Biology of bacteria

 The study of bacteria is known as bacteriology, a branch of microbiology.

 Constitute large group of single-celled, prokaryotic microorganisms
 Typically microscopic, and measured in micrometers (µ m) (1000 µ m = 1mm)
 Bacteria have a wide range of shapes, ranging from spheres to rods and spirals
Occurrence
 Ubiquitous occurrence in every habitat on Earth growing
– in soil (40 million bacterial cells/gram of soil )
– acidic hot springs, there are approximately
– radioactive waste five nonillion (5×1030)
– Water (million bacterial cells in a milliliter) bacteria on Earth, forming
– deep in the Earth's crust much of the world's
– in organic matter
biomass
– live bodies of plants and animals
Importance of bacteria
 Bacteria are vital in recycling nutrients(nitrogen fixation cycle and putrefaction)
 Some bacteria are pathogenic and cause infectious diseases (cholera, anthrax, TB)
 In industry, bacteria are important in sewage treatment, the production of cheese and yogurt
through fermentation, 1
 Used in biotechnology (antibiotics, interferon, genetic engineering)
 Phylogenetic tree of bacteria

 Most bacteria have not been characterized, and only about half of the phyla of bacteria have species that can be grown in the laboratory

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 Classification of bacteria
 Most widely used reference for classification of bacteria is Bergey’s manual of Systemic Bacteriology, published in 4 volumes.
1. Volume 1 contains ‘ordinary’ gram-negative bacteria
2. Volume 2 contains ‘ordinary’ gram-positive bacteria

Bergey’s manual Section Family

V1
gram-negative Spirochetes Spirochaetaceae
bacteria Leptospiraceae
Rickettsias & chlamydias Rickettsiaceae-Rickettsia (human)
Ehrlichieae (domestic animals)
Anaplasmataceae-Anaplasmosis
Mycoplasmas Mycoplasmataceae-
m.pneumonia(CBB)
Endosymbionts
Non-motile (or rarely motile) curved- Pseudomonadaceae-Xanthomonas
bacteria Rhizobiaceae-agrobacterium
Facultatively anaerobic rods Enterobacteriaceae-Esche richia
(e.coli), shigella, Salmonella, 3
Enterobacter
 Classification of bacteria
 Most widely used reference for classification of bacteria is Bergey’s manual of Systemic Bacteriology, published in 4 volumes.
1. Volume 1 contains ‘ordinary’ gram-negative bacteria
2. Volume 2 contains ‘ordinary’ gram-positive bacteria

Bergey’s Section Family

manual V2
gram- Gram-positive Cocci Staphylococcus-S. aureus
positive Streptococcus-S. pyogenes
bacteria
Endospore-forming Gram- Bacillus-B. thuringiensis
positive bacteria Clostridium-C. tetani
(tetanus)
Mycobacteria Mycobacterium-M.
tuberculosis
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 Biology of bacteria-Bacterial
morphology
Bacterial morphology is based on
A. Study of structure, appearance
B. Colony morphology - growth characteristics
C. Microscopic morphology - cell characteristics

Colony morphology
 A colony is clump of organisms growing on the surface of solid medium having
descended from a single cell
 Colony appearance vary and is characteristic of a genus
 Colony characteristics observed:
1. Shape, size
2. Margin
3. Elevation
4. Surface texture
5. Light transmitting property (color)
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6. Consistency
 Biology of bacteria-Bacterial
morphology
Microscopic morphology is based on
A. Size
B. Shape
C. Arrangement
D. Cell Structure
Basic cell structure
Special cell structures
Size
Bacterial size is measured in micrometers
(µ m) 1000 µ m = 1mm
Average Range:
Diameter = 0.1 µ m - 2 µ m
Length = 0.1 µ m - 8 µ m
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 Biology of bacteria-Bacterial
morphology
Cell shape, arrangement- variation of shape & arrangement is a characteristic of a genus
 Three groups according to shape. In addition,.
1. Cocci (us)-e.g. Stappylococus aureus; Streptococcus pneumoniae
2. Bacilli (us) -e.g. E. coli
3. Spirals-e.g. E. coli
 Cocci (us)
– Spherical, oval, egg shaped, bean shaped
– Size and shape varies
– Singles, pairs, irregular clusters, tetrads, cubical packets of 8.

