A Simplistic Look at Soil

Microbiology
 “We know more about the
movement of celestial bodies
than about the soil
underfoot”
Leonardo da Vinci, circa 1500
 CONTENT
1.Soil Organic Matter
2.Breakdown of Organic Matter
3.The Rhizosphere
4.Managing Soil for Biological Fertility
1.Soil Organic Matter
Organic matter in soil :
• Is required for microbiological activity
• Ensures microbiological activity
1.Soil Organic Matter
What is Organic Matter?
1.Soil Organic Matter
What is Organic Matter?
All carbon compounds formed by living organisms
1.Soil Organic Matter
What is Organic Matter?
All carbon compounds formed by living organisms

Three
components

Dead organic Living parts of Living microbes

matter plants (roots) and animals
(85%) (10%) (5%)
1.Soil Organic Matter
Dead organic
matter
(85%)

Dead plant Dead microbes

material and
insects/animals

Humus
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

(Hemi)- Chitin Simple molecules

Cellulose (sugars, acids, etc.)

Lignin Protein
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

(Hemi)-
Cellulose

• Carbohydrates composed of glucose that are bound together in long chains

• Prominent in woody substances, straw, stubble and leaves
• Initial hydrolysis of cellulose is often the rate limiting reaction in microbial
breakdown, therefore, mostly directly converted to CO2 and cell carbon
• Both fungi and bacteria involved in its breakdown
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

Lignin

• Plentiful in woody plants, especially older plants

• Contains only C, H and O, but is aromatic compared to cellulose
• Shows high resistance to enzymatic degradation, breaks down much slower than
cellulose
• Result is often well-composed materials that still have a high lignin content,
therefore one might find that compost (humus) contains little cellulose, but often
high lignin contents
• Mostly fungi that are involved in decomposing lignin
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

Lignin

• Plentiful in woody plants, especially older plants

• Contains only C, H and O, but is aromatic compared to cellulose
• Shows high resistance to enzymatic degradation, breaks down much slower than
cellulose
• Result is often well-composed materials that still have a high lignin content,
therefore one might find that compost (humus) contains little cellulose, but often
high lignin contents
• Mostly fungi that are involved in decomposing lignin
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

Chitin

• A polysaccharide with amino sugars as its basic structural unit

• It is a structural unit that gives mechanical strength to organisms
• Soil chitin originates from the remains of insects and fungi (and some
actinomycetes and yeasts)
• Mainly broken down by actinomycetes, which proliferate in its presence
• Especially actinomycetes that excrete anti-fungal substances, therefore helps
against pathogenic infections
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

Protein

• Consists of long chain amino acids that are linked together by peptide bonds
(CO-NH)
• Enzymes hydrolyse the peptide bonds to release the amino acids, which then
serve as C and N sources to innumerable heterothrophs
• They are broken down very easily
• Contribute to N in soil organic matter and therefore increases the C:N ratio
1.Soil Organic Matter
Dead organic

Humus
matter
(85%)

Simple molecules
(sugars, acids, etc.)

• Mostly soluble substances that are readily available for uptake/utilisation

1.Soil Organic Matter

Humus
• A mixture of colloidal degradation products
1.Soil Organic Matter

Humus
• A mixture of colloidal degradation products that accumulates in soil
because it breaks down slower than the products it was formed from
1.Soil Organic Matter

Humus
• A mixture of colloidal degradation products that accumulates in soil
because it breaks down slower than the products it was formed from –
relatively resistant to microbial breakdown
1.Soil Organic Matter

Humus
• A mixture of colloidal degradation products that accumulates in soil
because it breaks down slower than the products it was formed from –
relatively resistant to microbial breakdown
• Consists of a variety of substances, eg. (1) Colloidal substances
physically broken down; (2) Fenolic groups - residual lignin and dead
bacteria. Especially lignin is resistant to breakdown. It oxidises and
gives humus its black colour. The main substance in humus (3) Dead
microbial tissues – yeasts, fungi, bacteria, actinomycetes, insects, etc.
(4) Other (soluble) substances – humic/fulvic/amino acids, sugars
1.Soil Organic Matter

