Soil microbiology

1. Title:-Environmental
Microbiology
Subtitle:- Soil Microbiology
Presented by:- Ayesha, Emania,Arooj,
Ishra,kainat, Tooba
Roll No:-13,43,14,12,44,34
Bs Zoology (8 semester)
Submitted to:- prof. Kamran saeed paracha

2. Outline
• Physical Characteristics of Soil
• Microbial Flora of Soil
• Interactions among Soil
Microorganisms
• Biogeochemical Role of Soil
Microorganisms
• Biochemical Transformations of
Nitrogen and Nitrogen Compounds
• Biochemical Transformations of Carbon
and Carbon Compounds
• Biochemical Transformations of Sulfur
and Sulfur Compounds
• Biochemical Transformations of
Other Elements and Their
Compounds
• Biodegradation of Herbicides
and Pesticides

3. Introduction
Soil microbiology encompasses the study of microbial components in soil
and their significance in various ecological and agricultural contexts.
Definition of soil microbiology
Soil microbiology is a branch of microbiology that focuses on the
microorganisms present in the soil environment, including bacteria, fungi,
viruses, and protozoa. It examines their functions, interactions, and
contributions to soil health.

4. Physical characteristics of Soil
• Soil has been deĥned as that region on the earth's crust where geology
and biology meet. From a functional viewpoint, ihe soil may be
considered as the life. The characteristics of the soil environment vary
with locale and climate.Soils differ in depth, physical properties,
chemical composition, and origin.
• Mineral particles
• Organic residues
• Water
• Gases

5. Layers of Soil
A profile of soil is shown in figure:-

6. Cont…
1. Mineral Particles
• The dominant mineral particles in most soils are compounds of silicon,
aluminum, and iron, and lesser amounts of other minerals, including calcium
magnesium. potassium, titanium. manganese, sodium, nitrogen, phosphorus
and sulfur.
• The mineral constituents of soil range in size from small clay particles to large
gravel.
• The physical structure aeration, water- holding capacity,and availability of
nutrients are determined by the proportion of these particles which are
formed by the weathering of rock and the degradative metabolic activities of
microorganisms.

8. Cont…
(2) Organic residues
• A dark coloured soil has rich organic matter than a light coloured soil
• The plants and animals remain deposited on or in the soil contribute
organic substances
• In the last stages of decomposition, such material referred to as "humus"
and it makes the soil more fertile

9. Cont…
3:- Water
• It holds soil particles together
• The amount of water in soil depends on the amount of precipitation and
other adsorbed to the surfaces of particles.
• Various organic and inorganic component of soil are dissolved in soil
water and thus are made available as nutrients for soil inhabitants.

11. Cont…
(4) Gases
• The gaseous phase of soil consists mainly of carbon dioxide, oxygen, and
nitrogen.
• These gases exist primarily in the spaces between soil particles which are
not filled with water although a small amount of gas,especially carbon
dioxide, is dissolved in water.
• Obviously, then, the amount of gases in the soil is related to the amount of
moisture.

12. Microbial Flora of Soil
Function of microbial flora of soil
• They provide inorganic nutrients to plants especially nitrogen and
phosphorus
• They provide certain specific elements that may b limiting factors for plant
growth
• Soil is excellent culture medium for the growth of many kinds of
microorganisms
1. Bacteria. 2. Fungi. 3. Algae. 4. Protozoa
5. Viruses. 6. Rhizosphere

13. Cont…
1. Bacteria
• Bacteria are most dominant group of microorganisms in soil
• The soil bacteria may be autotrophs, heterotrophs,mesophiles,
thermophiles,aerobes, anaerobes,cellulose digesters,sulfur
oxidizers,nitrogen fixer,protein digesters e.t.c

14. Cont…
(2) Fungi
• Next to bacteria fungi are dominant in all types of soil and possess
filamentous mycelium composed of individual hyphae.
• They are usually found on the surface of soil.They exist both in spore and
mycelium stage.
• Fungi are dominantly acidic because acidic environment is not conducive for
the existence of either bacteria or actinomycetes
• The main function of fungi to decompose plant dead organic material
including cellulose,lignin and pectin,fungi improves the physical structure and
water holding capacity of soil.

