, 2007; Schmidt et al., 2011; Lehmann & Kleber, 2015).

What Actually Happens to Lignin and Polyphenols?

Lignin is indeed one of the key components determining long‑term preservation of organic matter. However, its role is not that it serves as a precursor for the synthesis of humic acids, but in its own recalcitrance.

Lignin is a three‑dimensional polymer with numerous strong bonds (including carbon‑carbon bonds). During decomposition of plant residues:

• Easily degradable carbohydrates and proteins mineralise quickly.
• Lignin, on the other hand, decomposes very slowly, and its relative content in the residues increases.
• White‑rot fungi can oxidise lignin, but this leads to the appearance of carboxyl and phenolic groups, not polymerisation into new macromolecules (White, 2006).
• These oxidised lignin fragments become more hydrophilic and adsorb more readily on minerals, further slowing their subsequent decomposition.

Thus, “humification” of lignin is largely its selective accumulation and chemical modification, not conversion into a new substance. The same applies to other resistant biopolymers – cutin, suberin, microbial polysaccharides, chitin (Scheffer et al., 2018).

The Role of Black Carbon (Char)

An important component of organic matter often ignored in the classical model is black carbon (char) – products of incomplete combustion of vegetation during fires (Weil & Brady, 2017; Scheffer et al., 2018). In soils subject to fires (savannas, steppes, boreal forests), black carbon can account for up to 40–50% of total organic carbon.

Black carbon is a highly aromatic, condensed material with a graphite‑like structure that is virtually non‑biodegradable. It has a huge specific surface area (up to 2500 m²/g) and high cation exchange capacity. It is black carbon, not synthesised “humic acids”, that often provides the dark colour, high water‑holding capacity, and fertility of some soils (recall the famous terra preta in Amazonia).

In classical humification schemes, black carbon was not taken into account and was attributed to “humin” or “non‑hydrolysable residue”. Modern research shows that many properties previously ascribed to humic acids are actually due to the presence of black carbon (Weil & Brady, 2017; Lehmann & Kleber, 2015).

Stabilisation as the Key Mechanism

If humification is not the synthesis of new compounds, then what ensures long‑term preservation of organic matter? The answer: stabilisation – physical and chemical protection from microbial attack.

As we discussed in Section 1, there are three main stabilisation mechanisms (Baldock & Skjemstad, 2000; Scheffer et al., 2018; Schmidt et al., 2011):

1. Chemical recalcitrance – resistance of the molecules themselves (lignin, black carbon, some lipids).

2. Physical protection – inaccessibility to microorganisms due to location within aggregates or micropores.

3. Organo‑mineral interactions – strong sorption on surfaces of clay minerals, Fe and Al oxides.

In modern views, it is these mechanisms, not the synthesis of special macromolecules, that determine how long organic carbon remains in soil. Humification is not an end‑product but a continuous process in which some molecules are protected, others are destabilised (e.g., by pH change or aggregate destruction) and re‑enter the cycle.

Humus as a Property of the System, Not a Substance

Modern science abandons the notion of humus as a substance with a defined chemical composition. Instead, humus is regarded as a property of organic matter that is in a state of stabilisation – that is, slowly cycling, protected, and tightly associated with the mineral matrix (Lehmann & Kleber, 2015; Schmidt et al., 2011).

Soil organic matter consists of:

• Molecules that can still be identified (derivatives of lignin, cutin, suberin, microbial polysaccharides, proteins, lipids, and black carbon);
• Fragments of these molecules, partially oxidised and hydrolysed;
• Products of their interactions with each other and with minerals through weak (hydrogen bonds, van der Waals) and strong (covalent, ligand exchange) interactions.

No fundamentally new types of bonds characteristic only of “humic substances” have been found. Everything present in soil is modified natural biopolymers and their fragments assembled into complex associations.

Practical Significance of Modern Views

The new view of humification has important practical implications:

1. Management of organic matter – instead of attempting to “create humus”, one should focus on creating conditions that favour stabilisation: preserving soil structure, maintaining high biological activity, adding organic material that will be processed rather than just “burned”.

2. Assessment of organic matter quality – important not only the total carbon content but also its distribution among fractions: free organic matter (easily mineralisable), aggregate‑protected, and mineral‑sorbed (Weil & Brady, 2017; Scheffer et al., 2018).

3. Understanding stability – the most stable forms of organic carbon are not those that are “chemically complex” but those that are physically inaccessible or tightly bound to minerals. Therefore, aggregate destruction (ploughing) leads to rapid carbon loss, even if the molecules themselves have not changed.

4. Carbon farming – carbon sequestration strategies in soils should rely on stimulating the formation of stable organo‑mineral complexes and aggregates, not on accumulation of “humus” per se.

