Microbiology

CSU-025: Fundamentals of Microbiology
Practical - 2: Compound Microscope

Compound microscope
Thank you
Dr Richa Kaushal
Faculty of Applied Sciences and Biotechnology
Shoolini University
Village Bajhol, Solan (H.P)
Lecture 1: Introduction of Microbiology
Topics to be covered today
1. Introduction of microbiology
What is microbiology
Study of Micro-organisms: Organisms that EXIST as Single Cells or
cell clusters and must be viewed individually with the aid of a
Microscope
1. EXIST (Webster definition)To continue to be, have life; live
HALLMARKS OF LIFE
1. METABOLISM (nutrient uptake, biomass, waste
output)
2. DIFFERENTIATION (Bacillus spp. Caulobacter)
3. REPRODUCTION (binary fission)
4. COMMUNICATION (Pseudomonas aeruginosa)
5. EVOLUTION (antibiotic resistance, pathogens)
Metabolism
• Take in nutrients from the environment
• glucose, lactose, other sugars, fats=lipids, proteins,
• toxic wastes, oils and petrol
• Assimilate the nutrients into BIOMASS

• DNA, proteins, carbohydrates and
• complex carbohydrates, lipids
• Release waste products into the environment

• gases, alcohols, acids and organic compounds
Differentiation— to form distinct structures
K.C. Keiler M. Dworkin

Differentiation— to form distinct structures
Anabaena spp. Cyanobacteria

Bacillus spp. endospore forming cells forming heterocysts
T.J. Deveridge M. Dworkin

Reproduction
To generate progeny of ones same type
A bacterium duplicates its DNA and forms a daughter cell via binary fission
Yeast duplicates its DNA and forms a daughter cell via budding, or mates with
another yeast cell and produces haploid progeny.
J. Pitocchelli E. Hettema
Communication
interaction with
other cells—response to other cells
Vibrio fischeri and Lantern fish
Kolter and
Losick
Communication
Biofilms and
Health
www.med.umich.edu
Evolution
• To change ones genetic make up (DNA sequence) to adapt to ones environment
• Bacteria can take up DNA from the environment or other cells via
• Transformation—uptake of naked DNA
• Transduction—phage (bacterial specific virus) mediated

• uptake of DNA
• Conjugation—uptake of DNA that requires the interaction

• of two bacteria
Antibiotic resistance, bacterial

pathogenesis
What is microbiology
• Study of Micro-organisms: Organisms that EXIST as Single
• Cells or cell clusters and must be viewed individually with the
• aid of a Microscope
2. KEYWORD single CELLS
(OR cell clusters)
• CHARACTERISTICS THAT MICROORGANISMS HAVE THAT MAKE THEM TRUE CELLS
1. CELL MEMBRANE –barrier that separates the inside of the cell from the outside
2. NUCLEUS OR NUCLEIOD – location of genetic information (DNA)
3. CYTOPLASM –location of the machinery for cell growth and function
4. MACROMOLECULES – proteins, nucleic acids, lipids, polysaccharides
3. KEYWORD exist as SINGLE cells
(OR cell clusters)
• We are multicellular creatures—made up of many cells

• What makes one of our cells different from a microbial cell??
• A single microbial cell can have an independent existence—our
• specialized cells need to interact with other cells in order to carry
• out their cellular functions for the good of the entire organism.
What organisms are considered to be microbial
cells and studied in microbiology
1. BACTERIA
2. FUNGI
3. ALGAE
4. PROTOZOA
5. Viruses(although not a cellular entity but an intracellular pathogen)
6. Prions (a biochemical anomaly—misfolded proteins)
7. Helminths Worms (multicellular)
Taxonomy
• The study of phylogenetic relationships between organisms
• (The sorting of all living things based on their related or differentiating features)
• KINDOM the highest level in classification
• PHYLUM related classes
• CLASS related orders
• ORDER related families
• FAMILY related genera

• GENUS closely related species
• SPECIES organisms sharing a set of biological traits and
• reproducing only with their exact kind
• Further classifications especially with bacteria:
• Strain—organisms within a species varying in a given quality
• Type—organisms within a species varying immunologically
Taxonomy::relatively easy to classify animals and plants
based on their behaviour and appearance—old school
Taxonomy::initially not easy to classify microorganisms
based on their behaviour and appearance
• Advancements in DNA amplification and DNA sequencing has greatly

helped
• The phylogenetic relationships between microorganisms can be
determined by sequencing the 16S and 18S ribosomal RNA of the
organisms in question
• (ribosomal RNA—structural RNA of the ribosome that plays a role in

protein synthesis)
Phylogenetic classification of micro-organisms
(new school) Eukaryotic
Algae
Prokaryotic Fungi
Eubacteria Archaeabacteria Protozoa
Universal Ancestor
Phylogenetic classification of micro-organisms
• EUBACTERIA most abundant of the bacteria found in soil, water and

animal digestive tracts
• ARCHAEACTERIA live in extreme conditions (temperature, pH etc)
mostly anaerobic (unable to live in the presence of oxygen)
• EUKARYOTES algae: live in soil and water, contains chlorophyll for
photosynthesis, has a cell wall
• fungi: yeast, molds. Lack chlorophyll and obtains energy from organic
compounds in soil and water, has a cell wall
• protozoa: colorless, lacks a cell wall, ingests other organisms or organic
particles
Major Differences between prokaryotic and
eukaryotic micro-organisms
• Prokaryotes
1. Nonmembrane bound nucleiod region
2. DNA-one circular molecule one chromosome
3. Haploid-One copy of a gene
4. Plasma membrane does not contain sterols
5. Reproduction—simple binary fission
• Eukaryotes
1. Membrane bound nucleus containing DNA
2. DNA-linear molecules arranged to form several chromosomes
3. Diploid-Two copies of a gene
4. Plasma membrane contains sterols
5. Reproduction—meiosis and mitosis
6. Presence of membrane bound organelles such as chloroplasts and mitochondria
Why study Microbiology ??
• Microbiology as a BASIC Science

• Bacteria and yeast are useful in studying molecular biology, biochemistry and genetics
• --reproduce rapidly
• --are genetically (DNA) and biochemically more simple than higher order organisms
• -working with bacteria and yeast for understanding life processes has no ethical
ramifications
• Microbiology as an APPLIED Science
• Medicine—Vaccine development, production of antibiotics,
• production of important biological enzymes (insulin)
• Industry—Production of beer, wine, cheeses and yogurt
• Agriculture—maintenance of soil fertility/digestion in cattle
• Ecology—Bioremediation—microorganisms that degrade toxic waste materials

Thank you
Dr Richa Kaushal
Shoolini University
FSU-008: Fundamentals of Microbiology
Lecture 2: History of Microbiology
Recap from last lecture
1. Introduction of microbiology
1. History of microbiology
Origins of
Microbiology
Outline
• Cells and cell theory

• Microbes and Germ Theory
• Classic Age of Microbiology
–Fermentation
–Pasteurization
–Vaccines
Primitive health codes
• Laws of Moses (Numbers, Deuteronomy)

• Venereal diseases
–acquired from infected individuals
–kill infected individual
• Trichinosis
–lack of fuel
–Undercooked pork spreads the parasite
–ban eating of pork
First Observations
• Robert Hooke cells
• Leeuweenhoek: microbes
Micrographia
• Robert Hooke
• First report of cell structure
1665
• ‘Little boxes’ in cork : CELL
First illustrated
book on
microscopy
Anton Van Leeuwenhoek
• First person to see bacteria

• Single lens microscope
Early Compound
Microscope
• beautifully crafted but had

severe chromatic distortion
Simple microscopes gave better
resolution
• Spermatozoa from man
and dog
• Leeuwenhoek
• 1678
Spontaneous Generation
vs
Biogenesis
The Great Debate

• Redi (1668)
• Needham (1745)
• Spallanzani (1765)
• Virchow (1858)
• Pouchet (1859)
• Pasteur(1861)
• Aristotle: any damp body gives rise to living things
– Miasma
– phoenix myths
– “Golam”
• Herodotus: Living organisms could arise from non living matter
– crocodiles from mud
• Van Helmont: small animals only
– maggots from meat
– mice from feed
Francesco Redi
• Italian poet physician 1668
• Tested hypothesis of Spontaneous Generation
–Meat in jars
- three jars open to air> maggots
- three jars sealed >no maggots
- three jars fine net>no maggots
• Concluded spontaneous generation did not still occur
John Needham
• Irish priest 1745
• Said microbes spontaneously generated
• Evidence
–Heated chicken soup
–poured into flasks
–covered flasks
–microbes appeared
Problems with experimental design??

Lazzaro Spallanzani
• Italian Monk 1765
• Said Needham’s broths contaminated after heating
• Evidence
–chicken soup poured into flasks
–covered flasks
– then heated soup
–microbes DID NOT appear
“ Production without parent of a new living organism” (Pouchet

1859)
• Required
– a solid organic substance just after death
–air containing “Life Force”
–water
Frankenstein??
Biogenesis
• Concept proposed by Rudof Virchow
–German Scientist 1858
• Virchow had No Evidence
Biogenesis or cell theory: cells can

only arise from preexisting cells
Biogenesis
Omne vivum ex vivo
Harvey
The Cell Theory
• All organisms composed of one or more cells
• Cells are smallest living things
• Cells arise only from previously existing cells
• Thus: all organisms are descendents of the first cells
Schwann Experiment
• Broth heated in flask

• Air heated
• Air and broth mixed
• No Growth
Pouchet argued that “Life Force”

destroyed
Academy of Sciences 1860
Award for a solution
21
And the Winner is..??
• Louis Pasteur
• Confirmed experiments of Redi and
Schwan
• Filtration Experiments
–air filtered through guncotton
–dissolve guncotton
–Examined residue
–contained microbes and dust
• Conclusion: microbes in the dust not in
air
Final Proof
Swan Neck Flask Experiment
• Add broth to flask
• Bend the neck of the flask(air can enter but dust cannot)
• Heat broth
• No bacterial growth
• Break neck of flask
–dust enters
–Growth occurs
Altitude Measurements
• Arbois (sea level ) 8/20 flasks contaminated
• Jara (850 meters) 5/20 flask contaminated
• Mer de Glace (2,000 meters) 1/20
Louis Pasteur
• Added 20 years to the

lifespan of every man
woman and child
• improved the quality of life
Golden Age of Microbiology
• Fermentation
• Pasteurization
• Disinfection
• Vaccines
French wine was spoiled during
shipment
Louis Pasteur
• Germ theory
• Fermentation
• Pasteurization
• Rabies vaccine
• Streptococcus pneumoniae causes lobar pneumonia
Fermentation
• Vintners thought sugar chemically converted to alcohol in air
• Pasteur, a chemist, was asked to help
• Discovered
–Yeast convert sugars to alcohol
–Bacteria change alcohol to vinegar
• Fermentation was biological process
Pasteurization
• Pasteur connected food spoilage

and microbes
• Pasteurization: Destroy microbes
that cause spoilage by heat
–Beer, wine, milk
• Critical to development of Germ
theory
Pasteur’s Original Flasks
Germ Theory of Disease
• Causal relationship between microbes and disease
• Disinfection controls surgical infection
• Microbes cause disease
Joseph Lister
Developed antiseptic surgery

Robert Koch
• Confirmed germ theory

• Discovered cause of
–anthrax
–cholera
–tuberculosis
• Developed
–pure culture techniques
–staining techniques
–solid media
Koch’s postulates
Rules to prove an organism
causes a disease
• Organism consistently isolated from diseased individuals

• Organism cultivated in pure form
• Signs and symptoms induced after inoculation
• Same organism isolated from experimentally infected individual
Vaccines:
Smallpox
• isolated smallpox virus from pustules on Egyptian mummies
• Father of Amhetop
Pustules Caused by Pox Virus
Edward Jenner
Edward Jenner
Vaccination
for smallpox
Jenner: Cowpox Cartoon
Rabies vaccine
• Pasteur described a rational

basis for the development of
vaccines
Thank you
Dr Richa Kaushal
Shoolini University
FSU-008: Disciplines of microbiology
Lecture 3
1. History of microbiology
1. Disciplines of microbiology
Microbiology
Microbiology - The science that studies very small living things
Usually requires a magnification tool – the microscope
Sub groups of Microbes we will study
Bacteria
Archaea
Fungi
Protozoans
Algae
Viruses
Bacteria
Fungi
Protozoans
Giardia Amoeba
Viruses
Bacteriophage Avian Flu

Various disciplines of study within microbiology
➢ Bacteriology
➢ Mycology
➢ Parisitology
➢ Immunology
➢ Epidemiology
➢ Biotechnology
➢ Virology
➢ Environmental Microbiology
➢ Bioremediation
Thank you
Dr Richa Kaushal
Shoolini University
FSU008: Bacteria
Lecture 4
1. Bacteria
What are bacteria?
• Single celled organisms
E. Coli O157:H7 can
make you very sick.
• Very small
• Need a microscope to see
• Can be found on most materials and Streptococcus

surfaces can cause strep
throat.
–Billions on and in your
body right now
This E. coli helps you digest
food.
Structure of Bacteria
What do they look like?
•Three basic shapes
–Rod shaped called bacilli (buh- Bacilli
sill-eye)
–Round shaped called cocci
(cox-eye)
–Spiral shaped Cocci
•Some exist as single

cells, others
cluster together
Cluster of cocci Spiral

Shapes of Bacteria
Size of bacteria
• Cocci are true spheres with diameter ranging between 0.75 to 1.25 μm (and
average of 1 μm).
• Bacilli varying length from 2-10 times their width.
• Coccobacilli are very short bacilli.
• Filaments are long threads of bacilli which have not separated into single
cells.
Bacteria are ALIVE!
• What does it mean to be alive?
– They reproduce (make more of

themselves)
– They need to eat

How do bacteria reproduce?
• Grow in number not in size

– Humans grow in size from child to adult
• Make copies of themselves by dividing in half

How do bacteria eat?
• Some make their own food from
sunlight—like plants Photosynthetic
bacteria
• Some are scavengers

–Share the environment around them
- Example: The bacteria in your stomach are now
eating what you ate for breakfast
Harmless bacteria
on the stomach
lining
• Some are warriors (pathogens)
–They attack other living things
- Example: The bacteria on your face can attack skin
causing infection and acne E. Coli O157:H7
is a pathogen
What is a pathogen?
• Bacteria that make you sick
– Why do they make you sick?
- To get food they need to survive and reproduce
– How do they make you sick?
- They produce poisons (toxins) that result in fever, headache, vomiting, and
diarrhea and destroy body tissue
Where do you get a
pathogen?
Indirect contact
• Contact with people who are sick
– Direct or indirect
• Food, Water, or other Surfaces that are contaminated
Foods that
could be
contaminated
Direct contact
A Closer Look – Where do you get a
pathogen
Direct
Contact
Indirect
Contact
Foods and water

may be
contaminated
Are all bacteria pathogens?
• No, most are harmless
• Some are even helpful

