Land Management

BLOG SERIES: Increasing carbon in soil – a holistic conversation. Part 1: The Different Pools of Soil Carbon

Perhaps the most complex of current agricultural carbon sequestration methodologies, understanding the mechanisms of soil carbon sequestration and how to increase carbon levels in soil requires a thorough understanding of, you guessed it – soil.

Philip Mulvey
January 31, 2022

If there’s one thing my team talks about on the daily, next to the weather and what’s for lunch, it’s how to increase carbon in soil. 

Perhaps the most complex of current agricultural carbon sequestration methodologies, understanding the mechanisms of soil carbon sequestration and how to increase carbon levels in soil requires a thorough understanding of, you guessed it – soil.

Comprehending carbon’s behaviour in soil, how carbon travels through different parts of the soil and what affects soil’s capability to store carbon for a meaningful time period, is essential to creating a land management practice that truly upholds climate integrity and creates a meaningful difference to our climate.

Though the industry talks widely about soil carbon farming, a general understanding of definitions and processes, even for those within the industry, is, in my observations, not well understood. A lively discussion with my team on soil carbon was deemed useful enough to convert to a series of articles.

Let’s begin our journey for this article with terms, types and processes. Following articles will address carbon outcomes in the soil under traditional agriculture and with regenerative practices. 

We hope this assists you in your understanding of soil carbon and your journey to pursue the right change to increase it.

What is soil – The difference between dirt and soil

Soil is defined as having three different matters (phases) and two mediums: 


— Mineral Matter

— Organic Matter

— Living Matter


— Air (having at least 15% oxygen)

— Water

Mineral matter is the rocks, pebbles, sand silt and clay that form the majority of the soil. In an agricultural soil, organic matter should be at least greater than 2% of the topsoil, and living matter – comprising of roots, micro-organsims and soil fauna, should be greater than 0.5% of the upper soil layers. As discussed in–depth in a previous article of ours, organic matter is 45% carbon and is the outcome of dead matter.

When a soil is primarily dominated (>98%) by mineral matter, particularly the fine mineral phase known as clay and silt, it is known colloquially as dirt.  A soil scientist rarely uses the term dirt, but will often use degraded soil to describe a soil devoid of organic matter and living matter and dominated by fine mineral matter.

Soil Profile – A soils fingerprint

A soil changes with depth and the unique nature of this vertical variability – typically in layers – is known as a soil profile.  

Typically a soil can be divided into 4 layers:  

Figure 1 - Soil Horizons

The topsoil, where most roots occur, is known as the A horizon, the upper subsoil is known as the B horizon, the lower subsoil that has only partially weathered floaters of rock (at greater than 20%) is known as the C horizon and the upper highly weathered surface of the rock known as the D horizon, in which rock fabric remains apparent. 

The top metre in which we measure carbon typically only intercepts the A and B horizon and occasionally the C horizon. The topsoil has more layers than just the A Horizon.  At the very surface is leaf litter (dead but not yet decayed) and a humus layer that’s not yet incorporated into the soil (ie does not contain mineral matter).  The Humus layer is called 0 horizon or A0.  The rich topsoil that has humus and mineral matter co-mixed is known as the A1 horizon.  The A horizon also often has a leached layer deficient in organic matter and nutrients beneath the A1 horizon known as the A2 horizon.  

The B horizon typically contains clay minerals – the product of weathering of the primary minerals typically found in rocks.  The boundary between the A and B horizon is often sharp (but can be gradual) and distinguished by a texture, colour and sometimes pH change. 

Colloquially A horizon is topsoil and B horizon is subsoil.  Topsoil is readily degraded and eroded and in Australia has often been completely removed from slopes in infilled  flats or washed or blown away. Many farms now grow crops directly in the B horizon. During a drought, dust–laden westerly winds cause algal blooms and resultant marine food chain bloom in the Southern Ocean and red-orange cover on the snow of the New Zealand Alps.  Our top soil provides benefits to our geological neighbours.

What stops soil washing or blowing away you may ask?  The answer is: Organic matter.

Forms of Carbon in Soil

Soil Organic matter is one form of carbon in the soil. Carbon essentially exists is three forms in the soil:

  1. Mineral carbon – which are carbonates and include calcrete and carbonate nodules
  2. Pyrolysed carbon –also known as black carbon, which include the natural soots and chars but also coke, breeze, clinker and carbonaceous slag from boilers and furnaces
  3. Organic Carbon – which makes up about 45% of all organic matter

Currently organic carbon can be sequestered using less energy and less cost than pyrolyzed carbon and sequestering carbonates is generally considered to take a long time.  