Brief Summary

Thus, humification from the standpoint of modern science is:

• Not synthesis of new macromolecules, but continuous transformation and selective preservation of organic compounds;
• A process in which stabilisation (physical protection and organo‑mineral interaction) plays the main role, not chemical polymerisation;
• A continuum, not discrete fractions; molecules gradually oxidise, hydrolyse, fragment, and interact with minerals, forming complex associations;
• Includes all resistant biopolymers (lignin, cutin, suberin, chitin, black carbon, microbial polysaccharides), as well as their fragments and interaction products;
• Does not create fundamentally new types of organic compounds – everything in soil can be traced back to plants, microorganisms, or combustion products;
• Determines long‑term carbon storage, but through a combination of molecular recalcitrance and protection by the soil matrix.

The modern understanding of humification shifts the emphasis from “synthesis chemistry” to “physics and chemistry of protection”. This allows a more meaningful approach to managing soil organic matter, viewing it not as a static stock but as a dynamic yet stabilised system that can accumulate or be lost depending on management.

In the next section, we will move on to microbial processing – the key link that ties together all the processes considered: it is microorganisms that are the main actors in mineralisation, immobilisation, and humification.

Introduction

We have already examined three key processes of organic matter transformation: mineralisation, immobilisation, and humification. However, behind all these processes lies the same driving force – microorganisms. They are the main actors that convert complex plant polymers into simple molecules, build their cells from them, secrete enzymes, create conditions for organic matter stabilisation, and determine what fraction of carbon will be rapidly returned to the atmosphere and what fraction will remain in the soil for a long time.

In this section, we will consider who exactly participates in the processing of organic matter, how the microbial “processing factory” is organised, how microorganisms interact with each other and with the soil environment, and why understanding these processes is so important for managing soil fertility.

What is Microbial Processing?

Microbial processing is the totality of processes by which soil microorganisms transform organic compounds, using them as a source of energy and building material for their own cells (Eash et al., 2016; White, 2006). It is not a separate process but an umbrella term that includes:

• Decomposition of complex polymers to monomers by extracellular enzymes;
• Uptake (assimilation) of monomers and mineral elements;
• Metabolism – oxidation of part of the carbon to obtain energy (mineralisation) and use of another part for synthesis of cellular components (immobilisation);
• Synthesis of new organic compounds – both inside cells and outside (extracellular polymers);
• Death and decomposition of microbial cells, which initiates a new cycle of processing.

Microbial processing is the “heart” of the carbon cycle in soil. Almost all organic carbon entering the soil passes through microbial biomass (Jenkinson, 1977; Weil & Brady, 2017). Figuratively speaking, microorganisms are the “eye of the needle” through which all carbon fluxes in terrestrial ecosystems pass.

Main Participants: Who Processes Organic Matter?

The soil microbial community is extremely diverse. One gram of soil can harbour billions of microorganisms belonging to tens of thousands of species (Eash et al., 2016; White, 2006). All of them contribute to organic matter processing, but their roles differ greatly.

Microbial Biomass: Magnitude and Dynamics

Microbial biomass is the total mass of living microorganisms in soil. It constitutes from 0.3 to 7% of total organic carbon, on average about 2–4% (White, 2006; Weil & Brady, 2017). In absolute terms, this is 500 to 2000 kg of carbon per hectare in the topsoil, and in some soils up to 5000 kg/ha.

Microbial biomass is not static. It grows rapidly when fresh organic matter arrives and declines rapidly when available substrate is exhausted. The turnover time of microbial biomass in soil ranges from a few days to several months depending on conditions (Eash et al., 2016; Weil & Brady, 2017).

It is through changes in microbial biomass that most effects of soil management manifest:

• Addition of organic fertilisers → biomass increase → enhanced immobilisation → temporary nitrogen binding → then gradual release.
• Ploughing → aggregate destruction → release of protected organic matter → burst of biomass growth → enhanced mineralisation → carbon loss.
• Drought → death of part of the biomass → upon rewetting – flush of mineralisation (“pulse” effect) (Weil & Brady, 2017).

Measuring microbial biomass is one of the most important methods for assessing soil “health”.

Ecological Strategies of Microorganisms

Microorganisms involved in organic matter processing can be divided into two groups according to their ecological strategies (Weil & Brady, 2017; Eash et al., 2016):

r‑strategists (“opportunists”):

• Rapid growth and reproduction upon input of easily available substrate;
• High metabolic rates;
• Consume simple sugars, amino acids, organic acids;
• Their numbers fluctuate sharply depending on food availability;
• Examples: most bacteria (Pseudomonas, Bacillus).

K‑strategists (“specialists”):

• Slow growth but efficient use of recalcitrant substrates;
• Enzymes with high affinity for substrate;
• Decompose lignin, cellulose, humus;
• Their numbers are more stable;
• Examples: fungi, actinomycetes, many oligotrophic bacteria.

In natural soils, both types coexist. When fresh organic matter arrives, r‑strategists “bloom” in numbers, then give way to K‑strategists, which continue slow processing of resistant fractions (Weil & Brady, 2017). It is this succession of strategies that determines the biphasic decomposition dynamics: a rapid initial stage and a slow long‑term stage (see Section 1, Fig. 3.15 in White, 2006).

