Soil Organic Matter and Carbon

1.1. Modern Definition of SOM (Soil Organic Matter)

Over the past two centuries, ideas about the nature of soil organic matter have evolved. Today, building on fundamental research and modern analytical techniques, we give the following definition.

Soil Organic Matter (SOM) is the totality of all naturally occurring organic materials present in and on the soil, including:

• Living components: plant roots, living microorganisms (bacteria, fungi, actinomycetes), and soil fauna (nematodes, earthworms, etc.);
• Dead plant residues at various stages of decomposition (from fresh litter to fine fragments);
• Dissolved organic matter (DOM) – organic compounds in the soil solution;
• Stable organic matter – products of deep biochemical transformation and synthesis, which we call humus, as well as decomposition‑resistant black carbon (pyrolysis products, soot‑derived carbon) (Baldock, 2012).

Thus, SOM is the entire assemblage of organic compounds in the soil. It is not merely a substance; it is a living, continuously renewing system.

1.2. How Does SOM Differ from Humus?

This is one of the key questions for understanding the nature of soil organic matter. In the traditional understanding, rooted in 19th‑century work, humus was viewed as an amorphous, dark‑coloured mixture of high‑molecular‑weight compounds resistant to decomposition. It was often divided into:

• Humic acids (soluble in alkalis, insoluble in acids);
• Fulvic acids (soluble in both alkalis and acids);
• Humin (insoluble in everything).

However, modern research based on in situ methods (solid‑state NMR spectroscopy, pyrolysis‑mass spectrometry) has shown that classical “humic substances” are largely artefacts of laboratory extractions, not real molecules existing in the soil (Lehmann & Kleber, 2015). Strong alkalis used for extraction disrupt complex organo‑mineral complexes and polymerise simple biomolecules.

Modern view:

Humus is not a specific chemical compound, but a functional and operational concept.

In modern soil science, humus is rather the stabilised, decomposition‑protected part of SOM. The main stabilisation mechanisms, in contrast to the outdated concept of “chemical recalcitrance” (resistance due to molecular complexity), are now attributed to:

1. Physical protection inside aggregates and micropores, inaccessible to microorganisms and their enzymes;

2. Chemical protection through sorption onto clay minerals and sesquioxides (formation of organo‑mineral complexes);

3. Molecular recalcitrance of certain compounds (e.g., lignin, cutin, black carbon), but this role is considered less important than previously thought (Marschner et al., 2008).

“Humus” is not a special class of molecules, but rather a collective characteristic of organic material that persists in the soil because of a combination of ecological and physicochemical constraints imposed on decomposer activity.

Hence, SOM is the general term for all organic material in the soil. Humus is its stable, protected fraction that determines the long‑term “capital” of soil fertility.

Key takeaways from Section 1:

1. SOM is a comprehensive category that includes living and dead organic matter, from fresh plant residues to stable organo‑mineral complexes.

2. Humus is not a synonym for SOM, but its stabilised component; its main function is long‑term storage of carbon, water, and nutrients.

3. The modern understanding of the nature of humus shifts from the notion of giant “mysterious” molecules toward the mechanisms of physical and chemical protection of organic matter within the soil profile.

In the second section of the lecture, we turn to a seemingly paradoxical question: why, given the enormous importance of organic matter, is its mass in most mineral soils so small?

2.1. The Balance “Input – Output”: The SOM Dynamics Equation

The content of organic matter in soil is not a constant; it is the result of a continuous competitive process between two fluxes:

Input is the annual supply of organic carbon in the form of:

• above‑ground litter (leaves, stems, fruits);
• below‑ground residues (dying roots, rhizodeposits – organic root exudates);
• organic fertilisers (manure, compost, green manures) in agroecosystems.

Output is the loss of organic matter, mainly through:

• mineralisation – decomposition to carbon dioxide, water, and mineral elements (under aerobic conditions);
• aerobic and anaerobic respiration of soil heterotrophs;
• erosion (wash‑off and wind‑blow of the surface, the most organic‑rich layer);
• leaching of soluble organic compounds (DOC) into groundwater.

In a stable, undisturbed ecosystem (e.g., virgin steppe or pristine forest), a dynamic equilibrium is established over time: the annual input of organic matter approximately equals the annual losses. SOM content fluctuates around an equilibrium level determined by climate, vegetation type, particle‑size composition, and topography (Foth, 1990; Baldock, 2012).

