Soil Processes

What is Soil

Structure Functions Decomposition Glomalisation Clay Biome Energy Entropy

A general picture of soil functioning includes nutrient cycling, active biodiversity, support for plant growth, decomposition of detritus and contaminants, carbon turnover, transport of water and solutes as well as stability and resilience of a soil system as a whole. For the soil to function like this, these processes need to operate.

Process

Soil is said to have many physical, chemical and biological processes that go on.

There are perhaps three dialectic dynamics which affect all of them: between wet and dry, aerobic and anaerobic, and electron transfer from + to -.

These dynamics also interact with each other and their environment. Soil environments have a wide range of functions, which exist alongside and react with each other in different ways according to soil type, climate, and land use.

Other chemical reactions

Human

As with the soil organisms, these soil functions and processes would not have arrived in one go, but appeared, survived and dispersed over millions of years.

Clay, both as particles and mineralogy, will have been reacting with organic matter for well over a billion (1000m) years. This would have firstly been with bacteria, making biofilms, then plant and fungal detritus, and with later animal products. 'Mineralisation' has probably been around for half a billion years, whereas 'aggregation' probably occurred in 2 waves the first 400mya providing micro-aggregation. A second stage of decomposition 'de-lignification' may only have appeared around 250mya. A third wave of decompostion, humification needed lots of animal guts running round to complete nutrient recycling, and macro aggregation probably less than 200mya.

Thin Fims

Many soil processes rely on thin water films that surround all sorts of sized soil particles and provide the soil pores with a moist atmosphere. Biofilms formed early on when clay reacted with bacteria. As well as providing a living substrate for creatures like nematodes, water films of various thicknesses impact two groups of processes - the transformation of minerals, and the breakdown of organics. Organic matter in water films can undergo various transformations, including decomposition, humification, and mineralisation, leading to changes in the composition and stability of organic carbon in the soil. Organic matter, such as organic acids and lignin, can undergo hydrolysis in water films, leading to the release of simpler organic molecules, Organic matter in water films can form complexes with metal ions, such as aluminum and iron, thus determining their availability.

In terms of mineral transformations,minerals in the soil can undergo weathering processes, like silicate minerals can react with water to form clay minerals. Ion exchange reactions occur on soil particles' surfaces in water films, which affects soil pH and nutrient availability to plants. Hydrolysis is a chemical reaction in which water molecules break down complex compounds. Redox (reduction-oxidation) reactions involve the transfer of electrons between different substances occur in the water films. In anaerobic (low-oxygen) conditions within water films, iron and manganese compounds in the soil can undergo redox reactions, eading to changes in their oxidation states. Water films can also dissolve and precipitate various minerals and compounds, like the leaching of calcium carbonate (CaCO₃) from soil particles.

These water films have increased the surface area for these processes many many times more than in water alone. An estimated surface area of the water film in a cubic meter of healthy soil in temperate climates might be in the range of approximately 10,000 to 50,000 square meters per cubic meter (m²/m³), nearer the top end when it comes to clay-like soils. So that it about 10,000 more surface area than a similar sized rock or puddle. No wonder we talk of the soil being alive. When we talk of ‘conquering the land’, it is these thin water films extended throughout soils, which enable a far greater range of chemical and organic reactions. Water holding capacity of soils is not just a physical matter - but a crucial chemical and biological one too.

Thin water films may have been the way marine organisms spread from water bodies across the land around half a billion years ago. In so dong they could carry the bacteria and animals that fed on them, thereby providing a crucial way to start to build soil..

Aggregation

There are at least two dozen soil functions, but this is probably the most important in making soil what it Aggregate formation occurs when soil particles and debris stick together, with various breakdown products providing the glue. These become larger when fungal hyphae wrap microaggrates into macroaggregates, which provide different water tensions, which influence water retention, aeration, and root penetration..

Aggregate formation

Aggregate formation is a very dynamic process. Soil aggregates are formed through physical, chemical and biological activity below ground and inluenced by us plowinthe land or running along. Formation of aggregates begins with finer soil primary particles binding together. Clay particles have a negative charge. Fertilizers (like potassium and nitrates) have + charged cations, so bind with the negative clay particles creating “floccules.” The type and amount of clay minerals in the soil often plays an influential role in aggregation formation.

