2nd Wave De-lignification

Humification Energy Entropy Mineralisation Decomposition Glomalisation

Soil Functions

Lignin is ‘recalcitrant to mineralisation’ by microorganisms because of its strong 3-D chemical structure (Ruiz-Duernas & Martinez 2009).

Widespread de-lignification probably didnt evolve till around 300mya.

Wood is made primarily of cellulose along with varying amounts of lignin. This latter compound is to cellulose what steel reinforcing rod is to concrete. There is far less of it but it imparts a great deal of strength and resilience. Even professional wood-eating bacteria in the gut of a termite cannot digest lignin. Only an exclusive coterie of fungi have that superpower.

White Rot Fungi (WRF)

What eats WRF?

Lignin & Humification

Enzymes

There is increasing interest in the enzymes that can break down lignin "Lignocellulose is the most abundant biomass available on earth, including wood and agricultural wastes such as rice straw, corn cobs, and oil palm empty bunches. The biopolymer content in lignocellulose has a great potential as feedstock for producing industrial raw materials such as glucose, sorbitol, xylose, xylitol, and other pharmaceutical excipients. Currently, scientists and governments agree that the enzymatic delignification method is an environmentally friendly green method to be applied. This review attempts to explain the proper preparation of the enzymes laccase, lignin peroxidase, and manganese peroxidase, as well as the important factors influencing their activity. " (Suriyadi 2022)

Does the soil have any answers?

Chemicals

Delignification, the process of extracting lignin from plant sources, can be done using a variety of methods. Its aim is the disintegration of the lignocellulosic structure into its fibrous components. The delignification processes in pulp mills can be divided into two major classes: chemical and solvent processes. The two conventional and industrially the two most widely used are sulfite and alkaline pulping, both of which are classified as chemical pulping processes.

How does the soil do it?

Structure

Lignin is one of the most abundant biopolymers in the terrestrial biosphere and protects other components of plant tissue from microbial attack. Traditionally, it was assumed that lignin limits litter decomposition1,2 and contributes substantially to soil organic carbon (SOC)3,4 . More recently, lignin’s importance in controlling litter and SOC decomposition has become controversial.

lignin

Abundance

Lignin is the most abundant aromatic biopolymer on earth, containing many active functional groups, e.g., aliphatic and phenolic moieties. Lignin is a three-dimensional, highly cross-linked macromolecule composed of three substituted phenols of coniferyl, sinapyl, and p-coumaryl alcohols generated by enzymatic polymerization, yielding a vast number of functional groups and linkages (Bross et al 2011) The primary source of lignin is plant biomass [24–27], mainly produced as the by-product of the pulping processes of wood and other plant resources. The chemical characteristics of lignin differ depending on the pulping processes and the origin of the lignin resources. Although unmodified lignin has a limited application today, many applications have been proposed for chemically modified lignin derivatives, such as fine chemicals, emulsifiers, flocculants, synthetic floorings, sequestering, binders, thermosets, paints, adhesives, and fuels [28–34]. There are various ways to modify lignin for valorization, such as pyrolysis [35–37], hydrolysis [38, 39], hydrogenolysis [40–42], gasification [43, 44], hydrothermal conversion [45], and oxidation [46–48]. Oxidation is the most popular route for lignin modification and depolymerization for vanillin and organic acid production [49, 50]. Oxidation can be conducted using different oxidizing agents or various catalysts and enzymes [47–49, 51–53]. Alkaline aerobic oxidation could be an efficient chemical process to convert lignin and lignocellulosic biomass into HS". (Sutradhar & Fatehi 2023)

White Rot Fungi (WRF)

The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also includes brown rot and ectomycorrhizal (evolved long after endomycorrhiza).

The name “white rot” derives from the white colour and rotting texture of the remaining crystalline cellulose from wood degraded by these fungi. Most knowledge of white-rot fungi comes from Coriolus versicolor and Phanerochaete chrysosporium.(Palmer, J. M., & Evans, C. S. (1983). The first way white-rot fungi can break down lignin involves a high-redox-potential catalyzed peroxidase attack on the heme pocket, thus reducing the stability of lignin. The second way involves a low-redox environment, enabling them to digest in all conditions.

Even though white-rot fungi have a very specialized process for acquiring carbon, they are still vulnerable to competitors. Researchers clarified that white-rot fungi survival is dependent on its ability to defend lignocellulose substrate against attack by soil microbiota and its ability to establish itself within the soil bulk. Brown-rot fungi and white-rot fungi have similar interspecific mycelial interactions. Together they form ‘decay columns’ with interspecific competition. Mutualism between two white-rot fungi was noted to be very rare. (Owens et al 1994)

White-Rot Fungi are increasingly being seen as a useful source of many useful products. "White-rot fungi exhibit a unique ability to decompose all wood components, contributing to carbon and nitrogen cycles and producing bioactive substances with several effects, such as antioxidant, antimicrobial, and anticancer properties" (Pinar & Rodriguez- Couto 2024).