2.2. Why Does Decomposition Dominate over Accumulation? The Energy Imperative

The main reason for the low organic‑matter content is that heterotrophic microorganisms and soil fauna use organic residues as their main source of energy and carbon for building their biomass. Under aerobic conditions, which prevail in most well‑drained soils, oxidation of organic matter (catabolism) proceeds very intensively.

During mineralisation:

• About 60–70 % of the carbon coming from plant residues is oxidised to CO₂ and returned to the atmosphere within the first year of decomposition (Weil & Brady, 2017; White, 2006).
• The remaining 30–40 % is partly assimilated into microbial biomass and partly transformed into more stable forms (humic substances).
• But even this stable part is not eternal – it decomposes, albeit much more slowly, with half‑lives ranging from decades to centuries.

Thus, in well‑aerated mineral soils, the rate of organic matter destruction in most cases exceeds or balances the rate of input, so organic matter does not accumulate in large quantities.

2.3. Climatic Factors: Temperature and Moisture

The rate of microbiological decomposition strongly depends on temperature and moisture. This is well described by models that include climatic corrections (Jenkinson, 1990; Parton et al., 1987).

• Warm and humid climate (tropics, subtropics): mineralisation proceeds year‑round, and microbial activity is extremely high. Organic input is large because of high productivity, but decomposition keeps pace and often outstrips it. Therefore, in tropical red soils (Oxisols), organic matter content often does not exceed 1–2 %, despite lush vegetation (White, 2006).
• Temperate climate (forest‑steppe, steppe): there is a clear seasonal rhythm – active decomposition in summer, slowdown in winter. Under these conditions, soils under perennial grasses (Chernozems, Mollisols) can accumulate up to 4–6 % organic matter because of massive root litter, which enters the soil directly and decomposes more slowly due to winter freezing (Weil & Brady, 2017).
• Cold and/or waterlogged climate (taiga, tundra, bogs): mineralisation is severely retarded by low temperatures or oxygen deficiency (anaerobiosis). Under these conditions, organic matter accumulates, sometimes forming thick peat horizons (Histosols, Gelisols) with organic carbon contents of 30–50 % (Huang, 2012). But these soils occupy a limited area.

Hence, globally, most of the land is covered by aerobic, moderately warm soils where decomposition is fast, and therefore the overall SOM content remains low.

2.4. The Role of Particle‑Size Composition (Texture)

Sandy soils with low specific surface area and weak aggregation cannot protect organic matter from decomposition. Organic matter in such soils is in a “free” state, easily accessible to microorganisms and rapidly mineralised. Therefore, organic matter in sands rarely exceeds 0.5–1.0 %.

Clayey and loamy soils, on the other hand, have high specific surface area and the ability to form organo‑mineral complexes. Organic matter sorbed on clay surfaces or trapped inside microaggregates becomes physically and chemically inaccessible to microbial enzymes, and its decomposition is slowed down. Thus, in heavy‑textured soils, organic matter content is usually 2–3 times higher than in light soils, even under similar climatic conditions (Foth, 1990; Weil & Brady, 2017).

“In sandy soil, organic matter is like money in the wind; in clayey soil, it is like capital in a secure bank, protected from inflation (but not completely).”

2.5. The Anthropogenic Factor: Tillage and Erosion

When virgin lands (steppes, forests) are brought into arable use, organic matter content drops sharply:

• Tillage destroys aggregates, aerates the soil, and mixes plant residues, creating ideal conditions for aerobic mineralisation.
• Reduced input of root residues (due to replacement of perennial vegetation by annual crops with smaller root mass).
• Erosion – removal of the top, most organic‑rich horizon.

Over 30–50 years of intensive farming, a soil can lose 30 to 60 % of its original organic carbon stock, which takes centuries to rebuild (Foth, 1990; Weil & Brady, 2017).

2.6. Take‑Home Message for Students: Small Does Not Mean “Bad”

The low absolute SOM content in most mineral soils is not degradation, but normal – the natural outcome of a dynamic balance between production and destruction. The problem arises when this equilibrium is shifted toward enhanced decomposition (tillage, erosion, deforestation). It is then that the soil loses its most important functions, which we will discuss in Section 3.

