SOIL ORGANISMS

Yum!
Tastes like
chicken!

http://www.lionking.org/imgarchive/Act_2/TimonGrabsBugs.jpg
Soil is an Ecosystem

• The Soil is nature’s original

recycling center:
-where leaves, wastewater, fecal
material, dead bodies are
converted into new biomass or
inorganic materials.
Recycling done
by:

Soil Organisms (fauna, flora)

Soil is an Ecosystem

Soil Ecosystem is among the most diverse

ecosystems in nature

Many different groups of organisms indicate that an

ecosystem that is more resilient/adaptable.
Soil Organisms
Macrofauna
1. Vertebrates (e.g. rodents)
2. Arthropods (insects, arachnids, crustaceans)
- ants, termites, beetles, centipedes
3. Annelids (e.g. Earthworms)
4. Mollusks (snails, slugs)
 Rice Field Rats
Soil Organisms

knowledgebank.irri.org

Wolf-spider urbanext.illinois.edu

David B. Richman
Centipede
Soil Organisms- Earthworm

• Hastens the cycling and increases the availability of

mineral nutrients
• Leaves soil borings

Check this video: http://www.agron.iastate.edu/~loynachan/mov/flash/earthworm.html

Soil Microorganisms - Microfauna
Nematodes
• Include threadworms,
eelworms
•Eukaryotic and
multicellular
•Have a body size of 200
to 1000 µm
•Typically slender,
cylindrical and

entnemdept.ufl.edu
unsegmented

Check this video: http://www.agron.iastate.edu/~loynachan/mov/flash/nematode.html

 Soil Microorganisms - Microfauna
Nematodes

• Some of them are

pests

USDA-ARS
J.W. Noling

A. M. Varela
Pepper infested with
Meloidogyne sp.
Soil Microorganisms - Microfauna
Protozoa
•Less than 200 µm long
•Eukaryotic and unicellular

Flagellates
micrographia.com

Amoeba
Ciliates
Check this Video: http://www.agron.iastate.edu/~loynachan/mov/flash/protozoa.html
Soil Microorganisms - Microflora
Bacteria
•single-celled, prokaryotic and
most are heterotrophic
•most numerous microbes in
the soil – 108 to 109 per gram
of soil
•Optimum moisture level for

sciencephoto.com
most plants are usually best for
most bacteria; prefers near-
neutral pH
Soil Microorganisms - Microflora
Bacteria
•“structurally simple but
functionally complex”

•may pack up to 1,000

enzymes in their bodies
(they are considered micro
bioreactors)

gbsbiology.pbworks.com
Why is bacteria
important?
Check this video: http://www.agron.iastate.edu/~loynachan/mov/flash/bacteria.html
Soil Microorganisms - Microflora
Archaea
•a domain of organisms that has previously be classified
as bacteria (previously names archaebacteria)

Example: Methanogens– used in biogas production

(production of methane; a biofuel) and in
sewage treatment.

Everly Conway de Macario

Methanosarcina acetivorans
Soil Microorganisms - Microflora
Cyanobacteria
•a phylum of bacteria that obtain energy through
photosynthesis and fix atmospheric nitrogen

biologie.uni-hamburg.de
Check this Video: http://www.agron.iastate.edu/~loynachan/mov/flash/cyano-algae.html
Soil Microorganisms - Microflora
Actinomycetes Also known as “thread bacteria”

• They look like fungi

(filamentous) and has spores
(conidia), but they are like
bacteria because they are
prokaryotic and their walls
are like that of bacteria.
• 2nd most abundant organism

soils.usda.gov
in the soil
• like pH 6-7.5

Check this video: http://www.agron.iastate.edu/~loynachan/mov/flash/actinomycetes.html

Soil Microorganisms - Microflora
Actinomycetes
Why are they Important?
1. decompose resistant organic
compounds (cellulose, lignin
and chitin)
2. some fix atmospheric Nitrogen

actinomycetes.pbworks.com
(Frankia)
3. some produce antibiotics such
as Streptomycin and
Chloramphenicol (from
Streptomyces)
Soil Microorganisms - Microflora
Fungi
•no chlorophyll --
heterotrophic organisms
(energy from organic
compounds)
•Exists in a wide range of soil
pH --- (widest pH range)
dominate at low pH due to Bebber et al (2007)
reduced competition

Check this Video: http://www.agron.iastate.edu/~loynachan/mov/flash/fungi.html

Soil Microorganisms - Microflora
Fungi
•Usually multi-cellular but
may include unicellular
organisms (yeast)
•Largely aerobic although
some can tolerate under
low oxygen
concentrations (e.g.
yeasts)
Fungus in agar culture
pmbio.icbm.de
 Soil Microorganisms - Microflora
Fungi
Why are they Important?