The second part of aggregate formation deals with bonding or binding. The clay floccules and other soil particles are bonded together by various bonds or adhesives, including organic matter (like humic substances and glomalin-related-soil-proteins), liming materials like calcium carbonate and various types of oxides, like iron and aluminum. In the case of organic matter, the breakdown products, following passage through a variety of small animal guts, are that “glue”. Also helping in aggregate formation are exudates from roots and the fungi feeding on them which again gpo through animal guts. These all help bind soil together near the root zone. Fungal hyphae also contribute to aggregate formation by entangling and weaving around soil particles.

Small creatures also play major roles in (macro)-aggregate formation. A study of upland grass found that “Uppermost organo-mineral horizon are dominated by excrement from meso- and macrofauna, a finding which highlights the importance of soil fauna in reprocessing organic material. Much of this excrement had fused into undifferentiable forms, but some could be associated specifically with enchytraeids and earthworms. New C found in between 0 and 40% of aggregates derived from faunal excrement.” (Davidson & Grieve 2005)

Micro & macroaggregates

Below are the difference between micro and macro aggregates.

Macroaggregates:
- Size: Macroaggregates are larger soil aggregates, typically ranging from 0.25 mm to several millimeters in diameter.
- Composition: Macroaggregates are primarily composed of sand, silt, clay, and organic matter.
- Formation: They are formed through the binding action of various organic materials, such as plant roots, fungal hyphae, and microbial byproducts (glomalin, polysaccharides, proteins, etc.).
- Stability: Macroaggregates tend to be more stable and resistant to disruption by water erosion or mechanical forces due to the strong binding agents that hold them together.
- Function: They provide pore spaces within the soil, facilitating water infiltration, aeration, and root penetration. Macroaggregates also help to protect organic matter from decomposition by physically sheltering it within their structure.
Microaggregates:
- Size: Microaggregates are much smaller than macroaggregates, typically ranging from 0.01 mm to 0.25 mm in diameter.
- Composition: Microaggregates are primarily composed of clay particles and organic matter.
- Formation: They are formed through the binding action of various organic substances, particularly microbial byproducts like polysaccharides, glues, and fungal hyphae.
- Stability: Microaggregates are less stable compared to macroaggregates and can be more easily broken apart by physical disturbances or changes in environmental conditions.
- Function: Microaggregates contribute to soil structure and stability by forming bridges between individual soil particles, which helps to prevent soil compaction and erosion. They also play a role in nutrient retention and microbial habitat.

In terms of glues or binding agents, both macroaggregates and microaggregates rely on organic substances produced by soil organisms:

Macroaggregates are often bound together by more stable and long-lasting organic substances like glomalin, polysaccharides, proteins, and humic substances. These substances are produced by fungi, bacteria, and roots, and they form strong bonds that hold soil particles together, contributing to the stability of macroaggregates.
Microaggregates, on the other hand, are primarily bound by microbial byproducts such as polysaccharides (extracellular polymeric substances or EPS), glues, and fungal hyphae. These substances are important for the formation and stability of microaggregates but may be more transient compared to the binding agents in macroaggregates.

It is part of my theory of soil evolution that micro-aggregation evolved 400-300mya primarily based on soil proteins while the building of macro- aggregation developed over 200 million years later when humic substances became more widespread.

In terms of glues or binding agents, both microaggregates and macroaggregates rely on organic substances produced by soil organisms:

Microaggregates are primarily bound by microbial by-products such as polysaccharides (extracellular polymeric substances or EPS), glues like GRSPs from breakdown of fungal hyphae (glomalisation) These substances are important for the formation and stability of microaggregates but may be more transient compared to the binding agents in macroaggregates.
Macroaggregates are often bound together by more stable and long-lasting organic substances like polysaccharides, proteins, and particularly humic substances. These substances are produced by bacteria in the guts of worms and mites, so their poo forms strong bonds that hold mineral soil particles together, contributing to the stability of macroaggregates.

