Soil solid phase (3-5)

Organic matter in soil: C cycle

Soil one of the most important C reserve on earth

Nitrogen important for soil, organism in the soil can catch it in the atmosphere and break it for the soil → fertilizer are Nitrogen already broken for the soil

OM → Source of C and energy

Organic matter composition

Composition of the OM: C (50%), H, O, N, S, P and metal cations

Changes from soil to soil, from season to season…

Content of OM in the topsoil:

Concentration vs Stock of organic C

Content*(density or area) → stock

Concentration is important but stock also

Global stock C distribution

More in the soil than in plants, more in colder places cause there are less organism

Soil OM: global fluxes and stocks

OM in soil definitions

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

Edaphon (soil biota): living organisms and roots → not part of the soil organic matter

Mineralization: complete microbial degradation to inorganic substances

Humification: formation of humus = protection of OM from further decomposition

Decomposition: breakdown of organic matter → transformation of organic residues by heterotrophic organisms leads to differentiation of the organic matter:

• Plant remains

• Microbial remains

• Mineral-bound organic substance

• Charcoal

• Dissolved organic carbon (DOC)

C/N Ratio

Indicator for the ease of decomposition of OM but also for biological activity

Mineralisation = release of CO2 while N is incorporated into microbial biomass → C/N becomes smaller → C/N ratio goes lower when you lose carbon, because Nitrogen doesn't get lost

Degradability of organic matter: the smaller the more degradable → spruce woods really degradable

Composition of OM: Plant remains

Parenchyma (basic tissue)

• Found in living green tissues (leaves, needles, fine roots)

• Cell walls mainly contain cellulose and hemicellulose

• Rich in proteins

• Low C/N ratio (< 50)

• Easily degradable

Lignified tissue

• Includes wood (xylem) and supporting tissue (sclerenchyma)

• Cell walls contain cellulose, hemicellulose, and lignin

• High C/N ratio (> 100)

• Structurally strong and resistant to decomposition

Cellulose

• Main structural component of plant cell walls

• Long chains of glucose forming strong microfibrils

• Mostly crystalline, partly amorphous

• Provides mechanical strength

• Usually associated with hemicellulose and lignin

Hemicellulose

• Cell wall polysaccharides made of different sugars

• Shorter and more branched than cellulose

• Amorphous and easily degradable

• Links cellulose microfibrils together

Lignin

• Very complex and highly cross-linked polymer

• Common in vascular and woody plant tissues

• Provides rigidity, protection, and resistance to microbes

• Very resistant to degradation (not easily broken down)

Composition of OM: Plant wax and fats

Lipids

• Mostly unbranched hydrocarbon chains

• Chemically diverse group (fatty acids, phospholipids, glycolipids)

• Key components of biological membranes

• Important for energy storage and waterproofing

• Generally more resistant to degradation than carbohydrates

Cutin

• Structural polymer forming the plant cuticle (wax layer)

• Found on the surface of leaves and stems

• Built from hydroxy fatty acids

• Provides protection against water loss and pathogens

• Contributes to plant resistance and durability

Suberin

• Cell wall component in outer tissues of woody plants

• Especially abundant in bark and roots

• Similar to cutin but made of longer-chain components

• Acts as a strong barrier to water, gases, and microbes

• Very resistant to biological degradation

Composition of OM: cellular constituent

Proteins

• Long chains of amino acids (polypeptides)

• Present in plant and microbial tissues

• Readily degradable by many microorganisms

• Important nutrient source (especially nitrogen)

• Less stable than structural compounds like lignin

Tannins

• Polyphenolic compounds

• Bind to proteins and reduce their availability

• Can slow down microbial decomposition

• Common in leaves, bark, and woody tissues

Other Cellular Compounds

• Pigments: e.g. chlorophyll

• Starch: energy storage compound in plants

Nitrogen, sulphur and phosphorus in OM

Nitrogen → Almost exclusively binding to OM in soil (95%) → First in microbial biomass, then stabilized in OM → Mostly in peptides

Sulfur: → up to 90% S in organic form, 30 - 75% as organo sulphates, rest as amino acids