1.decompose cellulose, lignins and

complex organic compounds
2.fungi are fewer in number than
bacteria and actinomycetes but
make up the largest biomass of

teknomadics.com
any microbe in soils – up to 80%
of microbial biomass.

Page 45
Soil Microorganisms - Microflora
Fungi
Why are they Important?
3. Plays a vital role in aggregate formation and
stabilization
4. Antibiotics

Gupta Vadakattu, CSIRO group

Soil Microorganisms - Microflora
Mycorrhizae
• “Fungus-Roots” symbiotic association.
• The fungus colonize plant roots in a
symbiotic relationship utilizing carbon from
the plant while benefitting the plants by
increasing uptake of phosphorus and
possibly other nutrients and water.
Mycorrhizae

Extended hyphal
network in Pine
ecto-mycorrhiza

Improved
Paul and Clark, 1994

absorptive capacity
of plant
 Mycorrhizae
Mycorrhizal Effect on Marigold
Mycorrhiza - No
treated Treatment
Asnar and Elhindi (2011)

Well-watered
 Mycorrhizae
Mycorrhizal Effect on Marigold
Mycorrhiza - No Mycorrhiza - No
treated Treatment treated Treatment
Asnar and Elhindi (2011)

Well-watered Water-stressed
Fungus-Algae Symbiosis
Lichen
• “Fungus-Algae” symbiotic
association.
• The fungus provides
growth factors (water
nutrients) to the algae
while the algae in
return provide
photosynthates to the
fungi.
Soil Microorganisms - Microflora
Algae
• They have chlorophyll
and are photoautotrophs

pondsolutions.com
• found in moist to wet
soils at or near a neutral
pH.

• live near the soil surface holistikhealth.com

(WHY?)
Soil Microorganisms - Microflora
Algae
Why are algae important?
1. Primary producers
2. Pioneer in soil formation

123rf.com
3. If growing in excess
amounts in water bodies –
environmental hazard students.chem.tue.nl

Check this Video:

http://www.agron.iastate.edu/~loynachan/
mov/flash/cyano-algae.html
 Microbial Groups with representative size
and number (top 10 cm of soil)

Microbial Group Example Size (µm) Population density

(organisms per g
soil)
Bacteria Pseudomonas 0.5 x 1.5 108-109
Actinomycetes Streptomyces 0.5 -2.0 107 -108
Fungi Mucor 8.0 105-106
Algae Chlorella 5 x 13 103 -106
Protozoa Euglena 15 x 50 103-105
Nematodes Pratylenchus 1,000 101-102

What trends do you see?

Page 46
Soil Microorganisms – Relative Sizes
Distribution of microorganisms along a soil profile

Depth Thousand of organisms per gram soil

Aerobic Anaerobic Actinomycetes Fungi Algae
(cm)
Bacteria Bacteria
3-8 7,800 1,950 2,080 119 25
20-25 1,800 379 245 50 5
35-40 472 98 49 14 <1
65-75 10 1 5 6 <1
135-145 1 <1 ND 3 ND

What trends do you see?

 Familiarize this….
Prokaryotic/ Unicellular/
Eukaryotic Mulitcellular Mouth Photosyn. Filamentous N-fixing Comments

MICROFAUNA
causes major
Nematodes Eukaryotic multicellular yes no no no plant diseases
Amoeba -
Protozoa Eukaryotic Unicellular no no no no pathogenic

MICROFLORA
most numerous,
structurally simple
but functionally
Bacteria Prokaryotic Unicellular no some no some complex
important source
Actinomycetes Prokaryotic Unicellular no no yes some of antibiotics
contributes a lot
to microbial
Fungi Eukaryotic both no no yes no biomass
Algae Eukaryotic both no yes both some needs light
What factors affect
microbial activity?
Factors that Affect Microbial Activity
1. Moisture Content:
Moist soils – around Field Capacity is best for
microorganisms. Soil moisture conditions that are too
dry or too wet inhibit microbial activity.