The Microbial “Conveyor”: Stages of Processing

The process of microbial processing of organic matter can be visualised as a conveyor belt on which different groups of microorganisms work sequentially:

Stage 1. Substrate preparation (reducers)

• Soil animals (worms, centipedes, mites, springtails) shred plant residues, break cell walls, increase surface area for enzyme action.
• Purely physical, but critically important for accelerating subsequent stages.

Stage 2. Hydrolysis of polymers (extracellular enzymes)

• Bacteria and fungi release enzymes into the external environment: cellulases, proteases, lipases, phosphatases, etc.
• Complex polymers are broken down to monomers: cellulose → glucose; proteins → amino acids; lipids → fatty acids and glycerol.
• This is the slowest stage, limiting the overall processing rate.

Stage 3. Uptake of monomers (assimilation)

• Monomers are transported across cell membranes (active transport, often energy‑dependent).
• Inside the cell, monomers enter metabolic pathways.
• Part of the carbon is oxidised to CO₂ for energy (mineralisation).
• Part of the carbon is used for synthesis of new cellular components (immobilisation).

Stage 4. Synthesis of secondary metabolites

• Microorganisms synthesise not only cellular components but also extracellular polymers – polysaccharides, glycoproteins (glomalin), melanins.
• These compounds play an important role in the formation and stabilisation of soil aggregates.

Stage 5. Cell death and decomposition

• Microbial cells have a limited lifespan (from a few days to months).
• After death, their contents become substrate for other microorganisms (secondary processing).
• Some microbial cell wall components (chitin, peptidoglycan, melanin) are resistant to decomposition and can persist in soil for a long time.

It is this “conveyor” that explains why added organic matter does not disappear instantly but passes through successive stages, each with its own time scales and participants.

The Rhizosphere: A “Hot Spot” of Microbial Processing

A special place in microbial processing is occupied by the rhizosphere – the zone of soil directly adjacent to plant roots (Eash et al., 2016; Weil & Brady, 2017). Here, microorganism concentrations are 10–100 times higher than in the rest of the soil.

Why is the rhizosphere so active?

1. Root exudates – plants release into the rhizosphere up to 20–40% of all carbon fixed during photosynthesis (White, 2006; Weil & Brady, 2017). These are sugars, organic acids, amino acids, vitamins – ideal food for microorganisms.

2. Root hair turnover – constantly renewing root hairs die and become an additional source of organic substrate.

3. Symbiotic interactions – mycorrhizal fungi and nitrogen‑fixing bacteria actively process organic matter in exchange for carbohydrates from plants.

4. High moisture and aeration – roots create favourable conditions for microbial activity.

In the rhizosphere, microbial processing is particularly intense. Here, the competition for nutrients (especially nitrogen) between microorganisms and plants fully manifests. It is in the rhizosphere that it is decided whether added organic matter will “feed” the plants or temporarily “starve” them.

Microbial “Turnover” and Carbon Binding

Can microbial processing be managed to maximise carbon retention in soil? Yes, and to do so one needs to understand the key principles:

1. Microorganisms are the main custodians of carbon. Almost all carbon that is not mineralised immediately passes through microbial biomass. The greater the microbial biomass, the more carbon can be temporarily fixed.

2. Stability is linked to reprocessing. The more cycles of processing organic matter undergoes through microbial biomass, the more stable products accumulate: microbial polysaccharides, glycoproteins, melanins, chitin. These compounds are themselves stable, and besides, they act as “glue” for aggregate formation, which protects organic matter from further decomposition (Weil & Brady, 2017; Scheffer et al., 2018).

3. Microbial community diversity is the key to efficiency. Different groups of microorganisms process different substrates at different stages. The higher the diversity, the more complete and efficient the processing, and the more carbon is “retained” in the soil.

4. Microorganisms create stable aggregates. By releasing extracellular polymers (polysaccharides, glomalin), microorganisms glue soil particles into aggregates. Inside aggregates, organic matter becomes protected from decomposition. This is a key mechanism for long‑term stabilisation.

Practical Implications for Soil Management

Understanding microbial processing allows us to formulate several practical recommendations:

1. Add diverse organic matter. A mixture of readily and slowly degradable materials (straw + manure, green manures + wood chips) supports microbial community diversity and promotes more complete processing.

2. Create favourable conditions for microorganisms. Optimal moisture (about 60% of water‑holding capacity), good aeration, near‑neutral pH, adequate nutrition (especially nitrogen, phosphorus, potassium) – all support high microbial activity.

3. Minimise mechanical disturbance. Ploughing destroys fungal mycelium and aggregates, reduces microbial diversity, and accelerates carbon loss. Minimum tillage and direct drilling are the best ways to preserve the microbial community.

4. Stimulate root exudation. Growing plants with high root activity (perennial grasses, legumes, cereals with strong root systems) stimulates microbial processing and carbon accumulation in soil.

5. Use symbiotic microorganisms. Inoculation with mycorrhizal fungi and nitrogen‑fixing bacteria can significantly enhance microbial processing and improve plant nutrition (Weil & Brady, 2017).

