3rd Wave - Humification

Energy Entropy Mineralisation De-lignification Decomposition Glomalisation

Soil Functions Secondary Aggregation

Widespread humification probably evolved less than 200mya as the third wave of decomposition. We have some mites, worms and insects to thank.

Human

The word human comes from the word humus. Human was first recorded in the mid-13th century, and owes its existence to the Middle French humain “of or belonging to man.” That word, in turn, comes from the Latin humanus, thought to be a hybrid relative of homo, meaning “man,” and humus, meaning “earth’.

The dominant thinking for many years has been that humus was the key ingredient of good soils.

Layer of humus (Organic O) with lower soil stained with HSs.

Signs of humus in the geological record seem to be elusive...

See why humification so important

Humification

Humification is the process that produces humus. In the process other substances, generally called humic acids (HAs) are formed. "During the past 225 years, most researches on the molecular structure and reaction of HA and SOM (Soil organic Matter) were done by soil chemists, with limited contribution from soil microbiologists. This may be one reason why progress in our knowledge of the molecular structure of SOM and HA has been slow. Closer cooperation between chemists and microbiologists would have been certainly beneficial." (Schnitzer 2011)

Humification is often seen as a key component in soil formation. Humification differs from mineralisation, in that the process of humification turns organic matter into organic polymers, which are stable and cannot be decomposed further. It remains as humus and that is what makes soil what it is in many parts of the world. Humification only became widespread less than 300mya (National Geographic) [National Geographic is not an academic journal, it is a popular magazine often containing non-specialist journalist written pieces, with few top flight academic authors and without peer reviewed articles - graduates will view it as a less reputable source]

After Stevenson

Humus

Humus is a black [and brown?] amorphous substance produced by the decomposition of dead and decaying organic matter.

This process of humification was developed, through chemical and biochemical pathways, to break down plant debris completely so there are no 'shapes' of debris. It just happened to create powerful humic substances(HSs) that became a building cement (see 'Concrete & Clay below).

Role of lignin

In the story of soil, the lignin-humification process is vital. "Currently, several chemical modification pathways can be followed to convert lignin into Humic Substances(HS)-like materials, such as alkaline aerobic oxidation, alkaline oxidative digestion, and oxidative ammonolysis of lignin. This review paper discusses the fundamental aspects of lignin transformation to HS comprehensively." (Sutradhar 2023)

"Earlier studies reported a direct connection between natural humification and lignin due to aromatic structures and other common functional groups found in HS and lignin [54, 55]. It was also illustrated that artificial humification by alkaline oxidation or oxidative ammonolysis/ammoxidation of technical lignin would be possible [56–61]. This review article describes the complete historical origin of HS and the similarities between HS and lignin comprehensively. Also, the natural humification process and recent approaches to transforming lignin into HS-like materials are extensively discussed. Furthermore, this review article extends the discussion on the application of lignin-derived HS". (Sutradhar 2023)
There is more on 'Relation between de-lignification & Humification' and their working together aerobically and anaerobically in De-lignifcation.

Compost

When composting, we are told to mix green and brown. The green represents leaves/grass while brown are the twigs and stalks. The green represent nitrogen (N) while the brown represents carbon (C). The genral recommendation is to have 10C to 1 N. They get decomposed but are still identifiable and still contain defined biological molecules.

However, making humus is quite different. It is like a ‘mud’ of substances, quite consistent although the chemicals can vary depending on the soil sources. They represent strongly altered organic materials that are not easily identifiable. Humic substances can provide up to 70% of Soil Organic Matter (SOM).

Terms

Humus

You may think the term humus is commonly understood. The term humus is used by some soil scientists synonymously with soil organic matter, that is to denote all organic material in the soil, including humic substances. Contemporary, the term humus is frequently used to represent only the humic substances.

It bears no morphological resemblance to the structures from which they were derived. These transformed components are referred to as the humification process products.

Types

Soil organic matter (SOM)

SOM is non-living components which are a heterogeneous mixture composed largely of products resulting from microbial and chemical transformations of organic debris.

SOM can exist in different morphological patterns, which are the bases of the classification of so called forms and types of humus.

The term SOM is generally used to represent the organic constituents in the soil, including undecayed plant and animal tissues, their partial decomposition products, and the soil biomass. Thus, this term includes:

identifiable, high-molecular-weight organic materials such as polysaccharides and proteins,
simpler substances such as sugars, amino acids, and other small molecules,
humic substances.

Humic substances

What are humic substances (HSs)?

They are a series of relatively high-molecular-weight, brown to black colored substances formed by secondary synthesis reactions. The term is used as a generic name to describe tocolored material or its fractions obtained on the basis of solubility characteristics:

humic acids (HA)
fulvic acids (FA)
humins

These are what determine soil colour.

