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Decompose
Decompose
A lot of people think that the main function of the soil is to decompose. It is certainly important, but can - logically - only come after growth, for which much of the soil is responsible too. Pushed further, many people will say that decomposition is carried out mainly by earthworms, mites and insects like termites - which we call detrivores (Latin: detrítus: scree, rock debris; voráre: to gobble, to gulp).
Process
Process
Decomposition is the process of breaking complex organic matter into simpler inorganic matter. There are five 'steps' of decomposition - fragmentation, leaching, catabolism, humiciation and mineralisation. The fragmentation process consists of breaking detritus into little pieces by detritivores. Leaching is the process of releasing nutrients in the water and seeping into the soil.
Hypothesis
Hypothesis
My hypothesis is that the first wave od decomposition was mineralisation has been around 400mya, while the second wave de-lignification was not substantial till 300mya and the third wave of widespread humification less than 200mya to be the sort of composition we know today.
Mineralisation is carried out primarily by bacteria and fungi, that have been around for 500my. De-lignification relies very much on white rot fungi, which do not appear till 300mya, while humification is mainly carried out by bacteria the guts of animals like higher oribatids, termites and earthworms. These are relative newcomers to soil arriving less than 200mya.
We will follow this story about how soil evolved, through decomposition, and how that is distributed around the world. How and when the various processes of decomposition evolved can help explain the composition processes of soil around the world.
2-ways
2-ways
The process of decomposition works in two main ways - aerobically and anaerobically.
Aerobic uses air to provide the energy, to turn dead matter into useful carbon compounds, very effectively and efficiently. That's why we turn our compost heaps, to let the air in. Anaerobic decomposition uses nitrogen and phosphates to breakdown the complex compounds,
All fungi (eg saprophytic, and white rot) that decompose, do so aerobically. The bacteria responsible can be aerobic or anaerobic. There are 'obligate' aerobes/anaerobes - meaning they have to stay the same. And there are those who can change between the two ways.
The two processes come together to make compost The best compost is a mixture of aerobic and anaerobic. Both these will have gone on for a billion years but they would have acted separately - almost by definition
Compost
Compost
"The key to good compost lies in getting the mix right. You need to keep your ‘greens’ and ‘browns’ properly balanced. If your compost is too wet, add more ‘browns’. If it’s too dry, add some ‘greens’. Making sure there is enough air in the mixture is also important." Eden project
400mya
400mya
There were decomposition processes around for a billion years, and from 400mya, saprophytic fungi break down the detritus aerobically. Springtails consumed the fungi, so aiding the decomposition indirectly. Surface millipedes were probably the most prolific detrivores at that time. There would have been pockets of anaerobic decomposition
200mya
200mya
The aerobic and anaerobic processes came together when soil-dwelling aerobic animals consumed detritus (chew or crunch) directly thus breaking it into smaller pieces so that it decomposed by anaerobic bacteria in their guts to produce humus.
Decomposition Today
Decomposition Today
Decomposition today consist of a mixture of mineralisation - releasing inorganic minerals compounds from detritus, de-lignification bought about by white rot fungi and humification carried out by bacteria in various animal gut. But it wasn't always like this. It is likely that these 3 major processes evolved a hundred million years apart.
Chitin, cellulose and lignin
Chitin, cellulose and lignin
The three main complex organic chemicals that are hard to break down are. Chitin is a polymer (similar structure to plastics), widespread in strong coverings – in mites, molluscs, and fish scales. Cellulose is on all plant cell walls. Lignin provides the strength of plant cell walls. Both provide the base to make paper and cardboard. Breaking these chemicals down is a crucial process in recycling plant life - a key part in the cycle of all life.
Various bacteria break these tough molecules into sugars, which they use for energy, as well as to make other complex chemicals like the enzymes. Cellulose decomposition is carried out in soils by Penicillium spp and other cellulose-degrading soil microbes, such as species of Streptomyces, have the ability to degrade chitin and use it as a nitrogen source (Regeura 2011). The main degraders of lignin are white rot fungi (WRF).
Detritus
Detritus
Remains of dead plants & animals
Plant Detritus
Plant Detritus
Cellulose:
Structure: A polysaccharide consisting of linear chains of glucose molecules.
Function: Provides structural support to plant cell walls.
Hemicellulose:
Structure: A group of polysaccharides that are more complex and heterogeneous than cellulose.