Key takeaways from Section 2:

1. SOM content in soil is the result of a balance between input (plant litter, roots) and losses (mineralisation, erosion, leaching).

2. Under aerobic conditions, which dominate the planet, decomposition proceeds faster than accumulation, so organic matter in mineral soils is scarce.

3. Climate (temperature, moisture) and texture (clay content) are the main natural regulators of this balance.

4. Anthropogenic impact (tillage, erosion) strongly shifts the balance toward losses, leading to fertility degradation.

5. A small amount of organic matter is not an anomaly but the natural state of most soils. The threat arises only when even this small stock is rapidly lost.

In the next section, we will show how exactly this “small” component determines virtually all key soil properties, uniting physics, chemistry, and biology into a single fertility system.

3.1. Organic Matter → Structure → Pores: The Foundation of Physical Soil Health

Perhaps the most visible effect of organic matter is on soil structure. Clay and silt particles tend to stick together into dense masses that poorly conduct water and air. Organic matter, especially its active components – microbial polysaccharides and glomalin (a glycoprotein produced by mycorrhizal fungi) – act as natural glues.

• Aggregation: These sticky substances cement fine mineral particles into water‑stable aggregates – crumbs of various sizes. Particularly important are root exudates and fungal hyphae, which literally “stitch” aggregates together, creating their framework (Tisdall & Oades, 1982; Weil & Brady, 2017).
• Pore space: As a result of aggregation, macropores (for air and rapid water infiltration) form between the crumbs, and micropores (for capillary water retention) form inside the crumbs. It is organic matter that creates the optimal pore ratio – roughly 50 % solid phase and 50 % pores, half of which are filled with water and half with air (Fig. 1.21 in Weil & Brady, 2017).
• Resistance to breakdown: Organo‑mineral aggregates are resistant to raindrop impact and mechanical stress. This is why soils rich in organic matter suffer less from erosion (see Section 6).

Thus, first cascade: organic matter → aggregates → macro‑ and micropores → optimal water‑air regime.

3.2. Pores → Water: Regulation of Water Regime

The structure created by organic matter determines how much water the soil can hold and how quickly it releases it to plants.

• Water‑holding capacity: Humus itself has an enormous specific surface area and hydrophilicity. It can hold 4–5 times its own weight in water (for mineral soils – 15–20 times) (Weil & Brady, 2017). But the main point is not that. The main point is that humus increases the volume of medium‑sized pores, where water is held with a force accessible to plant roots (from capillary potential to the wilting point). This is why adding organic amendments to sandy soil sharply increases its field capacity and available water (da Silva & Kay, 1997; Weil & Brady, 2017).
• Infiltration and runoff reduction: Macropores created by aggregates, earthworm burrows, and dead roots allow water to infiltrate quickly, preventing surface runoff. This is a key mechanism for protecting against water erosion.

Second cascade: organic matter → structure → pores → available moisture → drought resilience.

3.3. Pores → Air and Biota: Soil Respiration

Porosity is not only a reservoir for water but also a ventilation system for the soil.

• Gas exchange: Macropores ensure rapid gas exchange between the soil and the atmosphere. Oxygen (O₂) penetrates to roots and microorganisms, while carbon dioxide (CO₂) released by respiration leaves the soil. If organic matter is destroyed (e.g., by frequent tillage), aggregates break down, pores are filled with fine particles, aeration deteriorates – “oxygen starvation” sets in, which inhibits roots and aerobic microorganisms.
• Habitat: The aggregates themselves, their surfaces and internal cavities, are micro‑worlds where bacteria, fungi, protozoa, and nematodes live. Organic matter serves as their substrate (food) and energy resource. The richer and more diverse the organic matter, the higher the biodiversity of the soil and the intensity of nutrient cycling (Eash et al., 2016; Huang, 2012).

Third cascade: organic matter → aggregates → aeration → active soil “breathing” → biotic diversity.

3.4. Chemistry of Fertility: Organo‑Mineral Interactions

Now we turn to the chemical action of organic matter – that which directly determines the nutrient regime of the soil.