Humic acids - the fraction of humic substances that is not soluble in water under acidic conditions (pH < 2) but is soluble at higher pH values. They can be extracted from soil by various reagents and which is insoluble in dilute acid. Humic acids are the major extractable component of soil humic substances. They are dark brown to black in color.

Fulvic acids - the fraction of humic substances that is soluble in water under all pH conditions. They remains in solution after removal of humic acid by acidification. Fulvic acids are light yellow to yellow-brown in color.

Humin - the fraction of humic substances that is not soluble in water at any pH value and in alkali. Humins are black in color.

Aerobic & Anaerobic

Humification involves both aerobic and anaerobic pathways. The fermentation process by bacterial breakdown is anaerobic.

But the creatures carrying the bacteria in their guts need air to breathe and bite. In aerobic environments where oxygen is present, aerobic microorganisms contribute to humification by breaking down organic matter into simpler compounds.

However, in anaerobic environments where oxygen is limited or absent, anaerobic microorganisms, such as certain bacteria and archaea, can contribute through fermentation and other anaerobic processes. Humification occurs in soil but, is much more widespread in the guts of millions of small animals running round. Anaerobic bacteria are found in compacted soil, deep inside soil particles (microsites), and hydric soils where oxygen is limiting. One bacterium Trichonympha is known to be an active wood eater.(video).

However this process can happen most reliably - and become much more widespread - in animal guts. Those could be oribatid mites nematodes, termites or earthworms. Bacteria in this new anoxic environment would have spread the humification process through a lot more soil.

Concrete & Clay

The Humic Substances (Insight to Humic Substances) are attracted electrostatically to colloid particles like clay. This makes the clay particles sticky.

The humic substances cover particles and – because of the electrostatic, also attract others so the particles stick together to make crumbs. The Humus Substances are attracted electrostatically to colloid particles like clay, and thus help to build aggregates. Humification is one of the great soil processes, and links with another, soil particle formation. The sticky property of humic substances would have enabled the production of particles. Can you imagine the role this humus cement could make when surrounding root bits and fungal filaments? The production of particles would make the soil stronger to support the upper layers better.

Gram for gram, the capacity of humus to hold nutrients and water is far greater than that of clay minerals, with most of the soil cation exchange capacity arising from charged carboxylic groups on organic matter. It also has a great capacity to retain water. It is this mixture which now makes soil so powerful. Small amounts of humus may remarkably increase the soil's capacity to promote plant growth. Imagine the evolution of humus formation and the effect that was to have on all life.

Evolution

Humus may have provided a key step in the evolution of soil, but not much before 300mya. It is most likely to have spread worldwide sometime later than 200 mya.

“Trees would fall and not decompose back. When those trees died, the bacteria, fungi, and other microbes that today would have chewed the dead wood into smaller and smaller bits were missing, or as Ward and Kirschvink put it, they ‘were not yet present’.”

Bacteria existed, of course, but microbes that could ingest lignin—the key wood-eaters had yet to evolve in the new conditions. It’s a curious mismatch. Food to eat but no eaters to eat it. And so enormous loads of wood stayed whole.

“By not being there 350 million years ago, and by not arriving for another 60 million years, giant seams of black coal now warm us, light us, and muck up our atmosphere.” National Geographic

My hypothesis

While Ward and Kirschvink put it, they ‘were not yet present’ 300mya, the National Geographic predict humification a short time after. But no evidence is provided

I predict that widespread humification was not till another hundred million years later.

This was when earthworms, 'higher oribatid' mites and termites could spread the process within their guts throughout the soil.

This completed the nutrient cycles and provided a new cement to build better aggregates, from where angiosperms could take off.

Humus & Soil

The significant accumulation of soil humus, which contributes to the brown coloration in paleosols, became more pronounced as terrestrial vegetation evolved and diversified. Humus became mixed with mineral soils. This process accelerated especially from the mid-Jurassic period (around 170 mya) onward, providing secondary aggregation that led to better aeration.

I believe the widespread impact of humification was another 100 million years later than National Geographic. The fermentation process takes place in the guts of in many animals but particularly earthworms, termites and higher oribatid mites, all of which did not appear till atfer 200mya. As plants grew a plenty again then, their success was now ensured by the process of humification carried out in the new incumbents which now ensured nutreint recycling, further encouraging plant growth. This 'second coming' is the 'true terrestrialisation' that makes soil we know today.

What is humus? The answer is not that easy.

Basis of soil

For over 200 years, most research on the molecular structures and reactions which involved with Humic acids and SOM were done by soil chemists. However good they were, and Frank Stevenson is a fine example at drawing attention to this process, we now have a better idea how humus works, by including the biology of bacteria and the enormous impact they make. "In greater detail, humification involves three steps.