Brief Summary

Thus, microbial processing is:

• The central process of organic matter transformation in soil, uniting mineralisation, immobilisation, and humification;
• Carried out by a community of microorganisms – bacteria, fungi, actinomycetes, and also soil animals that prepare the substrate;
• Includes successive stages – hydrolysis of polymers by enzymes → uptake of monomers → metabolism → synthesis of new compounds → cell death and decomposition;
• Determined by ecological strategies of microorganisms – r‑strategists (opportunists, rapid growth on labile substrates) and K‑strategists (specialists, slow decomposition of resistant compounds);
• Most intense in the rhizosphere – the zone of active root influence;
• Creates conditions for stabilisation – through formation of extracellular polymers, aggregates, and accumulation of resistant microbial products;
• Controllable through agronomic practices – organic matter input, optimisation of conditions, minimum tillage, stimulation of root activity.

Microorganisms are not just “processors” but active builders of soil fertility. Understanding how the microbial “conveyor” works allows us to manage it so as to maximise carbon retention in soil, improve its structure, and supply plants with nutrients.

In the next section, we will examine what factors determine the rate of all these processes – microbial processing, mineralisation, and immobilisation.

Hierarchy of Factors

The influence of various factors on the rate of organic matter transformation can be represented as a hierarchical system (Weil & Brady, 2017; Scheffer et al., 2018):

First level – climatic factors (temperature, moisture), which act at regional and global levels and set the general background for processes.

Second level – soil properties (texture, structure, pH, aeration), which modify the effect of climate at the local level.

Third level – quality of the organic substrate (C:N, lignin content, polyphenols), which determines how quickly a given material will be processed by microorganisms.

Fourth level – management factors (tillage, fertilisation, crop rotations), which can drastically change process rates in agroecosystems.

Let us examine each of these levels in detail.

1. Temperature

Temperature is one of the most powerful factors determining the rate of microbial processing. Like all biochemical reactions, decomposition of organic matter follows the van’t Hoff rule: for every 10 °C rise in temperature, the reaction rate increases by a factor of 2–3 (in the range from 0 to about 35–40 °C) (Weil & Brady, 2017; White, 2006).

This indicator, called Q₁₀, for organic matter mineralisation is usually 2.0–2.5 (Eash et al., 2016; Scheffer et al., 2018). This means that when temperature rises from 10 to 20 °C, the decomposition rate roughly doubles.

However, the relationship is not linear across the entire range:

• At temperatures below 5 °C, microbial activity drops sharply, though it does not cease entirely even at sub‑zero temperatures (in unfrozen water films).
• The optimal range for most soil microorganisms is 25–35 °C. At these temperatures, mineralisation proceeds at maximum speed.
• At temperatures above 40–45 °C, activity of most mesophilic microorganisms begins to decline (enzyme denaturation, cell death), and only thermophiles continue to work (this is important for composting but not for ordinary soils).

The global significance of the temperature factor is well illustrated by comparing different climatic zones. In the tropics, where mean annual soil temperature is 15–20 °C higher than in temperate zones, decomposition proceeds about 3–5 times faster (White, 2006; Weil & Brady, 2017). This is why tropical soils have difficulty accumulating organic matter – it simply does not have time to “stay” in the soil without other protective mechanisms.

At the same time, it is important to distinguish the temperature sensitivity of different fractions of organic matter. Recent studies show that the most sensitive to warming are labile fractions, while stable, mineral‑associated fractions respond more weakly to temperature (Davidson & Janssens, 2006; Weil & Brady, 2017). This means that under global warming, it is the “active” carbon – the very carbon that supports fertility – that will be mineralised first, which could have serious consequences for agroecosystems.

2. Moisture and Water Regime

Water is essential for all metabolic processes of microorganisms. It serves as a medium for nutrient transport, participates in enzymatic reactions, and maintains cell turgor. However, excess water is as harmful as its deficit.

Optimal moisture for decomposition of organic matter is when soil pores are filled with water to about 50–70% of total porosity (Eash et al., 2016; Weil & Brady, 2017). At such moisture:

• Enough water for microbial activity;
• Air pores remain for oxygen supply;
• Normal diffusion of gases and nutrients is ensured.

With lack of moisture (below about 30–40% pore filling):

• Microorganisms enter a dormant state (form spores, cysts);
• Metabolic rate drops sharply;
• Diffusion of enzymes and substrates is hindered.

With excess moisture (above 80–85% pore filling):

• Aeration is impaired, oxygen does not enter the soil;
• Anaerobic processes develop, which are slower and less efficient;
• Toxic products for many microorganisms (organic acids, alcohols, H₂S) are formed.

Interestingly, fluctuating water regime (wetting‑drying cycles) can accelerate mineralisation. Upon drying, some microorganisms die and their cells break down; upon rewetting, the surviving microorganisms receive an abundant food supply – a flush of mineralisation occurs (Weil & Brady, 2017). This effect is especially noticeable in seasonally humid regions and during alternation of dry and wet periods.