• Cation exchange capacity (CEC): Humus contains many functional groups – carboxyl (-COOH), phenolic (-OH), and carbonyl groups. They can dissociate to form negative charges, especially at pH > 5. The specific CEC of humus is 2–5 times higher than that of the most active clays (e.g., montmorillonite). The contribution of organic matter to the total CEC of surface horizons ranges from 20 to 80 % (Weil & Brady, 2017; Foth, 1990). This means that humus retains cations (Ca²⁺, Mg²⁺, K⁺, NH₄⁺), preventing their leaching, and gradually releases them to plants.
• Buffering: Owing to the presence of weak acids and conjugate bases, humus has a high buffering capacity with respect to pH. It dampens changes in acidity when fertilisers or acid rain are applied (White, 2006).
• Complexation (chelation): Low‑molecular‑weight organic acids and fulvic acids form mobile complexes with metal ions, especially Fe³⁺, Al³⁺, Cu²⁺, Zn²⁺, and Mn²⁺. This serves two purposes:
• Increases the availability of micronutrients to plants by converting them into soluble but not leachable forms.
• Reduces aluminium toxicity in acid soils by binding Al³⁺ ions into non‑toxic chelates (Eash et al., 2016).
• Source of nutrients: Upon mineralisation of organic residues, nitrogen (as NH₄⁺ and NO₃⁻), phosphorus (H₂PO₄⁻), sulfur (SO₄²⁻), and many micronutrients are released. This is the main natural mechanism of plant nutrition, complementing dissolved mineral salts.

Fourth cascade: organic matter → negative charges → cation retention and buffering → chelation → availability of macro‑ and micronutrients → plant nutrition.

3.5. Generalised Scheme: Organic Matter as an Integrating Factor

Let us now try to represent a single chain of influence of organic matter on fertility, linking all the modules you have studied:

Increased input of organic matter (plant residues, manure, green manures) →

→ enhanced aggregation and creation of optimal porosity (physics) →

→ improved water infiltration and water‑holding capacity (water) →

→ enhanced aeration and respiration (air) →

→ stimulation of the microbial community (biota) →

→ accumulation of humus → increased CEC, buffering, chelation (chemistry) →

→ enhanced and balanced plant nutrition (plant physiology) →

→ increased productivity, accumulation of new organic residues – a closed positive cycle.

In the opposite direction – destruction of organic matter (intensive tillage, erosion) – triggers a degradation cycle leading to deterioration of all the above properties.

3.6. Conclusion: Organic Matter – the Conductor of the Soil Orchestra

Thus, organic matter is not one of the isolated components but the central integrative factor that:

• Binds mineral particles into structural aggregates,
• Controls the water‑air regime through pore space,
• Creates a habitat and regulates soil biota activity,
• Provides chemical fertility through CEC, buffering, chelation, and slow release of elements,
• Unifies soil physics, chemistry, and biology, creating its fertility.

This understanding is critically important for practice: by managing organic matter (through crop rotations, tillage, organic amendments), we simultaneously manage all other soil properties.

Key takeaways from Section 3:

1. Organic matter is the control centre for all soil functions, linking the mineral skeleton, pore space, water, air, biota, and chemistry.

2. The main physical effect is the creation of water‑stable structure and optimal pore space (capillary‑porous framework).

3. The water regime improves through increased water‑holding capacity and infiltration, reducing drought and erosion risks.

4. Chemical action is expressed through high CEC, buffering capacity, metal chelation, and serves as a nutrient depot.

5. The biological effect is providing energy and substrate for heterotrophic biota, closing the nutrient cycle.

6. Organic matter is an integral indicator of soil health and the main lever for fertility management.

In the next section, we move to the quantitative expression of this whole system – to organic carbon, its measurement, and its significance as a modern indicator of soil well‑being.

4.1. Why Carbon Rather Than “Organic Matter”?

1. Measurement accuracy: Modern analytical methods (dry combustion with CO₂ detection, high‑temperature catalytic oxidation gas chromatography) allow direct and accurate measurement of carbon content in a soil sample. Determining the entire mass of organic matter is much more complicated, because it also includes oxygen, hydrogen, nitrogen, phosphorus, sulfur, and other elements in variable proportions. Therefore, in international practice (ISO standards, USDA methods), organic matter content is expressed through organic carbon content.

