LESSON 2

prelims
microbiology 1st SEMESTER

DOMAIN, BACTERIA, AND ARCHAEA

EUKARYOTES VS PROKARYOTES II. Archaea

III. Fungi

IV. Algae

V. Virus

CLASSIFICATION OF MICROORGANISMS

Microorganisms
VI. Protozoa
I. Bacteria
 II. Cell Wall

 Made of peptidoglycan it gives the bacteria its

shape. The cell wall is thicker in some bacteria.

III. Plasma Membrane

 Found within the cell wall, this generates energy

and transports chemicals.

IV. Cytoplasm

 A gelatinous substance inside the plasma

membrane that contains genetic material and ribosomes.

THE PROKARYOTES: DOMAINS BACTERIA V. DNA

AND ARCHAEA
 It contains all the genetic instructions used in
I. BACTERIA the development and function of the bacterium.
 Singular: bacterium
 They exist in millions, in every environment. VI. Ribosomes
 Some are harmful, but majority are useful.
 It is where proteins are made, or synthesized.
What are Bacteria? Ribosomes are complex particles made up of RNA-rich
granules.
 Single-cell organisms that are neither plants nor
animals. VII. Flagellum
 Usually measure a few micrometers in length.
 Exist together in communities of millions.  It is used for movement, to propel some types of
 Example: A gram of soil typically contains about bacteria. There are some bacteria that can have more
40 million bacterial cells. A milliliter of fresh than one.
water usually holds about one million bacterial
cells. VIII. Pili
 The earth is estimated to hold at least 5
nonillion bacteria, and much of the earth’s biomass is
 These hair-like appendages on the outside of the
thought to be made up of bacteria.
cell allow it to stick to surfaces and transfer genetic
material to other cells. This can contribute to the spread
Bacterial Structure of illness in humans.

Types of Flagella
Arrangement

I. Polar / Monotrichous

 Single flagellum at one pole.

II. Lophotrichous

 Tuft of flagella at one pole.

I. Capsule

 A layer found on the outside of the cell wall in

some bacteria. Capsules prevent phagocytosis.
III. Amphitrichous

 Flagella at both poles.

IV. Peritrichous

 Flagella all over.

V. Amphilophotrichous

 Tuft of flagella at both ends.

III. Spiral

 These are known as spirilla (singular spirillum).

Types of Bacteria by  If their coil is very tight they are known as
Shape spirochetes.
 Examples: Leptospirosis, Lyme disease,
 There are three basic shapes: and syphilis are caused by bacteria of this shape.

I. Spherical

 Bacteria shaped like a ball are called cocci, and a

single bacterium is a coccus.
 Examples: include the streptococcus group,
responsible for “strep throat.”

Bacterial Shapes and

Arrangements

II. Rod-shaped

 These are known as bacilli (singular bacillus).

 Some rod-shaped bacteria are curved and are
known as vibrio.
 Examples: Bacillus anthracis (B. anthracis),
or anthrax.
 Bacterial Feeding III. Facultative anaerobes or facultative
anaerobic bacteria
 Bacteria feed in different ways:
 Can live either with or without oxygen, but they
I. Heterotrophic Bacteria or Heterotrophs prefer environments where there is oxygen.
 They are mostly found in soil, water, vegetation
 photosynthesis, and some normal flora of humans and animals.
using sunlight, water and
carbon dioxideGet their IV. Mesophiles or mesophilic bacteria
energy through consuming
organic carbon.  Are the bacteria responsible for most human
 Most absorb dead infections. They thrive in moderate temperatures,
organic material, such as around 37°C. This is the temperature of the human body.
decomposing flesh.  The human intestinal flora, or gut microbiome,
 Some of these contains beneficial mesophilic bacteria, such as
parasitic bacteria kill their host, while others help them. dietary Lactobacillus acidophilus.