Origins of white rot

"The earliest definitive fossil record of basidiomycete white rot is from Triassic conifer wood (Stubblefield & Taylor 1986), an earlier evolution of fungal-mediated lignin degradation is indicated by Devonian-to-Permian woods infiltrated with fungi and possessing damage consistent with white rot decay or other forms of fungal degradation of lignified tissue (Raymond et al 2001, Stubblefield & Taylor 1986,, Stubblefield et al 1985, Dieguez & Lopez-Gomez 2005)". (Nelson et al 2016)

Evolution of WRF

Peroxidases (PODs) developed after cellulolytic enzymes. White-rot mechanisms were an elaboration based on the already existing saprotrophic model, not just on the utilization of PODs.(Nagy et al 2017).

Insight on the evolutionary development of white-rot fungi comes from the evolution of lignin catabolism. During the Carboniferous (360-300 mya) and Permian (300-250 mya) there was a very high carbon accumulation, including lignin. However, near the end of the Permian there was a sharp decline in carbon accumulation. White-rot fungi and their ability to cleave lignin evolved at the end of the Permian period (Folman 2008) Researchers attempted to reconstruct the evolution of saprotrophic capabilities.

The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contain non–lignin-degrading brown rot and ectomycorrhizal species. WRF were the common ancestors of brown-rot fungi and ectomycorrhiza (ECM), but that in these two groups gene coding for PODs were lost. (Floudas 2012) Comparative analyses of 31 fungal genomes (12 generated for this study) suggest

"The lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and (ecto) mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period." (Floudas 2012)
But beware!! Molecular clocks usually predict earlier than fossil evidence

What eats WRF?

Few studies have been conducted on the effects of invertebrate grazing on the growth and activity of individual decomposing fungi, so an artificial microcosm was made to study the effects of invertebrate grazing on the enzyme pro (Crowther et al 2011) Invertebrates can directly increase the growth and enzyme activity of fungi through grazing. White-rot fungi adopt a “compensatory” growth strategy in the face of fauna grazing. These grazing effects in the grazing area can be transmitted through hyphae, increasing the growth and extracellular enzyme activities of fungi in the non-grazing area (decomposition area). The decomposition of fungi was affected by the litter species. In conclusion, invertebrate grazing is a crucial pathway of the carbon dynamics and nutrient cycling driven by decomposing fungi in the forests.

Animals partial to WRF

It is well known that many soil animals involved in decomposition - but which ones are partial to WRF? It would be likely that early beetles 'living on dead wood' would eat WRF, like Agaricales (Epps & Arnold 2017) - but that would be 100m years after WRF first appeared.

"The grazing of isopods on white-rot fungi was transitive and persistent. The grazed fungi appeared “compensatory” growing. The biomass of fungi increased after grazing. The activities of enzymes associated with nutrient cycling were increased under grazing. The zymography images showed the enzyme hotspots and activities also increased significantly in the grazing area. The results suggest that invertebrate grazing can significantly increase the fungal biomass and enzyme activity, accelerating litter decomposition in the unreached grazer area." Chen et 2022). This confirms how these little creatures control fungi (Crowther et al 2011) - along side their role in climate change as we will see later.

We would expect springtails, long-time fungivores to be involved in consumption of WRF. These would include Onychiurid (Hedlund et al 1991), Folsomia, often used in labs, Protaphorura decompose organic matter and control fungal populations, Sinella interact with fungal communities in soil.Orchesella consume various fungal species and Hypogastrura feed on a range of fungal species.

Oribatid role

Yet the most obvious to me is the role of higher oribatids linking the aerobic de-lignification with gut humification. "It could be shown (1) that oribatid mites prefer dark pigmented fungi (Dematiacea) over most other soil fungi, (2) that some Dematiacea (Alternaria alternata, Ulocladium sp.) were preferentially ingested compared to others,(3) that some ectomycorrhizal fungi are accepted as food substrates" (Schneider et al 2004). It may be that they do not consume the WRF itself may be attracted to any of the widespread bioactive products, like Quercetin, Taxifolin, Catechin, Coumaric acid ((Pinar & Rodriguez- Couto 2024).