2. Conversion from SOM to SOC: It is established that, on average, soil organic matter contains about 50–58 % carbon by mass (Baldock, 2012; Weil & Brady, 2017). This allows the use of simple empirical conversion factors:

• Traditional factor 1.72 (based on the assumption that C = 58 % of SOM, i.e., SOM = C × 100/58 ≈ 1.724).
• A more modern and often used factor 1.9–2.0, which acknowledges that carbon content in real soils may vary from 45 to 60 % depending on the degree of humification and the composition of organic matter (Foth, 1990; Eash et al., 2016).
• Important: in practice, especially in international reports and models, it is preferred to use SOC (g/kg or t/ha) rather than SOM, to avoid the uncertainty associated with the variable conversion factor.

3. Universality in models and global cycles: Carbon is the main element in the global biogeochemical cycle (which we will discuss in Section 5). All models of organic matter dynamics (ROTH‑C, CENTURY, APSIM) operate with carbon pools. This makes it possible to compare data from different soil‑climatic zones and assess the contribution of soils to the global CO₂ balance.

4.2. Organic Carbon Is Not All Organic Matter

It is important to emphasise: SOC is part of SOM, not its entire volume. Besides carbon, SOM includes:

• Nitrogen (N) – on average 4–6 % by mass (C:N ≈ 10–12:1) (White, 2006).
• Oxygen (O) – up to 35–40 %.
• Hydrogen (H) – 4–6 %.
• Phosphorus (P), sulfur (S), and micronutrients – in smaller amounts.

Nevertheless, carbon content is taken as the quantitative indicator of soil organic matter stocks, because it is easier to measure and correlates well with most organic matter functions (water retention, CEC, microbial activity) (Baldock, 2012).

4.3. Which Carbon Fractions Do We Measure?

In modern research and agronomic practice, it is increasingly important not only to know total organic carbon (Total SOC) but also its fractional composition, because different fractions perform different functions:

• Active (labile) pool: microbial carbon, dissolved organic matter, free POM (particulate organic matter >53 µm). It mineralises rapidly (years to decades) and is responsible for plant nutrient supply, structure formation, and stress resilience (Huang, 2012).
• Slow (stabilised) pool: carbon associated with clay minerals and inside aggregates, as well as black carbon (pyrolysis products). This pool has turnover times of hundreds to thousands of years and determines the long‑term soil “capital” – its buffering, water‑holding capacity, and CEC.

Modern fractionation methods (e.g., separation of POM and mineral‑associated carbon) allow not only estimation of total SOC stocks but also understanding which part of this carbon is active and vulnerable and which is stable and performs long‑term functions (Baldock & Skjemstad, 1999; Huang, 2012).

4.4. Why Is This Important for an Agronomist and an Ecologist?

1. Fertility assessment: SOC content is a key indicator of soil quality. The higher the SOC, the higher the potential productivity (other things being equal). But not only the quantity but also the quality (ratio of active/passive carbon) is important.

2. Management: Knowing the current SOC content and its fractions, an agronomist can plan measures to replenish it: choice of crop rotation, application of organic fertilisers, minimisation of tillage.

3. Carbon credits and climate policy: In recent decades, SOC has become a tradable asset in greenhouse gas emission trading systems. Increasing SOC stocks in soils is considered an effective way of sequestering (removing) carbon dioxide from the atmosphere (more on this in Section 5).

“Carbon is the currency in which soil health is measured, and at the same time the bridge between soil and global climate processes.”

4.5. Summary: From SOM to SOC – Evolution of Concepts

Thus, we see a historical and methodological shift:

• SOM – a broad, biological and chemical term denoting the entire set of organic materials in the soil (with emphasis on their nature, functions, and diversity).
• SOC – a quantitative, measurable, and standardised indicator used for stock calculations, modelling, and international comparisons.

In modern science and practice, we more often speak of organic carbon because it provides an accurate, reproducible, and comparable assessment of the soil’s organic wealth. At the same time, we always remember that behind this carbon lies a huge diversity of living and dead organic compounds that determine soil life.

Key takeaways from Section 4:

1. Carbon is the main quantitative element of organic matter, its “skeleton”.

2. SOC is the part of SOM that can be precisely measured. Conversion from SOM to SOC is done using factors (1.72–2.0), but the international standard is to use SOC directly.