Function: Works with cellulose to strengthen plant cell walls.
Lignin:
Structure: A complex polymer composed of phenolic compounds.
Function: Provides rigidity and resistance to decay in plant cell walls.
Starch:
Structure: A polysaccharide composed of glucose units.
Function: Serves as an energy reserve in plants.
Proteins:
Structure: Chains of amino acids.
Function: Serve various structural and enzymatic roles.
Lipids:
Structure: Includes fats, oils, and waxes.
Function: Serve as energy reserves and structural components of cell membranes.
Phenolic Compounds:
Structure: Aromatic compounds with hydroxyl groups.
Function: Act as antioxidants and contribute to plant defense mechanisms.
Animal Detritus
Animal Detritus
Proteins:
Structure: Chains of amino acids.
Function: Serve as enzymes, structural components, and signaling molecules.
Lipids:
Structure: Includes fats, oils, and phospholipids.
Function: Serve as energy storage, structural components of cell membranes, and signaling molecules.
Carbohydrates:
Structure: Includes monosaccharides (glucose, fructose) and polysaccharides (glycogen).
Function: Provide energy and serve as structural components.
Nucleic Acids:
Structure: DNA and RNA.
Function: Carry genetic information and are involved in protein synthesis.
Collagen:
Structure: A fibrous protein.
Function: Provides structural support in connective tissues, skin, and bones.
Chitin:
Structure: A polysaccharide composed of N-acetylglucosamine units.
Function: Provides structural support in the exoskeletons of arthropods and cell walls of fungi.
C/N Ratio
C/N Ratio
The carbon over nitrogen (C/N) ratio is a measure of the amount of nitrogen that can be released during decomposition of organic detritus.
"Divide the carbon by the nitrogen to get the C:N ratio. If it's between 25 and 35, your pile should compost beautifully" Calculation
If the C:N ratio is too high (excess carbon), decomposition slows down. If the C:N ratio is too low (excess nitrogen) you will end up with a stinky pile.
The C:N ratio in the organic matter of agricultural soils ideally averages about 10:1.
The lower the C/N ratio the more nitrogen is released during decomposition. Soil life is not served by low or high C/N ratio.
The lower the C/N ratio, the easier the breakdown. With a higher C/N ratio, the breakdown of organic matter is more difficult. A high C/N does not necessarily mean something is wrong.
A high C/N implies little decomposition of organic matter, and the organic matter that remains can improve workability, carbon sequestration, and water storage.
A low C/N ratio positively impacts nutrient availability, through nitrogen mineralisation, as it encourages microbial activity.
The ratio can be affected by soil management; input of straw and solid manure will eventually increase the C/N-ratio.
Guts
Guts
Anaerobic & fermentation
Anaerobic
Anaerobic
& Fermentation
Earthworms and Fermentation:
Earthworms and other soil animals play a crucial role in the decomposition of organic matter. In the guts of earthworms, fermentation processes break down organic compounds, including lignin, into simpler substances. This not only aids in the decomposition process but also produces nutrient-rich casts that enhance soil fertility.
"the nature of the microorganisms involved in gut fermentation in the earthworm is less well understood" (than ruminants) Zeibich et al 2019
Oribatid Mites and Humification:
Oribatid mites are perhaps the largest group of soil animals that contribute to humification. They consume decomposed organic matter, and the processes in their digestive systems help further break down complex organic compounds into humic substances. Their activity helps in the formation of stable humus, improving soil structure and nutrient retention.
"The changes consist in an increase of Humus Index and the density of mites, especially oribatids" Salmon 2018
Processes
Processes
Anaerobic decomposition and fermentation are both processes that occur in the absence of oxygen, but they differ in their mechanisms, conditions, and end products. Anaerobic decomposition encompasses a wider range of biological breakdown activities, whereas fermentation is a more specific biochemical process primarily focused on energy extraction from carbohydrates.
Anaerobic Decomposition (AD) is a broad, multi-stage process involving a variety of microorganisms, resulting in biogas (methane and carbon dioxide) and other compounds, commonly used in waste treatment and energy production. AD directly contributes to humification by breaking down organic matter into stable humic substances, especially in oxygen-poor environments. The slow decomposition rate under anaerobic conditions helps in the accumulation and preservation of organic carbon, leading to humus formation.
