SWAE 3411

Environmental Soil
Microbiology

16-Feb-20 Dr. B Shaharoona 1

Soil as a Microbial Habitat

16-Feb-20 Dr. B Shaharoona 2

Factors that influence microbial distribution in soil

Intrinsic factors Extrinsic factors

• Persistence mechanisms • Organic matter
(spores) • Soil structure
• Size • Soil atmosphere
• Motility • Precipitation and soil water
• Structural features • Soil pH
• Biochemical capacities • Soil Temperature
• Soil oxidation-reduction
potential
• Solar radiations
• Wind and relative humidity

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 Soil as a Microbial Habitat
• Soil physical characteristics
• Soil chemical characteristics
• Soil abiotic environmental factors

There is a need to
understand “soil” in order
to understand soil
microbiology. This concept
Is not an easy one.
Soil Porous Media
• Mineral Particles (sand + silt + clay)
• Organic Matter
• Pore Spaces
• water
• air

Organic Matter
5%
Air Mineral
25% Particles
45%

Water
25%
Soil Structure
Aggregation of sand, silt, and clay particles

Structure affects:
Macroporosity
Infiltration
Aeration
 Formation of soil structure
• Growth of roots and movement of organisms
create pores and aggregates
• BIOTURBATION (https://www.youtube.com/watch?v=Mxp1nnrUG0Q)
• Soil organisms break down organic residues,
producing glues that stabilize aggregates
• Fungi provide structural support to aggregates
• Physical and chemical processes are also involved
 Soil microbes may form microbial gums, polysaccharides,
and other external metabolites that act as glues that bind
sand, silt, and clay together into a secondary structure
called Soil aggregates or peds.
Aggregates held together by:
1. Fungal hyphae
2. Bacterial “glues”
3. Organic matter
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 Larger aggregates are often composed of an agglomeration of smaller aggregates. This illustration shows four levels in
this hierarchy of soil aggregates. The different factors important for aggregation at each level are indicated. (a) A
macroaggregate composed of many microaggregates bound together mainly by a kind of sticky network formed from
fungal hyphae and fine roots. (b) A microaggregate consisting mainly of fine sand grains and smaller clumps of silt
grains, clay, and organic debris bound together by root hairs, fungal hyphae, and microbial gums. (c) A very small
submicroaggregate consisting of fine silt particles encrusted with organic debris and tiny bits of plant and microbial
debris (called particulate organic matter) encrusted with even smaller packets of clay, humus, and Fe or Al oxides. (d)
Clusters of parallel and random clay platelets interacting with Fe or Al oxides and organic polymers at the smallest scale.
These organoclay clusters or domains bind to the surfaces of humus particles and the smallest of mineral grains.
(Diagram courtesy of R. Weil)
(a) packing pores (b) interped pores (c) ) Biopores
Texture and aggregation are also important in determining
the movement of microbial populations in in soil media.

Q = Quartz
CL = Clay
B = Bacterium
Gaseous Composition of the soil air
• Oxygen
• Atmosphere (21 %)
• Soil (upper layers) slightly below 20 %
• Soil (lower layers) less than 5 % or even
zero

• Carbon Dioxide
• Atmosphere(0.035 %)
• Soil (1-10 %)

• Other Gases
• Soil air has much higher water vapor
• Waterlogged soil may have higher CH4,
H2S, and C2H4
• N2 gas is similar in atmosphere and soil
 The process of diffusion between gases in a soil pore
and in the atmosphere. The total gas pressure is the
same on both sides of the boundary. The partial
pressure of oxygen is greater, however, in the
atmosphere. Therefore, oxygen tends to diffuse into
the soil pore where fewer oxygen molecules per unit
volume are found. The carbon dioxide molecules, on
the other hand, move in the opposite direction
owing to the higher partial pressure of this gas in the
soil pore. This diffusion of O2 into the soil pore and
of CO2 into the atmosphere will continue as long as
the respiration of root cells and microorganisms
consumes O2 and releases CO2.