–
Examples of helpful bacteria:
- Lactobacillus: makes cheese, yogurt, & buttermilk and
produces vitamins in your intestine
- Leuconostoc: makes pickles & sauerkraut
- Pediococcus: makes pepperoni, salami, & summer

sausage
How can I avoid pathogens?
• Wash your hands often so you won’t transfer bacteria to your
mouth or food
– Warm water with soap for 20 seconds, rub hard between

fingers and nails
How can I avoid pathogens?
• Cook food thoroughly to kill any pathogens that may

be in your food
• Store food properly to limit pathogen growth
– Cold temperatures (40F)

Cell Wall
• The cell wall is the outer most layer of the cell. In many cases
the cell wall comes in direct contact with the environment.
Function:
✓ Protection of the cell.
✓ Maintains the shapes of the cell.
✓ Maintains the osmotic integrity of the cell.
✓ Play an essential role in cell division.
Bacterial classification
Peptidoglycan
• Peptidoglycan, also known as murein, is a polymer consisting of sugars and
amino acids
• The sugar component consists of alternating residues of β-(1,4) linked N-
acetylglucosamine and Nacetylmuramic acid.
• These subunits which are related to glucose in their structure are covalently
joined to one another to form glycan chains.
• Attached to the N-acetylmuramic acid is a peptide chain of three to five
amino acids.
Gram Positive Cell wall
• Usually thick, homogenous, composed mainly of
peptidoglycan.
• It accounts for 50-90% of the dry weight of the cell wall.
• Contain large amount of teichoic acids (polymers of glycerol or
ribitol joined by phosphate group).
Special components of Gram positive cell wall
Teichoic acid
• Teichoic acids are connected to either peptidoglycan or to plasma
membrane lipids.
• Absent in gram negative bacteria.
Function of Teichoic Acid:
• Antigenic determinant (receptor molecule for bacteriophages).
• Participate in the supply of Mg to the cell by binding Mg++
• Regulate normal cell division.
• For most part, protein is not found as a constituent of the G+ cell wall
except M protein on group streptococci.
Gram Negative Cell Wall
• Multi layered and more complex than Gram positive cell walls.
• Peptidoglycan of gram negative bacteria is thin and comprises
only 10% or less of cell wall.
• Outer membrane lies outside the thin peptidoglycan layer.
• Most abundant protein is Braun’s lipoprotein.
Special components of Gram negative cell wall
Periplasm
• The region between the cytoplasmic membrane and the outer
membrane is filled with a gel-like fluid called periplasm.
• In gram negative bacteria, all secreted proteins are contained
within the periplasm, unless they are specifically translocated
across the outer membrane.
• Periplasm is filled with the proteins that are involved in various
cellular activities, including nutrient degradation and transport.
Outer membrane
• Peptidoglycan layer is surrounded by outer membrane in the gram negative
bacteria.
• Its outside leaflet is made up of lipopolysaccharides, rather than
phospholipids.
• For this reason, the outer membrane is also called the lipopolysaccharide
layer or LPS.
• The outer membrane functions as a protective barrier and excludes many
toxic compounds.
Cont…
• Lipopolysaccharide molecule is extremely important from a
medical stand point.
• It consists of three parts, two of them are medically significant.
1. Lipid A…..embedded in membrane.
2. Core polysaccharide…..located on the surface of
membrane.
3.O antigens….which are short polysaccharides extended
out from core.
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 4: Structure and Morphology of Fungi

1. Structure and morphology of fungi

2. Fungal cell
Yeasts
• Unicellular fungi
• Reproduce asexually, often by budding
• Reproduce sexually by formation of spores
Molds
• filamentous fungi
–hyphae (s., hypha)
- the filaments of a mold
- may be coenocytic (no cross walls) or have septa (cross
walls)
–mycelium (pl. mycelia)
- bundles or tangled masses of hyphae
Hyphae
• Hyphae are designed to increase the surface area of fungi and
thus facilitate absorption
• May grow fast, up to 1 km per day, as they spread throughout
a food source
• May be coenocytic, having no septa between cells, or septa
may be present with pores through which cytoplasm can flow
moving nutrients through out the fungus
• Parasitic fungi have modified hyphae called haustoria, which
penetrate the host tissue but remain outside cell membrane
Hyphae
Hyphae
Pores
Septa
Coenocyti
c
The Body of a Fungus
• Fungi exist mainly in the form of slender filaments (hyphae).

–long chains of cells joined end-to-end divided by cross-walls
(septa)
- rarely form complete barrier
- cytoplasm freely streams in hyphae
–mycelium - mass of connected hyphae
- grows through and penetrates substrate
MYCELIUM
• Intertwined filamentous mass formed by hyphae, visible to

the unaided eye
• Forms when environmental conditions are right
• Vegetative mycelium: Mycelial portion remaining INSIDE the
substrate to obtain nutrition
• Reproductive mycelium: Mycelial portion extends into air
,responsible for SPORE reproduction
hypha
mycelia
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 6: General characteristics of algae
Algae
They can be defined as the

small autotrophs that fail to
show any cellular
differentiation & their sex
organs are unicellular & if
multicellular all cells are
fertile
Characteristics
 They are photoautotrophs
 They primarily inhabit aquatic habitats
 The vegetative body does not show any

differentiation into various tissue systems
 They show progressive complexity in
reproduction
 They do not develop embryo after fusion of gamates
during sexual reproduction
 Range in size from microscopic to single celled organisms
to large seaweed
 Many species occur as single cells others as
multicellular
Characteristics
❑ Algal cells are eucaryotic
❑ Study of algae is called phycology
❑ Cellwall is thin and rigid
❑ Motile algae such as euglena have flexible cell

membrane called periplasts
❑ Cell walls of many algae are surrounded by a flexible
gelatinous outer matrix
❑ A discrete nucleus is present
❑ Inclusions like starch granules, oil droplets and

vacuoles are present
❑ Chlorophyll and other pigments are present
❑ Chloroplasts may occur one,two or many per cell they may

be ribbon like ,bar like ,net like,or as discrete discs
THALLUS ORGANISATION:
a)Unicellular algae:
 single cells, motile with flagellate
(like Chlamydomonas and
Euglena) or nonmotile (like
Diatoms).
 Occor in all groups except
carophycae of phylum chlorophyta
and pheophyta.
✓ Rhizopodial
✓ Flagellate
✓ Spiral fillamentous
✓ Nonmotile
b)Colonial algae:
Motile or non motile algae may form a colony by
aggregation of the products of cell division with in a
mucillagenous mass.
 Coenobial :
The colony is formed with a definite shape, size
and arrangement of cells.
Ex: volvox
 Palmelloid :
Irregular arrangement of cells varying in number
,shape and size.
Ex: Chlamydomonas , Tetraspora
 Dendroid:
Looks like microscopic tree due to union of
mucilagenous threads present at base of each cell.
Ex: Chrysodendron
 Rhizopodial colony:
Cells are united through rhizopodia
Ex: Chrysidiastrum
c)Filamentous algae:
 Daughter cells remain attached
after cell division and form a cell
chain
 Adjacent cells share cell wall
Cladophora
(distinguish them from linear
colonies!)
 May be unbranched (uniseriate
such as Zygnema and Ulthrix) or
branched (regular mutiseriate such
as Cladophora or unreguler
mutiseriate such as Pithophora).
1
0
Pithophora
d) Coenocytic or siphonaceaous:
one large, multinucleate cell
without cross walls such as
Vaucheria
e) Parenchymatous:
mostly macro-scopic algae
with tissue of undifferentiated cells
and growth originating from a
meristem with cell division in three
dimensions such as Ulva
REPRODUCTION
MOST REPRODUCE BOTH SEXUALLY

AND ASEXUALLY
–Most sexual reproduction is triggered by
environmental stress
–Asexual Reproduction
- Mitosis
–Sexual Reproduction
- Meiosis
- Zoospores
- Plus and minus gametes
- Zygospore
REPRODUCTION IN
ALGAE
Sexual-
Gametes
Vegetative Asexual Reproduction

Cell .
divisions/Fragmentation
=part of the filament
breaks off from the rest
and forms a new one.
Sexual reproduction
 ISOGAMY-Both gametes have flagella and similar in size and morphology.
 ANISOGAMY-Gametes have flagella but are dissimilar in shape and size. One
gamete is distinctly smaller than the other one.
 OOGAMY-gamete with flagella (sperm) fuses with a larger, non flagellated

gamete (egg).
Reproduction in Multicellular Algae
• Oedogonium reproduction
–Antheridium-release flagellated
sperm that swim to the oogonium oogonium
–Oogonium-houses the zygote which

is a diploid spore
- The spore undergoes meiosis and
produces 4 haploid zoospores. One of the
four cells becomes a rootlike holdfast the
others divide and become a new filament.
holdfast
CLASSIFICATION OF ALGAE
 BASED ON SEVEN MAJOR DIVISIONS
1) Nature and properties of pigments
2) Chemistry of reserve food products
3) Morphology of flagella
4) Morphology of cells and thalli
5) Life history reproductive structures and methods
of reproduction
6) Food-storage substance
7) Cell wall composition
DIVIDED INTO 9 PHYLA
 Phylum Rhodophycophyta
 Phylum Xanthophycophyta
 Phylum Chrysophycophyta
 Phylum Phaeophycophyta
 Phylum Bacillariophycophyta
 Phylum Euglenophycophyta
 Phylum Chlorophycophyta
 Phylum Cryptophycophyta
 Phylum Pyrrophycophyta
Phylum Rhodophyta
•4000 species of RED Algae

•Most are marine
•Smaller than brown algae and are often found at a depth
of 200 meters.
•Contain chlorophyll a and C as well as phycobilins which
are important in absorbing light that can penetrate deep
into the water
•Have cells coated in carageenan which is used in
cosmetics, gelatin capsules and some cheeses
•Red algae GELIDIUM from which AGAR is made
PHYLUM XANTHOPHYCOPHYTA
 Yellow Green Algae
 Xanthophytes walls with cellulose and pectin
 Chlorophyll a,c and rarely e are present
 Cellular storage product is chrysolaminarin
 Flagella unequal in length
 Asexual reproduction by cell division and

fragmentation
 Vaucheria is a well known member of this division
VAUCHERIA
PHYLUM CHRYSOPHYCOPHYTA
❑ Golden Algae
⦁ predominately flagellates some are
amoeboid
⦁ Chlorophyll a and c present
⦁ Reserve food as chrysolaminarin and their
frequent incorporation of silica
⦁ Characteristic color due to masking of their
chlorophyl by brown pigments
⦁ Reproduction is commonly asexual but at
times isogamous
GOLDEN
ALGAE
PHYLUM PHAEOPHYCOPHYTA
⦿ 1500 species of Brown algae
⦿ Mostly marine and include seaweed
⦿ All are multicellular and large (often
reaching lengths of 147 feet)
⦿ Individual alga may grow to a length of 100m
with a holdfast, stipe and blade
⦿ Chlorophyll a and c present
⦿ Used in cosmetics and most ice creams
⦿ Many of them have holdfasts and air
bladders which give them buoyancy
Fucus sp. Nereocystis luekeana
PHYLUM BACILLARIOPHYCOPHYTA
❑ The Diatoms
❑ Diatoms provide abundant food supply for
aquatic animals
❑ Chlorophyll a and c present
❑ Shells of diatoms are called frustules
❑ Deposits of these shells from centuries of

growth are called diatomite or diatomaceous
earth
DIATOMS
PHYLUM EUGLENOPHYCOPHYTA
✓ Unicellular and motile by means of flagella
✓ Chl a & b present
✓ 1000 species of Euglenoids
✓ Have both plantlike and animal-like
characteristics
✓ Euglena cell with contractile vacoules and fibrils
✓ Carry out photosynthesis in chloroplast and is
facultatively autotrophic
✓ Reproduction by longitudinal binary fission
✓ Dormant cysts are formed
EUGLENA
PHYLUM CHLOROPHYCOPHYTA
 Green algae
 7000 diverse species
 green algae contain one chloroplast per cell

which contain pyrenoids
 Both green algae and land plants have chlorophyll
a and b as well as carotenoids and store food as
starch
 Both have walls made of cellulose
 Reproduction by asexual methods or

isogamous and heterogamous sexual means
PHYLUM CRYPTOPHYCOPHYTA
 Cryptomonads are biflagellate organisms
 Cells are slipper shaped and flattened occur
singly
 Some with cellulose wall others naked
 There are 1 or 2 plastids with or without

pyrenoids
 Reproduction by longitudinal cell division or by
zoospores or cysts
CRYPTOMO
NAS
PHYLUM PYRROPHYCOPHYTA
⦁ Flagella are inserted in the girdle and arranged with
one encircling the cell and other trailing
⦁ Many are covered only by plasmalemma and in some
there is a wall made of cellulose
⦁ Some have a series of cellulose plates with in
plasmalemma termed thecal plates
⦁ Dianoflagellates a diverse group of biflagellated
uni cellular organisms present
DIANO FLAGELLATES
Thank you
Dr Richa Kaushal
Shoolini University
FSU008: Fundamentals of Microbiology
Lecture 8: Viruses
Virus
• An infective agent that typically consists of a nucleic acid

molecule in a protein coat, is too small to be seen by light
microscopy, and is able to multiply only within the living
cells of a host.
Introduction
➢Viruses do not have cells that divide; new viruses are

assembled in the infected host cell
➢ But unlike still simpler infectious agents, viruses
contain genes, which gives them the ability to mutate
and evolve.
➢Over 5,000 species of viruses have been discovered.
Introduction
➢ A virus consists of two or three parts:

➢ genes, made from either DNA or RNA,
long molecules that carry genetic information
➢protein coat that protects the genes; and in some viruses,
an envelope of fat
➢Viruses vary in shape from the
simple helical and icosahedral to
more complex structures.
➢Viruses range in size from 20 to 300 nanometres; it
would take 30,000 to 750,000 of them, side by side, to
stretch to 1 centimeter.
SPREADING
➢Viruses spread in many ways. Just as many viruses
are very specific as to which host species or tissue
they attack,
➢Plant viruses are often spread from plant to plant by
insects and other organisms, known as vectors.
➢Some viruses of animals, including humans, are
spread by exposure to infected bodily fluids
➢Viruses such as influenza are spread through the air by
droplets of moisture when people cough or sneeze.
➢Viruses such as norovirus are transmitted by the
faecal–oral route, which involves the
contamination of hands, food and water.
➢The human immunodeficiency virus, HIV, is transmitted by
bodily fluids transferred during sex.
➢Dengue virus, are spread by blood-sucking insects.
➢Rotavirus is often spread by direct contact with infected
children.
➢Antibiotics have no effect on viruses,
but antiviral drugs have been developed to treat life-
threatening
infections. Vaccines that produce lifelong immunity can
prevent some viral infections.
DISCOVERY
➢In 1884 the French microbiologist Charles
Chamberland invented a filter, known today as
the Chamberland filter or Chamberland–Pasteur filter, that
has pores smaller than bacteria. Thus he could pass a
solution containing bacteria through the filter and
completely remove them from the solution.
➢In the early 1890s the Russian biologist Dmitri
Ivanovsky used this filter to study what became known as
the tobacco mosaic virus. His experiments showed that
extracts from the crushed leaves of infected tobacco-plants
remain infectious after filtration.
Characteristics
• Obligate intracellular parasites of bacteria, protozoa,
fungi, algae, plants, and animals.
• Ultramicroscopic size, ranging from 20 nm up to 450 nm
(diameter).
• Not cellular in nature; structure is very compact
and economical.
• Do not independently fulfill the characteristics of life.
• Inactive macromolecules outside the host cell and active
only
inside host cells.
• Basic structure consists of protein shell (capsid)
surrounding nucleic acid core.
• Nucleic acid can be either DNA or RNA but not both
•Nucleic acid can be double-stranded DNA, single-
stranded DNA single-stranded RNA, or double-stranded
RNA.
• Molecules on virus surface impart high specificity for
attachment to host cell.
•Multiply by taking control of host cell’s genetic material
and regulating the synthesis and assembly of new viruses.
• Lack enzymes for most metabolic processes.
• Lack machinery for synthesizing proteins.
•Most RNA viruses multiply in & are released from the
cytoplasm.
•l Viral infections range from very mild to life
threatening.
Comparison with cell
• Viruses have no nucleus, no organelles, no cytoplasm or
cell membrane—Non-cellular
Size of a Virus
• Smallest infectious agents

• Most are so small, they can only be seen
with an electron microscope
• Animal viruses
• Proviruses- around 20 nm in diameter
• Mimi viruses- up to 450 nm in length
• Viewing viruses
• Special stains and an electron microscope
• Negative staining outlines the shape
• Positive staining shows internal details
• Shadow casting technique
Structure
Viral components
• Nucleic acids
• Capsid
• Envelope
DNA Viruses
• ssDNA
(single stranded DNA)
• dsDNA
(double stranded DNA)
Medically relevant DNA Viruses group
RNA Viruses
• Mostly single-stranded
• Positive-sense RNA: genomes that are ready for immediate
translation into proteins
• Negative-sense RNA: genomes have to be converted into
the proper form to be made into protein
RNA Viruses
Tools for studying Viruses
• Electron Microscopy
• Excellent tool with some limitations
• High resolution
• Image can be a distortion due to specimen processing
• X-ray Diffraction
• Good for naked virions (no envelope)
• Cryoelectron Microscopy
Structural symmetry
• Icosahedral Symmetry
• 20 triangular faces
• It is a common capsid structure
• Examples of viruses with icosahedral symmetry
• Parvoviruses
• These are simple viruses
• ssDNA genome
• Capsid is formed with 60 copies of single protein
• Polio virus
• Uses 180 copies of 3 subunit proteins
• Much bigger virus
Capsid
• Constructed from identical subunits called capsomers

• Made up of protein molecules
Two different types
• Helical
• Rod-shaped capsomers
• Assemble in to helical nucleocapsid
Icosahedral
• Three-dimensional
• 20-sided figure
• 12 evenly spaced corners
• Although they all display this symmetry, there are wide
variations
Function of Viral capsid
• Protects nucleic acids

• Help introduce the viral DNA or RNA into a suitable host
cell
• Stimulate the immune system to produce antibodies that
can protect the host cells against future infections
Viral reproduction
• Viruses can reproduce only when they enter cells and
utilize the cellular machinery of their hosts. Viruses’ code
their genes on a single type of nucleic acid, either DNA
or RNA, but viruses lack ribosomes and the enzymes
necessary for protein synthesis. Viruses are able to
reproduce because their genes are translated into proteins
by the cell’s genetic machinery. These proteins lead to the
production of more viruses.
Viral reproduction
Viral multiplication proceeds as following manner.

• Adsorption,
• Penetration,
• Uncoating,
• Synthesis,
• Assembly and Release
• Adsorption.
Bacteriophage Life cycle
Cultivation
• Primary purposes of viral cultivation

• To isolate and identify viruses in clinical specimens
• To prepare viruses for vaccines
• To do detailed research on viral structure, multiplication cycles,
genetics, and effects on host cells
• Using Live Animal Inoculation
• Specially bred strains of white mice, rats, hamsters, guinea pigs, and
rabbits
• Occasionally invertebrates or nonhuman primates are used
• Animal is exposed to the virus by injection
Tissue culture technique
• Most viruses are propagated in some sort of cell culture

• The cultures must be developed and maintained
• Animal cell cultures are grown in sterile chambers with special
media
Classification
• 3 Types of systems were proposed to classify the viruses:

• Baltimore Classification.
• Classical System Classification.
• Genetic Classification.
Baltimore classification
7 groups were made.
Its principles are fundamental to an understanding of virus
classification and genome replication.
The Baltimore classification has + RNA as its central point.
I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses) II:
ssDNA viruses (+ strand or "sense") DNA (e.g. Parvoviruses) III: dsRNA
viruses (e.g. Reoviruses)
IV: (+)ssRNA viruses (+ strand or sense) RNA
(e.g. Picornaviruses, Togaviruses)
V: (−)ssRNA viruses (− strand or antisense) RNA (e.g.
Orthomyxoviruses, Rhabdoviruses)
VI: ssRNA viruses (+ strand or sense) RNA with DNA
intermediate in life-cycle (e.g. Retroviruses)
VII: dsDNA viruses (e.g. Heptadnaviruses)
On the basis of host
• Animal viruses:
• Viruses of animal host
• Rabies, Polio, Mumps, Chicken pox, Small pox, and
Influenza.
• Plant Viruses:
• viruses which show their live characteristics when
attached to plants.
• Tobacco mosaic virus (TMV), Banana streak virus,
Carrot thin leaf virus
• Bacterial Virus: Bacteriophages ( T1, T2, T3, and T4.)
On genetic basis
• According to genetic consequences viruses are classified as. DNA

Viruses and RNA Viruses
• Genes may be linear or circular
• The smallest have only 4 genes and largest have several hundred.
• DNA Viruses
• DNA Viruses are the viruses which consist of DNA genome . They
complete their activities by transcription and most of them attack on
organisms of similar genome.
• RNA Viruses
• RNAViruses are the viruses which consist of RNA genome. They
complete their activities by reverse transcription.
On structural basis
• With relevant to morphology of viral structure viruses are

organized as Enveloped and Nonenveloped viruses.
• However they are also arranges subclasses of DNA and
RNA viruses
Thank you
Dr Richa Kaushal
Shoolini University
Lecture- 10 - Culture media
Culture media
• Culture media contains nutrients and physical growth

parameters necessary for microbial growth. All
microorganisms cannot grow in a single culture
medium and in fact, many can’t grow in any known
culture medium.
• Organisms that cannot grow in the artificial culture

medium are known as obligate parasites.
Ex.:Mycobacteriumleprae, Rickettsia, Chlamydia, and

Treponema pallidum
Culture media
Classification
On the basis of consistency
Solid medium
• Agar – 1.5-2.0 %
• Solid medium has a physical structure and allows
bacteria to grow in physically informative or useful
ways.
• Solid medium is useful for isolating bacteria or for
determining the colony characteristics of the isolate.
Classification
Semisolid medium
• Agar - 0.5% or less.

• Semisolid medium has a soft custard-like consistency
and is useful for the cultivation of microaerophilic
bacteria or for the determination of bacterial motility.
Classification
Liquid (Broth) medium
• Contains nutrients but not solidifying agents.

• Broth medium serves various purposes such as
propagation of a large number of organisms,
fermentation studies, and various other tests.
Ex.: sugar fermentation tests, MR-VP broth.

Classification
On the basis of purpose
General-Purpose Media
• Basal media also called general-purpose media are

basically simple media that support the growth of
most non-fastidious bacteria.
• Ex.: Peptone water, nutrient broth, and nutrient agar

(NA)
• These media are generally used for the primary

isolation of microorganisms.
Classification
Enriched media
• Addition of extra nutrients in the form of blood,

serum, egg yolk, etc.
• Enriched media are used to grow nutritionally exacting
(fastidious) bacteria.
• Ex.: Blood agar, chocolate agar, Loeffler’s serum slope
• Blood agar is prepared by adding 5-10% (by volume)
blood to a blood agar base.
Classification
Selective and Enrichment Media
• These media are designed to inhibit unwanted

commensal or contaminating bacteria and help to
recover pathogens from a mixture of bacteria.
• While selective media are agar-based, enrichment
media are liquid in consistency. Both these media serve
the same purpose.
• Any agar media can be made selective by the addition
of certain inhibitory agents that don’t affect the
pathogen of interest.
• Various approaches to making a medium selective
include addition of antibiotics, dyes, chemicals,
alteration of pH, or a combination of these.
Classification
Selective Media
Principle: Differential growth suppression
• Selective medium is designed to suppress the growth

of some microorganisms while allowing the growth of
others.
• Selective medium is agar-based (solid) medium so that
individual colonies may be isolated.
• Ex.: Mannitol salt agar, MacConkey agar, Thayer Martin
agar, Pseudosel agar
MacConkey agar
Classification
Enrichment Media
• Enrichment medium is used to increase the relative

concentration of certain microorganisms in the culture
prior to plating on solid selective medium.
• Unlike selective media, enrichment culture is typically
used as a broth medium.
• Enrichment media are liquid media that also serves to
inhibit commensals in the clinical specimen.
• Selenite F broth, tetrathionate broth, and alkaline
peptone water (APW) are used to recover pathogens
from fecal specimens.
Classification
Differential/ Indicator Media
• Certain media are designed in such a way that different

bacteria can be recognized on the basis of their colony
color.
• Various approaches include incorporation of dyes,
metabolic substrates, etc, so that those bacteria that
utilize them appear as differently colored colonies.
• Such media are called differential media or indicator
media.
• Differential media allow the growth of more than one
microorganism of interest but with morphologically
distinguishable colonies.
• Ex.: Mannitol salt agar, Blood agar, MacConkey’s agar
Classification
Transport media
• Clinical specimens must be transported to the

laboratory immediately after collection to prevent
overgrowth of contaminating organisms or commensals
and maintain the viability of the potential pathogens.
This can be achieved by using transport media.
• Such media prevent drying (desiccation) of a specimen,
maintain the pathogen to commensal ratio, and inhibit
the overgrowth of unwanted bacteria.
• Some of these media (Stuart’s & Amie’s) are semi-solid
in consistency. Addition of charcoal serves to neutralize
inhibitory factors.
• Ex.: Cary Blair transport medium, Pike’s medium
Classification
Assay media
• These media are used for the assay of vitamins, amino

acids, and antibiotics.
• E.g. antibiotic assay media are used for determining
antibiotic potency by the microbiological assay
technique.
Sterilization
• Moist heat sterilization

• Dry heat sterilization
• Filter
• Chemicals
Thank you
Dr Richa Kaushal
Shoolini University
FSU008: Microbial nutrition
Lecture 14
1. Methods in microbiology
1. Microbial nutrition
Microbial Growth Conditions
1. Macronutrients
2. Micronutrients
3. Growth factors
4. Environmental factors: temperature; pH; Oxygen
Nutrient requirements
• Microorganisms require about ten elements in large quantities, because
they are used to construct carbohydrates, lipids, proteins, and nucleic
acids.
• Several other elements are needed in very small amounts and are parts of
enzymes and cofactors.
Macronutrients
• Required in large amounts, including: carbon, oxygen,
hydrogen, nitrogen, sulfur, phosphorus (Components of
carbohydrates, lipids, proteins, and nucleic acids ); potassium,
calcium, magnesium and iron (cations and part of enzymes
and cofactors)
–Sources
- Organic compounds
- Inorganic salts
Micronutrients
• Microbes require very small amounts of other mineral
elements, such as iron, copper, molybdenum, and zinc; these
are referred to as trace elements.
• Most are essential for activity of certain enzymes, usually as
cofactors
• Growth factors
–Organic compounds
–Vitamins
Growth Factors
• Amino acids: are needed for protein synthesis
• Purines and pyrimidines: for nucleic acid synthesis
• Vitamins: are small organic molecules that usually make up all
or part enzyme cofactors, and only very small amounts are
required for growth
Role of Oxygen in Nutrition
• Obligate aerobes – require O2
• Obligate anaerobes – O2 is toxic
• Facultative anaerobes
• Microaerophilic organisms
Nutritional classification
Nutritional types of microorganisms
Cont…
1 Photoautotroph: Which use light energy and CO2 as a source of carbon.
2 Photoheterotrophs: Which use light energy and organic compounds as a
source of carbon.
3 Chemoautotrophs: Which use chemical energy and CO2 as a source of
carbon.
4 Chemoheterotrophs: Which use chemical energy and organic compounds
as a source of carbon.
Phototrophs
• Use radiant energy (light)
• Divide in to 2 groups
➢Photolithotrophs: Use inorganic compounds as their source of electrons.
Ex.: Chromatium okenii uses H2S as its electron donor, oxidizing it to
elemental sulfur.
➢Photoorganotrophs: Use organic compounds such as fatty acid and
alchohols as electron donors. Ex.: Rhodospirillum rubrum can use
succinate.
Chemotrophs
• Use chemical compounds for their energy
• Divide in to 2 groups
➢Chemolithotrophs: Use inorganic compounds as their source of electrons.
Ex.: Nitrosomonas use ammonia as their electron source, obtaining energy
by oxidizing ammonia to nitrate.
➢Chemoorganotrophs: Use organic compounds as their electron donor such
as sugars and amino acids. Ex.: Arthrobacter
✓Certain bacteria can grow as either chemolithotrophs and
chemoorganotrophs. Ex.: Pseudomonas pseudoflava can use either the
organic compound glucose or the inorganic compound hydrogen.
Autotrophs
• Those organisms that can make use of external energy sources and
assimilate inorganic carbon. Ex.: Nitrosomonas obtaining sufficient energy
to assimilate the carbon of CO2 in to cell components (CO2 fixations).
Heterophs
• Used organic compounds as their carbon source.
• Studied more extensively than the autotrophs
• All microbe that can cause disease
Obligate parasites
• Some bacteria have not successfully cultivated on an artificial media
• Such bacteria can be propagated only in association with living host which
serves as the medium.
Ex.: Mycobacterium leprae, which can be cultivated by infecting mice
Thank you
Dr Richa Kaushal
Shoolini University
FSU-008: Fundamentals of Microbiology
Lecture 9: Pure culture and pure culture techniques
1. Different Sterilization Techniques