Fermentation is a more specific anaerobic process involving specific microorganisms, converting carbohydrates into simpler compounds like alcohols and acids, with applications in food, beverages, and biofuels. Fermentation plays a more indirect role by producing intermediate organic compounds that can be further decomposed into humic substances. Fermentation primarily contributes to the microbial activity and diversity in the soil, which supports the overall humification process.
While anaerobic decomposition has a more direct and significant role in humification, fermentation's contribution is indirect, supporting microbial communities that help form humus.
Anaerobic Digestion has taken on importance recently as a way to reduce waste and provide a source of energy, so there is much new research in this area.
AD - stages
AD - stages
Definition: Anaerobic decomposition is a broader term that refers to the breakdown of organic matter by microorganisms in the absence of oxygen.
Organisms Involved: It involves a diverse group of microorganisms, including bacteria, archaea, and fungi.
Conditions: It occurs in environments devoid of oxygen, such as deep soil layers, swamps, landfills, and the digestive systems of ruminants.
Stages: The process can be divided into several stages:
Hydrolysis: Breakdown of complex organic molecules into simpler ones.
Acidogenesis: Conversion of these simpler molecules into volatile fatty acids, alcohols, and gases.
Acetogenesis: Further conversion of products into acetic acid, hydrogen, and carbon dioxide.
Methanogenesis: Production of methane and carbon dioxide by methanogenic archaea.
End Products: The main end products are methane (CH₄), carbon dioxide (CO₂), ammonia (NH₃), hydrogen sulfide (H₂S), and other trace gases.
Applications: Anaerobic decomposition is used in waste treatment processes like anaerobic digesters, which produce biogas as a renewable energy source.
Fermentation - stages
Fermentation - stages
Definition: Fermentation is a specific type of anaerobic process where microorganisms, typically yeast or bacteria, convert organic compounds (usually carbohydrates) into simpler compounds to obtain energy.
Organisms Involved: It primarily involves specific microorganisms like yeast (e.g., Saccharomyces cerevisiae) and certain bacteria (e.g., Lactobacillus spp.).
Conditions: Fermentation takes place in anaerobic or low-oxygen conditions, often in controlled environments like fermenters or bioreactors.
Stages: The process generally involves:
Glycolysis: Breakdown of glucose into pyruvate, yielding ATP.
Fermentation Pathway: Conversion of pyruvate into various end products depending on the type of fermentation (e.g., alcoholic fermentation, lactic acid fermentation).
End Products: The end products vary based on the type of fermentation:
Alcoholic Fermentation: Ethanol and carbon dioxide.
Lactic Acid Fermentation: Lactic acid.
Other Fermentations: Various acids, alcohols, gases, and other metabolites.
Applications: Fermentation is widely used in food and beverage production (e.g., bread, beer, yogurt), pharmaceuticals (e.g., antibiotics), and biofuel production (e.g., ethanol).
AD - processes
AD - processes
Process Involvement: Anaerobic decomposition plays a crucial role in humification, especially in waterlogged or oxygen-poor environments like swamps, peat bogs, and wetlands where oxygen is limited.
Microorganisms: During anaerobic decomposition, a variety of microorganisms break down organic matter. While the end products of anaerobic decomposition include gases like methane and carbon dioxide, some of the intermediate products (such as volatile fatty acids and alcohols) can contribute to the formation of humic substances.
Formation of Humic Substances: As organic matter decomposes anaerobically, complex polymers and stable organic compounds, which are resistant to further decomposition, accumulate. These compounds contribute to the formation of humic substances, which are essential components of humus.
Conditions: Anaerobic conditions slow down the decomposition process, allowing for the accumulation of partially decomposed organic matter that can eventually become humus. This slow degradation process helps in the preservation of organic carbon, leading to the formation of stable humic substances.
Fermentation - processes
Fermentation - processes
Limited Direct Role: Fermentation, being a more specific and typically faster process compared to anaerobic decomposition, has a more limited direct role in humification. It primarily involves the conversion of carbohydrates into simpler organic compounds like ethanol, lactic acid, and other metabolites.
Intermediate Products: However, the by-products of fermentation can contribute to the pool of organic matter in the soil. For example, lactic acid and ethanol can be further decomposed by other microorganisms under anaerobic conditions, eventually leading to the formation of more complex humic substances.