1. where the soil microorganisms digest the dead matter to produce a complex polyketide-related synthases. The PKs involve complex alkylaromatic, aromatic, polyaromatic, phenolic, and polyphenolic structures which contribute to the formation of a central structure of Humus substances. They are part of SOM. SOM is quite varied materials that include humus but not just that. The synthesized PKs are adsorbed rapidly and strongly onto inorganic soil colloidal surfaces, thereby minimizing their potential decomposition by resistant soil organisms. This provides the Central Unit Structure (CUS).

2 many microorganisms utilize soluble, low-molecular-weight compounds, called ‘labile’ substrates such as sugars, amino acids, and organic acids. These small molecules are readily taken into bacterial cells and metabolized. Glucose provides the energy to capture nutrients such as nitrogen, phosphorus, or calcium into themselves. The CUS reacts electrostatically with these products to produce macromolecular assemblies.

3, the catalytic surfaces of soil colloids (like clay) provide means to trap both the PK’s and the assemblies in to even larger sized humified macromolecules, of a large and diverse range. We call them particles.)

Different clays enhance humification. It has been found that Oxisol clay is better than Mollisol clay. While Oxisol caught more carbon, each produce different humus substances (HSs) depending particularly on Iron and Manganese oxidation. This shows how important the presence of this chemical is in humification.

To provide the characteristics of humus, the CUS must have polyphenols, be kinetically stable, be devoid of carbohydrates, and have electrostatic attractions to other molecules, that generate new random structures" (Schnitzer & Monreal 2011

or human artifact

The contentious nature of soil organic matter 2015 Nature 528(7580) 10.1038/nature16069

Johannes Lehmann Markus Kleber

"The exchange of nutrients, energy and carbon between soil organic matter, the soil environment, aquatic systems and the atmosphere is important for agricultural productivity, water quality and climate. Long-standing theory suggests that soil organic matter is composed of inherently stable and chemically unique compounds. Here we argue that the available evidence does not support the formation of large-molecular-size and persistent 'humic substances' in soils. Instead, soil organic matter is a continuum of progressively decomposing organic compounds. We discuss implications of this view of the nature of soil organic matter for aquatic health, soil carbon-climate interactions and land management."

Don't pooh-pooh humus.

50 yrs ago

For my PhD in soil ecology, my external examiner Kenneth Mellanby (the then Director head of Terrestrial Ecology Research Station) asked the hardest question: ‘What is humus?’.

I mumbled something about ‘universal amorphous soil substance that can’t break down any further’.

Now

If asked this question, I would say: The answer is poo.

If humification takes place mainly in mite, termite and worm guts, the humus must reflect that.

In the past, we looked at the chemistry of plant breakdown, then with the role played by bacteria, but now we should also include the animals and the stuff from their guts. Just think about our poo.

Once we see humus as a product of digestion - we see it totally differently. It explains why plant decomposition doesn't follow a script of various processes but is more a digestive process. It helps explain its makeup - it is distinct - but differs all the time.

Those complex chemicals in humus come from the animals not the plants. It shows how we need to look in a new way when looking into the soil. More on mite poo

Wait! I said something similar about how the other main sticky soil substances -glomalin related glues - could have developed. This time the fungivores, like springtails, turned fungal exudates into sticky substances that held particles together.

Going Brown

When humification spread round the globe, the soil turned brown.

The Maillard reaction in food circles is the way some foods go brown. It explains the crust on bread and pork but also how milk can turn brown. It is also considered to be a major pathway in humification because of significant similarities between humic substances (HSs) and (browning) melanoidins formed through this pathway, involving sugar–amino acid condensation. These - humins and melanins - are also the chemicals involved in making higher oribatid mites go brown..

Humiifcation Index

Humification Index is the ratio of HSs to non-HSs. Using Laser Induced Fluorescence spectroscopy, we can measure the rate of humification (HLIF) in compost heaps, rubbish tips and between different trees rotting, and how various practices affect the HLIF

At first sight peat and humus look the same but.

Peat

Peat is partially decomposed plant material that accumulates in waterlogged, anaerobic conditions, such as bogs and mires. Its composition can vary depending on the types of plants from which it is derived and the environmental conditions.

Peat forms in waterlogged, acidic environments where the rate of decomposition is slower than the rate of organic matter accumulation. Over time, layers of partially decomposed plant material accumulate and undergo limited microbial decomposition due to the anaerobic conditions, leading to the formation of peat bogs or peatlands.

Peat is less stable and more acidic compared to humus. It has a spongy texture and retains a significant amount of water, making it important for water retention in ecosystems like wetlands. Peat also plays a role in carbon sequestration, although it releases carbon dioxide when disturbed or drained.