Phosphorus → > 50% bound in the form of orthophosphate

Mineralization and humification

Mineralization

• Microbial breakdown of organic matter into inorganic nutrients

• Produces carbon dioxide, water, and plant-available nutrients

• Fast for easily degradable compounds (carbohydrates, proteins)

• Leads to nutrient release into soil solution

Humification

• Transformation of organic residues into stable humic substances

• Favored by resistant compounds (lignin, fats, waxes, tannins)

• Slower process than mineralization

• Contributes to long-term carbon storage in soils

Decomposition of litter

• Plant litter is decomposed by microorganisms and soil fauna

• Early phase: biochemical breakdown of simple compounds

• Initial phase: leaching and rapid microbial growth

• Crushing phase: mechanical fragmentation by soil fauna

• Final phase: enzymatic degradation, nutrient release, accumulation of resistant compounds

Key idea: Litter decomposition drives nutrient cycling and soil organic matter formation.

Biochemistry of degradation processes

Biochemistry of Degradation Processes

• Easily degradable polymers are enzymatically hydrolyzed early

  • Proteins, starch, nucleic acids, simple lipids

• Complex and resistant compounds require prior physical breakdown

  • Cellulose: degraded by specialized enzyme systems

  • Lignin: broken down via oxidative reactions

• End result: small molecules that serve as microbial food

Speed of litter degradation

Litter factors (degradability):

• N content of the substance (C/N ratio)

• Lignin content (lignin/N ratio)

• Tannin content (polyphenol/N ratio)

External factors, environmental factors:

• Heat/temperature

• Availability of H2O and O2

• pH

• Inhibitors (bactericides, fungicides)

Stabilisation of OM

Stabilisation (Humification)

• Processes that slow down organic matter decomposition

• Leads to accumulation of humus in soil

• Stabilized organic matter is older and more persistent

Stabilisation by Recalcitrance

• Delayed degradation due to molecular structure

• Primary recalcitrance: plant-derived compounds with resistant structures (litter, roots)

• Secondary recalcitrance: microbial and animal products forming resistant macromolecules

• Includes pyrogenic (black) carbon, highly resistant

Key Idea → Chemical complexity increases resistance to microbial breakdown

Old and new concept of stabilisation

Old Concept

• Soil organic matter forms large, stable humic macromolecules

• Stabilisation driven mainly by chemical condensation reactions

• Humic substances (humic acids, fulvic acids, humin) seen as real soil entities

• Molecular complexity = long-term stability

New Concept

• Soil organic matter is mostly made of small, simple biomolecules

• Stability depends on environmental protection, not molecular size

• Key mechanisms: mineral association, physical protection, limited microbial access

• Carbon persistence is dynamic and can change with conditions

Key Idea → Soil carbon is stabilized by its environment, not by intrinsic “humic” polymers

Stabilization through sorption and aggregation

Stabilisation through Sorption

• Organic matter binds to mineral surfaces (clays, metal oxides)

• Sorption reduces accessibility for microbes and enzymes

• Strong organo-mineral associations increase persistence

• Particularly important for small organic molecules

Stabilisation through Aggregation (Physical Disconnection)

• Organic matter is physically protected inside soil aggregates

• Limited access of microorganisms, oxygen, and enzymes

• Larger aggregates store carbon short- to medium-term

• Mineral-associated organic matter enables long-term storage

Key Idea → Soil carbon stability is controlled by physical protection and mineral interactions, not by molecular complexity alone

Importance of organic matter for soil

• Major nutrient source for plants (especially nitrogen, phosphorus, sulfur)

• Improves nutrient retention and gradual release

• Enhances soil aggregation and structural stability

• Reduces erosion through clay–organic matter complexes

• Increases water-holding capacity

• Influences soil temperature via light absorption

• Supports decomposition of organic pollutants

• Key reservoir for carbon storage (e.g. peatlands, permafrost, biochar)

Key Idea: Soil organic matter is essential for soil fertility, structure, and climate regulation.