Microbial Contribution: The microorganisms involved in fermentation, like yeasts and lactic acid bacteria, can also contribute to the overall microbial biomass and activity in the soil, indirectly supporting the humification process by providing a diverse microbial community that can further decompose organic matter into humus.
Specific Contexts: In certain controlled composting or fermentation processes designed to manage organic waste, the intermediate products can contribute to the formation of humic substances. For example, composting with a combination of aerobic and anaerobic phases can produce humus-rich compost.
Gut bacteria & Fermentation
Gut bacteria & Fermentation
Several types of gut bacteria are known to be involved in fermenting the contents of the gut.
Fermentation is a metabolic process by which sugars and other organic compounds are broken down anaerobically, producing various byproducts such as organic acids, gases (e.g., hydrogen, methane), and alcohol. These byproducts play important roles in energy metabolism and the overall ecology of the gut microbiota. Some of the primary gut bacteria involved in fermentation include:
Bacteroides: Bacteroides species are abundant members of the human gut microbiota and are known for their ability to ferment a wide range of complex carbohydrates, including dietary fiber and mucin. They produce short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate through fermentation, which are important energy sources for the host and play roles in gut health.
Firmicutes: Various members of the phylum Firmicutes, including genera such as Clostridium, Lactobacillus, and Ruminococcus, are involved in fermentation in the gut. These bacteria can ferment different substrates, including complex polysaccharides, proteins, and other organic compounds, producing SCFAs, gases (such as hydrogen and carbon dioxide), and other fermentation byproducts.
Prevotella: Prevotella species are prevalent in the gut microbiota of individuals with diets rich in plant-based carbohydrates. They are capable of fermenting dietary fibers and other complex carbohydrates, producing SCFAs such as acetate and propionate, as well as gases such as hydrogen and methane.
Bifidobacteria: Bifidobacteria are commonly found in the gut microbiota of humans and other mammals, particularly in infants. They are known for their ability to ferment complex carbohydrates, including oligosaccharides in human milk, producing SCFAs and contributing to the development of a healthy gut microbiota.
Escherichia coli: While Escherichia coli is primarily known as a facultative anaerobe, certain strains are involved in fermentation within the gut, particularly under anaerobic conditions. They can ferment sugars and other organic compounds, producing various fermentation byproducts.
These are just a few examples of gut bacteria involved in fermentation, and the composition of the gut microbiota and their metabolic activities can vary depending on factors such as diet, host genetics, and environmental factors. Fermentation by gut bacteria plays a crucial role in nutrient metabolism, energy production, and maintaining gut health.
Calorespirometric ratio (CR)
Calorespirometric ratio (CR)
“Over the past two decades, measurements of heat produced during organic matter decomposition have been increasingly used to quantify microbial activity in soils. Combined aerobic and fermentation (anaerobic) pathways for substrate metabolism can contribute to the observed variation in calorespirometric ratio (CR) from soils. Further, it shows that the presence of fermentation pathways can alter the CR values depending upon their rates (i.e., the degrees of aerobicity and fermentation) and associated growth yields. CR can emerge as a unifying metric containing information on both the energy and the mass fluxes exchanged by soil systems" (Chakrawal 2020)
Come Together
Come Together
Angiosperm plants, which include a wide variety of flowering plants, generally have less lignin in their wood compared to gymnosperms. Lignin, the complex organic polymer found in the cell walls of many plants, contributes to rigidity and resistance to decay. Gymnosperms, such as conifers, typically have wood that is more heavily lignified than angiosperms, due to the distinct types of cells and structures that compose their wood. Gymnosperms primarily contain tracheids for water transport, which have thicker and more lignified walls, while angiosperms have a combination of vessel elements and fibres that generally have less lignin. Angiosperms evolved 200-150mya.
How Angiosperms helped decomposition
How Angiosperms helped decomposition
The relationship between anaerobic decomposition, fermentation, and humification, particularly in the context of the evolution of angiosperms, is an important part of Earth's ecological history. The emergence of angiosperms (flowering plants) around 200-150mya had a significant impact on terrestrial ecosystems, soil formation, and organic matter decomposition processes, producing soil we would recognise today. Here’s how these concepts come together in light of this evolutionary development:
Evolutionary Context
Evolutionary Context
Emergence of Angiosperms: Angiosperms appeared during the Mesozoic Era, roughly between 150 and 200 million years ago. They diversified and became the dominant form of vegetation by the Cretaceous period, significantly altering terrestrial ecosystems. We will discuss this more with Darwin's Dilemma.
