Summary
Samenvatting Principles of Soil Processes (SOC 22803)
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This is a summary of the bachelor's course Principles of Soil Processes. It includes everything you need to know for the exam (reader from 2020).
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Lecture 1 Soil forming starts with a parent material, e.g. a newly deposited sediment or a fresh rock
surface. Small organisms that survive extreme conditions invade the new space until nutri-
ents start to accumulate, resulting in a dark A horizon.
Usually it takes longer for an ecosystem to establish on fresh rock surfaces as compared to
sediments: rock first needs to be broken up into smaller pieces through physical weathering.
When the pieces get smaller, chemical weathering becomes more effective. At that stage mi-
croorganisms and plants will be able to establish and soil formation will start.
Weathering processes take place because most minerals are formed deep inside the interior
of the Earth at very different physical and chemical conditions: high pressure & temp., no
presence of water, no oxygen, high pH. When such a mineral comes to the Earth surface, it is
unstable. During weathering a mineral is physically and chemically adjusted to new equilib-
ria. Primary minerals weather into secondary minerals near the Earth surface.
Types of physical weathering:
o Pressure release: near surface, pressure from above will become negligible which
will cause rocks to expand in that direction -> rocks will crack parallel to the surface
which is called exfoliation.
o Decrease of temperature: changes in volume will cause random cracks.
o Daily temperature changes at surface may cause pressure differences inside
rock material which will result in cracks.
o Frost wedging: water inside pores in a rock freezes due to an increase of
volume.
o Root expansion: fine roots may grow into small cracks in rock material.
o Salt weathering: in arid environments, growth of salt crystals in small cavities may
increase cracks in rock material.
After physical weathering plants can grow in the new parent material. Plants produce bio-
mass. When plants die, they are food for many organisms in and on the soil. These pro-
cesses mess up the original parent material and create soil structure.
A soil consists of solid mineral particles (sand, clay, …), organic matter, water
and air. Based on volume, an average well-functioning soil has 40-60% mineral
matter, 2-10% organic matter, and 30-45% pore space, which is usually filled
with water and air.
In the figure, V is volume, m is mass, s is solid, w is water and g is gas. P is for
pores and t is for total.
The volume fraction of water V w is frequently called θ and is defined as:
Volume water m3
θ= ( ).
Volume total soil m3
The volume fraction of pores V p is frequently called φ (porosity):
Volume pores m3
φ= ( ).
Volume total soil m3
3
Volume gas m
The volume fraction of gas (air): φ g= ( 3 ).
Volume total soil m
3
Volume solid m
The volume fraction of solid material (mineral and organic): φ s= ( ).
Volume total soil m3
1
, The pores can be completely filled with water (saturated), completely filled with gas(dry soil)
or contain a mix of water and gas. The porosity φ equals the volume fractions water and gas.
ρd
o φ=φ w + φ g. ALSO: φ=1− .
ρs
The summation of volume fractions solid material and porosity equals 1: φ s +φ w + φg =1.
Therefore, the porosity can be expressed as: φ=1−φs .
Lecture 2
Soil particle density ( ρ p or ρ o ) is the mass per volume of individual soil particles.
o Mineral matter (clay, silt, sand) ρ p = 2.65 g/cm3 (average)
o Organic matter ρo = 1.0 – 1.3 g/cm3
o Water ρw = 1.0 g/cm3
The dry bulk density ( ρd ) is the weight of a soil (without water) per volume of the total soil:
mass of dry soil kg
ρd = ( )
volume total soil m3
o It is a frequently measured soil parameter which relates mass based observations to
soil volume and vice versa.
Soil bulk density is measured with metal rings with a precise volume (100 or 200 cm 3). The
rings are gently inserted into the soil to avoid compaction of soil inside the ring. When the
ring is excavated both sides are capped. In the lab, 1 cap is removed and the ring with sample
and 1 cap is weighted. Next, the ring is placed in the oven to dry. After emptying the ring, the
ring and cap are weighed -> soil water content at the time of sampling and the soil bulk dens-
ity can be calculated. Assuming a density of the mineral soil particles (e.g. 2.65 g/cm 3), the
porosity can be estimated as well.
When the soil volume is not known, it is easier to measure the mass of a soil sample (field
moist or dry). The mass fraction water is not the mass of water divided by the total mass of
the moist soil, but the wetness (w, gravimetric water content) is defined as the mass ratio of
mass water g
water and dry soil: w= ( ).
mass dry soil g
The wetness and the volumetric water content are related through the soil bulk density and
ρw V w ρ w ρd
the density of water: w= = θ. Or: θ= w ( ρ w = density water = 1.0 g/cm3).
ρd V t ρd ρw
Suppose a heavy rain shower leaves a water column of 250 mm on top of a
soil surface (1 m2); after penetration into a dry soil, the volumetric water
content θ of the soil is 0.25. The equivalent depth of soil water is defined as:
d w =θ d soil, where d soil is the total depth and d w and d soil have the same
units (m, cm or mm).
Mineral soil particles can be classified based on their size: soil texture or
particle size distribution. Most classification systems are based on the fine
earth fraction: the part of a soil sample that passes through a 2mm sieve.
Larger particles (>2mm) are classified as gravel or stones. The fine earth frac-
tion consists of sand(0.05-2mm), silt (0.002-0.05mm) & clay (<0.002mm).
o Clay: sticky, formable, soft, shiny surface, high plasticity.
o Silt: non-sticky, rough and floury surface after squeezing.
o Sand: cannot be deformed, feels grainy,
2
, After estimating the percentages of sand, silt and clay, the USDA texture triangle can be
used to estimate the texture class.