Humus forms

Mull

• Most favorable humus form

• Nutrient-rich soils

• Neutral to slightly acidic

• High microbial and soil fauna activity

• Fast litter decomposition

• No distinct organic (Oa) layer

• Typical of deciduous forests and species-rich grasslands

Moder

• Intermediate between Mull and Mor

• Neutral to slightly acidic

• Moist conditions

• Moderate biological activity

• Oi, Oe, and Oa horizons present with gradual boundaries

• Common in coniferous, mixed, and deciduous forests

Mor

• Least favorable humus form

• Nutrient-poor soils

• Acidic, often very wet or very dry

• Low microbial and animal activity

• Fungi-dominated decomposition

• Thick litter layer, slow decomposition

• Sharp boundaries between Oi, Oe, and Oa

• Typical of coniferous forests and harsh environments

Key Idea:
Humus forms reflect decomposition intensity, biological activity, and nutrient availability.

Parent material → Rocks

Soils are made of organic matter and rocks from the bedrock, also called parent material.

The parent rock of a soil largely determines the soil development and the mineral content.

Rocks are classified according to their history of origin: Magmatic, metamorphic and sedimentary

Magmatic rock soil properties:

• Basalt / Gabbro → base-rich, nutrient-rich

• Andesite / Diorite → intermediate

• Rhyolite / Granite → silica-rich, nutrient-poor

• Extrusive: fine-grained, chemical weathering dominant

• Intrusive: coarse-grained, physical weathering dominant

• Key idea: More silica → fewer bases → lower soil fertility.

Sedimentary rocks:

• Clastic: formed from mechanical weathering (e.g. sandstone, shale)

• Chemical: formed by precipitation from solution (e.g. rock salt, some limestones)

• Organic: formed from accumulated biological material (e.g. coal, some limestones)

• Key idea:
  Sedimentary rocks form from weathering, precipitation, or biological accumulation.

Lithosphere cycle

Most common minerals in earth crust and soil

Most commons elements in earths crust → O and Si → SiO2 most common mineral

This is also true for Soils

Primary → comes from the rock → broken down rock goes into the soil

Secondary → chemical composition changes

Minerals: silicates

Origin

• Main source of secondary (pedogenic) minerals

• Formation depends on temperature, pressure, cooling rate, and chemistry

• Crystallize in sequence from high to low temperature

  • Early: olivine, pyroxene

  • Late: feldspars, quartz

Silicate Structures

• Isolated tetrahedra → olivine

• Single chains → pyroxenes

• Double chains → amphiboles

• Sheets (layers) → micas, clay minerals

• Framework → feldspars, quartz

Properties

• Structures linked by oxygen bridges

• Negative charge attracts metal cations

• Isomorphic substitution creates chemical diversity

• Structure controls stability and weatherability

Key Idea → More complex silicate structures are more stable and weather more slowly

Micas (sheet)

Types

• Muscovite: light-colored mica

• Biotite: dark-colored mica

Structure

• Sheet (layer) silicates with a 2:1 structure

• Layers held together by potassium ions

Importance for Soils

• Important source of potassium

• Easily weathered minerals

• Biotite weathers faster than muscovite

Occurrence

• Magmatic rocks: mainly biotite

• Sedimentary and metamorphic rocks: mainly muscovite

Key Idea → Micas are nutrient-bearing, easily weatherable minerals important for soil fertility

Tectosilicate (3D) → Quartz and Feldspar

Quartz

• Pure framework silicate

• Very resistant to weathering

• Common as sand and silt in soils and sediments

• Does not supply nutrients

• Hard, irregular fracture surfaces

Feldspars

• Framework silicates with aluminum substitution

• Charge balanced by potassium, sodium, or calcium

• Most abundant minerals in magmatic rocks

• Easily weathered compared to quartz

• Smooth cleavage surfaces

Relevance for soil

• Feldspars release nutrients during weathering

• Weathering forms secondary (clay) minerals

• Quartz accumulates due to high resistance

Key Idea → Quartz persists; feldspars transform and feed soils

Weathering

• Weathering alters rocks and primary minerals

• Occurs at the interface with atmosphere, biosphere, and hydrosphere

• Transforms primary minerals into secondary minerals

• Produces clay minerals, oxides, and hydroxides

• Key process linking lithosphere to soil formation

Key idea:
Weathering is the bridge between rocks and soils.