3. Total SOC is an integral indicator, but it is more informative to measure carbon fractions (active, slow, passive), because they affect fertility differently.

4. SOC is the “currency” in the global carbon cycle and in soil fertility management.

5. Understanding SOC as a measurable indicator allows us to move to quantitative assessment of the soil’s role in the global carbon cycle – the subject of the next section.

In Section 5, we will consider the place of soil in the global carbon cycle, where SOC acts as a key link between the atmosphere, biosphere, and lithosphere.

5.1. Soil – The Largest Reservoir of Organic Carbon on Land

Carbon stocks in different Earth components differ sharply. To appreciate the scale, here are modern estimates (from IPCC, 2013; Batjes, 1996; Lal, 2004; Weil & Brady, 2017).

Note: Soil organic carbon (SOC) is 2–3 times larger than the carbon in all terrestrial vegetation and about twice the atmospheric carbon (as CO₂).

Considering that the top metre of soil contains about 1500 Pg C, and the layer down to 2 m – more than 2300 Pg C, it becomes clear why soils are the largest active carbon reservoir in terrestrial ecosystems. Even small changes in this reservoir (e.g., a loss of 5–10 % of SOC) can significantly affect atmospheric CO₂ concentration.

5.2. The Place of Soil in the Carbon Cycle: Fluxes and Balance

The carbon cycle is a continuous exchange of carbon between major reservoirs. Soil participates both through input (plant fixation of CO₂ → formation of organic matter → input into soil) and through loss (decomposition of organic matter → return of CO₂ to the atmosphere).

Annual fluxes:

• Total net primary production (NPP) of terrestrial ecosystems is about 60–65 Pg C/year. This is the amount of carbon that plants remove from the atmosphere each year.
• Of this, approximately 50–60 Pg C/year is returned to the atmosphere annually through mineralisation (soil respiration and decomposition of organic matter). The remainder (~5–10 Pg C) may temporarily accumulate in biomass or be transferred to stable humus forms, but on a global scale this accumulation is small.

Natural equilibrium: In undisturbed ecosystems (forests, steppes, wetlands), the carbon input and output are nearly balanced, and SOC stocks remain relatively stable over centuries (unless climate change or catastrophic events occur).

However, human activity disrupts this balance:

• Deforestation and ploughing of land: when natural ecosystems are converted to cropland, organic matter begins to mineralise intensively. In the first 20–40 years of cultivation, soils can lose 30 to 60 % of their original SOC stock (Foth, 1990; Weil & Brady, 2017). This is one of the largest anthropogenic sources of CO₂, alongside fossil fuel combustion.
• Current state: It is estimated that since the beginning of the Industrial Revolution, soils have lost about 60–80 Pg C, and this process continues in tropical regions. At the same time, in some regions (e.g., in temperate agriculture with a shift to minimum tillage), a slow recovery of SOC stocks is occurring, but it is extremely uneven.

5.3. “Soil Source” vs “Soil Sink”: When Does Soil Work for Us and When Against Us?

Soil can act both as a source of greenhouse gases and as a sink (absorber).

1. Soil as a source (emitter) of CO₂:

• As a result of mineralisation of organic matter under aerobic microbial respiration, CO₂ is released. This is a normal process, but it accelerates when structure is disturbed (ploughing, drainage of peatlands).
• Additional sources are burning of plant residues (agricultural stubble burning) and erosion, where organic carbon is removed and oxidised.

2. Soil as a sink (sequester) of CO₂:

• This is the soil’s ability to take up CO₂ from the atmosphere and retain it in stable forms – as humus, black carbon, or carbonates.
• The main mechanism of sequestration is increasing organic matter input (by increasing productivity, using green manures, returning crop residues) and reducing losses (minimum tillage, erosion protection, leaving crop residues on the surface).

5.4. Soil and Other Greenhouse Gases: A Brief Note

Although the main focus of the carbon cycle is on CO₂, we cannot omit two other gases closely linked to soil processes, to keep the picture complete:

• Methane (CH₄):
• Soil can be a source of methane under anaerobic conditions (rice paddies, wetlands, landfills), where methanogenic bacteria decompose organic matter without oxygen.
• In well‑aerated soils, there are methanotrophic bacteria that oxidise CH₄ to CO₂, so the soil acts as a sink for this gas (Weil & Brady, 2017). This process can be inhibited by excess nitrogen fertilisers (as we have already discussed in connection with the carbon cycle in agroecosystems).