Humus
• A mixture of colloidal degradation products that accumulates in soil
because it breaks down slower than the products it was formed from –
relatively resistant to microbial breakdown
• Consists of a variety of substances, eg. (1) Colloidal substances
physically broken down; (2) Fenolic groups - residual lignin and dead
bacteria. Especially lignin is resistant to breakdown. It oxidises and
gives humus its black colour. The main substance in humus (3) Dead
microbial tissues – yeasts, fungi, bacteria, actinomycetes, insects, etc.
(4) Other (soluble) substances – humic/fulvic/amino acids, sugars
• Humus is decomposed in two ways: (1) Oxidation of resistant
products in hot dry conditions (2) Microbial breakdown in moist
conditions. – FLUX of breakdown after a dry spell…
1.Soil Organic Matter

Compound Type of Tissue

Young leaves Old leaves Stems
Carbohydrates
Cellulose 30 50 60
Other 25 30 17
Proteins 25 6 1
Nucleotides 5 2 -
Lipids 5 2 1
Lignin 2 8 20
Simple molecules
Sugars,acids,etc. 8 2 1
100% 100% 100%
1.Soil Organic Matter
2. Breakdown of Soil Organic Matter

A complex process, which involves:

• Physical fragmentation of organic matter
• Chemical alteration of organic matter
• Finally, the release of mineral nutrients
2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

1. Dead organic material is colonised by micro-organisms.

Leaf- and root surfaces are colonised by micro-

organisms even before they die

They use enzymes to oxidise the organic

matter to obtain energy and C. In the process
CO2 is also released.
 2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

1. Dead organic material is colonised by micro-organisms.
2. Earthworms and other larger soil animals, such as mites,
ants, etc. fragment organic matter, increasing the surface
area to allow more micro-organisms to colonise and
decompose it .

Mites
2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

1. Dead organic material is colonised by micro-organisms.
2. Earthworms and other larger soil animals, such as mites,
ants, etc. fragment organic matter, increasing the surface
area to allow more micro-organisms to colonise and
decompose it
3. Soil animals such as earthworms assist by incorporating
organic matter into the soil (where conditions are more
Earthworm
favorable) and mixing it with intestinal burrow
microbes
2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

1. Dead organic material is colonised by micro-organisms
2. Earthworms and other larger soil animals, such as mites,
ants, etc. fragment organic matter, increasing the surface
area to allow more micro-organisms to colonise and
decompose it
3. Soil animals such as earthworms assist by incorporating
organic matter into the soil (where conditions are more
favorable) and mixing it with intestinal microbes
4. Fungi and bacteria secrete enzymes to break up the organic
matter, which are long and complex compounds, into simpler
molecules
2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

1. Dead organic material is colonised by micro-organisms
2. Earthworms and other larger soil animals, such as mites,
ants, etc. fragment organic matter, increasing the surface
area to allow more micro-organisms to colonise and
decompose it
3. Soil animals such as earthworms assist by incorporating
organic matter into the soil (where conditions are more
favorable) and mixing it with intestinal microbes
4. Fungi and bacteria secrete enzymes to break up the organic
matter, which are long and complex compounds, into simpler
molecules
5. These then require further decomposition into mineralised
nutrients
2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

Already said  Compounds vary in the ease by which they can
break down…

Amino acids/sugars  Cellulose  Phenols/lignin (Humus)

2. Breakdown of Soil Organic Matter

Stages of Breakdown Involves:

Mineralisation of organic matter
It is the biological process by which organic compounds
are chemically converted to simpler organic compounds
and finally to mineral nutrients.
Mostly done by bacteria and fungi.

EXAMPLE: A protein molecule contains C, P, N, S, O and H.