Pyrolysed carbon can have a role to play in increasing the amount of organic carbon sequestered in low charge soils but in The Australian Soil Carbon Farming Methodology and under VERRA soil carbon standards is not allowed to be considered as soil carbon when bio-char is  imported or produced from offsite

Forms of Organic Matter in the Soil

Dead matter/litter, though broken down to a limited extent by photo (sunlight) and chemical degradation, occurs almost entirely by microbial and microfauna degradation.

Organic matter is decayed dead matter.  It does not include litter but does include humus. Litter (dead matter), though broken down to a limited extent by photo (sunlight) and chemical degradation, occurs almost entirely by microbial and microfauna degradation. A common view is that organic matter is moved into the soil by being washed down by rain. Though this does occur for a small amount of organic matter the majority is moved downward by physical process such as gravity, but for the non– leachable components – principally by bioturbation (ie dragged down by ants, worms, flatworms, nematodes etc) and to a minor extent by gravity.  The mobility and migration of the organic matter depends on the chemical nature of that type of organic matter.

Organic matter can also be created at some depth below the surface by roots shedding sheath or dying, root and microbial exudates and death of soil fauna and microbes, as well as ongoing degradation of bioturbation from surface litter.  The mobility and fate of this source of organic matter also depends on the chemical nature of those compounds formed during the breakdown process by microbes.

Classification by Chemical Extraction Processes

Organic matter is a group name for numerous very complex chemicals that perform a myriad of functions in the soil.  There are numerous ways of subdividing organic matter. A traditional way of doing so was via alkalis and acid extraction producing compounds collectively known as:

Humic Acid

Fulvic Acid, and


Fulvic acid and humic acid are extracted from organic matter using a strong alkali (NaOH) leaving behind the insoluble humin. The extractant is then acidified with hydrochloric acid (HCl) to a pH of about 1 and the resulting precipitant is called humic acid – leaving fulvic acid in solution. 

The group of compounds known as fulvic acid are broadly considered the lightest and simplest structure of the chemicals that make up organic matter.  They are likely to have the most carboxyl bonds and therefore the highest nutrient complexing ability and a strong biostimulant and they don’t bind to pesticides.  

Temporal–Based Classification

Organic matter occurs in every layer in soil, but, subject to the physical, biological and chemical process, can be classified into different pools based on permanency.  These pools are not static and organic carbon can move between these pools or be released from the soil: to the atmosphere as carbon dioxide, washed away to groundwater, or used as the building blocks for additional living matter. Thus organic matter is a transient state in soil which can be divided into pools on how long carbon lasts in the soil. 

Classified this way, the three pools of carbon in soil are:

1. The Labile Pool

2. The Semi-Permanent Pool

3. The Intractable Pool

Figure 2 - 3 Pools of Soil Carbon in Natural Equilibrium

1) The Labile Carbon Pool

The labile carbon pool consists of simple compounds that are soluble in water or are rapidly made soluble by microbes. The labile pool is typically what is defined as bioavailable carbon, as microbes can rapidly consume it. 

Thus the labile pool consists of dissolved organic matter (DOM) and those compounds that are readily made soluble by microbes after approximately 24 hours in moist conditions.  This fraction of carbon only lasts from hours to just a few days (unless protected).

2) The Semi–Permanent Pool

The semi-permanent carbon pool consists of readily microbial degradable organic matter that is subject to low oxygen transfer, reasonable soil moisture that stimulates a fungal dominated biome and humification.

When oxygen transfer is high due to the soil having low moisture content and many macropores (cracks), this fraction is mineralised by bacteria to carbon dioxide and water. The duration of this fraction depends on whether conditions favour humification or mineralisation. Subject to which of these conditions occurs, typically carbon lasts from weeks to several years within this fraction. 

A slight deviation into chemistry is required to understand a bit about the semi-permanent pool. Not only is this pool dependent on whether the physical and biological conditions favour either humification or mineralisation, but what nutrients are present to play a chemical role. 

Certain divalent cations are important nutrients in soil. Dissolved atoms are called ions. Cations have a positive charge.  Divalent means double strength. Thus, an example of a divalent cation is calcium and magnesium, which are essential soil nutrients. Divalent cations attach to charged particles called colloids, which include clay minerals, using only one packet of charge, or more descriptively, one arm.  The other arm (charge) can grab the DOM floating by in the soil water and hold the DOM to the colloid via the divalent cation.  

