SOIL MICROBIOLOGY

 Soil Microbiology – the

study of soil organisms and
their processes. Soil
organisms are creatures
that spend all or part of
their life in a soil
environment.
Importance of soil organisms

1. Decomposer of plant and

animal residues.
2. Responsible for biochemical
changes promoting the
transformation of essential
elements and nutrient cycling.
3. Play an important role in
preserving environmental
quality.
Animals – (fauna)

 Macrofauna – earthworms,
millipedes, termites
 Mesofauna – nematodes to
single-cell protozoans
 Plants (flora) – include the
roots of higher plants,
macroscopic algae and diatoms
 Microorganisms are too
small to be seen with the
naked eye include fungi,
bacteria and
actinomycetes.
Kinds of Soil Microflora

A. Bacteria – very small,

single-celled prokaryotic
organisms without nucleus.
They range in size from
0.5 to 5 mm.
  Shape
⚫ Coccus – round
⚫ Bacillus – rodlike
⚫ Spirillum - spiral

 Psychrophilic – capable of growing at 0oC

 Mesophilic – optimum growth is at 25oC
to 39oC
 Thermophilic – microorganism that thrive
only at high temperature (50oC to 72oC)
 Source of energy and carbon

 Autotroph
⚫ Photoautotrophs – obtain their
energy from sunlight and carbon
from carbon dioxide. Ex.
Photospirillum– purple bacteria
Cyanobacteria – blue green algae
 Chemoautotroph – energy is
obtain from the oxidation of
inorganic constituents as
ammonium, sulfur and iron
and carbon from carbon
dioxide or dissolved
carbonates.
Example

 Nitrosomonas

 Nitrobacter

 Thiobacillus
 Heterotrophs – energy and
carbon sources are preformed
organic carbon from organic
matter. Ex.
⚫ Heterotrophic bacteria – Bacillus,
pseudomonas
⚫ Fungi – Rhizopus, Aspergillus
 Oxygen Requirements

 Aerobic – use O2 as the electron

acceptor in their metabolism. It
can grow only in the presence of
oxygen.
 Anaerobic – use substances other
than O2 as electron acceptor in their
metabolism. Can live in the
complete absence of oxygen.
 Facultative– can use either
aerobic or anaerobic
metabolism. Can live in the
presence or absence of
oxygen.
 Characteristics of bacteria

 Bacteria are either autotrophic or

heterotrophic
 Most common genera –
Pseudomonas, Rhizobium,
Bacillus, Clostridium and
Arthrobacter
 Another group is the
cyanobacteria previously
classified as blue-green
algae.
 Examples of Cyanobacteria
(blue-green algae), Anabaena,
Nostoc, Gleocapsa, Gleotrichia,
Lyngbya and Oscillatoria
 Bacteriagrow best under
neutral to slightly basic
conditions.
Importance of bacteria

 Help in the remediation of

polluted soils
 Breakdown of hydrocarbon
compounds such as gasoline
and diesel fuel
 Responsible for the
biological oxidation of
inorganic compounds
 Microbial action controls
toxicity and deficiency of
some nutrients such as iron
and manganese
 Organic matter decomposition
is the most significant
contribution of the soil fauna
and flora to higher plants
 Plant residue decomposition is
the process wherein dead
leaves, roots and other plant
tissues are broken down
converting organically held
nutrients into mineral forms
available for plant uptake and
recycle the elements.
 By-products of organic matter
decomposition, are utilize by
microorganism to synthesize
new compounds to stabilize
soil structure and contribute to
humus formation.
 Nitrogen fixation – fixation
of elemental nitrogen gas
which cannot be used
directly by higher plants.
Factors affecting the growth of soil bacteria
and other soil microorganism