The Dutch texture classification focusses on soil developed in river and marine sediments
and is largely based on clay percentage.
A typical Dutch particle size class is the ‘leem’ fraction, which is defined as all mineral
particles smaller than 0.05mm (<50μm). This is equal to USDA’s clay and silt fractions. The
‘leem’ particle size fraction should not be confused with the English ‘loam’ texture class.
Lecture 3
Photosynthesis (light energy + CO2 -> reduced organic C + O2) and plant growth include:
o Uptake of solar energy and conversion into chemical energy.
o Uptake of CO2 from the atmosphere.
o Uptake of water and nutrients from the soil.
o Production of ‘reduced’ carbohydrates (sugar, starch, etc.).
Several environmental factors control photosynthesis by a single leaf:
o Light energy (climate; season length; cloudiness).
o CO2 concentration in the leaf (gas exchange through stomata).
o Temperature (increases chemical reaction rates; too high temperature = damage).
o Water pressure in the plant.
o Soil nutrient availability (nitrogen, phosphorous, etc.).
The photosynthetic rate can be expressed as the uptake of C per leaf surface (or mass) per
unit time. At ecosystem scale this is called gross primary production (GPP) which is equal to
the combined photosynthesis of all leaves above a certain ground surface (g C m-2 y-1)
o GPP: photosynthesis per surface per year.
Part of the stored carbohydrates are used by the plant itself for physiological processes.
These oxidation processes produce CO2 and are collectively called plant respiration (Rplant).
o Respiration: reduced organic C + O2 -> release of energy + CO2
The carbohydrates that remain in the vegetation are referred to as
net primary production (NPP). NPP = GPP – Rplant (g C m-2 y-1)
There is a tight relationship between GPP and NPP at ecosystem scale.
About half of total photosynthetic productivity (GPP) is used by the
plants themselves (Rplant). The remaining productivity (NPP) is alloc-
ated to above and belowground plant parts. The NPP accumulates
into above and belowground plant biomass.
o Ratio of above and belowground biomass varies per biome.
Grassland ecosystems generally have relatively more belowground biomass as com-
pared to forests.
Next to annual NPP, part of the living biomass will die, which is called turnover (y-1). This in-
cludes leaf senescence and fine root turnover.
Above and belowground biomass turnover is input to litter layers and soil.
Just before plant senescence, plants resorb soluble nutrients from leaves into the stem.
Aside from these N, P and K-rich water soluble components, fresh litter has about the same
chemical composition as the original plant tissue.
3
, Carbohydrates in litter are present in various forms. Large organic molecules (hemicellulose,
cellulose) cannot be taken up directly by micro-organisms -> first need to be broken down.
Micro-organisms make extracellular enzymes that can catalyse specific chemical reactions.
Proteins are also too large to be taken up directly -> proteases (enzymes) catalyse the
breakdown of proteins into smaller polypeptides and amino acids. Amino-N is an im-
portant N-source to micro-organisms. Surplus amino-N is mineralised into inorganic
N, which can be taken up by plants. Whether all N is taken up by micro-organisms (N
immobilisation) or some inorganic N becomes available for uptake by plants, de-
pends on the C:N ratio of litter.
Generally, C:N ratios of litter are higher than C:N ratios of soil. So, relatively more C
is lost as compared to N when litter is taken up in the soil.
Organic acids are easily decomposed. Fats are less decomposable. Lignin, pigments,
waxes and resins are hard to decompose.
Soil biomass is defined as the mass of all organisms in a given volume or mass of soil.
Microbial biomass may be estimated by several methods:
o Extraction of adenosine triphosphate (ATP) – specific protein related to total micro-
bial biomass.
o Substrate-induced respiration (SIR) – measurement of biological activity when all or-
ganisms are active (no food limitation).
o Chloroform fumigation (killing all organisms) followed by extraction of organic C.
Bacteria
Soil bacteria live in water films around soil particles and in small water filled pores.
They prefer places where substrate (food) is likely to be abundant:
o Rhizosphere: root exudates and turnover of fine roots form suitable substrate.
o Macropores: flow of soil solution may supply fresh substrate.
o Interior of aggregates: decomposition of organic matter in the stabilized and protec-
ted intra-aggregate micro-environment.
They often form biofilms on particle surfaces to protect themselves from desiccation and
predation. Collectively they secrete a slime substance (mucus) to limit evaporation.
They prefer to feed on easily decomposable substrate (labile, low C:N). Can’t move or com-
bine sources of substrate from different places to match C:N ratio -> need to seize the mo-
ment once suitable substrate is available by quickly becoming active and start multiplying.
Bacteria can only transport small molecules across their cell walls -> most substrate needs to
be broken down by extracellular enzymes. Making enzymes costs a lot of energy and re-
sources -> bacteria only make them when there is a demand for C, N, P, etc.
Bacteria become inactive when substrate is exhausted (50-80% of soil bacteria are inactive).
Fungi
Most fungi are multi-cellular and form long hyphae. A mycelium is a network
of hyphae with fruiting bodies on which spores are formed.
Many fungi form symbiotic associations with plants species:
o Arbuscular mycorrhizal (endomycorrhizal) symbiosis:
Hyphae invade interior root cells of host plant.
Symbiosis with ~80% of terrestrial plant species.
Symbiosis is of mutual benefit: organic C from host plant; nu-
trients and water to the plant.
o Ectomycorrhizal symbiosis:
Hyphae form sheaths around roots of partner plant.
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