This document provides an overview of an agricultural microbiology course taught by Dr. Dawit getahun at ODA BULTUM UNVERSITY. The course covers topics such as the definition and historical development of microbiology, types of microscopes, microbial culture techniques, classification of microorganisms, characteristics of bacteria, microbes important in agriculture, plant pathogenic microbes, the role of microbes in nutrient cycles, and microbial interactions in soil. The objective is for students to learn about microorganisms important in agriculture and how to handle and identify them.

1. Agricultural Microbiology
Complied By Dr. Dawit getahun (Ph.D)
(Assistant professor in Plant Pathology)
ODA BULTUM UNVERSITY

2. Course Description
• Definition and historical development of Microbiology
• Types and structure of microscopes
• Culture techniques;
• Classification of microorganisms into different groups;
• Characteristics of bacteria;
• Microbes in rhizosphere and phyllosphere
– Morphology ,
– biology,
– nutrition,
– reproduction and classification of microorganism and other
microorganisms of agricultural importance;

3. Microbiology of plant pathogenic microbes;
Role of different microbes in nutrient transformations and
nitrogen fixation
Microbial interaction in the soil system;
 Like composting and decomposition of organic matter
through microbes; biodegradation of pesticides;
mycorrhizae and
 Their role in agriculture and commercial use of bio
Course Description

4. Objective of agricultural
microbiology course
By the end of the course, students will be able:
 To know microorganisms of agricultural importance and
techniques of their handling;
 To describe the importance of agricultural microbiology;
 To recognize microorganisms of agricultural importance:
bacteria, fungi and viruses;
 To understand laboratory techniques for culturing and
identification of microorganisms; and

5. 1.1. General Introduction and Scope of Microbiology
What is microorganism?
Technically a microorganism or microbe is an organism that is
microscopic
 So, they can be seen and studied only with the help of microscope
 They are an organism too small (less than 0.1 mm in size) to be seen by naked
eyes.
 The human eye is not able to perceive (see) objects with a diameter of less than
0.1 mm size, therefore an object must be required to magnify at least 0.1mm to
preferably 0.2mm for clear vision.
 Being too small to be seen with unaided eyes, these organisms are termed as
microorganisms.
Chapter 1. Introduction

6. What is microbiology?
 Microbiology often has been defined as the study of organisms and agents too
small to be seen clearly by the unaided eye.
 That is, the study of microorganisms.
 Because objects less than about 1mm in diameter cannot be seen clearly and
 Must be examined with a microscope, microbiology is concerned primarily
with organisms and
 Agents this small and smaller.
 The term microbiology derived from three Greek words mikros [small] bios
[life] and logos [study].
 The term microbiology was introduced by a french Chemist Louis Pasteur,
who demonstrated that fermentation was caused by the growth of bacteria and
yeast.
 He is known as father of microbiology.
1.1. General Introduction and Scope of
Microbiology

7.  Microbiology is the study of microorganisms which requires some form of
magnification ( Microscope) to be seen clearly
 Examples of microrganisim:
 Viruses
 Bacteria
 Fungi
 Algae
 Protozoa's
 Most microorganisms are unicellular in which all the life processes are
performed by a single cell.
 All living cells contain protoplasm which is a colloidal organic complex
consisting of largely proteins, lipids and nucleic acids.
1.1. General Introduction and Scope of Microbiology….

8.  Some organisms studies by microbiologists CAN be visualized without the aid
of amplification [bread molds (fungus) and filamentous algae]
 These organisms are included in the discipline of microbiology because of
similarities in properties and techniques used to study them
 Techniques necessary to isolate and culture microorganisms:
 Isolation
 Sterilization
 Culture in artificial media
1.1. General Introduction and Scope of Microbiology….

9. 1.1. General Introduction and Scope of Microbiology….
• It is concerned with microbial
• Form, Structure,
• Reproduction,
• Physiology,
• Metabolism and
• Classification.
• It includes the study of
• Their distribution in nature,
• Their relation ship to each other and
• Other living organisms, their effects on human beings and on other
animals and plants,
• Their abilities to make physical and chemical changes in our
environment and
• Their reactions to physical and chemical agents.

10. 1.1. General Introduction and Scope of Microbiology….
 Microbes Distribution in Nature:
They are Omnipresent: Generally microorganisms are everywhere in nature
and grows where they get food, moisture and temperature.
 Occurrence
• Air
• Soil
• Water, Oceans
• Food we eat
• Surfaces of our body (Skin) and inside alimentary canal also.

11. Scope of microbiology
 Microbiology has both basic and applied aspects
 Basic aspects are concerned with biology of microorganisms themselves and
includes fields like
 Bacteriology.
 Mycology.
 Phycology.
 Protozoology.
 Microbial cytology and physiology.
 Microbial genetics.
 Molecular biology.
 Microbial ecology.
 Microbial Taxonomy.