 Oxygen requirement
 Moisture
 Temperature
 Amount of organic matter
 pH
 Actinomycetes – unicellular
aerobic microorganism,
which form branched
mycelium and reproduced
by fragmentation or asexual
spore formation
 Generally aerobic and
heterotrophic living in decaying
organic matter in the soil.
 Common genera of soil
actinomycetes are Nocardia,
Streptomyces, Micromonospora
and Thermoactinomyces.
 Important in the
decomposition of resistant
compounds such as cellulose,
chitin and phospholipids to
simpler forms. They are the
groups of organisms
important in the final stage of
decomposition.
 Fungi – nucleated, spore-bearing,
achlorophyllous organism which
generally reproduce sexually and
asexually, and whose usually
filamentous, branched somatic
structures are typically surrounded
by cell walls containing cellulose or
chitin or both.
Nutrition and Growth

 Parasites – fungi obtain

their food by infecting living
organisms.
 Saprophyte – attack dead
bodies of animals and
plants.
 They decompose cellulose,
starch, gums and lignin as
well as the easily
metabolized proteins and
sugars. Common genera
are Penicillium, Aspergillus,
Trichoderma, Mucor and
Fusarium
 Mycorrhiza – association
between fungal hyphae and the
roots of higher plants
 Endomycorrhiza- the fungus
penetrates into the root cells and
arbuscules and vesicles are
formed.
example: wheat, corn beans,
tomatoes
 Ectomychorrhiza-mutualistic, the
fungus surrounds the root tip with
or sheath
example: pine trees
 Ectendomycorrhiza - orchids
 Algae – most important
photosynthetic microorganisms
in the soil. The blue green
algae are procaryotic and
contain chlorophyll, carotenoid
and phycocyanin pigments
which are diffused throughout
the cytoplasm.
Activities and Functions of Soil
Microorganisms

A. Decomposition of Organic
Materials – The decomposition
of organic residues with the
release of nutrient element
such as C, N, P and S so that
these may be utilize by plants
and new generation of
organisms.
 Decomposition – an oxidation process in a
well-aerated soil.
 General reaction decomposition
Decompositon

CHO + O2 CO2 + H2O + Inorganic

nutrients + Humus

Organic N NH4+ NO-3

ammonification nitrification
mineralization
Purpose of decomposition for the
microflora

 Provides energy for growth

 Supply carbon for the formation
of new cell materials
Course of decomposition

lignin

Total material
hemicellulose
cellulose

Days After Decomposition

 Humus – a dark colored,
heterogenous mostly colloidal
of newly synthesized organic
compounds that are resistant
to decay
Factors affecting organic matter
decomposition

 pH
 Temperature
 Moisture content
 Oxygen
 C:N ratio
 Mineralization – the conversion of
an element from an organic form to
an inorganic state as a result of
microbial decomposition
 Immobilization – the conversion
of an element from the inorganic to
the organic form in microbial tissues
or in plant tissues, thus rendering
the element not readily available to
other organisms or to plants
 Mineralization and Nitrification
 Nitrification – the oxidation sequence involved in the conversion of
ammonium to nitrate. In soils, this is brought about by two groups of
autotrophic bacteria which derive their energy from the oxidation of
ammonium to nitrate and nitrate.
 Nitrosomas oxidizes ammonium to nitrate and Nitrobacter oxidizes
nitrite to nitrate. The reactions are as follows:
(NH4)2 SO4 + H2O → 2NH4OH + H2SO4
2NH4OH → 2NH4+ + 2OH-
nitrosomonas
2NH4+ + 3O2 ----------→ 2NO2- + 4H+ + 2H2O
nitrobacter
2NO2- + O2 ---------→ 2NO3-
 The activities of the nitrifiers are affected by pH, aeration, moisture
content and temperature
 Denitrification – the microbial reduction of nitrate and
nitrite with the liberation of molecular nitrogen and nitrous
oxide. Under anaerobic conditions, such occurs
frequently in soils following heavy rains. NO3 can be
denitrified in a short time, particularly when sufficient
energy is available in the form of organic matter.