Through a series of chemical processes :
the C is converted to CO2 or microbial tissue,
the N is converted to NH3/NH4+ and NO3-,
the P is converted to PO43-
and the S to SO42-
2. Breakdown of Soil Organic Matter

N-mineralisation
Two steps:
1. Ammonification
Organic matterBacteria & fungi
H2O
R-C2HOOO-NH2  R-COOH + CO2 + NH4+

Urea
CO(NH2)2 + 2H2O 
Urease
(NH4)2CO3 + H2O  2NH4+ + H2O + CO2
Bacteria & fungi
2. Breakdown of Soil Organic Matter

N-mineralisation
Two steps:
1. Ammonification
2. Nitrification – two stages:

NH4+ + 3/2O2 
Nitrosomonas NO2- + H2O + 2H+
bacteria

NO2- + O2 
Nitrobacter 2NO3-
bacteria

• Urea requires biologically alive soil

• Use of NH4+ fertilisers acidifies soil
• Little NH4+ accumulates in soil, and NH4+
does not necessarily prevent leaching
• Uptake mostly in NO3- form
2. Breakdown of Soil Organic Matter
The role of the C:N ratio of organic matter
• Is an expression of how much more C than N there is
• Does not tell us what forms the C and N are in
• Do tell us what the potential N-availability is to both
soil micro-organisms and plants
• The short term effect of an addition of organic
matter with a high C:N ratio is to cause a N-
deficiency EXAMPLE
When a protein high in N (eg. dried blood) is added to soil, 80% of the
added N is liberated as NH4+  NO3-, while 20% is retained as microbial
tissue
If carbohydrates (eg. cellulose) is mixed with the protein, the amount of
microbial tissue that is built up increases, resulting in a lower proportion of
N being liberated as NH4+  NO3-
2. Breakdown of Soil Organic Matter
Immobilisation
• The opposite of mineralisation.
• Mineralised nutrients (especially N) are incorporated into
organic molecules within living cells.
• Prevent leaching of N because it is incorporated into pools
within the soil that have a relatively rapid turnover time –eg.
bacteria

C:N ratios
Fresh woody tissues 200:1 Rapid immobilisation

Fresh leguminous tissues 30:1 Little immobilisation

Stable soil organic matter (humus) 12-20:1 Steady mineralisation

Bacteria 10:1 Rapid mineralisation

2. Breakdown of Soil Organic Matter
Example:
We have a soil with 0,8% organic C.
What will the annual N-release be?
In the soil is 1 300kg/m3 x 10 000m2 x 0,15m x 0,008 = 15 600 kg C/ha
The C:N ratio of stable organic matter is 15:1
That means, there is 1 040 kg organic N per ha (up to 15 cm depth)
Of this, only 1-2% is mineralised per year, meaning that :
1040 x 1,5/100 = 15,6 kg N/ha per year is released
2. Breakdown of Soil Organic Matter
What if I can increase it to 1,2% organic C?

= 23 400 kg C/ha
C:N ratio is 15:1, therefore: 1 560 kg organic N per ha
Only 1-2% is mineralised, meaning that : 23,4 kg N/ha

It takes a lot of organic matter to move the C from 0,8 to

1,2, so is it worthwhile?

Yes, by applying organic matter regularly.

Of fresh organic matter, 50 % of its N is released in the 1st year.
In the 2nd year 20% (+ 50% of the new OM)
In the third year 5%.....(+ 20% of previous year + 50% of new year)
...
3. The Rhizosphere
The region of soil immediately adjacent to the
roots which is directly affected by the roots.
3. The Rhizosphere
The region of soil immediately adjacent to the
roots which is directly affected by the roots.
Active growing roots exude organic compounds (exudates) into the soil.
Due to these compounds, the environment directly around the root is very
different form the rest of the soil.
They are a food source for micro-organisms, causing their number to be far
larger than in the bulk soil.
The presence of micro-organisms attracts larger organisms, making the
concentration of soil organisms up to 500 times higher than in the rest of the
soil.
A constantly changing environment, due to changes in the characteristics of
the exudates, which depend on the age of the plant, season and inter-actions
between organisms, chemical inputs, water availability, etc. Eg., wilting
increase the amount of amino acids released
Bacteria are the most sensitive to environmental/nutritional changes, so they
will be affected the most to changes in the rihizosphere
3. The Rhizosphere
The effect of chemicals on the rhizosphere
Chemicals affect the microbial situation of the rhizosphere in three ways:
1. They become incorporated into the soil and affect the rhizosphere directly
2. They are absorbed by the leaves and translocated to other plant parts, altering
the plant’s metabolism and thus changing the composition of exudates
3. They are absorbed by the plant, translocated to the roots and exuded from the
roots into the rihizosphere

EXAMPLE
Application of Bordeaux mixture to the leaves of bean plants was
found to increase the level of Cu in the rhizosphere, reducing the
bacterial numbers therein
3. The Rhizosphere
The rhizosphere as the “first line of defence”
Within the rhizosphere are both saprohytes and parasytes
For a pathogen (parasyte) to successfully establish itself as a member in
the rhizosphere, it must be able to compete with the other saprophytes
for nutrients. It can only cause a disease by entering the root from the
rhizosphere.
Because of the high numbers of microbial organisms and their
enhanced activity, which is associated with antagonistic and competing
reactions, the rhizosphere generally protects the roots against infection.