Physicall weathering

• Mechanical breakdown of rocks without chemical change

• Reduces grain size and increases surface area

Main Processes

• Pressure release: cracking after erosion of overlying rock

• Gravity: impact and crushing

• Temperature changes: differential expansion of minerals

• Frost weathering: ice expansion widens cracks

• Salt weathering: crystal growth in pores and fractures

• Biological pressure: root growth

Transport & Abrasion

• Water: rolling, abrasion, scouring

• Wind: saltation and suspension of fine particles

• Ice: transport and abrasion at glacier base

Key Idea:
Physical weathering fragments rocks and prepares material for chemical weathering and soil formation.

Chemical weathering

• Chemical transformation or dissolution of minerals

• Driven by water, acids, and biological activity

• Continuous process because products are removed by water

Main Processes

• Hydration

  • Water molecules enter mineral structures

  • Weakens crystal bonds and promotes dissolution

  • Especially important for highly soluble minerals (e.g. salts)

• Hydrolysis / Protolysis

  • Reaction of minerals with acidic water

  • Carbonic acid from CO₂-rich water plays a key role

  • Very important for carbonate dissolution and silicate alteration

• Complexation

  • Organic acids released during decomposition bind metal ions

  • Increases mobility of metals such as iron and aluminum

  • Enhances mineral dissolution and element transport

• Oxidation

  • Reaction with O₂

  • Fe²⁺ → Fe³⁺, S²⁻ → SO₄²⁻

  • Produces H⁺, lowers pH

  • Forms Fe oxides/hydroxides (goethite, hematite)

• Protolyis (Hydrolysis) of Silicates

  • Reaction of silicates with H⁺ (water / carbonic acid)

  • Breaks Si–O–Al bonds

  • Releases K⁺, Na⁺, Ca²⁺

  • Forms clay minerals (e.g. kaolinite) + silica

• Weathering of Silicates – Overview

  • Early stage: loss of interlayer cations (e.g. K⁺), structure partly preserved

  • Advanced stage: complete lattice breakdown → new secondary minerals

  • Products: clays, oxides, hydroxides

Weathering Products

• Weathering residues (solid remains)

• Weathering solutions (dissolved ions transported away)

Key Idea → Chemical weathering transforms primary minerals and releases elements, driving soil formation and nutrient cycling.

Weathering stability of minerals

Water solubility → Easily soluble salts < gypsum < calcite < dolomite

Structure of the silicates → Island < chains < leaf < framework (feldspars < quartz)

Fe(II) content (oxidizability) → Biotite < Muscovite

In general → Olivine < Pyroxene < Amphibole < Biotite < Plagioclase < Muscovite ≈ Orthoclase < Quartz

Pedogenesis image

Secondary minerals

• Formed after partial or complete dissolution of primary minerals in the parent material

• Main products:

  • Clay minerals (from layer silicates, e.g. micas)

  • Fe, Mn and Al oxides and hydroxides

  • Secondary carbonates and salts

These secondary minerals form in soils during pedogenesis.

Clay Mineral

Origin

• Formed from silicate weathering

• Structure similar to mica (tetrahedral + octahedral layers)

• Doesn’t change structure → Still tetrahedra/octahedra but with different minerals and charge

• Particle size < 2 µm (clay fraction)

Identification

• Formula unit: smallest repeating crystal unit

• Basal spacing: distance between two consecutive layer units

Structural Types (classification)

• Based on Si tetrahedra / Al octahedra stacking:

  • 1:1 (e.g. kaolinite)

  • 2:1 (e.g. smectite, illite)

  • 2:1:1 (e.g. chlorite)

  • Special forms: tubes, spheres

• Different interlayer compositions (K⁺, water, cations, OH layers)

Isomorphic Substitution

• Tetrahedral: Si⁴⁺ → Al³⁺

• Octahedral: Al³⁺ → Mg²⁺ or Fe²⁺

• Creates permanent negative layer charge

Charge Compensation

• Exchangeable cations in interlayers

• Positively charged Al-hydroxide layers

Two layer clay mineral → Kaolinite

• Structure: 1 tetrahedral + 1 octahedral layer (1:1)
  → layers linked by H-bonds, no interlayer

• Basal spacing: ~0.72 nm

• Formula: Al₂(OH)₄Si₂O₅

Origin

• Forms in Si-poor, strongly weathered (tropical) environments

• End product of silicate weathering

Properties

• White, non-expanding, no swelling/shrinking

• Used for ceramics (porcelain)