 Volatilization – it is the conversion of ammonium to

ammonia gas in an alkaline aqueous medium NH
Denitrification

2HNO3 2HNO2 [2NO] N2O N2

a. Stimulated by anaerobic conditions
b. 10-15% of applied NO3- lost even under well-
drained conditions
c. Requires presence of OM
d. Rapid reaction
 Nitrogen fixation – nitrogen fixation is the
process by which gaseous nitrogen (N2) is
converted to ammonia (NH3) by
specialized group of microorganisms.
Nitrogen fixation is usually grouped into
two types:
⚫ Non symbiotic nitrogen fixation which is
brought about by certain free-living bacteria
and blue-green algae
⚫ Symbiotic nitrogen fixation which occurs in an
association of a higher plant root and a
microorganism (bacteria)
 Non symbiotic nitrogen fixation. Among
the non symbiotic nitrogen fixing
organisms are the following:
⚫ Azotobacter and related genera Azomonas,
Beijerinckia and Derxia
⚫ Clostridium pasteurianum and other species
⚫ Blue-green algae
 Symbiotic Nitrogen Fixation. The
legumes are one of the largest
groups of flowering plants belonging
to the family Leguminaseae.
Almost all species of these are
subject to nodulation.
 Associative symbiosis. Nodule
formation is not involved.
Associative symbiosis has been
reported in grasses such as
Paspalum notatum, Degitaria
decumbens and Pennisetum
purpuereum. The active organisms
from the root of Degitaria
decumbens was identified as
Spirillium lipoferrum (Azospirillum
basillens).
N - CYCLE N2
atmos.

symbiotic
fixation
Animals

NO3- Plants Soil OM

assimilation
Crop
leaching Removal erosion

NH4 fixation
Industrial NH3 Volatilization
fixation erosion
N - FIXATION
mechanism Approximate amount
lbs/acre/year

1. Electrical discharge 2–5

N2 NO3-

2. Biological
a. symbiotic – 40 – 200
Rhizobia – (various species)
b. Nonsymbiotic 5 – 50
Azotobacter (aerobic)
Clostridium (anaerobic)
Blue-green algae-Nostoc

3. Industrial
N2 NH3 fertilizer
MINIRALIZATION AND NITRIFICATION

Mineralization

Deaminization ammonification
OM R – NH2 NH3(+H+ NH4+)
(general purpose heterotrophic organism)
MINIRALIZATION AND NITRIFICATION

Nitrification

Nitrosomonas
2 NH4 + 3O2
+ 2 NO2- + 2H2O + 4H+

Nitrobacter
2 NO2 + O2
- 2 NO3-

(Special-purpose, autotrophic bacteria)

DENITRIFICATION

NO3- NO2- N2 O(g) N2(g)

(various heterotrophic bacteria)

a.Stimulated by anaerobic conditions

b.10-15% of applied NO3- lost even under

well drained conditions

c.Requires presence of OM

d.Rapid reaction
N-GAINS AND LOSSES

Gains
1. fertilizer

2. fixation, 18 to 34 kg/year

3. soil OM turnover (~2%), 50 lbs/year

4. crop residues, manure

N-GAINS AND LOSSES
Losses

1. Crop removal

2. Leaching
-significant on bare soil
-slight when crop growing

3. volatilization – denitrification
NH3 NO3 N2 O, N2
-surface applied -anaerobic conditions
-alkaline pH, >7.2 -need OM (heterophic
bacteria)

4. erosion
 REVIEW QUESTIONS FOR SOIL
MICROBIOLOGY

1. Net nitrogen immobilization in soil occurs

if the C/N is.

a. less than 20:1

b. Greater than 20:1
c. Greater than 35:1
d. Less than 15:1
e. None of the above
2. Individually, which among the following
soil organisms have the least biomass?

a. Actinomycetes d. Protozoa
b. Fungi e. Earthworm
c. Bacteria

3. Which among the following soil organisms

are acid-loving?

a. Fungi d. Actinomycetes
b. Protozoa e. A and B above
c. Bacteria
4. Ammonia volatilization from NH4+ -
bearing fertilizers is not favored by which
of the following?