15. Cont…
Fungi are generally classify into:
1 Ascomycota-ex.Aspergillus
2)zygomycota-ex.Rhizopus,Mucor
3.Basidiomycota-ex. Mushrooms

16. Cont…
(3) Algae
• Algal population in soil is smaller than that of fungi or bacteria
• Soil algal are ubiquitous in nature wherever moisture and sunlight are
available.
• They are generally visible to the unaided eye in the fom of green net on
thesutface of soil and water.
• They may be unicellular or filamentous and belong to the family.
1::Chlorophyceae(Green algae)·contain chlorophyll in their cell
ex.Chlorella,Chlamydomonas.
2:Cyanophyceae(Blue-green algae)-contain phycocyanin and chlorophyll
pigmentex.Oscillatoria,nostoc anabaena

17. Cont…
(4) Protozoan
• Soil protozoa are unicellular and achlorophyllous
• They are characterized by cyst stage in their life cycle which can help
the species to withstand adverse soil condition
• They produce sexually by fusion and asexually by fission
• The number of protozoa are generally found in moist richsol ranges
from a few hundred to several thousand per gram
• Most of the soil protozoa usually feed on bacteria and other organic
material.

18. Cont…
(5) Fungal Viruses
• Fungal virus affect the fungal hyphae and also infect the spores
• Fungal viruses have been reported affect in over 60 species of
fungi.is.Penicillium,Chrysogenum,Aspergillus
• Virus leads to the formation of irregular growth and abnormal
pigmentation
• The relationship between fungal virus and the metabolisms of their
host is poor understood.

19. Interaction among Soil Microorganisms
• The microorganisms that inhabit the soil exhibit many different types
of associations or interactions.Some of the associations are indifferent
or neutral:some are beneficial or positive: others are detrimental or
negative. As each different type of association or interaction is
discovered.
⚬ Neutral association (neutralism)
⚬ Positive or beneficial (mutualism and commensalism)
⚬ Negative or detrimental (antagonism, competition, parasitism,and
predation)

20. Cont….

21. Cont…
(1) Neutral Association (Neutralism)
• Two different species of microorganisms occupy the same environment
without affecting each other.
• For example, each could utilize different nutrients without producing
metabolic end products that are inhibitory.
• Such a condition might be transitory; as conditions change in the
environment, particularly availability of nutrients, the relationship
might change.

22. Cont…
(2) Positive Associations
a. Mutualism.
-Mutualism is an example of a symbiotic relationship in which each organism
benefits from the association. -
Mutualism One type of mutualistic association is that involving the exchange of
nutrient between two species, a phenomenon called Syntrophism.
-It is highly specific and obligatory interaction.
Example:- Rhizobium-legume association

24. Cont…
(B) Commensalism
• The phenomenon of commensalism refers to a relationship between
organisms in which one species of a pair benefits; the other is not
affected.
• It is unidirectional relationship between species.

25. Cont…
(3) Negative Associations
a. Antagonism
• One Species of an organism is inhibited by another species.
• One organism may directly or indirectly inhibited.
• Important for the production of antibiotics.
• Example
• Staphylococcus aureus and Pseudomonas pigments inhibit
germination of Aspergillus Spores.

26. Cont…
(B) Competition
• A negative association may result from competition among species for
essential nutrients.
• In such situations the best adapted microbial species will predominate
or, in fact, eliminate other species which are dependent upon the same
limited nutrient substance.

27. Cont….
© Parasitism
• Parasitism defined as a relationship between organisms in which one
organism lives in or on another organism.
• The parasite feeds on the cells, tissues, or fluids of another organism,
the host, which is commonly harmed in the process.
• The parasite is dependent upon the host and lives in intimate physical
and metabolic contact with the host.
• All major groups of plants, animals, and microorganisms are
susceptible to attack by microbial parasites.