3. Aeration (Oxygen Availability)

Most soil microorganisms involved in decomposition are aerobes. They require molecular oxygen for respiration (as the final electron acceptor). Without oxygen, aerobic respiration stops, and microorganisms either switch to anaerobic pathways or die.

Aerobic decomposition gives microorganisms significantly more energy than anaerobic:

• Aerobic: 1 mol glucose → 38 mol ATP;
• Anaerobic (fermentation): 1 mol glucose → 2 mol ATP.

The difference in energy yield is 19‑fold! This is why aerobic processes proceed much faster, and why in well‑aerated soils organic matter decomposes rapidly and completely.

When oxygen supply is limited (e.g., in waterlogged soils or inside large aggregates), aerobic decomposition is replaced by anaerobic. In this case:

• Decomposition rate decreases by tens of times;
• Incomplete oxidation products are formed – organic acids, alcohols, aldehydes, as well as methane (CH₄), hydrogen sulfide (H₂S), ammonia (NH₃);
• Part of the carbon is not mineralised to CO₂ but accumulates in reduced form (methane).

It is precisely because of the slowdown of decomposition under anaerobic conditions that wetland soils and peatlands accumulate huge stocks of organic carbon (Weil & Brady, 2017; Scheffer et al., 2018).

4. Soil Reaction (pH)

Microbial activity is strongly affected by soil pH. Most bacteria prefer neutral to slightly alkaline conditions (pH 6.0–7.5), while fungi are more active under acidic conditions (pH 4.5–5.5) (Eash et al., 2016; White, 2006).

In acidic soils (pH < 5):

• Bacterial activity is suppressed;
• Fungi and some acid‑tolerant bacteria dominate;
• Overall mineralisation rate is lower than in neutral soils;
• Decomposition of lignin and other resistant polymers is slowed.

In alkaline soils (pH > 8):

• Activity of many bacteria is also reduced;
• Specific microorganisms may develop, but overall decomposition rate is often lower than at neutral pH.

The optimum pH for most decomposition processes is 6.0–7.5. This is why liming of acidic soils often accelerates mineralisation of organic matter (Weil & Brady, 2017).

5. Composition and Quality of Substrate

The quality of the organic material (its chemical composition) is one of the most important factors determining its decomposition rate. We touched on this in the mineralisation section, but now we will examine it systematically.

5.1. Content of readily decomposable compounds

Materials rich in sugars, organic acids, amino acids, and other simple compounds (young green mass, root exudates) decompose very quickly – within days and weeks. This is the so‑called metabolic pool (Weil & Brady, 2017).

Materials rich in cellulose, hemicellulose, proteins (mature plant residues, straw) decompose more slowly – over months.

Materials rich in lignin, cutin, suberin, waxes (wood, bark, needles) decompose very slowly – over years and decades.

5.2. Lignin content

Lignin is one of the main factors slowing decomposition. As we already discussed (Section 2), lignin has a complex three‑dimensional structure with many strong bonds. Its decomposition requires specialised enzymes (peroxidases, laccases) found only in a few fungi (mainly basidiomycetes – white‑rot fungi) (White, 2006; Weil & Brady, 2017).

Moreover, lignin physically protects cellulose and other readily degradable polysaccharides by covering them from enzymes. The higher the lignin content in plant residues, the slower their decomposition.

5.3. Polyphenol content (tannins and other phenolic compounds)

Polyphenols are another important factor slowing decomposition. These substances, present in the leaves of many trees (especially conifers and oak), have “tanning” properties: they bind proteins, making them inaccessible to proteases (White, 2006). In addition, many polyphenols are themselves toxic to microorganisms or inhibit their enzymes.

High polyphenol content is one of the reasons why mor humus type forms under coniferous forests and oak groves – a slowly decomposing litter accumulating on the soil surface (White, 2006; Weil & Brady, 2017).

5.4. C:N ratio

As we discussed in detail in Section 3, the C:N ratio is a key factor determining whether decomposition will be accompanied by net mineralisation or immobilisation.

• C:N > 25–30 (straw, sawdust) → immobilisation, plant nitrogen starvation, slowed decomposition due to nitrogen deficiency.
• C:N = 20–25 (mature grasses, leaf litter) → balance between mineralisation and immobilisation.
• C:N < 20 (young legumes, manure, green manures) → net mineralisation, rapid nitrogen release.

It is important to understand that these are not rigid boundaries but approximate thresholds. They depend on the carbon use efficiency of microorganisms (which varies from 0.3 to 0.6) and on microbial community composition (bacteria have lower C:N than fungi) (Weil & Brady, 2017; White, 2006).

5.5. Physical availability (particle size, surface area)

The finer the plant residues, the faster they decompose. This is because:

• Specific surface area for enzyme action increases;
• Protective layers (cuticle, bark) are broken;
• Penetration of microorganisms inside is facilitated.

Therefore, shredding of plant residues (e.g., mulching, tillage) accelerates their decomposition.

