Soil Abiotic Environment

• The soil environment consists of a variety of physical,

biological and chemical factors that affect the
abundance and diversity of microbes found in the
soil.
• At its basic level, the soil environment consists of a
solid and porous fraction.
• Within these fractions, a variety of chemical and
physical factors are affected by and affect microbes.
• These include, but are not limited to texture,
temperature, pH, oxygen, cation exchange capacity
and redox reactions.
• The soil environment directly affects the types
of microbes, as well as the rates of processes
they perform. For example, microbial activity
increases with temperature, which in turn
affects rates of decomposition.
• On the other hand, microbial processes
directly affect their environments as well,
contributing to the carbon and nitrogen
cycles, which are important for microbial and
plant health
• At the micro scale, bacteria and other
microbes participate in a variety of reactions
that affect nutrient cycling, pH, as well as
oxygen and CO2 content.
• At the macro scale, these processes can
change the landscape in drastic ways, assisting
in weathering of the soil and development of
soil layers.
 Soil Environment Overview
Solid Fraction

• The solid fraction of the soil consists of mineral and

organic matter, which is typically about 50% of the soil
by volume, and it has a dominant influence on heat,
water, and chemical transport and retention process.
• Most of the solid particles are derived from mineral
sources such as decomposed rocks or sediments.
• Soil organic matter (SOM) consists of all of the organic
components of a soil, including living biomass,
decomposing tissue, and fully decomposed tissue
called humus.
• The rate and pathway of carbon
decomposition and SOM formation directly
affects the carbon cycle . Texture can also
influence chemical properties such as cation
exchange capacity (CEC).
• Finer textured soils with high clay content will
have great CEC than soils with low clay
content.
• Cation exchange capacity (CEC) is
the total capacity of a soil to hold
exchangeable cations.
• CEC is an inherent soil
characteristic and is difficult to
alter significantly.
• It influences the soil's ability to
hold onto essential nutrients and
provides a buffer against soil
acidification.
Soil Pores
• Soil pores consist of the air and water filled fractions of the
soil, and together they make up about 50% of the soil by
volume.
• Pore space is largely determined by size and arrangement of
aggregates and affects the movement of water, air, and
organisms in soil.
• Soil pores are typically classified based on size:
• Macropores ( >75µm)
• Mesopores ( 30-70µm)
• Micropores ( 5-30µm)
• Ultramicropores (0.1-5µm)
• Cryptopores ( < 0.1µm).
• The air filled pores of the soil typically have a similar
distribution of gases as the atmosphere above the soil,
with slightly lower oxygen and slightly more CO2 due to
the respiration of microorganisms.
• The soil atmosphere consists of about 18-20% oxygen near
the surface, which decreases with depth. CO2 is around
1%, and N2 is about 78% of the soil air filled pore space.
• Oxygen content will be lower when available carbon is
high (demand for high O2 to utilize carbon).
• Soil that is high in clay content and/or compacted may
have trouble exchanging gases to the atmosphere.
• Soil air generally has a very high moisture
content when compared to the atmosphere
(~100% unless the soil is very dry).
• The amount and composition of air in a soil is
largely determined by the water content in the
soil.
• The main source of soil water is rainfall and
overland flow.
• The amount of water that enters the soil is a
function of soil structure and texture. Water
moves in soil through mass flow and capillary
action.
• The water in soil is often called the soil
solution, which can move nutrients from
the surface through the soil column.
• The water fraction of the pores is typically
between 20% to 30% but can vary
depending on precipitation, soil texture,
and soil structure.
• The water content of a soil influences gas
exchange, nutrient movement and
concentrations of nutrients, and buffers
the temperature of the soil.
Soil Aggregates & Structure
• Soil aggregates are groups of soil particles that
bind to each other more strongly than to adjacent
particles.
• The space between the aggregates provide pore
space for retention and exchange of air and water.
• Aggregation affects erosion, movement of water,
and plant root growth.
• Polysaccharides produced by soil bacteria, and
humic substances and hyphae produced by fungi
improve aggregation.
• Soil structure is the arrangement of primary soil
particles into aggregates which describes the
arrangement of the solid parts of the soil and the pore
spaces between them.
• Soil structure has a major influence on water
movement, SOM leaching, and gas exchanges of the
soils.
• The water movement, affected by structure can bring
SOM in the surface to deep inside the soil.
• Soil with high clay content and/or poor structure, may
have reduced infiltration and will cause run off, erosion
and surface crusting. This can cause nutrient loss and
increase the potential of desertification.
 Physical & Chemical Factors that Control
Biological Activity in the Soil
Texture