II. Autotrophic bacteria or Autotrophs Reproduction and Transformation

 Make their own food, either through either:  Bacteria may reproduce and change using the
 Photosynthesis, using sunlight, water and following methods:
carbon dioxide.
 Chemosynthesis, using carbon dioxide, water, I. Binary Fission
and chemicals such as ammonia, nitrogen,
sulfur, and others.  An asexual form of reproduction, in which a cell
Types of Autotrophs continues to grow until a new cell wall grows through
Photoautotrophs Some types, for the center, forming two cells. These separate, making
bacteria that use example cyanobacteria, two cells with the same genetic material.
photosynthesis. produce oxygen.
Others, such as
heliobacteria, do not
produce oxygen.
Chemoautotrophs These bacteria are
bacteria that use commonly found in
chemosynthesis. ocean vents and in the
roots of legumes, such
as alfalfa, clover, peas,
beans, lentils, and
peanuts.

Where Do Bacteria Live?

 Bacteria can be found in soil, water, plants,

animals, radioactive waste, deep in the earth’s crust,
arctic ice and glaciers, and hot springs.
 There are bacteria in the stratosphere, between
6 and 30 miles up in the atmosphere, and in the ocean
depths, down to 32,800 feet or 10,000 meters deep.
 Bacterial type based on where they live: II. Transfer of genetic
material
I. Aerobes or aerobic bacteria  Cells acquire new genetic material through
processes known as conjugation, transformation, or
 Can only grow where there is oxygen. transduction. These processes can make bacteria
 Some types can cause problems for the human stronger and more able to resist threats, such
environment, such as corrosion, fouling, problems with as antibiotic medication.
water clarity, and bad smells.
A. Conjugation
II. Anaerobes or anaerobic bacteria
 Conjugation is the process where one bacterium
 Can only grow where there is no oxygen. transfers genetic material to another through direct
 In humans, this is mostly in the gastrointestinal contact.
tract.
 One bacterium serves as donor of the genetic
material, and the other serves as the recipient.
 The donor bacterium carries a DNA sequence C. Transfomation
called the fertility factor, or F-factor.
 The F-factor allows the donor to produce a pilus,  Transformation is a process where in bacteria
which the donor uses to contact the recipient. take up foreign genetic material (naked DNA) from the
 The pilus then draws the two bacteria together. environment.
 The donor bacterium transfers genetic material  The prerequisite for bacteria to undergo
to the recipient bacterium. transformation is its ability to take up free, extracellular
 The genetic material is in the form of a plasmid, genetic material, it is called as competent cells.
or a small, circular piece of DNA.  Once the transforming factor (DNA) enters the
 The genetic material transferred during cytoplasm, it may be degraded by nucleases if it is
conjugation often provides the recipient bacterium with different from the bacterial DNA.
some sort of genetic advantage.  If the exogenous genetic material is like
bacterial DNA, it may integrate into the chromosome.
 Sometimes the exogenous genetic material may
co-exist as a plasmid with chromosomal DNA.

B. Transduction
III. Spores
 Transduction is the process by which a virus
transfers genetic material from one bacterium to  Formed by bacteria when there is low resources.
another.  It hold the organism’s DNA material and contain
 Viruses called bacteriophages can infect the enzymes needed for germination.
bacterial cells and use them as hosts to make more  They are very resistant to environmental
viruses. stresses.
 After multiplying, these viruses assemble and  The spores can remain inactive for centuries,
occasionally remove a portion of the host cell's bacterial until the right conditions then they can reactivate and
DNA. become bacteria.
 Later, when one of these bacteriophages infects  Spores can survive through periods of
a new host cell, this piece of bacterial DNA may be environmental stress, including ultraviolet (UV) and
incorporated into the genome of the new host. gamma radiation, desiccation, starvation, chemical
exposure, and extremes of temperature.

IV. Endospores

 Resting cells
 Resistant to desiccation, heat, chemicals.
 Sporulation: Endospore formation.
 Germination: Return to vegetative state.
 Endospore formation:
 The Result
 Gram positive = purple
 Gram negative = red or pink
 Gram staining is nearly always the first step in
identifying a new sample or species of bacteria.

How to Classify Bacteria?

