Soils I - Part 2 - The Solid Phase

Organic matter is humus in a broad sense: all dead plant and dead substances in and on the mineral soil and their organic transformation products.

Edaphon (soil biota): living organisms, living roots (does not belong to the soil organic matter)

Complete microbial degradation to inorganic substances → when organic material becomes inorganic.

formation of humus = protection of OM from further decomposition (stabilisation of carbon in the soil)

Decomposition is the breakdown of organic matter into smaller molecules. Transformation of organic residues by heterotrophic (= organisms that need organic matter to survive/ feed on) organisms leads to differentiation of the organic matter (e.g. plant remains, microbial remains, mineral-bound organic substance (charcoal), dissolved organic carbon (highly reactive but stored in water).

The C/N ratio is an indicator for the level of decomposition of the OM and for biological activity. It is based on the finding that through mineralisation CO₂ is realeased while N is incorporated into the microbial biomass (and then the OM). Consequnetly the C/N ratio becomes smaller over time. Typically the smaller an organic matter is, the better it is degradable i.e. Mushroom mycelium (15-19), grass (18-25), spruce wood like pine needles (100-400).

1. Parenchyma tissue (basic tissue): is living green tissue, e.g. leaves, needles and fine roots (greenish mush/ fleshy part between the two outer layers of the leaf). It is made up of cellulose (what we make paper of, strands of glucose), hemicellulose (chain of sugars that are not glucose cell walls) and Proteins. Its C/N ration is < 50.
2. Lignified tissue (very hard material, due to lignin): this is made up of a wood part (xylem), supporting tissue (sclerenchyma) and a lignified cell wall made from cellulose, hemicellulose and lignin. Its C/N ratio is > 100 (much harder to degrade).

Different substances are either directly made inorganic (mineral substances, carbohydrates) or are first turned into humic substances (lignins, N-containing substances, fats, tannins and waxes). These processes usually reach an equilibrium. Humification is stabilized over a certain period of time and then goes back into the atmosphere as CO₂.

1. Preliminary phase of decomposition: Biochemical reactions of substances produced by the plant (hydrolysis and oxidation processes by tissue enzymes). This happens in the plant and not on the soil.

• Degradation of chlorophyll → autumnal discoloration (degraded by cold)
• Starch → Sugar
• Protein → amino acids

2. Initial phase

• Hydrolysis and oxidation of high polymeric compounds
• Leaching of water-soluble components (e.g. sugar, amino acids)
• Strong increase of microorganisms that live from the re- leased substances

3. Crushing phase

• Litter is partly bitten, partly eaten and modified by the macrofauna, and is excreted again in modified form
• Incorporation into the soil by earthworms, enchytraeids and arthropods = accessibility for mesofauna (collem- bola, mites, nematodes)

4. Dismantling and conversion phase

• Enzymatic cleavage of the organic fragments
• Formation of simple inorganic components like CO₂, H₂O, NH⁴⁺, NO3-, PO₄^2- (mineralization)
• Relative enrichment of hardly degradable compounds (e.g. tannins)

Easily degradable polymers like proteins, starch, ribonucleid acids and polar lipids are hydrolized in the initial phase. The more complex substances need to become subject to physicial degradation before they can be broken down by enzymes. 

Internal Factors

• N content of the substance (C/N ratio)
• Lignin content (lignin/ N ratio)
• Tannin content (polyphenol/ N ratio)

External Factors

• Heat/ temperature
• Availability of H2O and O2
• pH (the soil in forests are acidic, which is why the microorganisms cannot work under perfect conditions)
• Inhibitors (bactericides, fungicides)

Stabilization is a general term for processes and mechanisms that slow down the degradation of OM in soil and thus forms humus. In other words it is the accumulation of OM in the soil with slowed degradation (i.e. lower pH in forests and moors). Additionally stabilized OM is older than fresh organic matter.

Stabilization happens through...

... sorption: Once adsorbed to the surface of phyllosili- cates or neutral minerals, it is much harder for microorganisms to extract the nutrients.

... aggregation: Primary particles will be stabilized and shrink together by the organic compounds. These compounds make it harder for microorganisms to get to the organic matter and form CO2.

... physical disconnection (Fig. 63): The spatial location of OM in the soil influences the accessibility for organisms and enzymes, e.g. in aggregates.

... sorption and aggregation: The more molecules and nutrients that are either built into aggregates or bound to the mineral surface, the longer Carbon dioxide is stored in the soils.

... functional diversity:

a) molecular diversity: if only one type of organic substance is available (e.g. monoculture), only one type of microorganism will grows, which will be highly specialized in the degradation of that specific organic substance. If there are many different source of organic matter in the soil and there also add some difficult compound to degrade, numerous types of microorganisms will be in competition with each other and that will reduce the capacity of the microorganisms to release CO2. The more diverse the organic matter input is, the less carbon will be emit- ted.

b) spatial diversity: if everything is situated in the same pore size of the soil, microorganisms will be able to easily access the nutrients. If there is organic matter in different pore sizes, it is much harder for microorganisms to have access to it.

c) temporal diversity (can go in both directions): Too much temporal variability (hot/cold, wet/dry), the microorganisms will have a hard time to adapt and therefore not be able to flourish as much. At the same time it is possible that through temporal variability nutrients are released and made available to microorganisms more easily. Following this, they would be able to flourish more and release more CO2.