Both are now vital for soil functioning, but it may well be that microaggregates formation was the main vehicle 4-300mya, and that macro versions developed later, less than 200mya involving new glues - as well as the old.

Glomalisation

I have created this term to explain.. "In soils, glomalin is measured as glomalin-related soil protein (GRSP). GRSP is highly positively correlated with soil aggregate stability, because it is a new component of soil organic matter." (Gao et al 2019)

Sticky stuff

There has been research comparing the ability of various soil compounds to promote soil aggregation or stickiness.

Humic substances, which include humic acids, fulvic acids, and humin, have been studied extensively for their role in soil aggregation. They are known to interact with soil particles, promoting aggregation through mechanisms such as flocculation and bridging of soil particles.

Glomalin-related soil proteins (GRSP) are another group of compounds found in soils, primarily associated with arbuscular mycorrhizal fungi (AMF). GRSP have been shown to contribute to soil aggregation by binding soil particles together, thereby enhancing soil stability.

Several studies have compared the effects of humic substances and GRSP on soil aggregation in relation to soil carbon sequestration and soil structure stability. it's essential to consider the context-specific nature of soil systems and the various factors influencing soil structure when interpreting these comparisons.

And it terms of soil evolution we will see that the role of GRSPs probably predates humic substances widespread involvement by over 100 million years

Physical

Water Infiltration is the rate at which water enters the soil and the movement of water through the soil profile. . It is the downward movement of water from the ground surface into the soil, dependent on soil structure and compaction (below).
Hydraulic Conductivity measures a soil's ability to transmit water and describes the ability of a soil to transmit water through it and represents the soil's capacity to conduct water and is often measured in units of velocity (e.g., cm/s or inches/hour).It is influenced by soil texture, where coarser textures (eg sand) have higher conductivity.

Compaction

Soil Compaction occurs when soil particles are compressed, reducing pore spaces and restricting water and air movement. It can have negative effects on root growth and overall soil health. Electrical conductivity (below) measurements can be used to assess soil compaction indirectly.

Erosion

Soil Erosion is primarily caused by water or wind, and is a physical process that involves the removal of the topsoil layer from one location and its deposition elsewhere. It can lead to soil degradation, loss of fertile topsoil, and environmental problems. Soil organisms, such as earthworms, play a role in stabilizing soil structure and reducing erosion through their burrowing and casting activities.

Electrochemical

Electrical Conductivity(EC) measures the ability of a soil to conduct electrical current. It is influenced by factors like soil moisture content and the presence of dissolved ions (salts) in the soil solution. EC can be used to assess soil salinity, nutrient content, and moisture levels, making it a valuable tool for soil management.
Cation Exchange is a chemical process in which soil particles, particularly clay and organic matter, can adsorb and exchange positively charged ions. Clay is slightly negatively charged so attracts positively charged ions (cations) such as calcium (Ca²⁺), magnesium (Mgwhere ²⁺), and potassium (K⁺), which have lost a negative electron.
pH Buffering: Soil acts as a buffer, helping to maintain a stable pH level. Buffering capacity is defined as the soil's capacity to maintain a relatively stable pH despite the presence of acidifying or alkalizing factors.

Redox reactions

Oxidation is the loss of electrons by a reactant.

When a metal element is reacting to form a compound then it is being oxidised.

For example:

Mg(s)+O2(g)→MgO(s)

The metal atoms are losing electrons to form an ion. They are being oxidised.

Mg(s)→Mg2+(aq)+2e−

This is known as an ion-electron equation.

Reduction is the opposite of oxidation. It is the gain of electrons.

Compounds reacting that result in metal elements being formed are examples of reduction reactions.

For example:

Cu2+(aq)+2e−→Cu(s)

The metal ions are gaining electrons to form atoms of the element. They are being reduced.