6. Soil Texture and Structure

Physical properties of soil exert a strong influence on the decomposition rate of organic matter, mainly through two mechanisms:

6.1. Protection of organic matter

In clay soils, organic matter is better protected than in sandy soils (Baldock & Skjemstad, 2000; Scheffer et al., 2018). Reasons:

• Greater specific surface area of clay minerals → more sites for sorption of organic molecules;
• Developed microaggregate structure → organic particles become trapped inside aggregates, inaccessible to microorganisms;
• Presence of iron and aluminium oxides → additional sorption via ligand exchange.

This is why clay soils generally contain more organic carbon than sandy soils (all else being equal) (Weil & Brady, 2017).

6.2. Aeration and water regime

Soil structure determines how pores of different sizes are distributed, and hence how quickly water is drained and oxygen enters.

• Well‑structured soils (with developed macro‑ and mesoporosity) drain excess water quickly and ensure aeration → mineralisation proceeds faster (up to a point).
• Poorly structured, compacted soils have few large pores → water stagnates → anaerobiosis → slowed decomposition and organic matter accumulation.

7. Influence of Soil Biota (Direct and Indirect)

The activity of microorganisms and soil fauna is another factor determining process rates.

Direct influence:

• The higher the microbial biomass and diversity, the faster the processing of organic matter (given substrate).
• Enzyme activity in soil (extracellular) determines the rate of polymer hydrolysis (limiting stage) (Weil & Brady, 2017).

Indirect influence (through food webs):

• Soil animals (earthworms, springtails, nematodes) – shred organic matter, transport microorganisms, create favourable conditions (aeration, mixing) (White, 2006).
• Protozoa and nematodes, by feeding on bacteria, stimulate nitrogen mineralisation (up to 2–3 times) (Weil & Brady, 2017).

The more diverse and balanced the microbial community, the more efficient the processing. This is why monocultures and intensive tillage, which reduce biota diversity, often lead to slowed nutrient cycling and fertility degradation.

8. Management Factors (Anthropogenic)

In agroecosystems, humans can strongly influence the rate of organic matter transformation processes:

8.1. Tillage (ploughing)

Ploughing accelerates mineralisation of organic matter for several reasons:

• Destroys aggregates, releasing protected organic matter;
• Improves aeration (oxygen supply);
• Increases contact between organic matter and microorganisms;
• Mixes fresh plant residues with soil.

As a result, under ploughing, organic carbon losses can increase by 2–3 times compared to minimum tillage or direct drilling (Weil & Brady, 2017; Scheffer et al., 2018).

8.2. Application of organic and mineral fertilisers

• Organic fertilisers (manure, compost, green manures) directly increase substrate input, stimulating microbial activity. However, their effect depends on C:N and composition (see above).
• Mineral nitrogen fertilisers can accelerate decomposition of high‑carbon materials (straw) by relieving nitrogen limitation. But excess nitrogen sometimes slows lignin decomposition (inhibition of ligninolytic enzymes) (Weil & Brady, 2017).

8.3. Liming (addition of CaCO₃)

Raising pH in acidic soils stimulates bacterial activity and accelerates mineralisation of organic matter. However, on very acidic soils, liming can significantly improve biological activity and, paradoxically, lead to loss of some organic carbon (Weil & Brady, 2017).

8.4. Drainage

Drainage of waterlogged soils increases aeration and sharply accelerates mineralisation. This is why draining peatlands leads to rapid loss of organic matter (with surface subsidence) and CO₂ emissions (Weil & Brady, 2017; Scheffer et al., 2018).

8.5. Crop rotations and vegetation cover

• Perennial grasses and legumes (with high root mass and active root exudation) stimulate microbial processing and accumulation of organic matter.
• Monocultures with low organic matter return (bare fallow) lead to organic matter degradation.
• Cover crops prevent organic matter losses during fallow periods.

Interaction of Factors: Synergy and Compensation

It is important to understand that factors do not act in isolation. Often there is synergy (enhancement) or compensation (weakening) of effects.

For example:

• Temperature + moisture: at optimal moisture, the temperature effect is maximal. With moisture deficit or excess, the influence of temperature is reduced (Eash et al., 2016; Weil & Brady, 2017).
• C:N + temperature: at high C:N, temperature has a weaker effect on decomposition because nitrogen becomes limiting (its deficiency is not compensated by warmth).
• Texture + management: in clay soils, the effect of minimum tillage on carbon conservation may be greater than in sandy soils, because clays protect organic matter better.

This is why it is impossible to predict decomposition rate based on a single factor – a systematic account of all interactions is needed.

Brief Summary

Thus, the rate of organic matter transformation processes is determined by a complex of factors that can be grouped into four levels:

Climatic factors:

• Temperature – increase accelerates processes (Q₁₀ ≈ 2–2.5), but at extremely high temperatures – slows.
• Moisture – optimum about 60–70% pore filling; deviations slow processes.
• Seasonal fluctuations (freeze‑thaw, wet‑dry) – can cause pulses of mineralisation.