2. Physical Techniques
3. Chemical Technique
1. Pure Culture
2. Pure culture techniques
3. Serial Dilution
4. Pour Plate method
5. Spread plate method
6. Streak Plate Method
Pure Culture
➢ Isolate a single species from mixed culture known as

pure culture.
➢ In natural habitats microorganisms grow in complex,

mixed populations containing several species
➢ Pure culture are very important and developed by

“Robert Koch”
➢ Within 20 years after the development of pure culture

techniques most pathogens responsible for the major
human bacterial diseases had been isolated.
Serial Dilution
➢ A serial dilution is the stepwise dilution of a substance in
solution. Usually the dilution factor at each step is constant,
resulting in a geometric progression of the concentration in a
logarithmic fashion.
➢ The aim of this dilution is to inoculate a series of tubes with a
microbial suspension so dilute that there are some tubes
showing growth of only one individual microbe
➢ A microorganism that predominates in a mixed culture can
be isolated in pure form by a series of dilutions. The
inoculum is subjected to serial dilution in a sterile liquid
medium, and a large number of tubes of sterile liquid
medium are inoculated with aliquots of each successive
dilution.
Pour Plate Method
➢ This method involves plating of diluted samples mixed with
melted agar medium. The main principle is to dilute the
inoculum in successive tubes containing liquefied agar
medium so as to permit a thorough distribution of bacterial
cells within the medium.
➢ Here, the mixed culture of bacteria is diluted directly in tubes
containing melted agar medium maintained in the liquid state
at a temperature of 42-45°C (agar solidifies below 42°C). The
bacteria and the melted medium are mixed well.
➢ When bacterial colonies develop, one finds that isolated
colonies develop both within the agar medium (subsurface
colonies) and on the medium (surface colonies). These
isolated colonies are then picked up by inoculation loop and
streaked onto another Petri plate to insure purity.
Spread Plate Method
➢In this method, the mixed culture or microorganisms is not diluted in the
melted agar medium (unlike the pour plate method); it is rather diluted in a
series of tubes containing sterile liquid, usually, water or physiological
saline
➢A drop of so diluted liquid from each tube is placed on the center of an agar
plate and spread evenly over the surface by means of a sterilized bent-
glass-rod. The medium is now incubated
➢When the colonies develop on the agar medium plates, it is found that
there are some plates in which well-isolated colonies grow. This happens
as a result of separation of individual microorganisms by spreading over the
drop of diluted liquid on the medium of the plate
➢The isolated colonies are picked up and transferred onto fresh medium to
ensure purity. In contrast to pour plate method, only surface colonies
develop in this method and the microorganisms are not required to
withstand the temperature of the melted agar medium.
Streak Plate Method
➢This method is used most commonly to isolate pure cultures of bacteria. A
small amount of mixed culture is placed on the tip of an inoculation
loop/needle and is streaked across the surface of the agar medium. The
successive streaks “thin out” the inoculum sufficiently and the micro-
organisms are separated from each other.
➢It is usually advisable to streak out a second plate by the same loop/needle
without re-inoculation. These plates are incubated to allow the growth of
colonies. The key principle of this method is that, by streaking, a dilution
gradient is established across the face of the Petri plate as bacterial cells
are deposited on the agar surface.
➢Because of this dilution gradient, confluent growth does not take place on
that part of the medium where few bacterial cells are deposited.
Presumably, each colony is the progeny of a single microbial cell thus
representing a clone of pure culture. Such isolated colonies are picked up
separately using sterile inoculating loop/needle and re-streaked onto fresh
media to ensure purity
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 12- Microbial growth and control
Terminologies
Sterilization – is the process by which all living cells,

viable spores, viruses, and viroids are either destroyed or
removed from an object or habitat.
Disinfection – is the killing, inhibition or removal of

microorganisms that may cause disease.
Disinfectants are agents, usually chemical used to carry

out disinfection and does not necessarily sterilise an
object because viable spores and few microorganisms
may remain.
Terminologies
Sanitization is closed related to disinfection. It is sometimes

necessary to control microorganisms on living tissue with chemical
agents.
Antisepsis – is the prevention of infection or sepsis and is

accomplished with antiseptics. These chemical agents are applied to
living tissue and they prevent infection by killing or inhibiting
pathogen growth or they reduce the total microbial population.
Germicide – kills pathogens but not necessary endospores. A

disinfectant or antiseptic can be effective against a specific group and
may be called a bactericide, fungicide, algicide and viricide.
Bacteriostatic and Fungistatic: chemicals do not kill, but they do

prevent growth, and if these are removed, growth will resume.
Factors affecting the effectiveness of anti-
microbial agents
• Population size
• Population composition
• Duration of exposure
• Temperature
• Local environment
Use of physical methods on microbial control
Heat:
• Moist heat
• Dry heat
• Pasteurization
• Ultra high temperature
Low temperature
• -80° C
• -20° C
• 4° C
Filtration
• Membrane filters (0.2 to 0.5 µm in diameter)
• HEPA filters
Use of physical methods on microbial control
Radiations
• Ultraviolet radiation
• 260nm
• Ionizing radiation
• Gamma radiation
• Cold sterilization (antibiotics, hormones, plastic
disposables)
Use of chemicals as anti-microbial agents
• Phenols: cresols, xylenols, and orthophenylphenol

• Alcohols: Ethanol, isopropanol
• Halogens: Iodine, chlorine
• Heavy metals: mercury, silver, arsenic, zinc and copper
• Detergents
• Aldehydes
• Sterilizing gases
• Hydrogen peroxide
• Acids and alkalis
Use of chemotherapeutic agents
Antibiotics
Mechanism of action
1. Cell wall synthesis inhibition

2. Protein synthesis inhibition
3. Nucleic acid synthesis inhibition
4. Cell membrane disruption
5. Metabolic antagonism
Mechanism of action
Mechanism of action
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 13- Microbial metabolism
Metabolism
Sum total of all the chemical reactions occuring in the

cell ( i.e. biosynthetic and degradative)
Metabolism in bacteria is essential for their existance,

for environment , and products are commercially and
medically important for human beings.
Metabolism
Classification of carbon and energy source
Components of metabolism
COMPONENTS FUNCTIONS
Enzymes Biological catalyst, fascilitates each step of metabolic reaction

by lowering the activation energy of reaction.
Adenosine triphosphate serves as energy currency of cell ,

(ATP)
Energy source Compund that is oxidised to release energy

, also called an electron donor.
Electron carriers carry the electrons that are removed during the oxidation of
energy source (NAD⁺, NADP⁺ , and FAD ( their reduced form
NADH , NADPH , and FADH₂) .
Precursor metabolites Intermediate metabolite that link anabolic and catabolic

pathways, like pyruvate, acetyl-coA, glucose -6-p, etc.
Role of ATP
➢ Is energy currency of cell,
serving as ready and
immediate donor of free
energy.
➢ Energy is releases when
phosphate bond is broken,
hence it is called high
energy phosphate bond.
➢ Synthesis and breakdown
of ATP continuously
occurs in cell during
degradative and synthetic
process.
Generation of ATP
Bacteria uses three mechanism
of phosphorylation to generate
ATP from ADP.
1)Substrate level
phosphorylation
C-C-C-P + ADP C-C-C + ATP
In this mechanism , a high

energy phosphate from a
phosphorylated substrate is
directly transferred to ADP.
2) Oxidative phosphorylation:
ATP generation during ETC.
3) Photophosphorylation
⚫ Occurs in phototrophs.
⚫ Derive ATP using radiant energy of the sun.
⚫ These ATP are then utilized to synthesize mainly
glucose .
Carbohydrate Catabolism
The breakdown of carbohydrates to release energy
Glycolysis
Krebs cycle
Electron transport chain
Glycolysis
• Embden-Meyerhof Pathaway (EMP)

• Oxidation of glucose to pyruvic acid
• Produces ATP and NADH.
GLYCOLYSIS
⚫ Embden-Mayerhof Parnas pathway.
⚫ Stepwise Conversion of glucose to
pyruvate and each step require specific
enzyme.
⚫ Occurs in cytosol.
⚫ Does not require oxygen and hence
occur in both aerobic and anaerobic
bacteria.
⚫ Three phases :- preparatory phase,
splitting phase and energy generation
phase.
⚫ 2 molecules of pyruvic acids are formed
from each glucose .
⚫ Net gain of 2 ATP by substrate level
phosphorylation and formation of 2
reduced substrate
i.e. NADH(5 ATP).
Pathways alternative to glycolysis
Many bacteria have another pathway in addition to

glycolysis for degradation of glucose.
1) Pentose phosphate pathway, and

2)Entner Doudoroff pathway.
Pentose phosphate pathway
⚫ Hexose monophosphate shunt.
⚫ Occurs simultaneously with
glycolysis and provides breakdown
of both pentose sugar and glucose.
⚫ Important Feature :- intermediate

pentoses are used for nucleic acid
synthesis, amino acid synthesis
and glucose from CO2 in
photosynthetics.
⚫ Important producer of reduced

coenzyme i.e. NADPH , used for
biosynthetic reactions.
Entner –Doudoroff pathway
⚫ Bacteria having enzyme for
Entner –Doudoroff pathway
can metabolize without
glycolysis or PPP.
⚫ Found in some Gram negative

bacteria like Psedomonas spp,
Rhizobium,etc. and generally
not found in Gram positive
bacteria.
⚫ Produces 1 molecule NADH, 1

molecule NADPH and 1
molecule of ATP ( from 1
glucose).
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 16- Bacterial photosynthesis
History
S. Winogradsky, a German botanist observed that some

purple bacteria can utilize hydrogen sulphide to
sulphate with intracellular deposition of sulphur.
C.B. Van Niel (1930) defined various metabolic versions

of anoxygenic photosynthesis and demonstrated that it
is the characteristic mode of energy yielding
metabolism in both purple and green bacteria.
History
Parson and Cogdell (1975) isolated functional

complexes from photosynthetic bacteria. The reaction
centre from the purple non-sulphur bacterium,
Rhodopseudomonas sphaeroides, contains four
molecules of chlorophyll and two molecules of
bacteriopheophytin (like b chlorophyll but the Mg
replaced by two H+), one or two molecules of
ubiquinone and one atom of ferrous iron together with
three polypeptides of apparent molecular weight in the
region of 28, 24 and 21 KD.
Phototrophs
• The most important biological process on Earth is
photosynthesis, the conversion of light energy to chemical
energy.
• Organisms that carry out photosynthesis are called
phototrophs.
• Photosynthesis, in bacteria, is defined as “the
synthesis of carbohydrates by the chlorophyll in the
presence of sunlight, CO2 and reductants taken from
air and oxygen do not evolve as by product, except in
cynobacteria.
Photosynthetic Pigments
• Because of presence of carotenoids in all

photosynthetic tissues their role is anticipated
in photosynthesis.
• The cells rich in carotenoids devoid of
chlorophyll do not photosynthesize.
• Light energy absorbed by carotenoids appears
to be transferred to chlorophyll a or bacterio
chlorophyll a and utilized in photosynthesis.
Chlorophylls and
Bacteriochlorophylls
• Phototrophic organisms contain some form of chlorophyll

(oxygenic phototrophs) or bacteriochlorophyll (anoxygenic
hototrophs).
• Chlorophyll a is green in color because it absorbs red and
blue light preferentially and transmits green light.
• The absorption spectrum of cells containing chlorophyll a
shows strong absorption of red light(maximum absorption
at a wavelength of 680 nm) and blue light (maximum at
430 nm).
• There are a number of different chlorophylls and
bacteriochlorophylls, and each is distinguished by
its unique absorption spectrum.
• Chlorophyll b, for instance, absorbs maximally at
660 nm rather than the 680-nm absorbance
maximum of chlorophyll a.
• All plants contain chlorophylls a and b. Some
prokaryotes contain chlorophyll d, while
chlorophyll c is found only in certain eukaryotic
phototrophs.
• Among prokaryotes, cyanobacteria produce
chlorophyll a and prochlorophytes produce
chlorophylls a and b.
• Anoxygenic phototrophs, such as the
phototrophic purple and green bacteria,
produce one or more bacteriochlorophylls.
• Bacteriochlorophyll a, present in most purple
bacteria absorbs maximally between 800 and
925 nm, depending on the species.
• Prokaryotes do not contain chloroplasts. Their
photosynthetic pigments are integrated into
internal membrane systems. These systems arise
• from invagination of the cytoplasmic
membrane (purple bacteria);
• from the cytoplasmic membrane itself
(heliobacteria);
• in both the cytoplasmic membrane and
specialized structures enclosed in a nonunit
membrane, called chlorosomes (green
bacteria)
• in thylakoid membranes (cyanobacteria)
Carotenoids and Phycobilins
• Although chlorophyll or bacteriochlorophyll is
required for photosynthesis, phototrophic
organisms contain an assortment of accessory
pigments as well.
• These include, in particular, the carotenoids and
phycobilins. Carotenoids primarily play a
photoprotective role in both anoxygenic and
oxygenic phototrophs, while phycobilins function
in energy metabolism as the major light-
harvesting pigments in cyanobacteria.
Carotenoids
• The most widespread accessory pigments in
phototrophs are the carotenoids.
• Carotenoids are hydrophobic light-sensitive pigments
that are firmly embedded in the photosynthetic
membrane.
• Carotenoids are typically yellow, red, brown, or green
in color and absorb light in the blue region of the
spectrum.
• Carotenoids are closely associated with
bacteriochlorophyll in photosynthetic complexes, and
energy absorbed by carotenoids can be transferred to
the reaction center.
• Nevertheless, carotenoids primarily function
in phototrophic organisms as photoprotective
agents.
• Bright light can be harmful to cells;
Carotenoids quench toxic oxygen species by
absorbing much of this harmful light and
prevent these dangerous photooxidations.
Phycobiliproteins and Phycobilisomes
• Cyanobacteria and the chloroplasts of red algae contain

phycobiliproteins, which are the main light-harvesting
systems of these phototrophs.
• The red phycobiliprotein, called phycoerythrin, absorbs
most strongly at wavelengths around 550 nm, whereas the
blue phycobiliprotein, phycocyanin, absorbs most strongly
at 620 nm.
• Phycobiliproteins assemble into aggregates called
phycobilisomes.
• In a fashion similar to how light-harvesting systems
function in anoxygenic phototrophs, phycobilisomes
facilitate energy transfer to allow cyanobacteria to grow at
fairly low light intensities.
Classification
Oxygenic Photosynthesis
• The oxidation of H2O produces molecular

oxygen (O2) as a by-product. Because O2 is
produced, photosynthesis in these organisms
is called oxygenic photosynthesis.
• They are mostly represented by gram-negative