The fungal order Agaricales has the most WRF (Sanchez Ruiz et al 2021). A 'track analysis' of acaricoid fungi (includes Agaricales) found "agaricoid species is in close proximity to the node found by Morrone (2011) for weevils. Nodes found are also coincidental with those found by Ruiz et al.(2016) for oribatid mites (Acari: Oribatida)" (Romano et al 2017) and that the relation of the these nodes (WRF, Weevils & Oribatids) should be studied more. I agree.

Lignin & Humification

"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)

Relation between de-lignification and humification

The processes of de-lignification and humification in soil are closely related, as both are crucial components of the overall decomposition of organic matter.

Relationship Between De-lignification and Humification

Sequential Processes: De-lignification is a precursor to humification. Lignin's breakdown releases other organic compounds like cellulose and hemicellulose, which can then be further decomposed by microorganisms. Without de-lignification, these compounds would remain protected and less accessible for microbial action.
Enhanced Decomposition: De-lignification facilitates the overall decomposition process by breaking down one of the most resistant components of plant material. This accelerates the degradation of the entire organic matter, making more substrates available for humification.
Formation of Humic Substances: During the de-lignification process, some lignin-derived compounds can contribute directly to the formation of humic substances. The breakdown products of lignin, along with other microbial metabolites, undergo further biochemical transformations to form the complex structure of humus.
Microbial Interaction: The microorganisms involved in de-lignification (e.g., fungi) play a role in humification as well. They not only break down lignin but also contribute to the transformation and stabilization of organic matter into humus.

Summary

De-lignification breaks down lignin, a resistant component of plant material, making other organic compounds accessible for further decomposition.
Humification transforms decomposed organic matter into stable humus, improving soil properties.
De-lignification aids humification by facilitating the decomposition of lignin-protected compounds, and some lignin breakdown products contribute directly to humus formation.
Both processes are essential for efficient nutrient cycling and soil health, working in tandem to ensure the complete decomposition and stabilization of organic matter.

In essence, de-lignification and humification are interconnected stages in the broader process of organic matter decomposition in soil. De-lignification paves the way for humification by breaking down resistant lignin, thus supporting the formation of humus and contributing to soil fertility and structure.

The unique and vital nature of soil arises from the intricate balance and interaction between aerobic and anaerobic decomposition processes. Soil fauna play a crucial role in maintaining this balance by creating and mixing microenvironments, thus facilitating the complete breakdown and transformation of organic matter. This dynamic interplay not only supports nutrient cycling and soil fertility but also enhances soil structure and contributes to carbon sequestration, making soil an essential component of terrestrial ecosystems.

On a global scale, about 20-30% of lignin carbon eventually contributes to stable soil organic matter (humus). In forest ecosystems, approximately 25-40% of lignin input contributes to long-term soil carbon storage, including humus. In grasslands, the proportion may be lower with about 10-20% of lignin contributes to stable humus .In agricultural soils, the proportion of lignin is influenced by soil management practices, crop type, and residue management, with a rough range 10-25%.

Factors

Several factors influence how much lignin ends up as humus:

Microbial Activity: Fungi, especially white-rot and brown-rot fungi, play a critical role in lignin degradation. Their activity levels and presence significantly impact the proportion of lignin that becomes humus.
Soil Conditions: Soil pH, moisture, temperature, and aeration affect microbial activity and the chemical breakdown of lignin.
Lignin Composition: The chemical structure of lignin varies between plant species, affecting its degradability and subsequent conversion to humus.
Environmental Conditions: Climate and seasonal changes impact decomposition rates and microbial efficiency in transforming lignin to humus.

References

[Kögel-Knabner, I. (2002). The macromolecular organic composition of plant and microbial residues as inputs to soil organic matter. Soil Biology and Biochemistry, 34(2), 139-162.]
[Crawford, R. L. (1981). Lignin Biodegradation and Transformation. John Wiley & Sons.]
[Harmon, M. E., Franklin, J. F., & Swanson, F. J. (1986). Ecology of coarse woody debris in temperate ecosystems. Advances in Ecological Research, 15, 133-302.]
[Amelung, W., & Zech, W. (1999). Lignin transformation in decomposing grass litter studied by acidic cupric oxide oxidation and direct pyrolysis mass spectrometry. Soil Science Society of America Journal, 63(3), 657-662.]
[Leinweber, P., & Schulten, H. R. (1998). Non-living soil organic matter: Composition, environmental relevance and existing definitions. European Journal of Soil Science, 49(2), 293-305.]

Anaerobic & Aerobic together

De-lignification and humification processes occur under different conditions, but their primary modes are typically associated with specific environments.