 Gram staining is a method used to classify
bacterial species into two large groups.
 Staining methods are designed and invented by
Christian Gram in 1882 to make a staining agent bind to How does Gram Staining Work?
the cell wall of the bacteria.
 You will find bacteria referred to as ‘Gram +’  Gram positive bacteria retain crystal violet stain
(Gram Positive) and ‘Gram -‘ (Gram Negative). during the decolorization process because it has a
 This is a reference to how the bacteria responds thicker peptidoglycan layer.
to the Gram staining method.  Gram negative bacteria lose the crystal violet
 Testing for gram stain response microbiologists stain and are instead stained by the safranin in the final
first spread some bacteria on a slide, then ‘fire it’ by staining process because it has thinner peptidoglycan.
passing the slide briefly through a flame.
1. The next step is to flood the slide with crystal
violet solution for 1 minute.
2. Then they add iodine solution for 3 minutes –
at this stage, all cells are purple.
3. Adding alcohol for 20 seconds.
4. Lastly, the cells are restrained with safranin.
 II. ARCHAEA
 Consist of prokaryotic cells. Groups of Archaea
 They lacked peptidoglycan which is common to
most bacteria. I. Methanogens
 They are found in extreme environments.
 Strict anaerobes that produce methane from
Characteristics of Archaebacteria carbon dioxide and hydrogen.

 Some archaea are aerobic, obligate or facultative II. Extreme halophiles

anaerobes - they flourish in the absence of oxygen.
 The cell membranes of the Archaebacteria are  Require high concentration of salt for survival.
composed of lipids.
 The rigid cell wall provides shape and support III. Extreme thermophiles / hyperthermophiles
to the Archaea and protects the cell from bursting under
hypotonic conditions.
 Normally grow in extremely hot environment.
 The cell wall is composed of Pseudomurein,
which prevents archaebacteria from the effects of
Lysozyme. IV. Thermoacidophiles
 Lysozyme is an enzyme released by the immune
system of the host, which dissolves the cell wall  Thrive at extremely low pH values (pH optima of
of pathogenic bacteria. growth typically between 0.7 and 3) and high
 Nutritionally, they include photoautotrophs and temperatures (above 50°C).
chemoautotrophs.
 These do not possess membrane-bound Types of Archaebacteria
organelles.
 Its thick cytoplasm contains all the compounds
required for nutrition and metabolism. I. Crenarchaeota
 Can be spherical, rod, spiral, lobed, rectangular
or irregular in shape.  They exist in a broad range of habitats.
 Exist as single cells, others form filaments or  They are tolerant to extreme heat or high
clusters. temperatures.
 They can live in a variety of environments and  They have special proteins that help them to
are hence called extremophiles. function at temperatures as high as 230 degrees Celsius.
 They can survive in acidic and alkaline aquatic  They can be found in deep-sea vents and hot
regions, and in temperature above boiling point. springs, regions with superheated water.
 They can withstand a very high pressure of  These include thermophiles, hyperthermophiles,
more than 200 atmospheres. and thermoacidophiles.
 Indifferent towards major antibiotics because
they contain plasmids which have antibiotic resistance
enzymes.
 The mode of reproduction is asexual; binary
fission, fragmentation and budding.
 The differences in their ribosomal RNA suggest
that they diverged from both prokaryotes and
eukaryotes.

II. Euryarchaeota

 These can survive under extremely alkaline

conditions and can produce methane, unlike any other
living being on earth.
 These include methanogens and halophiles.

III. Korarchaeota
 They possess the genes common
with Crenarchaeota and Euryarchaeota.
 All three are believed to have descended from a
common ancestor.
 These are supposed to be the oldest surviving
organism on earth. These include hyperthermophiles.

IV. Thaumarchaeota

 These include archaea that oxidize ammonia.

V. Nanoarchaeota

 This is an obligate symbiont of archaea

belonging to the genus Ignicoccus.

Importance of
Archaebacteria
 Archaebacteria have compelled the scientists to
reconsider the common definition of species. Species are
a group with gene flow within its members. The
archaebacteria exhibit gene flow across its species.
 The Archaebacteria are methanogens, they can
produce methane. They act on the organic matter and
decompose it to release methane which is then used for
cooking and lighting.