Soil relevance

• No nutrients in structure

• Very low CEC (little isomorphic substitution)

• Typical of low-fertility soils

 

Everything that could leach or so has happened, really ancient, not fertile, really deep

Three layer clay minerals (Illite, Smectite, Vermiculite)

Illite (2:1)

• Derived from mica

• Basal spacing ~1 nm

• K⁺ fixed in interlayer → almost no swelling → K keeps layers together, not exchangeable

• Important K source for soils

Smectite (2:1)

• Often from basic igneous rocks

• Expandable (1–2 nm)

• Strong swelling/shrinking

• Interlayer: hydrated, exchangeable cations

• High CEC, high water retention

• Hydrated cations in the middle

• Available for plants, really fertile

Vermiculite (2:1)

• Forms from biotite/muscovite

• Expandable up to ~2 nm

• Strong water retention

• Interlayer cations partly fixed, partly exchangeable

Four layer clay mineral (Chlorite)

Chlorite (2:1:1 clay mineral)

• Primary and secondary clay mineral

• Structure: 2:1 layers + hydroxide interlayer (Mg-, Al-, or Fe-hydroxides)

• Not expandable

• Very low to no cation exchange capacity (CEC)

Layered clay minerals

• Kaolinite (1:1)
  No true interlayer; layers held by H-bonds (O–H···O) → non-expandable, very low CEC → no shrink or swell

• Illite (2:1)
  K⁺ fixed in the interlayer → strong layer bonding, no swelling, moderate CEC → hold by K

• Smectite / Vermiculite (2:1)
  Hydrated, exchangeable cations + H₂O in the interlayer → expandable, high CEC → lot’s of exchange, swelling and shrinking

• Chlorite (2:1:1)
  Mg/Al hydroxide interlayer → rigid structure, non-expandable, very low CEC.

Further clay minerals

Mixed layers → transitions between layered forms, more reactive than pure minerals

Examples → Imogolite and Allophane

Clay mineral transformation

• Phyllosilicates (layer silicates)—especially micas—are the main precursors of clay minerals.

• Physical weathering opens layer edges and removes interlayer K⁺, which is replaced by larger Ca²⁺ and Mg²⁺.

• This drives the transformation sequence mica → illite → vermiculite / smectite, and with further alteration can lead to kaolinite or chlorite.

Short summary clay minerals

• Important secondary new formations in the soil (see «Weathering» for details)

• They are subject to constant change, but their stability is usually significantly higher than that of primary silicates

Importance for soil

• Clay minerals are components of the finest fraction of the soil, < 2 µm, = clay fraction

• Storage for nutrients whose leaching is prevented

• Microstructure makers in soil: particles adhere to each other, bind to themselves and to other coarse particles, expand and shrink etc..

Oxide and hydroxide of Fe, Al, Mn

• They are final products of weathering of silicate minerals.

• Weathering releases Fe, Al and Mn ions into the soil solution.

• These ions are oxidised and then precipitate.

• This forms iron, aluminium and manganese oxides and hydroxides.

Aluminium hydroxides: gibbsite

• An aluminium hydroxide mineral formed during strong weathering.

• Colourless to white.

• Built from Al-octahedra (layered structure).

• Forms only when silicon is very low in soil water.

• Typical of intense weathering, especially in tropical regions.

Iron oxides and hydroxides

Iron oxides & hydroxides (overview)

• Form during weathering of silicates when Fe²⁺ is released and oxidized to Fe³⁺

• Give soils yellow–brown–red colours

• Stable in oxic (aerobic) conditions, dissolve under reducing (anaerobic) conditions

• Very important for nutrient and trace-element binding

Main types

• Hematite (α-Fe₂O₃)

  • Red colour

  • Forms in warm, dry, well-aerated conditions

  • Typical of tropical and subtropical soils

• Goethite (α-FeOOH)

  • Yellow–brown colour

  • Forms at moderate temperatures

  • Very stable, common in temperate soils

• Lepidocrocite (γ-FeOOH)

  • Orange colour

  • Forms under reducing / waterlogged conditions

  • Metastable, often local and temporary

• Ferrihydrite (poorly crystalline Fe oxide)

  • Brown

  • Very young, poorly ordered (“rust”)