The colloid (charge in the soil) working together with divalent cations prevents DOM being washed away deep down into the groundwater.  

More importantly, DOM with divalent cations and colloids is an important soil building process. DOM in turn binds compounds of the  non-soluble semi-permanent  pool of organic matter to it.  These compounds cover the DOM so that the microbes cannot access it to break it down.  This binding action together with glomalin from fungi and exudates from roots glues the soil together to microaggregates which are further bound together again by these weak glues to form aggregates. When the soil dries these weak glues break.

The fraction of the semi-permanent carbon pool that is degraded or converted to soluble within a few weeks is known by some practitioners as semi-labile carbon pool, but this is not considered a separate pool, just the fraction of the semi-permanent that is rapidly converted to labile.  

3) The intractable Carbon Pool

The final pool is the intractable carbon pool.  It is defined by the permeance of the nature of the bonding.  It comprises the following types of compounds:

  • Simple organic compounds that could be readily degraded but are physically entrapped by clumps of clay minerals called domains in the centre of micro-aggregates.
  • Chemically difficult to break down compounds including polyaromatic residues that are also physically difficult for fungi to access, including in pores of char.
  • Soots and small particles of char surrounded by semi-permanent pool of organic matter.  Highly pyrolyzed carbon is very difficult for the biome to breakdown and some persist in the soil for thousands of years 
Many people think increasing one type of organic matter is more important than another. This is not necessarily the case, particularly when it is realised that all three pools can include and sometimes need the labile pool as a component. 

These pools are shown graphically in Figure 2.

All pools have a two–way movement between them. When humification dominates, organic matter is converted from the labile pool to the semi-permanent to the intractable and at equilibrium the semi-permanent pool dominates until all the charge and divalent cations are covered by organic matter. 

Once this stasis has been met, humification and mineralisation are balanced.  If mineralisation dominates then all pools reduce until the intractable and semi-permanent pool are independent of each other and the labile pool.  At this stasis only the labile pool increases or decreases in size in relation to the litter and humification is almost non-existent. 

You may wonder – what pool of carbon is more important ?

No pool of carbon is more important than another for sequestration. 

Water is essential for human life and comprises some 60% of our body mass overall but is 73% of our heart and 83% of our lungs.  Water is transient in every part of the body and essential for nutrient energy transfer.  Water does not just go in and out but round and round.  Thus it does not matter what water is partitioned to what organs or whether it just passes into the blood, as long as you are hydrated. So too for pools of carbon in the soil.  

When you are dehydrated water is lost via perspiration; when you rehydrate water comes back into the system. Carbon is the same. Carbon is lost when practices used on the land promote mineralisation of organic matter over humification, effectively mining the carbon from every pool. Carbon is gained when practices are used that increase carbon for every pool; promoting humification over mineralisation, effectively sequestering organic matter.

Thus, if you want to farm carbon effectively, increasing the total carbon levels of every pool, and not just one, is the goal.  

The movement between the pools is controlled by interplay and ultimately which has long-term dominance of the two processes: humification and mineralisation.  When humification dominates, all pools increase in size and the movement of organic matter in Figure 2 is from left to right. Carbon dioxide is removed from the atmosphere. However agriculture practice for the last 10 000 years since its inception has mostly mineralised organic matter, decreasing the pool size from right to left.  

Carbon dioxide is added to the atmosphere. We need to know how we mineralise organic matter and what are the signs first before we can explore how to sequester carbon and what are the early signs of success. Consequently the next blog will be on the topic of soil carbon mining, what causes it and how to recognise it by understanding the rate of change and the amount of the three pools of carbon. 

We are soil carbon farming experts*. If you would like to find out more about your possibilities, how our platform works and how to get started, reach out!

* An expert is someone who knows what they don’t know is infinite and what they know is just the beginning

Upcoming in part 2 of this blog series on how to increase carbon in soil.....

For over 10 000 years, agriculture has mined soil carbon and led to the rise and fall of civilisation; as the soil upon which they grew was destroyed by soil carbon mining.  These civilisations destroyed the basis of their existence, Natural Capital, which is foundered on soil organic matter – soil carbon.  They collapsed for want of soil carbon. 

Soil carbon mining is essentially caused by both tillage agriculture, mechanised agriculture and set pasture management.  The development in the last 15 years of conservation agriculture, so called because this system conserves soil carbon, and regenerative agriculture whose focus is to restore carbon are addressed in later blogs. The focus of this blog is on how mismanagement of the three pools of carbon led to soil carbon mining; and the ultimate outcome of desertification.

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