cyanobacteria.
• Because of presence of carotenoids in all
photosynthetic tissues their role is anticipated
in photosynthesis.
Photosynthetic Electron Transport System
• In the photosynthetic light reactions, electrons travel

through a series of electron carriers arranged in a
photosynthetic membrane in order of their increasingly
more electropositive reduction potential (E0).
• This generates a proton motive force that drives ATP
synthesis.
Oxygenic Photosynthesis
Anoxygenic Photosynthesis
• However, in many phototrophic bacteria H2O is not

oxidized and O2 is not produced, and thus the
process is called anoxygenic photosynthesis.
• Ex: Purple-Sulphur Bacteria, Purple non- Sulphur
Bacteria, Green-Sulfur Bacteria, Green non-Sulfur
Bacteria.
• Anoxygenic photosynthesis depends on electron
donors such as reduced sulphur compounds,
molecular hydrogen or organic compounds.
• They are found in fresh water, brackish water, marine
and hypersaline water.
Calvin cycle
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 17- Chemolithotrophy
CHEMOLITHOTROPHY
•Chemolithotrophs-These microbes obtain electrons for the electron transport
chain from the oxidation of inorganic molecules rather than NADH generated by
the oxidation of organic nutrients.
• The acceptor is usually O2, but sulfate and nitrate are also used.
•The most common electron donors are hydrogen, reduced nitrogen compounds,
reduced sulfur compounds, and ferrous iron (Fe2).
Chemolithotrophs
• Energy yield is always lower than that for a glucose molecule.
• Much less energy is available from oxidation of inorganic
molecules than from the complete oxidation of glucose to
CO2(∆G=686 kcal/mole). This is because the NADH that
donates electrons to the chain has a more negative reduction
potential than most inorganic substrates.
• Thus the P/O(Phosphate/Oxygen)ratios for oxidative phosphorylation in
chemo-lithotrophs are probably around 1.0 (although in the oxidation of
hydrogen it is considerably higher).
• Because of low ATP yield, chemolithotrophs must oxidize a large quantity of
inorganic material to grow and reproduce.
• This is particularly true of autotrophic chemolithotrophs, which fix CO2 into
carbohydrates. For each molecule of CO2 fixed, these microbes expend three
ATP and two NADPH molecules.
• Because they must consume a large amount of inorganic material,
• chemolithotrophs have significant ecological impact.
Chemolithotrophs
• Hydrogen Oxidizers:
– Most efficient (P/O > 1); εH2 <εNADH
– Hydrogenase may donate electrons to NAD+
• Sulfur Oxidizers:
– ATP by Substrate level phosphorylation in addition to oxidative
phosphorylation
– Substrate level phosphorylation is via adenosine 5’-phosphosulfate (APS)
• Iron Oxidizers
– Acidophilic Thiobacillus ferrooxidans Fe+2 → Fe+3
– Acid Mine Drainage if pyrite is exposed to O2 and H2O!
– Circumneutral Gallionella ferruginea Fe+2 → Fe+3
• Nitrifying Bacteria:
– Ammonium Oxidizers (NH4 + → NO2 -)
– Nitrate Oxidizers (NO2 -→ NO3 )-
– Process of “Nitrification” (NH4 + → NO3 -)
Hydrogen oxidizers
• Several bacteria can oxidize Hydrogen gas to produce energy

because they possess hydrogenase enzyme.
H2 2H+ + 2e-
• Because the H2 / 2H+ , 2e- redox couple has a very negative

standard reduction potential, the electrons are donated either to
ETC or NAD+.
• If NADH is produced, it can be used in ATP synthesis by electron
transport and oxidative phosphorylation with O2, Fe2+, S, and CO
as the terminal electron acceptor.
• Eg. Caminibacter, Aquifex, Ralstonia and Paracoccus

Nitrifying bacteria
Some bacteria use the oxidation of nitrogenous compounds as a source
of electrons.
Nitrification: It is the oxidation of ammonia to nitrate.
1. 2 NH4+ + 3 O2 → 2 NO2– + 2 H2O + 4 H+ (Nitrosomonas)
2. 2 NO2– + O2 → 2 NO3– (Nitrobacter, Nitrospina)

Reverse electron flow
• Energy released upon the oxidation of ammonia and nitrite is used to make
ATP by oxidative phosphorylation.
• Since the molecules like ammonia and nitrite have more positive reduction
potential than NAD+, they cannot directly donate their electrons to form the
required NADH and NADPH.
• So the nitrifying bacteria and sulphur oxidizers move the electrons which are
derived from the oxidation of inorganic substrate up the ETC to reduce
NAD(P)+ to NAD(P)H. This is called reverse electron flow.
Sulfur oxidizers
▪ Reduced sulfur compounds are oxidized by most organisms, including higher animals and
higher plants.
▪ Some organisms can conserve energy (i.e., produce ATP) from the oxidation of sulfur.
▪ Sulfur is the sole energy source for some lithotrophic bacteria and archaea.
▪ Reduced sulfur compounds, such as hydrogen sulfide, elemental sulfur, sulfite, thiosulfate,
and various polythionates (e.g.,tetrathionate), are used by various lithotrophic bacteria and
are all oxidized by Acidithiobacillus.
▪ Sulfur oxidizers utilize enzymes such as sulfur oxygenase and sulfite oxidase to oxidize sulfur
compounds to sulfate. Lithotrophs that can produce sugars through chemosynthesis make
up the base of some food chains.
▪ Food chains have formed in the absence of sunlight around hydrothermal vents, which emit
hydrogen sulfide and carbon dioxide. Chemosynthetic archaea use hydrogen sulfide as an
energy source for carbon fixation, producing sugars.
•Biological oxidation of hydrogen sulfide to sulfate is one of the major
reactions of the global sulfur cycle. Reduced inorganic sulfur compounds are
exclusively oxidized by prokaryotes, and sulfate is the major oxidation
product. Sulfur oxidation in members of the Eukarya is mediated by
lithoautotrophic bacterial endosymbionts .
The sulfur-oxidizing prokaryotes are phylogenetically diverse. In the

domain Archaea aerobic sulfur oxidation is restricted to members of the
order Sulfolobales, and in the domain
Bacteria sulfur is oxidized by aerobic lithotrophs or by anaerobic phototrophs.

The non-phototrophic obligate anaerobe Wolinella succinogenes oxidizes
hydrogen sulfide to polysulfide during fumarate respiration.
•The metabolism of Thiobacillus has been best studied. These bacteria oxidize
sulfur (So), hydrogen sulfide (H2S), thiosulfate (H2S2O3), and other reduced
sulfur compounds to sulfuric acid; therefore they have a significant ecological
impact.
•Interestingly they generate ATP by both oxidative phosphorylation and

substrate level phosphorylation involving adenosine 5′-phosphosulfate (APS).
APS is a high- energy molecule formed from sulfite and adenosine
monophosphate.
•Some sulfur-oxidizing procaryotes are extraordinarily flexible metabolically.
•For example, Sulfolobus brierleyi, an archaeon, and some bacteria can grow
aerobically by oxidizing sulfur with oxygen as the electron acceptor; in the
absence of O2, they carry out anaerobic respiration and oxidize organic material
with sulfur as the electron acceptor.
Energy Generation by Sulfur Oxidation.
(a) Sulfite can be directly oxidized to provide electrons for electron transport and
oxidative phosphorylation. (b) Sulfite can also be oxidized and converted to adenosine 5′-
phosphosulfate (APS). This route produces electrons for use in electron transport and ATP
by substrate-level phosphorylation with APS. (c) The structure of APS.
Iron-oxidizing bacteria
• They are chemotrophic bacteria that derive the energy they need to live and
multiply by oxidizing dissolved ferrous iron.
• The oxidation of Fe2+ to Fe3+ yields very little energy to the a cell (∆G°=29kJ
mol−1 /∆G°=-90kJ mol−1 acidic and neutrophilic environments respectively)
compared to other chemolithotrophic metabolisms, therefore the cell must
oxidize large amounts of Fe2+ to fulfill its metabolic requirements.
• The photoferrotrophic bacteria use Fe2+ as electron donor and the energy
from the light to assimilate CO2 into biomass through the Calvin Benson-
Bassam cycle (or rTCA cycle) in a neutrophilic environment (pH5.5-7.2),
producing Fe3+oxides as a waste product that precipitates as a mineral.
Lecture 18- Sulphate and nitrate reduction
NITRATE REDUCTION
• The reduction of nitrate into ammonia and its incorporation in organic
material is known as assimilatory nitrate reduction.
• The nitrogen in nitrate much more oxidized than that in ammonia.
Therefore nitrate must first be reduced to ammonia before the
nitrogen can be converted into an organic form.
• This process is widespread among bacteria, fungi, and photosynthetic
protists and it is an important step in nitrogen cycle.
Assimilatory nitrate reduction takes place in cytoplasm in bacteria.
• The ammonia is then incorporated into amino acids.

SULFATE REDUCTION
• Sulfur is needed for the synthesis of the amino acids cysteine and
methionine.
• The sulfur atom in sulfate is more oxidized than it is in cysteine and
other organic molecules; thus sulfate must be reduced before it can
be assimilated. This process is known as assimilatory sulfate
reduction.
• Assimilatory sulfate reduction involves sulfate activation through the
formation of phosphoadenosine 5′-phosphosulfate, followed by
reduction of the sulfate.
• Cysteine can be synthesized from hydrogen sulfide in two ways. Fungi
appear to combine hydrogen sulfide with serine to form cysteine
(process 1), whereas many bacteria join hydrogen sulfide with O-
acetylserine instead (process 2).
• Once formed, cysteine can be used in the synthesis of other sulfur-

containing organic compounds.
METHANOGENESIS
• Methanogens are strict anaerobes that obtain energy by converting
CO2, H2, formate, methanol, acetate, and other compounds to either
methane or methane and CO2. This process is called methanogenesis.
• This is the largest group of archaea. There are five orders
(Methanobacteriales, Methanococcales, Metha- nomicrobiales,
Methanosarcinales, and Methanopyrales) and 26 genera.
• As might be inferred from the methanogens’ ability to produce
methane anaerobically, their metabolism is unusual. These
prokaryotes contain several unique cofactors:
tetrahydromethanopterin (H4MPT), methanofuran (MFR), coenzyme
M(2-mercaptoethanesulfonic acid), coenzyme F420, and coenzyme
F430.
Habitat:
⚫ They are found in diverse habitats which are associated
with decomposition of organic matter, bogs, anaerobic
digestors, aquatic sediments, hydrothermal submarine
vents and geothermal springs.
⚫ In animals, they are found in rumens of herbivores,

mammalian intestines, human oral cavity, guts of insects.
⚫ Methanogens produce methane from substrates such as
H2/CO2, acetate, formate, methanol and methylamines by
a process called methanogenesis.
CO2 + 4H2 → CH4 + 2H2O
Example: Methanobacterium bryantii, Methanococcus

deltae
Application:
Methane production, biogas production, waste water
treatment
ACETOGENESIS
• Acetogenesis is a process through which acetate is produced from CO2 and
an electron source (e.g., H2, CO, formate, etc.) by anaerobic bacteria via the
reductive acetyl-CoA or Wood-Ljungdahl pathway. The different bacterial
species that are capable of acetogenesis are collectively termed acetogens.
Biochemistry
• The precursor to acetic acid is the thioester acetyl CoA. The key aspects of
the acetogenic pathway are several reactions that include the reduction
of carbon dioxide to carbon monoxide and the attachment of the carbon
monoxide to a methyl group. The first process is catalyzed by enzymes
called carbon monoxide dehydrogenase. The coupling of the methyl group
(provided by methylcobalamin) and the CO is catalyzed by acetyl CoA
synthetase.
2 CO2 + 4 H2 → CH3COOH + 2H2O
Organics Conversion in Anaerobic Systems
COMPLEX ORGANIC MATTER
Proteins Carbohydrates Lipids
hydrolysis
acidogenesis
Amino Acids, Sugars Fatty Acids, Alcohols

acetogenesis
INTERMEDIARY PRODUCTS
(C>2; Propionate, Butyrate etc)
Acetate
methanogenesis
Hydrogen, Carbon dioxide
Methane
Carbon dioxide
• Microbiology
The anaerobic degradation of complex organic matter is carried out
by a series of bacteria and archae. There exists a coordinated
interaction among these microbes.
✓ FERMENTATIVE BACTERIA
This group of bacteria is responsible for the first stage of anaerobic
digestion - hydrolysis and acidogenesis. These bacteria are either
facultative or strict anaerobes.
The anaerobic species belonging to the family of Streptococcaceae
and Enterobacteriaceae and to the genera of Bacteroides,
Clostridium, Butyrivibrio, Eubacterium, Bifidobacterium and
Lactobacillus are most common.
✓HYDROGEN PRODUCING ACETOGENIC BACTERIA
This group of bacteria metabolizes propionate and other organic acids
(>C-2), alcohols and certain aromatic compounds (i.e. benzoate)
into acetate and CO2.
CH3CH2COO - ➔ CH3COO - + CO2 + H2
Syntrophic association of acetogenic organisms with methanogenic H2-
consuming bacteria helps to lower the concentration of H2 below
inhibitory level so that propionate degrading bacteria are not
suppressed by excessive H2 level.
✓ HOMOACETOGENS
Homoacetogenesis has gained much attention in recent years in
anaerobic processes due to its final product: acetate, which is the
important precursor to methane generation.
The bacteria are, H2 and CO2 users. Clostridium aceticum and
Acetobacterium woodii are the two homoacetogenic bacteria
isolated from the sewage sludge.
Homoacetogenic bacteria have a high thermodynamic efficiency; as a
result there is no accumulation H2 and CO2 during growth on multi-
carbon compounds.
CO2 + H2 → CH3COOH + 2H2O
OBLIGATE SYNTROPHY
Both species (e.g., a methanogen and an acetogen) require the other:
the acetogen provides the hydrogen; the methanogen prevents a build-
up of hydrogen which inhibits the acetogens.
Lecture 19- Mycorrhiza
Mycorrhizae
• Mycorrhizae are mutualistic symbiotic

associations formed between the roots of higher
plants and fungi.
• The word mycorrhiza was coined by the German
scientist Albert Bernhard Frank in 1885.
• The word mycorrhiza is derived from the Greek words –
‘mukes’meaning fungus and ‘rhiza’meaning roots.
Classification of mycorrhiza
Based on tropic level by A.B. Frank