BUT,
if the balance and activity of this micro-habitat is disturbed by a
chemical or environmental conditions (drought, water-logging,
nutritional deficiencies, pH) the effectiveness of the
saprophytes to compete with the parasites/pathogens reduces
and results in infections taking place
3. The Rhizosphere
Example of nematodes
There are 20 000 known species, making them a diverse
group that play many roles in the soil system
Most eat bacteria, fungi protozoa and other nematodes
Some nematodes eat cut worms, caterpillars and beetle
larvae
But some are plant parasites…
3. The Rhizosphere
Example of nematodes
There are 20 000 known species, making them a diverse
group that play many roles in the soil system
Most eat bacteria, fungi protozoa and other nematodes
Some nematodes eat cut worms, caterpillars and beetle
larvae
But some are plant parasites…

The plant parasites feed on specific hosts, so… you

remove their food source.
Increased organic matter increases nematode predators
such as fungi, mites and other nematodes, so… you
increase the organic matter content of the soil.
Fungi, especially, pray on nematodes by trapping them,
or exuding a toxin whereby they are immobilised, so…
you incorporate fungal food regularly.
3. The Rhizosphere

The plant parasites feed on specific hosts, so… you

remove their food source.
Increased organic matter increases nematode predators
such as fungi, mites and other nematodes, so… you
increase the organic matter content of the soil.
Fungi, especially, pray on nematodes by trapping them,
or exuding a toxin whereby they are immobilised, so…
you incorporate fungal food regularly.
3. The Rhizosphere
Biological control
The use of living organisms to control the numbers and activity of
pathogenic organisms.
This means that soils must be managed so that the soil environment is
suitable for growth of the beneficial organisms that naturally control
pathogens.
3. The Rhizosphere
Biological control
The use of living organisms to control the numbers and activity of
pathogenic organisms.
This means that soils must be managed so that the soil environment is
suitable for growth of the beneficial organisms that naturally control
pathogens.

Responsible
Soil
Healthy Management
4. Managing Soil for Biological
Fertility
4. Managing Soil for Biological
Fertility
To manage the soil biological fertility you need to
keep in mind the following:
• Soil organisms are most abundant in the surface layers of
the soil
4. Managing Soil for Biological
Fertility
To manage the soil biological fertility you need to
keep in mind the following:
• Soil organisms are most abundant in the surface layers of
the soil
• Soil organic matter is required for nutrient cycling and soil
aggregation - humus
• Soil amendments can alter the physical and chemical
environment of the soil and, therefore, of soil organisms
• Soil biological processes can develop slowly, and it can take
time before changes are noticed. Some processes can take
place at enormous rates, affecting the soil’s situation within
days
• An abundant variety of soil organisms promote plant health
4. Managing Soil for Biological
Fertility
Examples of how an abundant variety of soil
organisms promote plant health
• Some bacteria release growth factors that directly increase
plant growth, eg. vitamins & hormones
• Some actinomycetes, bacteria and fungi excrete anti-biotics
• Fungi specialize in decomposing high C substances, eg.
cellulose and lignins, decreasing the C:N ratio. But
actinomycetes also do this job, resulting in other products
• Occurrence of a healthy ecosystem, ensures the occurrence
of mychorrhiza, promoting P-nutrition and water uptake
• Streptomyces, an actinomycete, liberate an enzyme which
lyse bacteria (digest their cell walls)
• Blue-green algae and rhozobium bacteria can fix N.
4. Managing Soil for Biological
Fertilityof how mineral fertilisation affect soil biota
Examples
4. Managing Soil for Biological
Fertilityof how mineral fertilisation affect soil biota
Examples
I. Short term stimulation of biological activity (BA) due to mineral N
&P
• Super-phosphate was found to stimulate bacterial
actvity in soil.
• The “priming-effect”, where added N stimulate micro-
organism activity, is well-known. This is probably
due to a removal of nutrient limitations.
• The priming effect, however, also leads to breakdown
of stable OM.
4. Managing Soil for Biological
Fertilityof how mineral fertilisation affect soil biota
Examples
I. Short term stimulation of biological activity (BA) due to mineral N
&P
II. •No short-term
More effect or depression
often, however, of no
studies show BA effect
due to mineral N N
of mineral
applications on soil microbiological activity.
• Effect of urea…
4. Managing Soil for Biological
Fertilityof how mineral fertilisation affect soil biota
Examples
I. Short term stimulation of biological activity (BA) due to mineral N
&P
II. No short-term effect or depression of BA due to mineral N
III. No short-term effect or depression of BA due to mineral P or S