a. high pH d. a and b above

b. high temperature e. b and c above
c. high CEC
5. Soil microorganisms degrade organic
residues primarily for

a. phosphorus and ATP

b. carbon and energy
c. nitrogen and energy
d. phosphorus and energy
e. nitrogen and phosphorus
6. The root-nodule bacteria belong to
the genus

a. Clostridium
b. Azotobacter
c. Rhizobium
d. Agrobacterium
e. none of the above
7. The anaerobic non-symbiotic
nitrogen fixing bacteria belong to
the genus

a. Derxia
b. Clostridium
c. Azotobacter
d. Bradyrhizobium
e. Nitrobacter
8. Algae are considered as

a. Autotrophs
b. Photoautotrophs
c. Chemoautotrophs
d. both a and b
e. none of the above
9. The source of energy for blue
green algae is

a. sunlight
b. metabolism of glucose
c. organic matter decomposition
d. oxidation of inorganic compounds
e. none of the above
10. The predominant available form
of N under flooded soil condition is

a. NO3-N
b. Organic-N
c. NH4-N
d. NO2-N
e. NH2-N
11. The available form of nitrogen
which predominates under upland
condition is

a. ammonium
b. nitrite
c. nitrate
d. microbial biomass N
e. fixed N
12. The conversion of NO3 to N2 is
referred to as

a. nitrogen fixation
b. denitrification
c. immobilization
d. immobilization
e. none of the above
13. The percentage of organic N in
the soil is approximately

a. 96-98%
b. 80-85%
c. 68-75%
d. 50-60%
e. 60-70%
14. Nitrogen is added to the soil
system by which of the following
processes?

a. leaching
b. nitrogen fixation
c. ammonia volatilization
d. a and b above
e. b and c above
15. The conversion of organic N to
inorganic or mineral N is termed as

a. immobilization
b. nitrification
c. mineralization
d. ammonification
e. none of the above
16. The conversion of N2 to NH4 is
referred to as

a. denitrification
b. nitrate reduction
c. nitrogen fixation
d. volatilization
e. none of the above
17. Microorganisms which do not
require oxygen are called

a. aerobes
b. anaerobes
c. obligate aerobes
d. microaerophillic
e. none of the above
18. The fixation and regeneration of
CO2 in the biosphere is referred to
as

a. carbon cycle b. CO2 evolution

c. respiration d. nutrient cycle
e. none of the above
19. The optimum temperature
requirement of thermophiles is

a. greater than 450C

b. less than 450C
c. greater than 250C
d. less than 300C
e. 30-400C
20. Microorganisms which require
organic compounds as sources of
carbon and energy are

a. autotrophs
b. heterotrophs
c. chemoautotrophs
d. photoautotrophs
e. none of the above
21. It refers to the entrapment of
ammonium ions in-between crystal
lattices of clays thus rendering them
unavailable for plant use. This
process is called

a. nitrogen fixation
b. microbial fixation
c. ammonium fixation
d. nutrient fixation
d. none of the above
22. Rhizobia are generally associated
with nitrogen fixation in

a. rice
b. peanut
c. corn
d. sorghum
e. sugarcane
23. Bacteria belonging to this genus
are non symbiotic nitrogen fixers

a. Nitrobacter
b. Aerobacter
c. Azotobacter
d. Arthrobacter
e. Nitrosomonas
24. If a crop residue contains 75%
organic carbon and 5% total
nitrogen, its C/N ratio is

a. 10:1 b. 12:1
c. 15:1 d. 20:1
e. 25:1
25. The C/N ratio of soil microbial
biomass is about

a. 5-8:1 b. 12-15:1
c. 15-20:1 d. 20-25:1
e. none of the above
26. The most abundant
microorganisms found in the soil
are generally the

a. fungi b. bacteria
c. actinomycetes d. algae
e. protozoa
27. The incorporation of inorganic
nitrogen into microbial tissues is

a. mineralization
b. immobilization
c. nitrification
d. denitrification
e. ammonification
28. Which of the following
microorganisms is very sensitive to
potassium levels in soil and
therefore useful in diagnosing
potassium deficiency?