• Soil texture is defined as the distribution of sand (0.05-2.0

mm), silt (0.002-0.05mm), and clay (< 0.002mm) in soil.
• Soil texture indirectly influences properties such as: water
holding capacity, porosity, aeration and nutrient availability.
• Clay particles have a very high surface to volume ratio, which
makes them very chemically active and have high nutrient
availability.
• Due to the adhesion of water, soils high in clay will also have a
high water holding capacity.
• Soils with a high clay content will often have a very active
microbial community, especially in areas of the rhizosphere.
Temperature
• Soil temperature changes with depth: the surface
soil (~0-20cm) is highly affected by the solar
radiation. Moving deeper (~below 27cm)
temperatures are very stable over time
• This is because heat moves in soil mainly by
conduction, which does not allow much heat to
reach deep in the soil profile.
• Soil temperature is also affected by the soil color,
soil cover, and the water content of the soil.
• A darker soil can absorb more heat compared to
lighter color soil.
• A dry soil is more easily heated than a wet one
due to the higher heat capacity of water.
• Heat moving in soil is analogous to the
movement of water. Generally, the higher the
temperature, the more active microbes are,
with microbial activity typically doubling with
a 10° rise in temperature.
• However, some bacteria thrive at very low
temperatures (psychrophiles) and very high
temperatures (extremophiles)
Microbial growth rate as a function of temperature for different types of bacteria
pH
• pH change in soils is due to both biotic and
abiotic processes. Microbes consume and release
H+ through redox reactions and fermentation.
• Abiotic processes such as rainfall can also affect
the pH of the soil.
• In areas of high rainfall, acidic soils can be
created through leaching of bases from the soil,
while more basic soils are typically located in arid
environments.
• pH affects microbial diversity because many
microbial species cannot tolerate extreme levels of
pH (high or low).
• Alterations in pH can render essential microbe
enzymes inactive and/or denature proteins within
the cells and prevent microbial activity from
occurring.
• However, there are microbes that can withstand
extreme pH environments.
• At pH below 5, fungi and acidophilic bacteria have
a competitive advantage over other bacteria that
thrive at a more neutral pH.
• pH can also affect the availability of nutrients in
this soil.
• Below a pH of 5, essential plant nutrients such as
phosphorous, calcium and magnesium are not
available.
• Low pH can also cause aluminum (Al3+) to be
released from soil minerals.
• Al3+ in soil solution is not only toxic to plants and
microbes, it can combine with OH- ions causing
the free H+ ions to lower the pH further.
• The effect of pH on nutrient availability and
microbe survivability can be seen :
Nutrient availability and microbial diversity as a function of pH
Oxygen
• Oxygen (O2) is a very important component of the
productivity of both microbes and plant roots.
• Oxygen has a very high electrical potential (Eh),
meaning that it has a lot of potential to produce
energy when used as an electron acceptor in an
oxidation-reduction reaction.
• An example oxidation-reduction reaction can be seen
in equation 1, where glucose is being oxidized, and
oxygen is being reduced.