28. Cont…
Example:-
• An interesting example of a parasitic relationship between microbes is
the bacterial parasite of Gram-negative bacteria named Bdellovibrio
bacteriovorus, which is widespread in soil and sewage. This unusual
motile bacterium attaches to a host cell at a special region and
eventually causes the lysis of that cell. As a consequence, plaque like
areas of lysis appear when these parasites are plated along with their
host bacteria.
• There are also many strains of fungi which are parasitic on algae and
other fungi by penetration into the host.

29. Cont…
(D) Predation
• The prey-predator relationships where predator (hunter)feeds on its
prey (hunted).
• The prey can be larger or smaller than predator and this normally
results in death of prey.
• Interaction is of short duration.
• Example:- Bdellovibrio, Vampirococcus, Daptobacterete are examples
of predator bacteria that can feed on wide range of bacterial
population.

30. Biogeochemical Role of Soil
Microorganisms
Soil microorganisms serve as biogeochemical agents for the conversion OF
SOIL MICROORGANISM constituent elements. The overall process is called
mineralization. This conversion of complex organic compounds into
inorganic compounds or elements provides for the continuity of elements
(or their compounds) as nutrients for plants and animals including people.
In the following paragraphs we shall discuss the role of soil microorganisms
with respect to the transformations they bring about on nitrogen, carbon,
sulfur,phosphorus. and their compounds.

31. The Nitrogen Cycle
Nitrogen Cycle is a biogeochemical process through which nitrogen is converted
into many forms, consecutively passing from the atmosphere to the soil to
organism and back into the atmosphere.
• Nitrogen fixation
• Ammonification
• Proteolysis
• Nitrification
• Reduction of nitrate to ammonia
• Denitrification

32. Cont…
1. Nitrogen Fixation
A number of microorganisms are able to use molecular nitrogen in the
atmosphere as their source of nitrogen. The conversion of molecular
nitrogen into ammonia is known as nitrogen fixation Two groups of
microorganisms are involved in this process:
(1) those living freely and independently in the soil; and.
(2) symbiotic microorganisms, those living in roots of plants.

33. Cont…
Symbiotic Nitrogen Fixation
Symbiotic nitrogen fixation is a process in which certain microorganisms,
typically bacteria, form a symbiotic relationship with plants and convert
atmospheric nitrogen (N2) into a form that can be used by the plant.
Example:-
Legume-Rhizobia Symbiosis:- Legumes, such as beans and peas, form
symbiotic relationships with Rhizobia bacteria.

34. Cont…
Non- Symbiotic Nitrogen Fixation
Non-symbiotic nitrogen fixation refers to the process by which certain
microorganisms, such as bacteria and cyanobacteria, convert atmospheric
nitrogen (N2) into a usable form, such as ammonia (NH3) or nitrate (NO3-),
without forming a symbiotic relationship with plants.Example:-
• Azotobacter: A genus of bacteria that can fix nitrogen in soil.
• Cyanobacteria:: Certain species of cyanobacteria, such as Anabaena
and Nostoc, can fix nitrogen in aquatic environments.

35. Cont…
2:-Ammonification
The end products of proteolysis are amino acids. Their fate in the soil may
be utilization as nutrients by microorganisms or degradation by microbial
attack. Amino acids are subject to a variety of pathways for microbial
decomposition.
An example of a specific deamination reaction is

36. Cont…
3:- proteolysis
The nitrogen in proteins (as well as in nucleic acids) may be regarded as the
end of the line as far as synthesis of nitrogenous compounds is concerned.
The nitrogen in proteins is "locked' and is not available as a nutrient to
plants.
In order to set this organically bound nitrogen free for reuse, the first
process that must take place is the enzymatic hydrolysis of proteins
(proteolysis).

37. Cont…
4:- Nitrification
Microorganisms convert ammonia to nitrate, and the process is called
nitrification. The process occurs in two steps, each step performed by a group
of bacteria

38. Cont…
5:-Reduction of Nitrate to Ammonia
Several heterotrophic bacteria are capable of converting nitrates into nitrites
or ammonia. This normally occurs under anaerobic conditions, e.g., in
waterlogged soil. The oxygen of the nitrate serves as an acceptor for electrons
and hydrogen. The process involves several reactions, and the overall result is

39. Cont…
6:-Denitrification
• The transformation of nitrates to gaseous nitrogen is accomplished by
microorganisms in a series of biochemical reactions. The process is
known as denitrification.
• From the standpoint of agriculture, this is an undesirable process in
that it results in loss of nitrogen from the soil and hence a decline in
nutrients for plant growth.
• Species of several genera of bacteria are capable of transforming
NO3to N2,e.g., Achromobacter, Bacillus, Chromobacterium,
Flavobacterium, Pseudomonas.