Changes in the concentration of CO2 in soil air with depth

into the profile of a Haplustox soil under a tropical
rainforest in the Brazilian Amazon region. The source of the
CO2 was likely a combination of root and microbial
respiration. Although by far the highest rates of CO2
production were in the upper soil layers, gas produced
there had little distance to travel to reach the atmosphere
and many large pores to travel through. The concentration
of CO2 increased with depth because the increasing travel
distance to the surface and the much lower macroporosity
at depth greatly slowed the movement of gases, causing
CO2 to accumulate. [Data from Davidson and Trumbore
(1995)]
 Clay particles

• The high surface area exerts

important influences on many
chemical and physical properties of
soils.
• Most of the surfaces are electrically
charged.
clay particles are particularly dominant in
• Clays are where most chemical determining the physical and chemical
characteristics of the soil or porous media
reactions in soils happen.
Cation Exchange
Soil Temperature
Microbial processes are doubled by every 10oC rise in temperature
Temperature affects physical, biological, and chemical processes
occurring in soils.
Soils biological decomposition is very slow under cold temperature
Soil borne plant pathogens are
influenced by the temperature
of the soil
Destruction of toxic organic
pesticides and pollutants are
influenced by warm soil
temperatures

Effect of soil temperature on cumulative microbial respiration (CO2

release) and net nitrogen and sulfur mineralization in surface soils
from hardwood forest in Michigan
Diversity and distribution of microorganisms
• Soil Quality is the measure of the ability of soil to carry out its ecological
functions
• Microbial number usually decrease with depth

• Microbial biomass is proportional to

the number of cells
• Number of taxa – different levels
• Functional diversity
• Functional redundancy
• Diversity indexes –
• DIRECTLY proportional to number of
taxa and
• INVERSELY proportional to dominance

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 The rhizosphere
Width not to scale • Layer of soil surrounding the
growing root that is affected by the
root
• Usually a few mm wide*
• Extent depends on plant
properties; e.g.
- Root hair length & density
- Rhizodeposition (exudates etc)
- Nutrient uptake versus supply

* ‘Mycorrhizospheres’ can extend

many cm
 Distribution of microorganisms along roots

Bacterial population in the rhizosphere of

different plant species

mucilage
Many soil microorganisms utilise root exudates. Microorganisms can
be beneficial (e.g. improving nutrient availability) or harmful (e.g.
competition for soil nutrients, or root disease)
 Soil Water and Microbial Activity
• Water affects movement of nutrients and microbial mobility.
• Water-film thickness and continuity of water films are the
two factors controlling nutrient diffusion and mobility.
• Water movement and availability in soil is described by the
term potential ()

( Soil) = m + o + g

 Water availability to microbes depends on matric

and osmotic potentials.
 Matric potential = water attraction to surfaces

 osmotic potential = water attraction to solutes

High matric and osmotic forces reduce free flow of water and
increase the amount of effort needed to obtain water for
microbe bodies
 FIGURE 5.32 Volumes of water and air associated with 100 g of soil solids in a representative well granulated silt loam.
The top bar shows the situation when the soil is completely saturated with water. This situation will usually occur for short
periods of time when water is being added. Water will soon drain out of the larger pores (macropores). The soil is then said
to be at field capacity. Plants will remove water from the soil quite rapidly until they begin to wilt. When permanent wilting
of the plants occurs, the soil water content is said to be at the wilting coefficient. There is still considerable water in the
soil, but it is held too tightly to permit its absorption by plant roots. The water lost between field capacity and wilting
coefficient is considered to be the soil’s plant available waterholding capacity (AWHC). A further reduction in water
content to the hygroscopic coefficient is illustrated in the bottom bar. At this point the water is held very tightly, mostly by
the soil colloids.

Soil Moisture Availability Increase

 Water content–matric potential curve of a loam soil as related to different terms used to describe water in soils. The
wavy lines in the diagram to the right suggest that measurements such as field capacity are only approximations. The
gradual change in potential with soil moisture change discourages the concept of different “forms” of water in soils. At
the same time, such terms as gravitational and available assist in the qualitative description of moisture utilization in
soils.
 Response of Microbes to Change in Water
Potential

At low potential (dry or salty soil environment), water

is pulled from microbe body unless microbe
counteracts the potential change

Halophiles (withstand salt) and xerophiles (withstand

dryness) can change the water potential in their bodies
by producing extra solutes
Producing extra solutes may have harmful effects such as:
 Salt toxicity
 Enzymes inhibitions
 More energy demand
Most microbes prefer moist soils
Plasmolysis: loss of water due to the extremely low
water potential in Soil environment may cause the cell
Membrane to pull away from the cell wall.
 Favorite water potential varies by organism

 Hygrophile: prefers wet soil (some are anaerobes), many

algae, protozoa, facultatives

 Mesophile: prefers near filed capacity

 Xerophile: occur mostly in dry soil many fungi,

actinomycetes,
spore-forming bacteria
Water effects on organisms depend on depth in soil profile
Deeper in soil, variations water content are reduced therefore
hydrophiles or xerophiles isolated from subsoil (in deep, well-drained
profile)
Drivers of soil microbial diversity

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