• Little info on the effect of mineral P and S on BA,

but in Canada a slight decrease in diversity was
observed.
• Was mainly a decrease in arbuscular mycorrhiza (AM)
4. Managing Soil for Biological
Fertilityof how mineral fertilisation affect soil biota
Examples
I. Short term stimulation of biological activity (BA) due to mineral N
&P
II. No short-term effect or depression of BA due to mineral N
III. No short-term effect or depression of BA due to mineral P or S
IV. Short-term toxicity effects of mineral fertilisers

• Metal contaminants (Cd, Pb) often found in P-

fertilisers can affect BA
4. Managing Soil for Biological
Fertilityof how mineral fertilisation affect soil biota
Examples
I. Short term stimulation of biological activity (BA) due to mineral N
&P
II. No short-term effect or depression of BA due to mineral N
III. No short-term effect or depression of BA due to mineral P or S
IV. Short-term toxicity effects of mineral fertilisers
V. Long-term effects of mineral fertilisation
• NH4+ and Urea fertilisation decreases soil pH over
time, affecting BA, especially bacteria.
• “Piming effect” which decreases total OM in soil leads
to decreased BA, due to less food sources.
4. Managing Soil for Biological
Fertility
Examples of how mineral pesticides affect soil biota
Pesticides impact BA through (a) direct or (b) indirect ways

(a)Eg.: A herbicide may not directly influence soil

biota, but through weed-control, less vegetative
material is introduced to the soil, therefore the BA
reduces.

(b)Eg.: Direct impacts can occur when a pesticieds

reaches the soil and affects a group or all of the
soil biota
Roundup

Roundup & Gramoxone

Goal EC
Dursban

Copper
Copper
4. Managing Soil for Biological
Fertility
A few management guidelines:
1. Soil erosion removes the habitat for micro-organisms
2. Retain and produce plant organic matter – more NB than
minerals
3. Disturb soil from time to time to stimulate activity of diverse
microbes
4. Calculate N fertiliser applications in consideration of N-
cycling from organic matter
5. Assess chemical inputs on account of their effect on soil
biology
6. Since mycorrhizal activity reduces in the presence of high P
concentrations, be conservative with P fertilisation
7. Use and rotate cover crop species to promote a diverse
microbial population
4. Managing Soil for Biological
Fertility
A few management guidelines:
9. Remember a large amount of external OM is required to
make a short-term impact on the soil’s OM content.
Therefore use cover crops.

Example
To increase the SOM (organic C = 0.6 x SOM) content of the
soil from 0,5% to 1% over a depth of only 15 cm, 65 ton of
OM is required.
However, of this 65 ton of OM, 80-90% of this added OM is
lost due to decomposition during the first several years
4. Managing Soil for Biological
Fertility
A few management guidelines:
9. Remember a large amount of external OM is required to
make a short-term impact on the soil’s OM content.
Therefore use cover crops.
10. Bacteria are more sensitive to changes, but their
populations are quickly restored (if impact is short-term).
Worry about the other groups.
11. Beware of acidifying fertilisers – also remember that
agricultural activity and also OM inputs acidifies the soil.
Apply lime from time-to-time (every few years check the
pH)
THANK YOU /