Physico‑chemical soil properties:

• Aeration – oxygen accelerates aerobic decomposition; its absence sharply slows it.
• pH – optimum 6.0–7.5; deviations (especially acid) slow bacterial activity.
• Texture and structure – clay soils protect organic matter and slow its decomposition compared to sandy soils.

Quality of organic substrate:

• C:N ratio – determines whether net mineralisation or immobilisation will occur.
• Content of lignin, polyphenols, cutin, suberin – the more of these, the slower decomposition.
• Physical availability – shredding accelerates decomposition.

Management factors:

• Tillage – ploughing accelerates mineralisation; minimum tillage slows it.
• Fertilisation – organic and mineral may accelerate or slow processes depending on composition and rates.
• Drainage, liming, crop rotations – all influence decomposition rate.

Interaction of factors – synergy and compensation make the system complex and non‑linear, so integrated models are needed for prediction.

Understanding these factors is the foundation for managing soil organic matter. Knowing what accelerates or slows decomposition allows the agronomist to consciously choose strategies: when to leave organic matter on the surface so it decomposes slowly and protects the soil, and when to incorporate it into the soil for rapid nutrient release.

In the next, concluding section, we will consider how modern models describe this entire complex of processes and how they help predict the behaviour of organic matter in soil.

Introduction

We have come a long way: we analysed the transformation cycle, mineralisation and immobilisation, humification, microbial processing, and the factors determining the rate of all these processes. Now a natural question arises: how can all this diversity of processes, interactions, and factors be quantitatively described? How can we predict how much carbon will remain in the soil after 10, 50, or 100 years under changing climate, tillage, or vegetation type?

The answer to this question is provided by modern models of soil organic matter (SOM) formation. These models are not merely abstract mathematical exercises. They are working tools that allow agronomists, ecologists, and policy makers to make informed decisions: how much carbon can be sequestered in soil, how greenhouse gas emissions will change under a switch to minimum tillage, how much organic fertiliser is needed to maintain fertility.

In this concluding section, we will get acquainted with the main models, their structure, key assumptions, and how they help us understand and manage soil organic matter.

Why Are Models Needed?

Soil organic matter is a complex, dynamic system in which hundreds of processes occur simultaneously. It is impossible to measure all these processes experimentally. Models allow us to:

1. Synthesise knowledge – formalise understanding of processes in mathematical equations.

2. Predict – forecast changes in SOM under changing climate, management, or vegetation.

3. Test hypotheses – compare model predictions with experimental data and refine our understanding.

4. Make decisions – evaluate the effectiveness of different management strategies (organic matter input, tillage, crop selection).

Modern SOM models are built on several key principles, which we will now examine.

Basic Principles of SOM Modelling

Major SOM Models

There are many models, differing in complexity, number of pools, and application domain. We will consider two of the most well‑known and widely used models.

From Conceptual Pools to Measurable Fractions

One of the main problems in SOM modelling is that pools in models do not correspond to what can be measured (Baldock et al., 2012; Scheffer et al., 2018). ROTH‑C uses DPM, RPM, BIO, HUM, and IOM, but we cannot simply take soil and say “here is BIO, here is HUM”. These are conceptual pools, not laboratory fractions.

However, in recent decades, significant progress has been made in linking model pools to measurable fractions (Baldock & Skjemstad, 1999; Scheffer et al., 2018; Weil & Brady, 2017).

Modern approach suggests the following correspondence (Baldock et al., 2012):

1. RPM (resistant plant residues) → POM (Particulate Organic Matter) – organic particles of size 53–2000 µm, separable by sieving after soil dispersion.

2. HUM (humified organic matter) → mSOM (mineral‑associated SOM) – organic matter associated with mineral particles <53 µm.

3. IOM (inert organic matter) → ROC (Resistant Organic Carbon) – black carbon and other pyrogenic substances, determined by special methods (UV oxidation + NMR).

Such correspondence allows calibration of models with real data, not just total carbon content. This significantly improves prediction accuracy and confidence in models.

Use of Modern Methods for Model Verification

Modern models are increasingly verified using isotopic methods (Baldock et al., 2012; Scheffer et al., 2018; Weil & Brady, 2017):

• ¹⁴C (radiocarbon) – allows determination of the “age” of organic carbon in different pools. Radiocarbon dating confirms that the stable pool indeed contains carbon that has been in the soil for hundreds to thousands of years (White, 2006).

• ¹³C (stable isotopes) – used to trace carbon sources upon vegetation change (e.g., C₃ to C₄). This makes it possible to determine what fraction of carbon in pools is “old” (from natural vegetation) and what is “new” (from crop plants).

• Bomb ¹⁴C – traces of nuclear tests from the 1960s serve as a label for carbon that entered the soil after 1963. This allows estimation of turnover rates of the youngest pools.

These methods show that models (especially ROTH‑C) describe real dynamics well when properly calibrated (Baldock et al., 2012; White, 2006).

What Models Tell Us About Long‑Term Dynamics

Modelling yields several important conclusions about SOM behaviour:

1. Most carbon is stable. Even in arable soils, 60–80% of organic carbon resides in slow and stable pools (Weil & Brady, 2017). This means that rapid changes in management give a rapid but limited effect – building truly stable carbon takes decades.