2. Adequate Temperature Range:

Activity of microorganisms is limited below 5 oC
(“biological zero”)
a.Psychrophiles: -5 to 25 oC
b.Mesophiles : 15- 40 oC
c.Thermophiles: 40-70 oC
d.Hyperthermophiles: at least above 60oC, usually at
80 – 100 oC
Factors that Affect Microbial Activity
3. Adequate Carbon
Organic matter is a carbon and energy source for
most microorganisms.

4. Adequate Soil pH
Different microorganisms work in specific pH ranges.
a.Bacteria prefers near neutral pH and is adversely
affected by acidic conditions
b.Fungi are more resistant to acidic conditions.
Factors that Affect Microbial Activity
pH Effect
How are microbes affected by pH?
1. Microbial enzymes can be denatured due to
pH change.
2. pH may affect the solubility of other chemicals
--- which may become toxic to microbes at
high concentrations or may be limiting at very
low concentrations
Low pH High Aluminum Activity of some bacteria
Concentrations may be affected
 Factors that Affect Microbial Activity
5. Competing Organisms
To be able to survive, microbes must be
able to compete or have a favorable
association with the microbes around them.

6. Aeration
The need of presence or absence of oxygen.
a.aerobic – requires oxygen to survive
b.anaerobic –survives in the absence of
oxygen
c.facultative -can undergo either aerobic or
anaerobic metabolic processes

Page 46
Factors that Affect Microbial Activity
How do you deal with soil microbes
that can cause diseases?
To kill pathogenic microbes, you have to make sure they are not in a
position to compete with native microorganisms.

surface

Anaerobic Aerobic
Groundwater
Factors that Affect Microbial Activity
5. Competing Organisms
To be able to survive, microbes must be
able to compete or have a favorable
association with the microbes around them.

6. Aeration
The need of presence or absence of oxygen.
a.aerobic – requires oxygen to survive
b.anaerobic –survives in the absence of
oxygen
c.facultative -can undergo either aerobic or
anaerobic metabolic processes
Factors that Affect Microbial Activity

1. Soil Moisture
2. Soil Temperature
3. Adequate Carbon
4. Soil pH
5. Competing Organisms
6. Aeration Questions?
Why are soil microbes
important?
Beneficial Activities of Soil Organisms

1. Decomposition
- microbially-mediated process whereby complex
organic matter are reduced to simpler ones.

What affects the rate of decomposition?

3 Factors:
1. The substrate
2. The environment
3. The microbe
Decomposition – Substrate quality
C/N Ratio
• Ratio of carbon to nitrogen in organic residues.
This can range from 10:1 to 30:1 in legumes
and as high as 600:1.
What do microbes need?

Need carbonaceous materials to Need sufficient N to

synthesize organic compounds and synthesize cellular
generate energy components such as DNA,
amino acids, enzymes

To grow normally, microbes need 24 C for every 1 N.

Decomposition – Substrate quality
C/N Ratio
To grow normally, microbes need 24 C for every 1 N.
Alfalfa:13:1(narrow) Wheat Straw: 80:1(wide)

24:1.85 24:0.3
Can Alfalfa residues supply Can wheat straw residues
the nitrogen need of effectively supply the nitrogen
microbes? need of microbes?

Microbes grow and multiply at Microbes are going to compete for

a high rate because nothing is the limited N & they will not grow
limiting. and multiply as effectively

Decomposition is effective Decomposition is slower

Decomposition – Environ./Microbial Effects
Why do organic matter accumulate in wetland areas?
When oxygen
is sufficient C6H12O6 + 6O2 6CO2 + 6H2O + 36ATP 686 kcal/mol

Wetland

Pores are saturated with water – re-supply of O2 is poor

In the absence
C6H12O6 2CO2 + 2C2H5OH + 2ATP 47 kcal/mol
of Oxygen
Beneficial Activities of Soil Organisms
2. Nutrient Transformation
•Transformations that are agriculturally relevant:
Nitrogen Fixation – conversion of
Atmospheric nitrogen (N2) to ammonia

N2 ===> NH3 ------ done by Rhizobium sp in

nodules in roots of legumes.