• Nitrous oxide (N₂O):
• This greenhouse gas has a global warming potential about 300 times that of CO₂. Its formation is linked to denitrification and nitrification processes in soil, especially under excessive nitrogen fertilisation and waterlogged conditions. This is an important aspect, but it belongs more to the nitrogen cycle, which we only touch upon indirectly.

5.5. Practical Conclusion: By Managing Organic Matter, We Manage Global Climate

Understanding the role of soil in the global carbon cycle gives us a powerful lever:

• Restoration of degraded soils (increasing SOC by 0.4–1.0 t/ha/year) could sequester up to 1–2 Pg C annually, comparable to annual emissions from fossil fuel combustion.
• The “4 per 1000” initiative: The Ramsar Convention and many countries support the goal of increasing global SOC stocks by 0.4 % per year, which is estimated to fully offset anthropogenic CO₂ emissions. This shows that soil carbon has become a strategic resource not only for food security but also for climate policy.

“Every decision we make in the field – whether to leave straw, whether to till, whether to sow green manures – has not only a local but also a global carbon footprint.”

5.6. Summary of Section 5:

1. Soil is the largest reservoir of organic carbon on land, containing more C than the atmosphere and vegetation combined.

2. Natural soils are in dynamic equilibrium with the atmosphere, but human activity disrupts this, turning soils from a sink into a source of CO₂.

3. Soil can serve both as a source (through mineralisation, erosion) and as a sink (through increased input and stabilisation of organic matter) for CO₂.

4. Managing soil organic carbon is a real tool for mitigating climate change, and this is reflected in international initiatives (e.g., “4 per 1000”).

5. Knowledge of the global carbon cycle gives every agronomic practice a climate dimension, elevating agronomy to the level of geoengineering.

In the final section, we will discuss why loss of organic matter is one of the main dangers for soils and ecosystems, and how these losses manifest in practice – in structural degradation, reduced fertility, impaired water regime, and other processes.

6.1. Structural Degradation and Loss of Aggregates

The first and most noticeable consequence of organic matter loss is destruction of water‑stable structure.

• Mechanism: Humus, microbial polysaccharides, and glomalin glue mineral particles into aggregates. When organic matter content decreases (e.g., because of intensive tillage or erosion), these “binding” substances are destroyed faster than they are synthesised. Aggregates break down into individual particles (Tisdall & Oades, 1982; Weil & Brady, 2017).
• Visual sign: The soil becomes structureless, dusty, or cloddy, which is clearly visible on severely eroded fields. Upon drying, such soil forms a dense crust; upon wetting, it slumps.
• Consequence: Pore space deteriorates: macropores responsible for aeration and rapid water infiltration disappear, leaving only fine capillaries. This triggers the next step.

6.2. Deterioration of Water‑Physical Properties

Structural degradation directly affects the soil water regime:

• Reduced infiltration: Because macropores are destroyed, water infiltrates more slowly. This leads to increased surface runoff – water does not have time to infiltrate and flows off the surface, unavailable to plants.
• Decreased water‑holding capacity: Humus, like a hydrophilic sponge, holds water in plant‑available forms. With the loss of organic matter, field capacity (the amount of water the soil can retain against gravity) decreases. This is especially critical for sandy soils, where organic matter was the only reservoir of available moisture (da Silva & Kay, 1997).
• Increased drought susceptibility: Soil with low water‑holding capacity dries out faster even during short dry spells, making plants more vulnerable to drought. This is one of the main reasons for yield decline on degraded lands.

6.3. Reduced Biological Activity and Simplification of Food Webs

Organic matter is the energy base for the entire soil biota.

• Loss of substrate: Heterotrophic microorganisms that derive energy from organic matter lose their food source. The abundance and diversity of bacteria, actinomycetes, and fungi decline. Especially affected are specialised decomposers (e.g., cellulose‑ and lignin‑degrading organisms) that ensure plant residue breakdown (Eash et al., 2016; Huang, 2012).
• Food‑web disruption: With reduced microbial biomass, the numbers of micro‑feeders (nematodes, protozoa) and macrofauna (earthworms) decrease. In particular, earthworms, which actively mix the soil and create burrows, disappear from degraded fields. This deprives the soil of its “natural ploughs”.
• Slowed nutrient cycling: The decline in decomposer activity means that new plant residues decompose more slowly, nutrients are not mineralised at the required rate, and their availability to plants decreases. The cycle closes in a negative direction.