• Ectotropic Mycorrhiza
• Endotropic Mycorrhiza
Based on morphological and anatomical feature
• Ectomycorrhiza
• Endomycorrhiza
• Ectendomycorrhiza
Ectomycorrhizae
• Ectomycorrhizas, or EM, are typically formed

between the roots of around 10% of plant families,
mostly woody plants including the birch, dipterocarp,
eucalyptus, oak, pine, deodar and rose families ,
orchids, and fungi belonging to the Basidiomycota,
Ascomycota and Zygomycota.
• Commonly associated with trans temperate forest
trees.
Ectomycorrhizae (ECM) are
association, where fungi form a
mantle around roots. There is
no hyphal penetration of cells.
Fungal hypha is generally
separate. A distinct Hartig’s net
is present between the cells.
• Ectomycorrhizal fungi form a sheath or mantle
around the root, and hyphae emanate through the
soil increasing the surface area.
• The fungus grows within the root cell wall but never
penetrates the cell interior.
• It grows between the cells of the cortex to form
Hartig net.
• The Hartig net present outside the endodermis and
meristematic zones is the site for nutrient
exchange.
• Colonization of root tips induces marked
changes in the host root morphology.
Fungus forming ectomycorrhizae
• Amanita muscaria
• Boletus variegatus Amanita muscaria
• Paxillus invalutus
• Rhizopogon vinicolor
• Entomoloma
• Sclerodendran Entomoloma
Advantages of ectomycorrhiza
• Extensive multibranching hyphae increases the water
holding capacity of plants.
• Increase the tolerance to drought, high soil temperature,
organic and inorganic soil toxins, extremes of soil acidity to
sulphur and aluminium.
• Deter infection of feeder roots by some rot pathogens.
• Enhance the uptake of many nutrients. (P, Cu, Zn through
Hartig net)
• Disease control through barrier effect, competitive exclusion.
• Play a key role in afforestation.
Endomycorrhiza mycorrhiza
• Arbuscular mycorrhizae (often called AM) are

the most common and widespread of all
mycorrhizae and are found in as many as 85%-
90% of the world's plant species.
• Commonly associated with agricultural,
horticulture crops in addition to tropical
trees.
• The external hyphal mantle or sheath is absent or
scanty. The fungal hyphae enters inside the root
cortex and penetrates the cortical cells.
• This is not a destructive parasitic association but
endomycorrhiza are present at certain times as a part
of normal root development.
• AM fungi penetrate the cell walls of root cells.
• They grow between the cell wall and cell membrane
forming arbuscules.
• VAM fungi produce vesicles for lipid storage.
Two main types of root colonization in
arbuscular mycorrhizae (AM).
1: extraradical hyphae; 2: appressorium/hyphopodium; 3:

arbusculum; 4: vesiculum; 5: intercellular hyphae; 6: intracellular
hyphae; 7: hyphal coils.
• In the Arum-type the fungal hyphae grow
intercellularly and well-developed arbuscules
are formed on branches entering the
neighboring cells.
• In the Paris-type the hyphae grow intracellularly,
develop hyphal coils in some cortical cells and
smaller arbuscules develop on these coils. Both the
fungal and the plant partner influence the type
developed
Fungi forming endomycorrhizae
• Endogone
• Glomus
• Sclerocystis
• Acaulospora
• Gigaspora Glomus Gigaspora
• Enterophophora
• Scutellispora
Endomycorrhizae Ectomycorrhizae
Generally fungi produce its typical Fungi produce majority of its

structures, vescicles and arbuscules structure outside the root system.
inside the root system.
Commonly associated with Commonly associated with trans

agricultural, horticultural temperate forest tree roots.
and tropical trees.
Have a loose network of hyphae in Form a complete mantle or sheath

the soil and an extensive growth over the surface of the root and
within the cortex cells of the plants. hyphae grows out into the soil.
Cannot be cultured on Can be cultured on artificial media.

artificial
media.
Doesn’t cause Cause morphological changes in
morphological roots.
changes in roots.
Ectendomycorrhizae
The fungi belong to Basidiomycotina, which covers
both gymnosperms and Angiosperms plants.
Ectendomycorrhizae show many of the same
characteristics’ of Endomycorrhizae but also show
extensive intercellular penetration.
The formation of Ectendomycorrhizae begins with

formation of a hartig’s net, which grows behind the
apical meristem of the growing root. The hartig net
penetrates between the epidermal and outer cortical
cells and later extends to the inner cortex.
Other types of mycorrhizae
• Orchids – orchid seeds are very small and do

not contain enough organic reserves to allow
development of the plant
• Must be infected soon after germination –
fungus provides seedling with carbohydrates
• Basidiomycetes involved in this mycorrhiza
are litter decomposing species of Rhizoctonia,
Armillaria that produce cellulases
Orchid mycorrhizae
• Some orchids are non-photosynthetic and

others produce chlorophyll when mature.
• They are completely dependant on
mycorrhizae for organic carbon and
nutrients.
Ericoid mycorrhizae
• Plants are Ericaceae – Erica,
Vaccinium - heathland plants
• Fungi are Ascomycota and
Deuteromycota
• Form loose network on surface
& hyphal coils inside
epidermal cells of hair roots
where nutrient exchange is
thought to take place
• Shown to supply N to plant –
fungi secrete proteinases
Arbutoid mycorrhizae
• Plant are also Ericaceae – Arbutus,

Arctostaphylose, Pyrola
• Fungi are basidiomycetes that also form
ectomycorrhizae
• Fungi form sheath and Hartig net, hyphae
also penetrate outer coritcal cells
Monotropoid mycorrhizae
• Plants are nonchlorophyllous
– Monotropa
• Fungi are basidiomycetes –
boletes that form
ectomycorrhizae with other
plants (conifers)
• Plant depends on its
mycorrhizal fungus - for its
organic nutrients as well as
inorganic nutrients
Importance
• 95% of all the world's plant species form mycorrhizal

relationships with fungi and that in the majority of cases the
plant would not survive without them.
• Present in 95% of plants (83% Dicots, 79% Monocots and
100% Gymnosperms).
• Brassicaceae, Cyperaceae, and Juncaceae- do not
have mycorrhizal associations (10-20%).
• The Orchidaceae are notorious as a family in which the
absence of the correct mycorrhizae is fatal even to
germinating seeds
Applications of Mycorrhizae
• Increase nutrient uptake of plant from soil. P nutrition and other elements:
N, K, Ca, Mg, Zn, Cu, S, B, Mo, Fe, Mn, Cl
• Increase diversity of plant. Produce uniform seedling.
• More tolerant to adverse soil chemical constraints which limit crop
production.
• Increase plant resistance to diseases and drought. Stimulate the growth of
beneficial microorganisms. Improve soil structure.
• Stable soil aggregate – hyphal polysaccharides bind and aggregate soil
particles.
• Significant role in nutrient recycling.
• Increases absorption of phosphate by crops.
• uptake of zinc also increases.
• Increases uptake of water from soil.
• Increases uptake of sulphur from the soil
• Increases the concentration of cytokinins and
chloroplast in plants.
• They protect plants during stress condition.
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 20- Microbial Fermentation
Fermentation
• Fermentation is a metabolic process that converts sugar to acids, gases or

alcohol. It occurs in yeast and bacteria, and also in oxygen-starved (Deficient )
muscle cells. Fermentation, chemical process by which molecules such as glucose
are broken down anaerobically.
• More broadly, fermentation is the foaming (Un-healthy) that occurs during the
manufacture of wine and beer, a process at least 10,000 years old. The frothing
results from the evolution of carbon dioxide gas, though this was not recognized
until the 17th century.
• French chemist and microbiologist Louis Pasteur in the 19th century used the
term fermentation in a narrow sense to describe the changes brought about by
yeasts and other microorganisms growing in the absence of air (anaerobically); he
also recognized that ethyl alcohol and carbon dioxide are not the only products
of fermentation.
TRADITIONAL FERMENTATION
• Traditional fermentation technology, as mentioned in the literary texts, is several

thousand years old.
• The fermentation technology employed a variety of processes and was put to a large
number of uses.
• Fermentation has been widely used for the production of a wide variety of substances
that are highly beneficial to individuals and industry.
• Over the years, fermentation techniques have gained immense importance due to their
economic and Environmental advantages.
• Ancient techniques have been further modified and refined to maximize productivity.
• This has also involved the development of new machinery and processes. Two broad
fermentation techniques have emerged as a result of this rapid development:
• 1. Solid State Fermentation (SSF). 2. Submerged Fermentation (SmF).
TYPES OF FERMENTATION
There are basic two type of fermentation:
1. Alcoholic fermentation, is the alcoholic fermentation, is the

production of ethanol and carbon dioxide
2. Lactic acid fermentation refers to two means of producing lactic acid:
– Homolactic fermentation is the production of lactic acid exclusively
– Heterolactic fermentation is the production of lactic acid as well as other acids

and alcohols.
ALCOHOLIC FERMENTATION
• The chemical equation below shows the alcoholic fermentation of glucose

• One glucose molecule is converted into two ethanol molecules and two carbon dioxide
molecules.
• C6H12O6 → 2 C2H5OH + 2 CO2
• Before fermentation takes place, one glucose molecule is broken down into two pyruvate
molecules. This is known as glycolysis.
• Alcoholic fermentation, is a biological process which converts sugars such as glucose,
fructose, and sucrose into cellular energy, producing ethanol and carbon dioxide as a side-
effect.
• Ethanol fermentation has many uses, including the production of alcoholic beverages, the
production of ethanol fuel, and bread cooking.
• Examples: Sacharomyces cereviseae, Pseudomonas
ALCOHOLIC FERMENTATION
LACTIC ACID FERMENTATION
• It is a metabolic process by which glucose and other six-carbon sugars (also,

disaccharides of six- carbon sugars, e.g. sucrose or lactose) are converted into
cellular energy and the metabolite lactate.
• If oxygen is present in the cell, many organisms will bypass fermentation and
undergo cellular respiration; however, facultative anaerobic organisms will both
ferment and undergo respiration in the presence of oxygen.
• Lactate dehydrogenase catalyzes the interconversion of pyruvate and lactate

with concomitant interconversion of NADH and NAD+.
LACTIC ACID FERMENTATION
HOMOLACTIC FERMENTATION
• It is the simplest type of fermentation.

• The pyruvate from glycolysis undergoes a simple redox reaction, forming lactic
acid.
• Overall, one molecule of glucose (or any six-carbon sugar) is converted to two
molecules of lactic acid: C6H12O6 → 2 CH3CHOHCOOH
• It occurs in the muscles of animals when they need energy faster than the blood
can supply oxygen. It also occurs in some kinds of bacteria (such as lactobacilli)
and some fungi.
• Homolactic bacteria: Streptococcus thermophiles, Streptococcus lactis,
lactobacillus lactis, Lactobacillus bulgarius, Pediococcus, Enterococcus
• Homolactic fermentation is important in dairy industry for
souring of milk to produce various fermented products
• Streptococcus mutant, a bacteria responsible for dental caries is a
homolactic fermenting bacteria.
• Lactobacillus spp in the digestive tract of human helps in
digestion of lactose present in milk.
• Lactobacillus spp are used as probiotic.
HETEROLACTIC FERMENTATION
• In hetero lactic fermentation, end product is ethanol and CO2 in

addition to lactic acid.
• In this reaction glucose is first metabolized to pyruvate, acetic
acid and CO2 by Pentose phosphate pathway.
• Pyruvate is then reduced to lactic acid whereas acetic acid is
reduced to ethanol and CO2.
• Heterolactic bacteria: Leuconostoc mesenteroides, Lactobacillus
bifermentous, Leconostoc lactis
Mixed acid fermentation
• In mixed acid fermentation, mixture of acids such as lactic acid, acetic acid,
ethanol, formic acid etc are produced as the end product.
• At first pyruvate is cleaved by the enzyme Pyruvate formate lyase to yield
formic acid and Acetyl coA.
• From formic acid various other end products such as acetic acid, lactic acid,
succinic acid, ethanol or CO2 and water are formed according to types of
pathway and types of bacteria. However formic acid is always the
intermediate product in this pathway.
• This pathway is followed by member of Enterobacteriaceae family such as E.
coli, Salmonella, Klebsiella etc.
• This fermentative pathway is the basis of Methyl red test.
Mixed acid fermentation
2,3-Butanediol fermentation
• In this pathway 2,3-butanediol is the end product.
• Some Pyruvate produced during glycolysis is
metabolized as in mixed acid fermentation but
most of the pyruvate is condensed to form α-
acetolactate.
• α-acetolactate undergoes decarboxylation in the
presence of enzyme pyruvate decarboxylase to
produce Acetoin (acetyl methylcarbainol) which is
reduced by NADH2 to form 2,3-butanediol.
• This pathway is followed by some member of
Enterobacteriaceae family. Eg. Klebsiella
• This fermentative pathway is the basis of VP test.
Butanol fermentation
• In this pathway pyruvate is converted into butanol or butyrate.
Other end product such as Acetone and CO2 or Isopropyl
alcohol and CO2 may formed by this pathway.
• This pathway is present in Clostridium spp
• At first Clostridium spp convert pyruvate into AcetylcoA
aerobically.
• Two molecule of acetylcoA condenses in the presence of
enzyme acetyl-transferase to from AcetoacetylcoA.
• AcetoacetylCoA is reduced to β-hydroxybutyrylcoA by NADH
in the presence of enzyme hydroxybutyrate dehydrogenase.
• β-hydroxybutyrylcoA is reduced by enoylcoA hydratase to form
CrotonylcoA and water.
• CrotonylcoA is further reduced to butyrylcoA by an enzyme
NAD-linked dehydrohenase.
• ButyrylcoA and acetate act together with fatty acid coA
transferase to form acetylcoA and butyrate. Acetyl coA then
recycle in the reaction.
Propionic acid fermentation
• In this pathway propionic acid and CO2 is the end product.