This process contributes between 40--300 lbs N/ha/yr

Nodules

N2

Rhizobium sp

NH3
 Beneficial Activities of Soil Organisms
2. Nutrient Transformation
•Transformations that are environmentally relevant:

Photo: www.algae.info Photo: www.hobbyfarms.com

bacteria
-
NO3 ===➔ N2, NO and N2O Denitrification
Nitrate Gaseous forms
Beneficial Activities of Soil Organisms
3. Weathering Reactions/ Soil Formation
Carbon and nitrogen are two essential
elements that are lacking in the soil parent
material.

davidhanauer.com
•Cyanobacteria, algae and
lichens are considered pioneer
organisms in soil formation
because of their dual roles in
acquiring carbon and nitrogen

shutterstock.com
from the atmosphere.
Beneficial Activities of Soil Organisms
3. Weathering Reactions/ Soil Formation

•Microorganisms produce
acidic exudates which
can contribute to
dissolution of the parent
materials.
 Beneficial Activities of Soil Organisms

4. Treatment of Waste
•Nitrate from septic systems, for example can
be denitrified by denitrifying organisms.

•Industrial wastes such as PCE or TCE (can cause

cancer) and pesticides may be degraded via
microbially-mediated reactions.

Page 47
Beneficial Activities of Soil Organisms

Figure 11.32
Beneficial Activities of Soil Organisms

5. Improve Soil Physical Properties

•Fungal hyphae may wrap soil particles
encouraging the formation of aggregates.

•Mucilaginous exudates of some bacteria may

serve as “glue” in aggregate formation.
Brady and Weil
Problems Related to Soil Organisms
1. Damage by soil fauna
lib.colostate.edu

apsnet.org
Rat Damage Root-knot nematode

Citrus root weevil

Problems Related to Soil Organisms
1. Damage by soil fauna

http://www.ces.ncsu.edu
Problems Related to Soil Organisms
2. Damage by Soil Microflora

Fusarium Wilt: Banana

Fusarium Wilt: Tomatoes
Problems Related to Soil Organisms
3. Some are pathogenic
micrographia.com

musee-afrappier.qc.ca
Amoeba

Clostridium tetani
How is microbial activity
affected by human
activity?
Effects of Management on Soil Microbes
1. Extensive Tillage/Disturbance
- Generally reduces diversity and abundance of
soil microorganisms
Ratio of Microbes in No tillage vs Tilled
Microbial Group Soil (for 23 years)
0 to 7.5 cm

From Handayani, 1996

Effects of Management on Soil Microbes
1. Extensive Tillage/Disturbance
- Generally reduces diversity and abundance of
soil microorganisms
Ratio of Microbes in No tillage vs Tilled
Microbial Group Soil (for 23 years)
0 to 7.5 cm

Total Aerobic Bacteria 5.6

Actinomycetes 5.5

Fungi 1.2

From Handayani, 1996

Effects of Management on Soil Microbes
2. Monoculture
- Generally increase the population of a few species

3. Water Management
- Soils that are continually saturated will favor the
proliferation of anaerobes

4. Soil Amendment (fertilizers, lime, manures)

- Fertilizers and lime – promotes plant growth and hence,
organic matter production
- Manures –directly increases organic matter
Effects of Management on Soil Microbes
5. Pesticide Use
- Generally reduce abundance and diversity of
microorganisms

Fig. 11.37
Metabolic Classification
Based on Energy Source:
• Phototrophic – microbes that use light as their
primary source of energy
Example: Algae, Cyanobacteria

• Chemotrophic – microbes that use chemical

compounds and reactions as their source of
energy
Example: Nitrifying bacteria, Sulfur oxiding
bacteria
Metabolic Classification

Based on Carbon Source:

• Heterotrophs - microbes that obtain carbon from
organic compounds ; most numerous type
Example: Fungi, most bacteria, Protozoa

• Autotrophs: Obtains carbon (C) from by fixation

of CO2
Example: Algae, cyanobacteria