6.4. Loss of Chemical Buffering and Deterioration of Nutrient Supply

• Decrease in cation exchange capacity (CEC): Humus is the main carrier of negative charges in surface horizons (along with clays). Loss of organic matter reduces soil CEC, especially in sandy and loamy sand soils where clay is scarce. This means that the soil retains Ca²⁺, Mg²⁺, K⁺, NH₄⁺ less effectively – they are more easily leached into groundwater, becoming unavailable to plants (Foth, 1990; White, 2006).
• Reduced buffering: Thanks to weakly acidic groups (carboxyl, phenolic), humus dampens sharp pH changes. When it is lost, the soil becomes less resistant to acid loads (acid rain, application of physiologically acid fertilisers). This is especially critical for acid soils, where loss of buffering can lead to a sharp drop in pH and activation of toxic aluminium.
• Reduced availability of micronutrients: Chelation provided by low‑molecular‑weight organic acids is the main mechanism for retaining and making Zn, Cu, Mn, Fe available. With the loss of organic matter, these micronutrients form sparingly soluble mineral forms and become unavailable to plants, causing hidden deficiencies (Eash et al., 2016).
• General impoverishment of nutrients: Organic matter is the main reservoir of nitrogen (N) and a significant portion of phosphorus (P) and sulfur (S). Its loss means a direct decrease in the stocks of these elements in the soil, requiring higher doses of mineral fertilisers to maintain productivity.

6.5. Intensified Erosion – The Final Chord

Structural degradation, loss of infiltration, and reduced plant cover (due to declining fertility) make the soil extremely vulnerable to water and wind erosion.

• Water erosion: The structureless surface poorly absorbs rainwater; surface runoff forms and washes away the top, most fertile layer. Not only mineral particles but also the remaining organic matter are washed off – the process accelerates.
• Wind erosion: In arid regions, fine dust‑sized particles are easily lifted by wind, creating dust storms. This is evident on severely eroded lands where the top horizon is completely lost and infertile subsoil is exposed.

“Loss of organic matter makes the soil not just “poorer” but physically disappearing – it is literally washed and blown away from the fields.”

6.6. The Vicious Circle of Degradation: Positive Feedbacks

All the described processes are not isolated. They organise into feedback loops where each negative effect amplifies the next (Bird et al., 2001; Weil & Brady, 2017):

Intensified tillage → ↓Organic matter content → ↓Aggregation → ↓Infiltration and ↑Runoff → ↓Moisture and ↑Erosion → ↓Plant cover → ↓Input of new organic matter → ↓Organic matter content (even more) → ...

Thus, loss of organic matter is not just a quantitative decline of an indicator, but a shift of the soil into a new, degraded state (an ecological threshold). Recovery from such a state requires decades and much greater inputs (fertilisers, amelioration, sowing perennial grasses) than maintaining the original level.

6.7. Agronomic Significance: What Does This Mean for Practice?

For the agronomist, understanding this cascade means that:

1. Prevention of degradation is far more effective than restoration.

2. The main measures should be aimed at preserving and replenishing organic matter: returning crop residues, using green manures, applying organic fertilisers, minimum tillage, maintaining plant cover during the off‑season.

3. Even a small loss of organic matter (e.g., 0.1–0.2 %) already sets off a degradation cycle that may be difficult to stop.

4. Soils with high organic matter content (Chernozems, dark chestnut soils) are a national treasure that must be protected, because their loss is irreplaceable over historically foreseeable timeframes.

Key takeaways from Section 6 (and the entire lecture):

1. Loss of organic matter triggers a chain reaction of deterioration in all soil properties: structure, water regime, biota, chemical fertility.

2. This leads to erosion, which makes the loss of organic matter irreversible on a human timescale.

3. Degradation develops through positive feedback – the worse the soil condition, the faster it further deteriorates.

4. Preserving and accumulating organic carbon in soils is not only an agronomic but also a global climate task, directly linked to food security and ecosystem sustainability.