Oil Rig

Oxidation is Loss, Reduction is gain - of an electron

Biological

Rhizosphere Interactions occur in the region around plant roots where complex interactions between plant roots, soil microorganisms, and soil chemistry occur. These interactions influence nutrient uptake, plant health, soil structure and soil biology.
Mycorrhizal Associations are the symbiotic relationships between plants and mycorrhizal fungi which enhance nutrient uptake, and provide glomalin, a feed source for many arthropods..
Biological Diversity indicates the diverse community of soil organisms that contributes to soil health and the value of this diversity is becoming more apparent and only recently was it found that nearly 60% of all organisms are in the soil.

Decomposition

Decomposition occurs when soil bacteria, fungi, small arthropods and worms break down dead plant and animal material into organic matter, helping to improve soil structure and nutrient availability for plants. The soil microorganisms break down organic matter, releasing - thus recycling - vital nutrients like nitrogen (N), phosphorus(P), and potassium(K) for plant uptake, crucial for plant growth.

Plant Residue incorporation into the soil improves organic matter content and is related but distinct from Bioturbation. This is the disturbance and mixing of soil and sediment by various living organisms, particularly burrowing animals and soil-dwelling creatures like earthworms, ants, termites, and other invertebrates.

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Decomposition in soil is a complex process involving the breakdown of organic matter, such as plant and animal residues, into simpler substances. This process is crucial for nutrient cycling and soil fertility. Decomposition occurs through various processes, including humification, fermentation, and de-lignification, and can be either aerobic or anaerobic, depending on the environmental conditions

Soil decomposition is a multifaceted process driven by microorganisms that break down organic matter through various pathways. Aerobic decomposition is more common and efficient, leading to the formation of stable humus. Anaerobic decomposition, occurring in oxygen-depleted environments, is slower and results in the production of gases like methane. Both processes are essential for maintaining soil health and fertility. They work best together as we know from 'composting'

Primary decomposition is the first stage and is carried out by bacteria and fungi. Various bacteria decompose cellulose, pectin, chitin and certain fungi decompose cellulose and lignin. The species that continue the process of decomposition are known as detrivores, meaning ‘feeders on dead or decaying organic matter’ and they work in tandem with one another. Collectively they are known as the detritivore community”.

Aerobic Decomposition

Aerobic decomposition requires oxygen and is the most common form of organic matter breakdown in soils. It involves several stages:

Initial Breakdown: Organic matter is first broken down by soil fauna like earthworms, beetles, and other decomposers into smaller pieces. This increases the surface area available for microbial attack.
Microbial Decomposition: Bacteria and fungi play a pivotal role in further breaking down the organic material. Aerobic bacteria and fungi metabolize complex organic compounds, producing carbon dioxide, water, and heat as by-products. The key processes include:
- Hydrolysis: Enzymes break down complex molecules like proteins, fats, and polysaccharides into simpler molecules such as amino acids, fatty acids, and sugars.
- Oxidation: Microorganisms oxidize these simpler compounds, releasing energy for their growth and reproduction.
Humification: During this process, partially decomposed organic matter is transformed into humus, a stable organic component of soil. Humus formation involves the polymerization of organic molecules, which are then stabilized by binding with soil minerals. Humus improves soil structure, water retention, and nutrient supply.

Anaerobic decomposition

Anaerobic decomposition occurs in environments with little or no oxygen, such as waterlogged soils, swamps, and compost piles. The absence of oxygen leads to different microbial processes:

Fermentation: Anaerobic bacteria and fungi carry out fermentation, breaking down carbohydrates to produce energy. This process results in the formation of organic acids, alcohols, methane, hydrogen sulfide, and carbon dioxide. Fermentation is less efficient than aerobic respiration, resulting in slower decomposition rates.
Methanogenesis: In highly anaerobic conditions, methanogenic archaea convert organic matter into methane and carbon dioxide. Methanogenesis is significant in wetlands and rice paddies, contributing to greenhouse gas emissions.