• This pathway is carried out by Propionic acid bacteria (PAB).
• These bacteria ferment glucose or lactate to propionic acid under
anaerobic condition.
• Pyruvate reacts with methyl malonyl coA to form Propionyl coA and
Oxaloacetate.
• Oxaloacetate give rise to malate, fumarate and succinate by reverse TCA
cycle.
• Propionyl coA transfer its coA to succinate to form succinylcoA and
propionate
• Example: Propionibacterium
Thank you
Dr Richa Kaushal
Shoolini University
FSU008- Fundamentals of Microbiology
Lecture 21: Nitrogen Fixation
Nitrogen Fixation
• The conversion of atmospheric nitrogen into the

nitrogenous compounds through the agency of living
organisms is called biological nitrogen fixation.
• Microorganism involved:
• those which live in close symbiotic association with
other plants
• those which are “free living” or non-symbiotic.
• Nitrogenase: Rhizobium and Frankia, or the free-living
Azospirillum and Azotobacter and BGA.
Symbiotic nitrogen fixation
Rhizobium sp. and Frankia are free living in soil, but only
as symbionts, can fix atmospheric di-nitrogen
Nodule formation
Mechanism of nitrogen fixation
• The nodule serves as site for N2 fixation.
• Nitrogenase and leghaemoglobin.
• The nitrogenase has 2 components i.e. Mo-Fe protein
(molybdoferredoxin) and Fe-protein (azoferredoxin).
Assimilation of Ammonia
Reductive amination
Catalytic amidation
Transamination
Glutamate (amino donor) + Oxaloacetate (amino acceptor) → Aspartate (amino

acid) + 2 oxyglutarate
Symbiotic association by Frankia
Actinorhizal symbioses
220 spp incl. 8 families form endosymbioses with the actinomycete
bacterium Frankia
Rosales: Rosaceae, Eleanaceae, Rhamnaceae

Cucurbitales: Datiscaceae, Coriariaceae
Fagales: Betulaceae, Casaurinaceae, Myricaceae
Actinomycetes (e.g., Frankia)
Gram positive
Mycelial growth—bind soils in a netlike structure
Very abundant in soils
Fix N as free-living bacteria and in plant nodules (unlike Rhizobium)
Metabolically more active in nodules
Vesicles are sites of N-fixation, protect from O2 poisoning
Produce Geosmins—distinctive smell of soils
Warmth in compost piles
Form nodules similar to those in Rhizobium-legume symbiosis

Symbiotic association by Frankia
Infection process and nodule development
Intracellular infection (e.g., Fagales)
1. Root hairs deformed by “Frankia signals”

2. Hyphae enmesh with root hairs, penetrate root
3. Penetration causes cell divisions in root forming a prenodule
4. Nodule primordium arises from root pericycle
5. Nodule is a modified lateral root. Vesicles form at tips of hyphae
Intercellular infection (e.g., Rosales)
1. No root hair deformation

2. Frankia grow in middle lamella, spread through the apoplast
Mature Nodules are modified lateral roots from pericycle
Multilobed, each lobe with vascular bundle

Periderm, endodermis, expanded cortex.
In Casuarina, plant cell wall lignification = O2 protection (no vesicles)
Thank you
Dr Richa Kaushal
Shoolini University
Lecture 22: Conjugation
BACTERIAL CONJUGATION WAS FIRST
DISCOVERED BY
Lederberg And Tatum

IN 1946
IN Esch.coliK12 STRAINS
F factor and Conjugation
• F (fertility) factor is a conjugative plasmid transferred from
cell to cell by conjugation
• F factor is an episome = genetic element that can insert into

chromosome or replicate as circular plasmid
• The F plasmid is a low-copy-number plasmid ~100 kb in

length, and is present in 1–2 copies per cell
• It replicates once per cell cycle and segregates to both

daughter cells in cell division
3
WHO IS A DONOR?
F PLASMID ABSENT
DONOR RECIPIENT
F+ F–
MALE CELL FEMALE
F factor and Conjugation
• Conjugation is a process in which DNA is
transferred from bacterial donor, F+ cell to a
recipient, F- cell by direct contact.
• The transfer is mediated by a tube-like

structure called a pilus, formed between the
cells, through which the plasmid DNA passes.
• Once in contact, conjugation, DNA transfer is

unidirectional. The lagging strand template
peels away… and is transferred to the
recipient.
• The leading strand template is replicated in

the donor while the lagging strand template is
replicated in the recipient… so that both cells
wind up with the plasmid.
5
THISF PLASMID ENCODES FOR THE
SEX PILUS
WHAT HAPPENS DURING
CONJUGATION?
What is Hfr cell?
When F factor/ plasmid exists in

an integrated state with the host
chromosome
Hfr
• F factor can integrate into chromosome via
genetic exchange between IS elements
present in F and homologous copy located
anywhere in bacterial chromosome
• Cells with the F plasmid integrated into the

bacterial chromosome are known as Hfr
cells
• When an Hfr cell undergoes conjugation,
the process of transfer of the F factor is
initiated in the same manner as in an F+ cell
• However, because the F factor is part of

the bacterial chromosome, transfer from
an Hfr cell also includes DNA from the
chromosome
• Hfr = high frequency of recombination
9
Hfr CONJUGATION
• Transfer begins within an
integrated F factor and proceeds Hfr and Conjugation
in one direction
• A part of F is the first DNA

transferred, chromosomal genes
are transferred next, and the
remaining part of F is the last
• The conjugating cells usually

break apart long before the
entire bacterial chromosome is
transferred, and the final
segment of F is almost never
transferred
The recipient cell remains F-
11
12
F+ (free plasmid) Hfr ( integrated )
REVERSIBLE
TURNS A (F-) CONJUGATION WITH A

INTO A (F+) UPON Hfr , AN (F-) RARELY
CONJUGATION BECOMES (F+) BUT IT
RECEIVES CHROMOSOMAL
DNA FROM THE
DONOR
F+ Hfr
REVERSIBLE
WHEN THE F FACTOR REVERTS FROM

INTEGRATED FREE STATE IT MAY
SOMETIMES CARRY WITH IT SOME
CHROMOSOMAL DNA FROM ADJACENT SITE OF
ITS ATTACHMENT
SUCH AN F FACTOR IS KNOWN AS F’ FACTOR

( F’) + ( F-) SEXDUCTION
WHEN (F’) CONJUGATES WITH A RECIPIENT (F-

), IT TRANSFERS, ALONG WITH THE F
FACTOR, THE HOST DNA INCORPORATED
WITH IT.
Lecture 23: Transformation
DNA exchange among bacteria
• DNA can be exchanged among bacteria in three ways:
1. Conjugation
The transfer of genetic material between bacterial cells
by direct cell-to-cell contact or by a bridge-like connection
between two cells.
2. Transduction
A phage carries DNA from one bacterium to
another.
3. Transformation
Cells take up free DNA directly from their
environment.
Transformation
• Incorporation of naked DNA from
extracellular environment.
•Cells that can be used

for transformation are
called competent.
History
• In 1928, Fred Griffith found that one form of the
pathogenic pneumococci (now called
Streptococcus pneumoniae) could be
mysteriously “transformed” into another form.
• Griffith made a conclusion that the dead
pathogenic bacteria gave off a “transforming
principle” that changed the live nonpathogenic
rough-colony-forming bacteria into the
pathogenic smooth-colony form.
Competence
• The ability of some bacteria to take up naked
DNA from their environment.
• It is genetically programmed. Generally, more
than a dozen genes are involved, encoding both
regulatory and structural components.
• The general steps that occur in natural
transformation differ in Gram-negative
and positive bacteria.
Steps involved
Types of Transformation
There are two types of transformation:
1. Natural transformation
2. Artificial transformation
Natural Transformation
• In this case DNA take-up occurs without outside
help.
• Naturally competent bacterium – They can
take up DNA from the environment without
requiring special treatment.
• About 40 species have been found to be
naturally competent or transformable.
• Examples: Bacillus subtilis, Streptococcus
pneumoniae, Haemophilus influenzae, Neisseria
gonorrhoeae, Helicobacter pylori, Acinetobacter
baylyi, and some species of marine
cyanobacteria.
Steps involved in natural
transformation
Following proteins are involved in this process:
▪ ComEA: binds directly extracellular double-stranded DNA.
▪ The comF genes encode proteins that translocate the DNA into the
cell.
▪ ComFA provides the energy for translocation of DNA through
the membrane.
▪ ComEA, ComEC, and ComFA form a sort of ATP- DNA
into the cell.
▪ The genes in the comG operon encode proteins that might
form a “pseudopilus” which helps move DNA through the
ComEC channel.
▪ They might bind to extracellular DNA, perhaps acting
through the ComEA DNA-binding protein, and then retract,
drawing the DNA into the cell.
•The comE, comF and comG operons are all under the
transcriptional control of ComK.
•Some of genes involved in the transformation process are not
designated as com, because such genes were first discovered
on the basis of their involvement in other processes.
1.The nucA gene product makes double-strand breaks in
extracellular DNA.
2.Other examples are single-stranded-DNA binding protein
(SSB), and RecA functions in the recombination of
transforming DNA with chromosome DNA.
▪ The lengths of single-stranded DNA
incorporated into the recipient chromosome
are about 8.5 to 12 kb on co-transformation
of genetic markers
▪ Incorporation takes only few minutes to be

completed.
Natural transformation of Gram
positive bacteria
Natural transformation in gram
negative bacteria
Artificially induced competence
•Bacteria can be sometimes be made competent by certain

chemical treatments or DNA can be forced into bacteria by a
strong electric field in a process called electroporation.
1. Chemical Treatment (with calcium ions).
• Chemically induced transformation is usually
inefficient, and only a small percentage of the cells
are ever transformed.
• The cells must be plated under conditions,
selective for the transformed cells.
• Therefore, the DNA used for the transformation
should contain a selectable gene such as encoding
resistance to an antibiotic.
Artificially induced competence
2. Electroporation
• The bacteria are mixed with DNA and briefly
exposed to a strong electric field.
• The bacteria first be washed extensively in buffer

with very low ionic strength such as distilled
water.
• The brief electric field across the cellular

membranes might create artificial pore of H2O lined
by phospholipid head groups. DNA can pass
through these temporary hydrophilic pores.
• Electroporation requires specialized equipment.

Applications of Transformation
Bacterial transformation is used:
• To make multiple copies of DNA, called
DNA cloning.
• To make large amounts of specific human
proteins, for example, human insulin, which
can be used to treat people with Type I
diabetes.
• To genetically modify a bacterium or other
cell.
Lecture 24: Transduction
● Definitions:
●1) The transfer of genetic material from one bacterium to
another through bacteriophages is called Transduction.
● 2)Transduction is the process by which foreign DNA

is introduced into a cell by a virus or viral vector.
The experiments implicated a bacteriophage as the vector or
transducing agent.
• What is Bacteriophage?
• The virus that infect the bacteria

are known as bacteriophage.
Most bacteriophage, the virulent
phages, undergo a rapid lyric
growth cycle in their host cells.
They inject there nucleic acid,
usually DNA, into the bacterium,
where it replicates rapidly and
also directs synthesis of new
phage proteins.
• Transduction occurs by either the lytic or lysogenic cycles.
•In a lytic infection, the host cells fills with virions and bursts.
•The result is cell death.
•Lysogenic infections are also known as latent infections.

•The viral genome becomes incorporated into the host cell’s DNA.
•It can remain this way for an extended period.
•The host cell lives.
❖Occurance:
-Various members of enteric group of bacteria
-Pseudomonas, Staphylococcus, Bacillus
-Temperate phages:
Ex- λ- E. coli, P22-S. typhimurium,
● Types of Transduction:
● 1. Specialised/restricted transduction:
This is the transduction in which phages
transfer only a few restricted genes from one cell to
another cell.
● 2.Generalized transduction:
This is the transduction in which phages
transfer any fragment of bacterial DNA from one cell
to another cell.
Specialized Transduction
●Also called Restricted transduction as only restricted
genes are transferred from one cell to another.
● Example- λ and Ø 80 (Lysogenic phages)
●These phages integrates their genome in host genome
at specific sites. But sometimes under certain
inductions they detaches from host genome.
●During detachment they take some gene portion of
host genome and leaves some of their own genes into
host genome.
● Such phage is called Transducing Phage.
Specialized transduction in Ø80 phage-
Host- E. coli
Integration site- Between Lactose utilization genes or Tryptophan

utilization genes.
Resulting phage is either λd trp or λd lac.
GENERALIZED TRANSDUCTION:
➢This is the transduction in which phages transfer any
fragment of bacterial DNA from one cell to another cell.
➢Example- P1 and P22 phage
➢It occurs only during Lytic cycle of Virulent as well as

temperate phage.
➢After infection viral genome may or may not integrate in
host chromosome. If integrate then site of infection may
not be fixed.
➢It means each and every gene has equal chance of getting
transferred from one cell to another.
GENERALIZED TRANSDUCTION IN P1 PHAGE:
● Host: E. coli
● Genome: dsDNA
● Many times does not integrate genome in host chromosome but
multiplies separately.
● After penetration of DNA in host it degrades host genome into fragments.
● Phage DNA replicates and also transcribed to produce mRNA for capsid
protein production.
● During assembly (Maturation) phage DNA is packed in head, but
sometimes it packs host gene fragment.
● Such phage(carrying host genes) when infects another host then it transfer
the genes from previous host.
● Such phage is called as “Generalized transducing phage”
● Frequency of Generalized Transduction: One in 106 TO 107 cells.
GENERALIZED TRANSDUCTION IN P22 PHAGE:
● Host: Salmonella typhimurium

● Genome: dsDNA
●Integrates its genome in host genome, but integration site
is not fixed.
●After induction detaches from hot genome and takes
adjacent gene sequence from host.
●Such phage(carrying host genes) when infects another
host then it transfer the genes from previous host.
ABORTIVE TRANSDUCTION:
●Transduction in which the Phage genome has no

capacity of integration into the host genome and also
lacks genes for its own replication then it remains as
it is in the host cell.
●When host cell divides then it will be transferred to
only one of the daughter cell. In this way it gets
diluted from generation to generation.
● This is known as Abortive Transduction.
PHAGE CONVERSION
●Temperate phage induces change in the phenotype of

infected bacteria. This is referred as Phage conversion or
Lysogenic conversion.
●lysogenic conversion lasts only as long as phage or
prophage is present in the host cell.
●Some lysogenic phage carry genes that can enhance the
virulence of the bacterial host.
●For example, some phage carry genes that encode toxins.
These genes, once integrated into the bacterial
chromosome, can cause the once harmless bacteria to
release potent toxins that can cause disease.
GENERAL USES OF THE TERM AND APPLICATIONS
• More generally, transduction is the process by which genetic

material e.g:
DNA or siRNA, is inserted into a cell by a virus.
• Common techniques in molecular biology are the
use of viral vectors(including bacteriophages).
• Some medical applications are:-

• It provide resistance to anti-biotic drugs.
• Helps in the correction of genetic diseases by direct modification of
genetic
errors.
• It is a common tool used by molecular biologists to stably
introduce a foreign gene into a host cell’s genome.
Lecture 25: Mutations
 Due to by physical, chemical & environmental
agents.
 Broadly classified into four categories.

1. Single base alterations (e.g. depurination,
deamination).
2. Two-base alterations (e.g. pyrimidine dimer)
3. Chain breaks (e.g. ionizing radiation)
4. Cross-linkages (e.g. between bases).
 Mutation refers to a change in the DNA
structure of a gene.
 The substances (chemicals) which can induce
mutations are collectively known as mutagens.
 The changes that occur in DNA on mutation are
reflected in replication, transcription &
translation.
 Two major types
1. Point mutations
2. Frameshift mutations
 Point mutations:
 The replacement of one base pair by another
results in point mutation.
 They are of two sub-types.
 Transitions:
 In this case, a purine (or a pyrimidine) is
replaced by another.
 Transversions:
 These are characterized by replacement of a
purine by a pyrimidine or vice versa.
Silent mutation:
 The codon (of mRNA) containing the changed
base may code for the same amino acid.
 UCA codes for serine & change in the third
base (UCU) still codes for serine.
 This is due to degeneracy of the genetic code.