12. • Applied aspects are concerned with practical problems.
• These are:
 Disease study.
 Water and waste water treatment.
 Food spoilage and food production.
 Industrial uses of microbes.
 Medical microbiology,
 Immunology,
 Industrial microbiology,
 Agricultural microbiology are widely studied fields of microbiology.
Scope of microbiology….

13. What is agricultural microbiology
Scope of microbiology…
 Agricultural microbiology is a field of study concerned about
 Plant-associated microbes .
 Plant and animal diseases.
 It also deals with the microbiology of soil fertility, such as microbial
degradation of organic matter and soil nutrient transformations.
 Agr. Microbiology also deals with BIOGEOCHEMICAL CYCLES like
 carbon cycle
Nitrogen cycle
Sulfur cycle
 Plant Microbe Interactions
Symbionts: beneficial relationships
Pathogen: harmful relationship

14. Therefore, getting inside into the causes,
 mode of dissemination, prevalence and control of those diseases requires
basic understanding of microbiology under sub-discipline called
A. Plant Pathology is basically the study of microorganisms that cause
disease in plants.
• The microorganisms which cause diseases in the plants are called as plant
pathogens.
Scope of microbiology…

15. B. Antagonism: In contrasting to plant pathogens, certain native microorganisms present
in the soil feed upon (or antagonistic to) these pathogens and can prevent the infection of
crop plants.
 This particular behavior of microorganisms is called antagonism.
 Literally, antagonism is an interaction between two organisms where one
organism benefits at the cost of harm to another organism.
 In case of plant pathogens, antagonism usually involves competition between
two microorganisms for
such as antimicrobial metabolites, secondary metabolites, antibiotics
and extracellular enzymes.
Scope of microbiology…

16. 1.2. Historical Development of Microbiology
Discovery of Microbiology
 Robert Hooke (1665) is the first person to report seeing microbes
under the microscope.
 He is working with a crude compound microscope and he saw the
cellular structure of plants around.
 He also saw fungi which he drew.
 However, because his lenses were of poor quality he was apparently
unable to "see" bacteria.

18. History
One of the most important discoveries of biology
occurred in 1665, with the help of a crude
microscope, when Robert Hooke stated that life’s
smallest structural units were cells.
ANTONY VAN LEEUWENHOEK (1632-1723) was
the first one to provide somewhat accurate
information about microorganisms.
His microscope had a magnification of 50-300X.

19. Theory of Spontaneous Generation
Early belief that some forms of life could arise from
“vital forces” present in nonliving or decomposing
matter, abiogenesis. Or simply, organisms can arise
form non-living matter.
But this theory was later challenged by many scientists.

20. Francesco Redi (1626-
1697)

21. John Needham and Lazzaro Spallanzani were still
supporting theory of spontaneous generation by
proving that air carried germs to the culture media.
Schwann, Friedrich Schroder and von Dusch (1830s)
disproved them by allowing air to enter flask but only
after passing through a heated tube or sterile wool, so
no growth appeared.
Still some scientists believed in theory of spontaneous
generation.

22. Pasteur’s Experiment
• These assumptions provoked Louis Pasteur (1822-
1895) to settle the matter once and for all.
• He first trapped airborne organisms in cotton, then
showed , that piece of cotton caused microbial growth
when placed in sterile medium. Then he did another
experiment to solve the controversy.
• Considered by many as “ Father of Microbiology”

23. Pasteur’s
Experiment

24. • John Tyndall (1820-1893) – dealt a final blow to
spontaneous generation theory in 1877 by
demonstrating that Omission of dust no growth
of microorganisms.
• He also provided evidence for heat resistant forms of
bacteria.
• A German botanist Ferdinand Cohn (1828-1898)
discovered existence of bacterial endospores.

25. Demonstrations that microorganisms cause
disease
• The first direct demonstration of the role of bacteria
in causing disease came from the study of anthrax by
German Physician Robert Koch (1843-1910).
• His criteria (is still used) to establish the link between
a microorganism and a particular disease that it cause,
is known as Koch's postulates.

26. Koch’s Postulates
• The causative agent must be present in all affected
organisms but absent in healthy individuals.
• The agent must be capable of being isolated and
cultured in pure form.
• When the cultured agent is introduced to a healthy
organism, the same disease must occur.
• The same causative agent must be isolated again from
the affected host.

27. Classification
• Classifying microorganisms has always
been a challenge for taxonomists, as they are
diverse.
• Some microorganisms are motile like animals,
but also have cell walls and are photosynthetic
like plants…..
• These observations eventually led them
to the development of a classification

28. Five Kingdom
System
➢Monera
➢Protista
➢Fungi
➢Animalia
➢Plantae

29. Three Domain
system
➢Bacteria
➢Archea
➢Eucarya
➢Carl Woese in 1970’s proposed this system.

30. Bacteria
• Prokaryotes
• Single-celled organisms
• Cell wall Peptidoglycan.
• Abundant in Soil, water, air and are the normal
resident of skin, nose, mouth and intestine.
• Some live in extreme temperatures.
• They have harmful aspects but are usually beneficial
as well.