2. Losses upon disturbance are rapid, recovery is slow. When virgin land is ploughed, most losses occur from labile and slow pools over the first 20–30 years (Weil & Brady, 2017; Scheffer et al., 2018). Recovery to the initial level under minimum tillage may take 50–100 years.

3. Stabilisation is limited by soil protective capacity. The amount of carbon that can be protected (bound to minerals and hidden within aggregates) is finite. When this capacity is filled, further carbon accumulation slows – a phenomenon called saturation (Weil & Brady, 2017). In clay soils, the capacity is higher than in sandy soils.

4. Climate change can accelerate losses. Rising temperature increases decomposition rates, especially in cold regions where much organic matter is stored (permafrost, peatlands) (Weil & Brady, 2017; Scheffer et al., 2018). Models predict that with 2–3 °C warming, soil carbon losses could amount to 10–30% of current stocks (Davidson & Janssens, 2006).

Practical Application of Models

For an agronomist, farmer, or land manager, models are useful because they allow:

1. Evaluating the effect of switching to minimum tillage. How much carbon can be accumulated over 10 years? How much does this offset greenhouse gas emissions?

2. Optimising organic fertiliser application. How much manure or compost should be added not only to maintain fertility but also to increase carbon stock?

3. Choosing vegetation type. Which crops (or combinations) give maximum organic matter input with minimum losses?

4. Predicting fertility changes. How will organic matter content and, consequently, nitrogen and other element availability change under different management scenarios?

Limitations of Models

It is important to understand that models are simplifications of reality. Their limitations include:

1. Do not account for all microbial diversity. The microbial community is represented by one or two pools, although in reality it is extremely diverse (Baldock et al., 2012).

2. Do not describe all stabilisation mechanisms. In particular, the role of microaggregates, hydrophobicity, and spatial heterogeneity is often simplified (Schmidt et al., 2011).

3. Require calibration. For new regions or soil types, models need to be tuned (calibrated) using experimental data.

4. Sensitive to input data quality. Errors in estimating organic matter input or temperature can severely distort predictions.

5. Do not account for all interactions. For example, the influence of root exudates on decomposition rate (priming effect) is often ignored or greatly simplified (Baldock, 2007).

Nevertheless, when properly applied, models remain the best available tool for predicting SOM dynamics over long time periods and under different management scenarios.

Prospects for Model Development

Current research is directed towards:

1. Accounting for spatial heterogeneity – moving from “homogeneous layer” to accounting for uneven distribution of organic matter in the profile and across the landscape.

2. Incorporating microbial ecology – considering that different microorganisms respond differently to conditions and substrates.

3. Integration with agro‑economic models – accounting not only for carbon but also for economic efficiency of different management strategies.

4. Better accounting for black carbon – its role in the stable pool is still poorly quantified for many soils (Weil & Brady, 2017; Scheffer et al., 2018).

5. Application of machine learning – to improve predictions based on large datasets (carbon content, climate, management) without explicitly specifying all mechanisms.

Brief Summary

Thus, modern SOM models are:

• Tools for knowledge synthesis – formalising understanding of processes into mathematical equations;
• Based on the pool concept – dividing SOM into labile, slow, and stable pools with different rate constants;
• Use first‑order kinetics – decomposition rate proportional to pool mass;
• Apply the cascade principle – part of the carbon moves to more stable pools during decomposition;
• Include modifying factors – temperature, moisture, protection, availability;
• Most well‑known models – ROTH‑C (UK) and CENTURY (USA);
• Allow prediction – changes in SOM under changed management, climate, or vegetation;
• Linked to measurable fractions – POM, mSOM, ROC;
• Verified by isotopic methods – ¹⁴C and ¹³C;
• Have limitations – simplification of microbial diversity, stabilisation mechanisms, require calibration.

Models cannot replace experiments or observations, but they allow extrapolating knowledge beyond experimental conditions and making informed decisions in managing soil fertility and carbon balance.

Concluding Remarks

We have travelled the entire path: from input of organic matter into soil through decomposition, mineralisation, immobilisation, humification, and microbial processing, to the quantitative description of all these processes in models.

The main conclusion we should draw is: soil organic matter is not a static stock but a dynamic system in which synthesis and decomposition processes continuously occur. The rate of these processes is determined by climate, soil properties, substrate quality, and management. It is the balance between input and decomposition that determines whether carbon will accumulate in soil or be lost to the atmosphere.

For the agronomist, this means that managing organic matter is managing the balance. One must simultaneously:

• Ensure sufficient organic matter input (plant residues, fertilisers, green manures, cover crops);
• Create conditions for its stabilisation (minimum tillage, structure preservation, maintenance of biotic diversity);
• Understand when rapid mineralisation is desirable (nutrient release) and when it is undesirable (carbon loss).

Modern models provide tools for such management, but they do not replace field experience and understanding of local conditions. Like any tool, models are useful when properly applied and interpreted.