6O2+C6H12O6→6CO2+6H2O
• The amount of oxygen available in a soil depends
on a number of factors, including soil porosity,
water content, and consumption by respiring
organisms.
• If soil pores are large and interconnected, oxygen
can flow easily. However, even in a well aerated
soil, micro-aggregates may contain anaerobic
zones in which oxygen flow is very limited.
• In a flooded soil environment oxygen content will
be very limited because oxygen diffuses about
10,000 times more slowly through water than
through air.
• In areas where oxygen is not present, soil
microbes may use alternative electron
acceptors such as nitrate, manganese, iron,
sulfate, and carbon dioxide.
• An example of the result of the use of an
alternative electron acceptor can be seen in
figure : Without oxygen, bacteria can
potentially use iron as an electron
acceptor, reducing it, and
creating the blue/gray soil in the
photo. The mottled red areas are the
result of oxygen getting in (perhaps
through root canals) and oxidizing
the iron.
Cation Exchange Capacity
• Cation exchange capacity (CEC) is the ability of
a soil to hold and exchange cations.
• The amount of CEC in soil is highly dependent
on the texture and organic matter of the soil.
• The high surface area and negative charge of
clay allows it to bind and exchange with soil
solution, which contains cations that are
important for plant and microbial health.
• For many soils, especially those with low clay
and organic carbon content , CEC is dependant
upon soil pH.
• As pH decreases , an increasing amount of H+
ions are attracted to negatively charged clay
particles and functional groups in SOM. This
causes other cations, that were attached to
these surfaces to fall off into the soil solution.
• CEC will increase as pH increases as less
cations are being pushed out by H+ ions.
Redox Reactions
• Reduction-oxidation (redox) reactions are
chemical reactions in which reactants experience
a change in oxidation number (which means these
reactants either gain or lose electrons) .
• Many reactions in the soil involve the gain or loss
of electrons, obtaining or releasing energy.
• Redox reactions are important in the soil, because
microbes obtain energy through redox reactions
for their metabolism, and the redox state can also
determine the microbial processes that will occur.
• Redox reactions include anabolism and catabolism
process, both of which play important roles in
microbial metabolism.
• Anabolism is the biosynthesis of cellular components,
linked to energy requirements, while catabolism is the
the biochemical processes leading to breakdown of
organic substances, linked to energy production.
• For example, the photosynthesis and respiration
processes are the coupled reactions in the soil, where
plants required energy from light and reduce carbon
dioxide to glucose, which then be used by microbes in
the soil as the energy for their metabolism.
Salinity

• Soil salinity refers to the salt content in the soil. The

concentrations and types of ions in solution in the soil
can cause modifications in the dispersion of the clay
fraction, degrading the original soil fraction.
• The sodium ion, being monovalent, increases the width
of the diffuse double layer on the surface of the clays,
reducing the attractive forces between them with a
consequent increase in particle dispersion.
• The consequence of this dispersion of the clay is also
shown by a reduction in stability of the soil aggregates,
which are thus easily transported by rain or irrigation.
• Soil salinization is a big problem for soils in arid or
semi-arid regions and agricultural soils throughout
the world.
• Salts can adversely affect plant and microbial
growth, due to destruction of the soil structure
and its consequent compacting.
• The stress of high salt concentration can be
detrimental for sensitive microorganisms and
decrease the activity of surviving cells, due to the
metabolic load imposed by the need for stress
tolerance mechanisms.
Bioavailability
• Bioavailability assesses what proportion of a
contaminant present at a contaminated site is
available for uptake by organisms.
• Bioavailability processes are the biological, chemical
and physical processes that result in an organism
being exposed to a contaminant present in the soil.
• These processes are: release of the contaminant
from the solid phase, transport of the contaminant
to and across a biological membrane and,
incorporation into a living organism.
• Bioavailable molecules must cross a biological
membrane, which means the molecules have to
interact with the aqueous phase.
• Therefore, soil properties which control partitioning
between the solid phase in soil and the pore water,
such as pH, organic matter content, Eh, cation
exchange capacity (CEC), and the concentration of clay
minerals, have a significant impact on bioavailability.
• Increasing exchange sites aids the retention of
molecules in the pore water in a bioavailable form, but
molecules sorbed strongly to surfaces or in solid form
are generally not bioavailable.