31. Archea
• These are bacteria but are different due to their rRNA
sequence.
• Cell wall composition is change as they lack
peptidoglycan but contains lipids.
• Unique feature is that some are methanogens.
• Archea are found in environments that are too hostile
for other life forms.
• No pathogenic archea have yet been identified.

32. Eucarya
• Multicellular organisms.
• The true nucleus is one of the distinguishing features
of eukaryotes
• Contains microbes classified as protists or fungi.
• Animals and plants are also included in this group.

33. Protists
• These are larger than prokaryotes.
• It includes unicellular algae, protozoa, slime molds
and water molds.

34. Algae
• The term algae has long been used to denote all
organisms that produce Oxygen as a product of
photosynthesis.
• All algae contain chlorophyll in their chloroplast.
• Many algal species are unicellular.
• Other algae may form extremely large multicellular
structures.

35. • A number of algae produce toxins that are poisonous to
humans and other animals.
• Dinoflagellates, a unicellular alga, cause algal blooms, or red
tides, in the It produces neurotoxins which is
accumulated in
ocean.
the shellfish, as shellfish feeds on this
organism. Ingestion of these shellfish by humans results in
paralytic shellfish poisoning and can lead to death.
• Together with cyanobacteria (blue green algae), it produces
about 75% of planet’s Oxygen.
• It forms foundation of aquatic food chains.

36. Protozo
a
• Protozoa are unicellular non photosynthetic protists.
• It seems likely that the ancestors of these protozoa
were algae that became heterotrophs—the nutritional
requirements of such organisms are met by organic
compounds.
• Adaptation to a heterotrophic mode of life was
sometimes accompanied by loss of chloroplasts, and
algae thus gave rise to the closely related protozoa.
Similar events have been observed in the laboratory
to be the result of either mutation or physiologic
adaptation.

37. • Many free living protozoa's are hunter of microbes.
• They obtain nutrients by digesting organic matter and
microbes.
• They are present in different environments, some are
normal inhabitants of intestines of animals and helps
them in digesting cellulose.
• Few of them causes diseases in animals and humans.

38. Fungi
• Diverse group of microorganism that range from
unicellular (yeasts) to multicellular fungi (molds and
mushrooms).
• They absorb nutrients from environment including
organic molecules, that they use as carbon and
energy source.
• They have metabolic capabilities, so many fungi are
beneficial in making bread rise, producing antibiotics,
decomposition of dead organic matter.
• Some causes diseases in humans, animals and plants.

39. • The fungi are non photosynthetic protists growing as a mass of
branching, interlacing filaments (“hyphae”) known as a
mycelium.
• These tubes, made of polysaccharides such as chitin, are
homologous with cell walls. Yeasts, do not form a mycelium
but are easily recognized as fungi by the nature of their sexual
reproductive processes.
The fungi probably represent an evolutionary offshoot of the
protozoa; they are unrelated to the actinomycetes, mycelial
•
superficially resemble. The major
of fungi are Chytridiomycota,
bacteria that
subdivisions
Zygomycota
they
(phyla)
(the zygomycetes), Ascomycota (the
ascomycetes), Basidiomycota (the basidiomycetes), and the
“deuteromycetes” (or imperfect fungi).

40. Slime molds
• These organisms are characterized by the presence, as a stage in their life
cycle, of an ameboid multinucleate mass of cytoplasm called a plasmodium.
The plasmodium of a slime mold is analogous to the mycelium of a true
fungus. Both are coenocytic (an organism made up of a multinucleate,
continuous mass of protoplasm enclosed by one cell wall). In slime molds
the cytoplasm can flow in all directions. This flow causes the plasmodium to
migrate in the direction of its food source, frequently bacteria.
• The life cycle of the slime molds depends upon interdependency of living
forms. The growth of slime molds depends on nutrients provided by
bacterial or, in some cases, plant cells. Reproduction of the slime molds via
plasmodia can depend on intercellular recognition and fusion of cells from
the same species.

41. Scope of microbiology
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42. • Microbiology has both basic and applied aspects.
• Basic aspects are concerned with biology of microorganisms
themselves and includes fields like
➢ Bacteriology.
➢ Mycology.
➢ Phycology.
➢ Protozoology.
➢ Microbial cytology and physiology.
➢ Microbial genetics.
➢ Molecular biology.
➢ Microbial ecology.
➢ Microbial Taxonomy.

43. Applied aspects are concerned with practical problems.
These are:
Disease study.
Water and waste water treatment.
Food spoilage and food production.
Industrial uses of microbes.
Medical microbiology, Immunology, Industrial
microbiology, Agricultural microbiology are also
widely studied fields of microbiology.