Organic matter is so important for soils because it...

• is a nutrient source for plants (N, P and S)
• has exchange properties and can both bind/adsorb cations and attach itself to clay minerals; gradual release of (nutrient) cations
• promotes aggregation of clay particles (clay-humus complexes): stabilizes aggregates, thus reducing erosion
• has a high water-binding capacity (3-5 times its own weight)
• has the capacity to adsorb light (soil temperature)
• it catalyzes organic pollutant decomposition
• functions as a carbon storage
  • Biochar/Terra preta
  • Permafrost carbon
  • Peat and moors

Rocks are classified according to their history of origin.

• Rhyolite
• Granite
• Basalt

These form through the crystallization of melted silicates on the earth's surface (Intrusive rocks/ plutonic rochs are slow cooling and extrusive rocks/ volcanic rocks are fast cooling). The soil development depends on the way of crystallization of the mineral.

• Gneiss
• Slate
• Phyllite

These rocks consist of already produced minerals and are formed through high temperatures (~200°C (rock does not melt)) and very high pressure. They are formed in the depths of the earth's crust (not on the surface).

• Breccia
• Conglomerate
• Claystone

These rocks cover 75% of the earth's surface but  are only a very small part of the lithosphere. They are formed through the mechanical weathering of debris (breccia, conglomerate, sandstone, shale), through precipitation (rock salt, iron ore, flint, dolomite*, limestone*) or accumulation of plant or animal debris (dolomites*, limestones*).

* some types of xx

There is no sharp boundary between diagenesis and metamorphism.

Diagenesis: the process that describes physical and chemical changes in sediments first caused by water-rock interactions, microbial activity and compaction after their deposition. The increase of pressure and temperature only starts to play a role as sediments get buried much deeper in the Earth's crust.

Metamorphosis: occurs at higher temperatures and pressures than diagenesis. 

(source: Wikipedia)

Things are always evolving and changin. When living things die, they can become sediments. Diagenesis makes sedimentary rock from loose materials which then either build soil, go through metamorphosis again or sinks down, melts and becomes magma.

properties: homogenous components of the earth's crust in terms of physical and chemical properties

composition: solid chemical compounds such as salts, oxides, hydroxides. They occur in pure form.

structure: with a specific crystal structure or without a crystal structure (= amorphous minerals)

importance: important soil components, starting products for weathering and the formation of secondary minerals

47% Oxygen, 27% Silicone (Si), 8% Aluminum, 5% Iron, 5% Calcium, 2% Magnesium, 2% Sodium, 2% Potassium, Other elements

Silicates (SiO₄) and Silica (SiO₂; also known as quartz) mainly originate from magmatic rocks (80%). They are the most important chemical (= base unit) for the building of secondary/ pedogenic minerals. They come in different shapes and sizes (isolated, chained/ banded, tetra-/ octahedral layers, etc.) which depends on temperature, pressure, cooling rate and chemical composition.

Silicates connect to other molecules via oxygen bridges. Together they build bands, layers and chains. Because the molecule is negatively charged, it also attracts positively charged ions like K⁺, Na⁺, Al³⁺, Fe^2/3+, Mg²⁺ and Ca²⁺. Because of the charge there can be isomorphic substitution and e.g. Al³⁺ takes the place of Si⁴⁺. One extra charge then needs to be compensated by other cations entering the structure. 

Olivine (Gg, Fe)₂SiO₄

• greenish
• easily weathered due to structure
• no oxygen bridges: silicates are loosely bound via Mg²⁺ or Fe²⁺.
• no isomorphic substitution
• nutrient-rich (cations)

Characteristic: networking via O atoms in corners of the tetrahedrons.

Mineral groups

• Pyroxene: Chain silicates (Ca,Mg,Fe,Al,Ti)₂(Si,Al)₂O₆ → representative; Augite (very sensitive to weathering, easily builds on volcanic rock, good nutrient supplier to soil)
• Amphibole: Band silicates Ca₂(Mg,Fe,Al)₅(Si,Al)₈O₂₂(OH)₂ → representative: Hornblende

1. flat 2D structure
2. aluminum (octahedral structure) is not an isomorphic substitution (→ negative charge)
3. the negative charges in the structure are stabilized by the inclusion of potassium (K⁺)
4. layers can bind together to form a specific structure
5. Example minerals in this group: Muscovite (light mica) and Biotite (dark mica)

Importance for soils

• K content 5-9%
• easily weatherable, biotite weathers more easily than muscovite

Occurrence

• Magmatic rocks: Mostly biotite
• Sediments and metamorphic rocks: Mostly muscovite