De-lignification

De-lignification is primarily an aerobic process. Here's why:

Aerobic Fungi: The main organisms responsible for de-lignification are fungi, particularly white-rot and brown-rot fungi. These fungi are predominantly aerobic, requiring oxygen to produce the enzymes (ligninases) necessary to break down lignin.
Enzymatic Activity: The enzymes involved in de-lignification, such as lignin peroxidase, manganese peroxidase, and laccase, function optimally in the presence of oxygen. These oxidative enzymes catalyze the breakdown of the complex lignin polymer into smaller molecules.
Environmental Conditions: De-lignification typically occurs in environments where oxygen is readily available, such as the surface layers of soil and decomposing plant material exposed to air.

Humification

Humification can occur under both aerobic and anaerobic conditions, but it is more complex:

Aerobic Conditions: In the presence of oxygen, humification involves aerobic microbes (bacteria and fungi) that decompose organic matter into simpler substances, which then polymerize and stabilize to form humus. Aerobic humification is generally more rapid and leads to the production of well-structured humus.
Anaerobic Conditions: Humification can also occur under anaerobic conditions, such as in waterlogged soils, wetlands, and compost piles where oxygen is limited. In these environments, anaerobic bacteria and fungi contribute to the breakdown and transformation of organic matter. However, anaerobic humification tends to be slower and may result in partially decomposed organic matter and different types of humic substances compared to aerobic conditions.

Summary

De-lignification: Primarily an aerobic process, as it relies on aerobic fungi and oxidative enzymes that require oxygen.
Humification: Can occur under both aerobic and anaerobic conditions. Aerobic humification is typically faster and more efficient, producing well-structured humus, while anaerobic humification is slower and may lead to partially decomposed organic matter.

In conclusion, while de-lignification is mainly aerobic due to the oxygen-dependent nature of the organisms and enzymes involved, humification is a more versatile process that can proceed in both aerobic and anaerobic environments, although the efficiency and nature of the resulting humus can vary significantly between these conditions.

The interplay between aerobic and anaerobic processes in soil decomposition is what makes soil a dynamic and vital ecosystem. This is how these processes work together and contribute to the uniqueness and vitality of soil.

Interplay of Aerobic and Anaerobic Processes

Soil Structure and Microenvironments:
- Soil is not a uniform environment; it has various microenvironments with differing levels of oxygen availability.
- Aerobic Zones: Typically found in well-aerated soils, near the surface, and around plant roots (rhizosphere). These zones support aerobic decomposition processes, including the activity of bacteria, fungi, and soil fauna that require oxygen.
- Anaerobic Zones: Found in waterlogged soils, deeper soil layers, and compacted areas where oxygen is limited. Anaerobic microbes thrive here, carrying out fermentation and other anaerobic decomposition processes.
Role of Soil Fauna:
- Soil fauna such as mites, springtails, earthworms, beetles, ants, and termites play a critical role in creating and maintaining these microenvironments.
- Bioturbation: Activities of soil fauna, like burrowing and mixing, help aerate the soil and facilitate the movement of organic matter and microbes between aerobic and anaerobic zones. This mixing promotes a dynamic interplay between different decomposition processes.
Sequential Decomposition:
- Decomposition in soil often occurs in a sequential manner, where initial breakdown by aerobic organisms is followed by further decomposition under anaerobic conditions.
- Aerobic Phase: Organic matter is initially broken down by aerobic bacteria and fungi into simpler compounds. This phase includes processes like hydrolysis, oxidation, and de-lignification.
- Transition to Anaerobic Phase: As organic matter gets buried or becomes more compact, oxygen levels decrease, and anaerobic microbes take over. They further decompose the remaining organic matter through processes like fermentation and methanogenesis.
Nutrient Cycling:
- The combination of aerobic and anaerobic processes is essential for the complete mineralization of organic matter, releasing nutrients in forms that plants can uptake.
- Aerobic Decomposition: Produces carbon dioxide, water, and inorganic nutrients like nitrate, phosphate, and sulfate.
- Anaerobic Decomposition: Produces methane, hydrogen sulfide, and organic acids, which can further break down into simpler compounds over time.

Importance of the Combined Processes

Soil Fertility: The interplay between aerobic and anaerobic decomposition processes ensures a continuous supply of nutrients, enhancing soil fertility and supporting plant growth.
Soil Structure: The activities of soil fauna and the formation of humus improve soil structure, porosity, and water retention, which are critical for root development and overall soil health.
Carbon Sequestration: Humification, particularly under anaerobic conditions, helps stabilize organic carbon in the form of humus, contributing to long-term carbon sequestration in soils.

Humification

Permian

200mya

The evolution oof the process of de-lignification, with the emergence of WRF around 250 mya, provided the fuel for humification carried out by microbes and small soil animals enabled the distribution of humus widely between 200-150may and the creation of soil, very much like we know it today

Click to start

Page updated

Google Sites

Report abuse