Processes

Humification: As mentioned earlier, humification is the formation of humus from decomposed organic matter. It involves complex biochemical processes where microbial metabolites and plant residues polymerize into stable, dark-colored substances that resist further decomposition. This process enhances soil fertility by improving nutrient availability and soil structure.
Fermentation: This anaerobic process breaks down sugars into simpler compounds like alcohol and organic acids. Fermentation occurs in the absence of oxygen and is characteristic of waterlogged soils and compost heaps. It produces less energy than aerobic respiration and results in partially decomposed organic matter.
De-lignification: Lignin is a complex, recalcitrant polymer found in plant cell walls, particularly in wood and bark. De-lignification refers to the breakdown of lignin by specific fungi, such as white-rot and brown-rot fungi, and some bacteria. This process is crucial for the complete decomposition of plant residues, as lignin protects cellulose and hemicellulose from microbial attack. De-lignification requires specialized enzymes (ligninases) and is slower than the decomposition of other organic compounds.

Aerobic v anaerobic

Aerobic Decomposition: Faster, more efficient, and leads to the production of carbon dioxide, water, and humus. It enhances soil aeration and nutrient availability.
Anaerobic Decomposition: Slower, produces methane, organic acids, and alcohols. It occurs in oxygen-poor environments and can lead to the accumulation of partially decomposed organic matter.

Mineralisation is where organic matter is converted into inorganic forms through microbial activity. The process increases the bioavailability of nutrients by decomposing organic compounds, into nitrates, phosphates, (both below) but also sulphur. Hence these minerals are more available for plant uptake. More

Earthworm impacts on mineralisation and humification

Bityutskii 2012

Humification is a slower specific stage within the decomposition process. The decomposed organic matter is transformed into more stable, complex organic substances known as humus, highly resistant to further decomposition. It has a complex molecular structure, which plays a vital role in forming aggregates. More

Nitrogen

- Nitrification is the biological [If we're linking to wikipedia here, should we not do this for previous sections to explain a mechanism? ANS - going to replace Wiki links to more original] oxidation of ammonia to nitrate via the intermediary nitrite. Nitrification is an important step in the nitrogen cycle in soil. The transformation of ammonia to nitrite is usually the rate-limiting step of nitrification. Nitrification is an aerobic process performed by small groups of autotrophic bacteria and archaea.
- Denitrification occurs in anaerobic (low-oxygen) conditions, where certain bacteria convert nitrates (NO3-) into nitrogen gas (N2), which can be lost to the atmosphere. This process can impact nitrogen availability and environmental nitrogen cycling.
- Biological Nitrogen Fixation: There are free-living soil bacteria known as diazotrophs that can fix atmospheric nitrogen into forms usable by plants. This biological process contributes to soil nitrogen availability. Some other bacteria, like Rhizobia, form symbiotic relationships within leguminous plants and fix atmospheric nitrogen into ammonia (NH3), providing a nitrogen source for the plants.

Phosphates

Phosphorus (P) is an essential nutrient ( energy transfer, photosynthesis, and nucleic acid synthesis) for plant growth, and is made more available for plant uptake by converting insoluble forms of phosphorus into soluble forms. In most soils, phosphorus exists in insoluble forms, primarily as phosphates that are not readily available for plant uptake. Phosphate-solubilizing microorganisms (PSMs) play a key role in making phosphorus more accessible to plants, as they produce produce organic acids, enzymes (phosphatases) and other substances that can break down or convert insoluble phosphates (rocks, calcium phosphates) into soluble forms.

Phosphate solubilization is crucial for sustainable agriculture because it enhances phosphorus availability to plants, reducing the reliance on synthetic fertilizers, by contributing to improved nutrient uptake and plant growth. Here's a general overview of the process:

Microorganisms: Phosphate-solubilizing microorganisms (PSMs) are the key players in this process. These can include bacteria such as Bacillus, Pseudomonas, and Enterobacter, as well as fungi like Aspergillus and Penicillium.
Production of Organic Acids: PSMs release organic acids as byproducts of their metabolic activities. These organic acids, such as citric, oxalic, and gluconic acids, play a crucial role in breaking down the insoluble forms of phosphorus.
Enzymatic Activity: Phosphate-solubilizing microorganisms also produce enzymes, especially phosphatases. These enzymes work to hydrolyze the phosphate ester bonds in organic or inorganic phosphorus compounds, making the phosphorus more soluble and available for plant uptake.
Chelation: Some microorganisms can produce substances that chelate or bind with metal ions associated with insoluble phosphates. This binding action helps in the release of phosphorus into the soil solution.
Conversion of Insoluble Phosphates: The combined action of organic acids, enzymes, and chelating substances helps convert insoluble phosphates, such as rock phosphate or calcium phosphate, into soluble forms like orthophosphate. Mycorrhizal fungi are particularly good at this.
Plant Uptake: Soluble orthophosphate is readily available for plant roots to absorb and utilize for various physiological processes, promoting plant growth.

The effectiveness of phosphate solubilisation can be influenced by various factors, including soil pH, temperature, moisture, and the types of microorganisms present in the soil. I have to note that encouraging bacterial PSMBs does not solve the issue of phosphate pollution of rivers (involved in Nutrient Neutrality') as they release more soluble phosphates - which can find their way into rivers more easily. We need the mycorrhizal fungi to transfer the soluble phosphates (as orthophosphate) directly to plants. More on phosphates and mycorrhiza 400mya

Carbon Sequestration

This is now probably the most famous soil process. Soil contains more carbon than all the above-ground biomass and atmospheric carbon together. Soil, quite simply, stores large amounts of carbon, mainly in the form of organic matter. The storage capability depends on what sorts of organic matter the carbon is found in.

The idea of storage or sequestration may give the idea of static stable carbon. In reality, much of the carbon is found in microbes and creatures running or creeping around. The recognition of this process is relatively recent as carbon sequestration helps mitigate climate change by removing carbon dioxide from the atmosphere and storing it as carbon in many organic forms, many running around. It is the best place to keep carbon from affecting global warming rather than emitting carbon dioxide or methane.

Soil - Air interface

The interface between soil and air is the greatest chemical exchange system in the world. Over the millions of years, we have seen soil can affect the air in terms of temperature and water saturation/humidity..

The main chemical reactions that take place now have been around forever:

Carbon Dioxide

There is the important carbon dioxide exchange where soils exchange carbon dioxide (CO2) with the atmosphere. Soil respiration, carried out by microbial and plant root activity, releases CO2 into the air - as a by-product. On the other hand, plants absorb atmospheric CO2 through photosynthesis and store carbon in the as 'soil organic matter' (SOM). This basic function has been going up and down over hundreds of millions of years. Where respiration is not taking place, because of lack of oxygen, then methane (CH4) is given off.

Acid-Base Reactions

Acid-Base reactions are where soil minerals and organic matter can undergo reactions when exposed to air - like carbonates in the soil can react with atmospheric carbon dioxide to form bicarbonates, contributing to the buffering capacity of soils. Certain microorganisms, influenced by moisture and temperature, release Volatile Organic Compounds (VOCs) such as methane (CH4), nitrous oxide (N2O), and various sulphur-containing compounds, into the air.

Other chemical reactions

Other chemical reactions in the soil-air interface contribute to nutrient cycling. Nitrification converts ammonium (NH4+) into nitrate (NO3-), and de-nitrification converts nitrate back into nitrogen gas (N2) under anaerobic conditions. These processes impact the availability and form of essential nutrients in the soil.

Human

Soil Conservation occurs where the soil surface is protected by natural leaf fall. Increasingly regenerative practices reflect how important keeping the surface covered is.
Soil is managed for farming in 70% of all land In the last 40 years, machines and chemicals have replaced labour
Contaminant Degradation is where Soil microorganisms can break down various contaminants, including pesticides and organic pollutants, helping to detoxify the soil and keep water clean. These processes must have been around before the modern contaminants arrived.

Mineralisation
Humification
Decomposition Energy
De-lignification
Glomalisation

These functions and processes are essential for soil life now, but when did they get here? It is unlikely they all arrived together in the water films, or dropped from the skies. Some processes crucial in soil, like nitrification, could have been around long before soil evolved, while others may have arisen out of the particular circumstances in soil later. Can we work out more clearly what processes arrived when?

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