40. Cont…
The overall biochemical reaction which expresses the process of denitrification is as :

41. Fig:-Nitrogen Cycle

42. The Carbon Cycle
The ultimate source of organic carbon compounds in nature is the carbon
dioxide present in the atmosphere (or dissolved in water). Although green
plants and algae are the most important agents of carbon dioxide fixation,
1:-Carbon dioxide Fixation
1:-Utilization of carbon dioxide by autotrophic bacteria; the carbon dioxide
represents the sole source of carbon for these organisms and is transformed by a
reduction reaction to carbohydrates. The general reaction is

43. Cont…
2:-Organic Carbon Compound Degradation
The organic carbon compounds that eventually are deposited in the soil are
degraded by microbial activity. The end product, carbon dioxide, is released
into the air and soil. Fresh air contains approximately 0.03 percent carbon
dioxide by volume. Bacteria and fungi are the principal microorganisms that
degrade organic carbon compounds.
The most abundant organic material in plants is cellulose. It is readily
attacked by many species of bacteria and fungi.

45. Fig:-Carbon Cycle

46. The Sulphur Cycle
Some of the biochemical changes by microorganisms involved in this cycle
may be summarized as follows:
1:- Sulfur in its elemental form cannot be utilized by plants or animals.
Certain bacteria, however, are capable of oxidizing sulfur to sulfates. The
classical example is Thiobacillus thiooxidans, an autotroph; the reaction
involved

47. Cont…
2:- Sulfate is assimilated by plants and is incorporated into sulfur-containing
amino acids and then into proteins. Degradation of proteins (proteolysis)
liberates amino acids, some of which contain sulfur. This sulfur is released
from the amino acids by enzymatic activity of many heterotrophic bacteria.
The following reaction is an example:

48. Cont…
3:- Sulfates may also be reduced to hydrogen sulfide by soil microorganisms.
An example of bacteria involved in this process is the genus
Desulfotomaculum, and the reaction suggested is

49. Cont…
4:- Hydrogen sulfide resulting from sulfate reduction and amino acid
decomposition is oxidized to elemental sulfur. This reaction is characteristic
of certain pigmented (photosynthetic) sulfur bacteria and is expressed as

51. Biochemical Transformations of Others
Elements And Their Compounds
The preceding discussion was concerned with transformations of nitrogen
carbon and sulphur and their compounds.But this represents only a part of
the elements and their compounds that are subject to assimilation and
dissimilation by microorganisms (production of acids ) solubilizes phosphate
from insoluble calcium, iron, and aluminum phos- phates. Phosphates are
released from organic compounds such as nucleic acids by microbial
degradation. Bacteria change insoluble oxides of iron and man- ganese to
soluble manganous and ferrous salts. The reverse is also possible .

52. Biodegration of Herbicides and
Pesticides
Herbicides are chemical substances that kill plants, especially weeds;
pesticides,as the term denotes, are chemical substances that destroy
pests.
An ideal pesticide compound would be one that destroys the pest quickly,
and, in turn, the pesticide compound would be degraded to more
elementary nontoxic substances. The soil is the”sink" which receives the
pesticide, and it is the soil microbiota that we depend upon to degrade
the compound.

53. Cont…
As an example to illustrate the
results of research on this topic, Fig.
25-17 shows the rate of
disappearance (degradation) of a
pesticide deposited in the soil. This
aspect of soil microbiology, namely,
the impact of and the fate of,
pesticides deposited in the soil, is a
subject of growing concern.
Degradation of PCP (pentachiorophenol) in so
by indigenous and inoc- ulated bacteria under
labo- ratory conditions at 30°C.