a. Pseudomonas denitrificans
b. Aspergillus flavus
c. Aspergillus niger
d. Azotobacter chroococcum
e. Nitrobacter agilis
29. A deficiency of this element will
not enable a legume and its
bacterial partner to perform
nitrogen fixation. This element is

a. Boron
b. Phosphorus
c. Molybdenum
d. Zinc
e. Magnesium
30. The group of soil microorganisms
which is responsible for decomposing
organic matter is the

a. Heterotrophs b. Autotrophs
c. Phototrophs d. Chemoautotrophs
e. none of the above
31. Organic materials with wide C/N
ratios are not ready sources of
available nitrogen because the
nitrogen that they contain is subject
to

a. nitrification b. volatilization
c. immobilization d. fixation
e. none of the above
32. The soil microbial population is
generally highest in the

a. A horizon b. B horizon
c. C horizon d. B2 horizon
e. A3 horizon
33. Chemoautotrophs are those
organisms which derive their energy
from

a. sunlight
b. oxidation of organic material
c. fermentation
d. oxidation of inorganic substances
e. none of the above
34. For soil bacteria, growth results in
an increase in the

a. size of the individuals

b. number of the individuals
c. form of the individuals
d. size and number of the individual
e. none of the above
35. The most efficient organic matter
decomposers under acidic soil
conditions are the

a. bacteria b. actinomycetes
c. fungi d. protozoa
e. algae
36. Pesticides will be retained much
longer in soils with

a. low organic matter

b. high moisture content
c. 2:1 dominant clay type
d. low pH
e. 1:1 dominant clay type
37. Net mineralization of organic
nitrogen in the soil will occur if the
C:N ratio is less than

a. 20:1 b. 30:1
c. 40:1 d. 50:1
e. 60:1
38. The initial substrate for
nitrification is

a. nitrite
b. nitrate
c. ammonia
d. amine
e. none of the above
39. The ultimate end product of
denitrification is

a. N2 b. NO
c. N2O d. NH3
e. none of the above
40. A gas which can be used as an
indicator of the level of microbial
activity in the soil is

a. nitrogen b. oxygen
c. hydrogen d. carbon dioxide
e. methane
41. Associative nitrogen fixation is
undertaken by bacteria in
association with

a. rice b. corn
c. sugarcane d. pasture grasses
e. all of the above
42. Frankia spp. are soil
microorganisms which are
responsible for the nodulation in

a. Casuarina b. Alnus
c. Eleagnus d. Coriaria
e. all of the above
43. The number and activity of
bacteria in the soil are affected by

a. pH
b. moisture
c. oxygen supply
d. salinity
e. all of the above
44. A type of microscope which
provides a three dimensional view
of the soil microorganisms is called

a. light microscope
b. scanning electron microscope
c. transmission electron microscope
d. immuno-fluorescent microscope
e. none of the above
45. A 1:1000 soil water dilution
means that 1 part of soil is
suspended in

a. 9 parts of sterile H2O

b. 99 parts of sterile H2O
c. 999 parts of sterile H2O
d. 1000 parts of sterile H2O
e. none of the above
46. In a legume biological nitrogen
fixing system, the microsymbiont is

a. bacteria b. actinomycetes
c. algae d. fungi
e. none of the above
47. CO2 evolution in soil is a function
of

a. microbial population
b. aeration
c. pH
d. temperature
e. all of the above
48. The amount of molecular nitrogen
(N2) in the atmosphere is about

a. 88% b. 78%
c. 68% d. 58%
e. 48%
49. When NO3 is denitrified all the
way to N2, there is a shift in the
valence of N from +5 to

a. +4 b. +3
c. +2 d. +1
e. 0
50. Which of the following bacterial
genera had been known to be
capable of denitrification?

a. Agrobacterium
b. Azospirillium
c. Pseudomonas
d. Thiobacillus
e. all of the above