 There are no detectable effects.
Missense mutation:
 In this case, the changed base may code for a
different amino acid.

 UCA codes for serine while ACA codes for
threonine.
 The mistaken (or missense) amino acid may be
acceptable, partially acceptable or
unacceptable with regard to the function of
protein molecule.
 E.g. Sickle-cell anemia.
Nonsense mutation:
 The codon with the altered base may
become a termination (or nonsense) codon.
 Change in the second base of serine codon
(UCA) may result in UAA.
 The altered codon acts as a stop signal &
causes termination of protein synthesis.
Frameshift mutations:
 These occur when one or more base pairs
are inserted in or deleted from the DNA,
respectively causing insertion or deletion
mutations.
 The insertion or deletion of a base in a gene results
in an altered reading frame of the mRNA.
 The machinery of mRNA (containing codons) does
not recognize that a base was missing or a new
base was added.
 No punctuation in the reading of codons, translation
continues.
 The result is that the protein synthesized will have
several altered amino acids and/or prematurely
terminated protein.
 The cell possesses an inbuilt system to
repair the damaged DNA.
1. Base excision-repair
2. Nucleotide excision-repair
3. Mismatch repair
4. Double-strand break repair
 The bases cytosine, adenine & guanine can
undergo spontaneous depurination to
respectively form uracil, hypoxanthine &
xanthine.
 These altered bases do not exist in the
normal DNA & therefore need to be
removed.
 This is carried out by base excision repair.

 A defective DNA in which cytosine is
deaminated to uracil is acted upon by the
enzyme uracil DNA glycosylase.
 This results in removal of defective base uracil

 An endonuclease cuts the back bone of DNA
strand near the defect & removes a few bases.
 The gap is filled up by the action of repair DNA
polymerase & DNA ligase.
 The DNA damage due to ultraviolet light,
ionizing radiation & other environmental
factors results in modification of certain
bases, strand breaks, cross-linkages.
 Nucleotide excision-repair is suited for large-
scale defects in DNA.
 After the identification of the defective piece
of the DNA.
 The DNA double helix is unwound to expose
the damaged part.
 An excision nuclease (exinuclease) cuts the
DNA on either side (upstream &
downstream) of the damaged DNA.
 This defective piece is degraded.

 The gap created by the nucleotide excision is
filled up by DNA polymerase which gets
ligated by DNA ligase.
 Despite high accuracy in replication, defects
do occur when the DNA is copied.
 For instance, cytosine (instead of thymine)
could be incorporated opposite to adenine.
 Mismatch repair corrects a single mismatch
base pair e.g. C to A, instead of T to A.
 The template strand of the DNA exists in a
methylated form, while the newly
synthesized strand is not methylated.
 This difference allows the recognition of the
new strands.
 The enzyme GATC endonuclease cuts the
strand at an adjacent methylated GATC
sequence.
 This is followed by an exonuclease digestion
of the defective strand & its removal.
 A new DNA strand is now synthesized to
replace the damaged one.
 Hereditary nonpolyposis colon cancer
(HNPCC) is one of the most common inherited
cancers.
 This cancer is now linked with faulty mismatch
repair of defective DNA.
 Double-strand breaks (DSBs) are dangerous.
 They result in genetic recombination which
may lead to chromosomal translocation,

broken chromosomes & finally cell death.
 DSBs can be repaired by homologous
recombination or non-homologous end joining.
 Homologous recombination occurs in yeasts
while in mammals, non-homologous & joining
dominates.
Mechanism Damage to DNA DNA Repair
Damage to a single base Removal of the base by

due to spontaneous N-glycosylase; abasic
Base excision repair alteration or by chemical or sugar removal,
radiation means replacement
Damage to a segment of
Removal of the DNA
Nucleotide excision- DNA by spontaneous
fragment (- 30 mt
repair chemical or radiation
length)& replacement
means
Damage due to copying Removal of the strand (by

Mismatch repair errors (1-5 base exonuclease digestion) &
unpaired loops). replacement
Damage caused by ionizing

Double-strand break unwinding, alignment &
radiations, free radicals,
repair ligation
chemotherapy.
CSU-186: Soil Microbiology
Practical-1: Lab Instruments
Analytical Balance
An analytical balance is a type of balance that is commonly used

for the measurement of mass in the sub-milligram range.
Principle:
• These types of balances are made with a measuring pan
enclosed in a transparent covering that prevents smalls
particles or air currents from getting collected on the pan.
• An electric analytical balance uses the force necessary to

counteract the mass rather than measuring the mass itself.
• An electromagnet is used to create a force required to achieve

a balance with the mass of the substance, and the resulting
force is displayed.
Analytical Balance
Autoclave
An autoclave is a pressurized chamber used for the process of

sterilization and disinfection by combining three factors: time,
pressure and steam
Principle:
• Autoclaves use steam as their sterilization agent. The basic
principle of an autoclave is that all the items within the
autoclave come in direct contact with the steam for a particular
period irrespective of the nature of the material- whether it is
liquid, plastic ware, or glassware.
• The amount of time and the temperature depends on the type

of material being sterilized and the increase in temperature of
the cycle allows for shorter periods.
Autoclave
Bunsen Burner
Bunsen burner is a standard tool used in laboratories, named

after Robert Bunsen. It is a gas-fueled single open flame.
Principle:
• This burner is made with a metal tube on a flat base with a gas
inlet at the bottom of the tube, which may have an adjustable
valve. On the sides of the tube are openings which can be
adjusted with a collar to control the amount of air that can
enter.
• Once the burner is connected to a gas source, the gas is forced

by the gas pressure so that the gas reaches the top where the
flame is ignited with a match or a lighter.
Bunsen Burner
Centrifuge
• A centrifuge is a device that allows the rotation of an object

about a single axis, where an outward force is applied
perpendicularly to the axis.
• A laboratory centrifuge is motor-based and allows the rotation

of a liquid sample resulting in the separation of the
components of the mixture.
Centrifuge
Principle:
• A centrifuge works on the principle of sedimentation, where
the high speed of the rotation causes the denser particles to
move away from the center while smaller, less dense
particles are forced towards the center.
• Thus, the denser particles settle at the bottom while the

lighter particles are collected at the top.
• In a laboratory tabletop centrifuge, the sample tubes are

aligned at an angle so that the particles have to travel a
shorter distance before they hit the bottom.
Centrifuge
Colony counter
A colony counter is used to estimate the density of a liquid culture

by counting the number of CFU (colony forming units) on an agar
or culture plates.
Principle:
• This instrument can accommodate different sizes of plates
which are scanned on top with UV, white light and/or
fluorescent illumination.
• One can accomplish the counting either manually with the

touch pressure or with a digital counter.
Colony counter
Deep freezer
Principle:
• Deep freezers are based on the principle that under extremely
low temperatures, there is minimum microbial growth which
allows for the protection and preservation of different
substances.
• Based on this principle, we can even preserve cultures over a

long period of time without any change in the concentration of
the microorganisms.
Deep freezer
Hot Air Oven
• A hot air oven is an electrical device that is used for sterilization

of medical equipment or samples using dry heat.
• Principle:
• Hot air oven is a type of dry heat sterilization which is performed on dry
materials and on substances that do not melt or catch fire under high
temperature.
• There are two types of hot air oven based on the working principle
• Forced air hot air oven: In this type of hot air oven, the heated air inside
the oven is distributed throughout the oven with a fan. This prevents
the rising of hot air towards the top while keeping the cold air at the
bottom. This allows for the adequate heating of materials inside the
oven.
• Static air hot air oven: In this type of oven, the heat is produced by coils
present at the bottom of the oven with no fan. The hot air rises and
doesn’t allow the effective sterilization of the materials.
• The equipment inside the oven acquire heat and pass the heat towards the
center, one layer at a time which allows for effective dry heat sterilization.
Hot Air Oven
Incubator
An incubator is a device that is used in the laboratories for the

growth and maintenance of microorganisms and cultures.
Incubator provides an optimal temperature, pressure, moisture,
among other things required for the growth of microorganisms.
Principle:
• The incubator is based on the principle of maintaining a proper atmosphere
for the growth of microorganisms.
• Incubators have a heating system that allows for the temperature within the
incubator to be adjusted according to the type of organism cultivated
inside.
• Similarly, they are provided with adjustments for maintaining the
concentration of CO2 to balance the pH and humidity required for the
growth of the organisms.
• Variation of the incubator like a shaking incubator is also available, which
allows for the continuous movement of the culture required for cell
aeration and solubility studies.
Incubator
Laminar Air Flow
Laminar Hood is a closed device primarily for processes or

instruments sensitive to microbial contamination.
Principle:
• A Laminar Hood is made up of stainless steel, avoiding joints
and corners to prevent the accumulation of bacterial spores.
• This device creates a sterile environment with the flow of

sterile air through a High-Efficiency Particulate Air (HEPA) filter
and shortwave ultraviolet germicidal lamp that sterilizes the
workstation.
• Laminar Air Flow has to turn on 15 minutes before to ensure

complete sterilization and the workstation should be cleaned
with ethanol before and after use.
Laminar Air Flow
Microscope
Microscopes are devices that allow the observer to an exceedingly

close view of minute particle
Principle:
• There are many different types of microscopes, each of which
works on their respective principles. However, there is some
commonality in them.
• The basic principle in a microscope is magnification. Based on

the relative position of the object from the lens or
electromagnets, different positions, nature, and magnification
of the image can be achieved.
• Different types of microscopes are developed to cater to the

specific needs of the observation. However, the common
theme is magnification.
Microscope
pH Meter
pH meter is a device used in laboratories that measure the H-ion

concentration in water-based solutions to determine the acidity
or alkalinity of the solution.
A pH meter is often termed as “potentiometric pH meter” as it
measures the difference in electric potential between the
reference and a pH electrode.
Principle:
• In a potentiometric pH meter, single or multiple glass
electrodes, connected to a bulb selective to hydrogen ions, are
attached to a metal rod.
• When the bulb with the electrodes is dipped into a solution,

hydrogen ions in the solution exchange with positive charges
on the electrode generating an electrochemical potential which
is displayed in terms of pH units on display.
pH Meter
Spectrophotometer
The spectrophotometer is an optical instrument for measuring the

intensity of light in relation to the wavelength.
Based on the amount of light absorbed by a colored solution, a
quantitative analysis of the solution can be done.
Principle:
• Spectrophotometry is based on the Beer-Lambert Law, which
states the absorbance of light by a solution (of a particular
wavelength) is directly proportional to the concentration of the
substance.
• Different wavelengths of lights are passed through a solution as

different substances have better absorbance at different
wavelengths. Based on the absorbance of a particular
wavelength, the quantitative analysis of a solution can be done.
Spectrophotometer
Vortex mixer
A vortex mixture is one of the basic technologies used for the

mixing of samples in glass tubes or flasks in laboratories.
Principle:
• It is based on the simple principle of causing reactions and
homogenization by agitating the mixture.
• Motorized draft shafts present on the mixer oscillates and

transfers the movement to the sample tubes causing the
sample fluids to undergo turbulent flow.
Vortex mixer
Water Bath
Water Bath is a conventional device that is used for chemical

reactions that required a controlled environment at a constant
temperature.
Principle:
• A sensor in the device transfers water temperature to a
reference value which is then amplified and a control system
generates a signal for the heating system which heats the water
to the desired temperature.
Water bath
Water Distiller
This instrument is commonly used in medical laboratories,

microbiology laboratories, organic chemistry laboratories and
medical industries.
Principle:
• A water distiller is based on the principle of distillation.
• According to this process, water is first brought to a boil and

then condensed into liquid form to obtain pure distilled water.
Water Distillation Unit
Thank you
Dr Richa Kaushal
Assistant Professor
Shoolini University, Solan (H.P)

Microbiology

Uploaded by

Document Information

Copyright

Available Formats

Share this document

Share or Embed Document

Sharing Options

Did you find this document useful?

Is this content inappropriate?

Copyright:

Available Formats

Microbiology

Uploaded by

Copyright:

Available Formats

CSU-025: Fundamentals of Microbiology

Practical - 2: Compound Microscope

1. EXIST (Webster definition)To continue to be, have life; live

• Assimilate the nutrients into BIOMASS

• Release waste products into the environment

K.C. Keiler M. Dworkin

Anabaena spp. Cyanobacteria

T.J. Deveridge M. Dworkin

• Transduction—phage (bacterial specific virus) mediated

• Conjugation—uptake of DNA that requires the interaction

Antibiotic resistance, bacterial

• We are multicellular creatures—made up of many cells

• FAMILY related genera

• Advancements in DNA amplification and DNA sequencing has greatly

• (ribosomal RNA—structural RNA of the ribosome that plays a role in

• EUBACTERIA most abundant of the bacteria found in soil, water and

• Microbiology as a BASIC Science

• Industry—Production of beer, wine, cheeses and yogurt

• Agriculture—maintenance of soil fertility/digestion in cattle

• Ecology—Bioremediation—microorganisms that degrade toxic waste materials

• Cells and cell theory

• Laws of Moses (Numbers, Deuteronomy)

• First person to see bacteria

• beautifully crafted but had

The Great Debate

Problems with experimental design??

“ Production without parent of a new living organism” (Pouchet

Biogenesis or cell theory: cells can

• Broth heated in flask

Pouchet argued that “Life Force”

Award for a solution

• Added 20 years to the

• Pasteur connected food spoilage

Developed antiseptic surgery

• Confirmed germ theory

• Organism consistently isolated from diseased individuals

• Pasteur described a rational

Bacteriophage Avian Flu

• Need a microscope to see

• Can be found on most materials and Streptococcus

•Some exist as single

Cluster of cocci Spiral

• What does it mean to be alive?

– They reproduce (make more of

– They need to eat

• Grow in number not in size

• Make copies of themselves by dividing in half

• Some are scavengers

– Why do they make you sick?

- To get food they need to survive and reproduce

– How do they make you sick?

• Food, Water, or other Surfaces that are contaminated

Foods and water

• Some are even helpful

- Leuconostoc: makes pickles & sauerkraut

- Pediococcus: makes pepperoni, salami, & summer

– Warm water with soap for 20 seconds, rub hard between

• Cook food thoroughly to kill any pathogens that may

• Store food properly to limit pathogen growth

– Cold temperatures (40F)

Lecture 4: Structure and Morphology of Fungi

1. Structure and morphology of fungi

• Fungi exist mainly in the form of slender filaments (hyphae).

• Intertwined filamentous mass formed by hyphae, visible to