  • Forms during rapid oxidation, very reactive

• Schwertmannite

  • Yellow–brown

  • Forms in acidic, sulphate-rich waters

  • Typical product of pyrite (FeS₂) weathering

Mn oxides

Manganese (Mn) oxides

• Form during weathering of silicates

• Mn²⁺ is oxidized to Mn⁴⁺, precipitating as Mn oxides

Main form

• MnO₂

  • Black colour

  • Forms black mottles/concretions in hydromorphic soils

  • Immobile under aerobic conditions

Redox behaviour

• Under reducing and acidic conditions:

  • Mn oxides dissolve

  • Mn²⁺ becomes mobile and colourless

• Acid soils and permanently waterlogged soils → low Mn content

Soil importance

• Bind trace elements under aerobic conditions

• Release trace elements under anaerobic conditions

• Behaviour very similar to Fe oxides

Oxides: indicators of soil formation

• Goethite (FeOOH)

  • Forms in humid, wet climates

  • Indicates moderate weathering

  • No hematite → conditions too wet

• Hematite (Fe₂O₃)

  • Forms in hot, tropical climates

  • Indicates intense weathering

  • Often together with goethite

• Fe and Mn translocation (shifting)

  • Occurs in acidic, wet soils (e.g. Podzols)

  • Fe and Mn are mobilized under reducing conditions

  • Bleaching = loss of Fe/Mn

  • Accumulation horizons = re-precipitation under oxic or pH change

Salts

Carbonates

• Main types:

  • Calcite (CaCO₃): white, reacts with HCl → CO₂

  • Dolomite (CaMg(CO₃)₂): less soluble, Mg source

• Origin:

  • Primary minerals (e.g. limestone)

  • Secondary carbonates from weathering

• Soil importance:

  • Neutralize acids (CO₂, organic acids)

  • Buffer soil acidification

  • Increase soil pH

Sulphates & Phosphates

• Sulphates (from sulphuric acid):

  • Anhydrite: CaSO₄

  • Gypsum: CaSO₄·2H₂O

• Phosphates (from phosphoric acid):

  • Apatite: main primary P mineral

  • Vivianite, Strengite: secondary Fe–phosphates

• Soil importance:

  • Phosphates = key P source for soils and biosphere

Grain size

• Grain size = particle size of soil (also called texture).

• It describes how soil particles are distributed by size.

Why grain size matters

• Controls porosity (pore size and distribution)

• Regulates water and air movement

• Affects transport and retention of substances (filter function)

• Influences biological activity

• Controls erosion risk

• Important for soil structure (microstructure)

Basic soil fractions

• Fine earth: particles < 2 mm

• Soil skeleton (coarse fraction): particles > 2 mm

Typical characteristics

• Coarse fraction: mostly rounded grains, mainly SiO₂ (quartz)

• Fine fraction: mostly flat/leafy particles, rich in mica and clay minerals

Soil skeleton

Fine earth fraction

It's used the logaritmic scale, and if you take 2 (the border between gravel and sand) then it's 63 the middle on the logaritmic scale

Mineral content in the grain fractions

• Quartz: mainly sand (also silt)

• Primary silicates (feldspars, pyroxenes, etc.): sand → silt

• Micas: mainly silt (can weather to clay)

• Clay minerals: clay (< 2 µm)

• Fe/Al/Mn oxides & hydroxides: clay (very fine particles/coatings)

Rule of thumb:
Sand = quartz

silt = a bit of everything

clay = clay minerals and others

Grain size determination in the field

Finger test

• Sand: gritty, loose, not sticky, no ribbon

• Silt: smooth–floury, weak cohesion, no ribbon

• Clay: sticky, plastic, shiny, forms long ribbon

• Loam: intermediate; slightly plastic, short ribbon

Lab grain size determination

• Sieve < 2 mm (fine soil only)

• Remove binding material (salts & organic matter)

• Measure with laser diffraction

• Smaller particles → stronger laser scattering

Grain size triangle

Grain size and soil functions

Physical effects

• Sand: drains fast, low water storage

• Silt: best water available to plants

• Clay: slow drainage, high water storage (often stagnant)

Chemical effects

• Sand: few nutrients, low buffering

• Clay: many nutrients, high buffering

Pollutants

• Finer grains (silt–clay) retain pollutants more than sand