Generally, the chemical constituents of peat include:

Carbon (C): Peat is rich in carbon, often making up around 50-60% of its dry weight. This high carbon content is due to the accumulation of plant material that has not fully decomposed.
Hydrogen (H): Present in smaller amounts, hydrogen is found in the organic compounds within peat.
Oxygen (O): Oxygen is also a significant component, particularly in the form of water content and oxygen-containing organic compounds like carbohydrates.
Nitrogen (N): Nitrogen content in peat is relatively low compared to carbon and oxygen but is present in proteins and other nitrogenous compounds.
Sulfur (S): Sulfur can be found in small amounts, often derived from the original plant material or from microbial activity.
Ash: This refers to the inorganic mineral content remaining after combustion, which can include elements like silicon, aluminum, iron, and calcium.

The primary compounds in peat include:

Lignin: A complex organic polymer found in the cell walls of plants, particularly woody plants.
Cellulose and Hemicellulose: Carbohydrates that make up the structural components of plant cell walls.
Phenolic Compounds: Various aromatic compounds derived from the decomposition of plant material.
Humic Substances: Including humic acids, fulvic acids, and humins, which are large, complex molecules formed through the decomposition and transformation of organic matter.

Humus

Humus is a stable, highly decomposed form of organic matter found in soil. It results from the microbial breakdown of plant and animal residues and is critical for soil fertility.

Humus forms through the further decomposition of organic matter by soil microorganisms such as bacteria, fungi, usually in the guts of mites and earthworms. This decomposition occurs in aerated soils with sufficient oxygen and moisture levels. As organic matter breaks down, it transforms into humus, which is a more stable and nutrient-rich form of organic material.

Humus improves soil structure by enhancing its ability to hold water and nutrients. It contributes to soil fertility by releasing nutrients slowly over time and promoting microbial activity. Humus also helps to stabilize soil pH and reduce erosion.

The chemical constituents of humus include:

Carbon (C): Humus is also carbon-rich, with a significant portion of its mass composed of complex carbon compounds.
Hydrogen (H): Present in various organic compounds within humus.
Oxygen (O): Found in a variety of functional groups, including carboxyl, hydroxyl, and carbonyl groups.
Nitrogen (N): Higher than in peat, nitrogen in humus is found in amino acids, proteins, and other nitrogenous organic molecules.
Phosphorus (P): Found in nucleic acids and phospholipids, and also as inorganic phosphates.
Sulfur (S): Present in organic compounds like amino acids (e.g., cysteine and methionine) and sulfate esters.

The primary compounds in humus include:

Humic Acids: Large, complex molecules that are not soluble in water under acidic conditions but soluble at higher pH.
Fulvic Acids: Smaller molecules than humic acids, soluble in water at all pH levels.
Humin: The fraction of humus that is insoluble in water at all pH levels.
Microbial Biomass: Includes the remnants of microorganisms that contribute to the formation of humus.
Resistant Organic Compounds: Such as lignin derivatives and other complex molecules that are highly resistant to further decomposition.

Humification turns a lot of organic matter into energy. What potential is there for us harnessing that?

Anaerobic digestion

We now know quite a lot about anaerobic digestion as many waste disposal units now use the process for breaking down biological debris. Anaerobic digestion is a treatment option for stabilisation of biogenic wastes leading to a residual product called digestates, enabling the sanitation and the recycling to use as a fertilizer. It is also a means to obtain energy from wastes as well as from dedicated energy crops.

Future Energy

Decomposition unlocks a lot of energy locked in the compressed plant debris. Imagine how much energy that entails. All that dead kerogen turned into coal during the short 'Late' Carboniferous period has run our civilisation for the last 150 years. What if, instead of kerogen, humus was formed, and in so doing released energy? A lot more energy starts going back into the soil, enabling the build-up of many more metabolic processes.

But just let us pause. The plant debris that has yet to be broken down, and which would produce vast amounts of kerogen and thence coal, is at the bottom of the swamp. Bacteria can get there, but they can also be washed away pretty easily. How do other creatures feature? There must be some sort of mixing between the mites and myriapods already in the soil and the debris and bacteria in the swamp. Water would flow to and forth, and the animals can move sideways, as they can already live deep down – but would need oxygen. Now with much more attention being applied to dealing with biological waste commercially, we may find out more about what goeson in the soil. And we may even find some natural process that can produce hydrogen for energy. Check out Anaerobic solid-state fermentation (ASSF) where many are now examining this process, like humification, only a 2-stage fermentation process started on solid plant plant (like straw sugar cane) to make hydrogen, the clean fuel of the future..learnt just as the soil did taking over from coal.

Humification in higher oribatids

Why humification important

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