Impact on Soil Formation: The proliferation of angiosperms contributed to the development of more complex and fertile soils. Their diverse root systems, litter production, and the variety of organic compounds they produced (e.g., lignin, cellulose), particularly those which helped aggregation, influenced soil structure and organic matter content.
Anaerobic decomposition & Humification
Anaerobic decomposition & Humification
Organic Matter Input: The abundant and varied organic matter from angiosperms provided a substantial input for anaerobic decomposition. Leaf litter, wood, and other plant materials from angiosperms decomposed in various environments, including oxygen-poor conditions.
Humic Substance Formation: The complex organic compounds from angiosperms, particularly lignin, are more resistant to decomposition and can contribute to the formation of humic substances. In anaerobic environments, the slower decomposition rates allowed for the accumulation of these stable organic materials, enhancing humus formation.
Fermentation & Soil Microbiology
Fermentation & Soil Microbiology
Increased Microbial Activity: The diverse organic inputs from angiosperms also supported a wider variety of microorganisms, including those involved in fermentation. While fermentation itself is a more specialized process, it contributed to the overall microbial activity and diversity in the soil.
Indirect Contributions: The products of fermentation, such as organic acids and alcohols, provided substrates for other microbial processes that could further decompose these compounds into more stable forms, indirectly contributing to humification.
De-lignification
De-lignification
Prior to 300mya lignin wasnt broken down much but I believe de-lignification provided the fuel for anaerobic processes incorporated into soil animal guts (eg fermentation in earthworm guts and humification in oribatid guts, to produce more humus, thus recycle the nutrients most fully for the first time. And angiosperms thrived. ChatGPT: "You're absolutely right about the significant role lignin played in the history of organic matter decomposition and how the evolution of decomposer organisms and processes influenced nutrient cycling and the success of angiosperms. Here's a more detailed look at these interconnections:"
Lignin's Resistance to Decomposition: Before the evolution of efficient lignin-degrading microorganisms, lignin was highly resistant to decomposition. This led to the accumulation of plant material and some believe the formation of coal deposits during the Carboniferous period (around 360-300 mya).
Evolution of Lignin-Degrading Microorganisms: Over time, certain fungi, particularly white-rot fungi, evolved the ability to break down lignin. This development was crucial for the decomposition of woody plant material and the recycling of carbon in terrestrial ecosystems
Integration of processes
Integration of processes
Enhanced Decomposition Dynamics: The evolution of angiosperms likely enhanced the dynamics of organic matter decomposition by providing a continuous and diverse supply of organic materials. This would have supported both aerobic and anaerobic decomposition processes, leading to more effective humification.
Stable Humus Formation: With angiosperms contributing to greater organic matter input and microbial diversity, the formation of stable humus in soils would have been more pronounced. The interactions between different decomposition processes, including fermentation, anaerobic decomposition, and the activities of various microorganisms, created a more complex and efficient system for humus formation.
Ecological Balance: The balance between organic matter input from plants and its decomposition by microorganisms and soil animals is crucial for maintaining healthy and productive ecosystems. This balance ensures the continuous formation of humus and the recycling of essential nutrients.
Co-Evolution: The co-evolution of angiosperms and decomposer organisms created a synergistic relationship. Angiosperms provided diverse and abundant organic matter, while decomposer organisms and processes enhanced soil fertility and full nutrient cycling, supporting plant growth.
Angiosperm Success: The efficient recycling of nutrients allowed angiosperms to thrive and diversify.
Nutrient Recycling and Soil Fertility: The enhanced decomposition and humification processes, facilitated by soil animals and microorganisms, improved nutrient recycling.
This integration marked a crucial turning point in the history of terrestrial ecosystems, shaping the soils and biological processes today.
ChatGPT:
"The evolution of efficient lignin decomposition and humification particularly through the activities of fungi and soil animals like earthworms and oribatid mites, played a critical role in transforming terrestrial ecosystems. These processes improved nutrient cycling and soil fertility, creating conditions that favored the proliferation of angiosperms. This dynamic interplay underscores the importance of decomposition processes in the development and maintenance of fertile soils and thriving plant communities. The integration of anaerobic processes in soil animal guts and their contribution to humification and nutrient cycling highlights the complex interdependencies in soil ecosystems."
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