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 Biology of bacteria-Bacterial
Bacilli (us) morphology
 Elongated, cylindrical, rod-like
 Vary in diameter, length, shape of ends, arrangement.
 Singles, pairs, chains, parallel packets

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 Biology of bacteria-Bacterial
Spirals morphology
 Curved rods, varying in diameter, length, number of curves, tightness of curves
& flexibility
 Three groups of spirals:
1. Vibrios – Vibrio cholera single curve, comma shaped
2. Spirillum- C. fetus rigid, two or more curves, cork screw shape
3. Spirochetes – flexible, two or more curves, wavy - move by flexing bodies.
Vibrios Spirillum Spirochetes

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 Biology of bacteria-Bacterial morphology
Basic cell structure
Flagellum

Capsule
Cell wall
Cell membrane Pilus

Cytoplasm

Inclusion

Nucleoid (circular DNA)

Plasmid
Ribosomes 10
 Biology of bacteria-Bacterial morphology
Basic cell structure-Structure and contents of a typical Gram positive bacterial cell
Extracellular structures
•Cell wall
•Cell (plasma) membrane
Intracellular structures
• Nuleoid (circ. DNA)
• Cytoplasm
• Ribosomes
• Inclusions
• Vacuoles
Special cell structures
• Capsule
• Flagellum(a)
• Pilus (pili)
• Plasmids
• Endospores

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 Composition & function of structures
Structure Property Composition Function
Cell wall -Rigid -Peptidoglycan (murein)- 1) Shape of the cell
-Porous major compound 2) Protection from ∆ in internal and
-80% murein Gram +ve external osmotic pressure
-40% murein Gram-ve
-20% murein Acid fast
Cell membrane -Thin, flexible Phospholipids & proteins 1Controls movement of nutrients,
-Semi permeable wastes across the membrane
2) Site of some metabolic reactions
- production of energy

Cytoplasm Viscous fluid 1. Filling of cell (“cell sap”)

Consistency of egg 2. Suspension medium
whites 3. Site of most metabolic processes

Nucleoid -Long, circular -DNA Control center of the cell

-Highly folded, -Single molecule Controls reproduction
suspended in -Lacks histones Controls metabolism
cytoplasm Contains genetic code (inherited
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characteristics)
 Composition & function of structures
Structure Property Composition Function
Ribosomes -Large, dense granules -RNA Sites of protein synthesis
-Scattered throughout -Proteins
cytoplasm
Cytoplasmic -Very small, numerous a.Volutin granules Storage of nutrients
Inclusions -Scattered throughout polyphosphate 1).Phosphates
cytoplasm b. Polysaccharide granules 2).Glycogen
b. Poly-B hydroxybutyrate 3.Carbon & energy source
(PHB) 3). Sulfur
c. Elemental sulfur
Gas vacuoles -Scattered in cytoplasm -Protein -Provide buoyancy
-Gases, lipid droplets Identifying feature of
-Bright retractile bodies vacuoles-can collapse und
pressure
Capsule -Jelly-like layer secreted by cell -Complex polypeptides and -Protects the bacterium from
(D.pnemonia) -Adheres to cell wall polysaccharides phagocytes
-Capsule - thick layer, regular -Exact composition varies in -Enhances bacterium’s
-Found only on some Cocci, each individual species ability to produce disease
bacilli
-Will not absorb dyes, need Bacteria 13
special staining techniques
 Composition & function of structures
Structure Property
Flagellum -Long, thin, thread-like appendage
-Attached to the cell membrane from a flagellin
basal granule
-Number and Location:
a. Number - single, two, or more
b. Location - at one end, both ends, all
over cell
-Found only on some bacilli, spirals
-Requires special stain to
demonstrate
Plasmids -Small circles of DNA
-Are not connected to the nucleoid
Composition Function
Protein called -Responsible for motility
-Rotates clockwise or counter
clockwise
-Chemotaxis - movement
toward nutrients, away from
harmful chemicals
-DNA -Contains genetic information that
is not essential to the cell’s
survival
-May contain genes for R factors
(drug resistance), toxins
-May be involved in conjugation
-Used in genetic engineering
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 Composition & function of structures
Structure Property Composition Function
Endospores -Dense, round to oval structure occurring -DNA -Survival-protection from
(spores) in cytoplasm surrounded by an adverse environmental
-Extremely resistant to environmental endospore cortex conditions
conditions (heat, drying, lack of nutrients, formed of -Produced by bacteria of
chemicals, radiation)
repeated layers genus Bacillus & clostridium
Remains viable but dormant after
vegetative cell dies of cell wall and
-Will germinate when introduced into a cell membrane
favorable environment producing a cell
identical to the parent cell
Pilus -Thin, shorter, hair-like appendages Protein - pilin Attachment pili :
-Vary in length 1).Allow bacteria to adhere to the
-Extend from entire surface of cell surface of mucus membranes and
to each other
-Two types:
2).Enables the cells to colonize
1).Attachment pili (Shorter in length 3).Enhances the bacteria’s ability
2).Conjugation (sex) pili (Longer in to cause disease
length) Conjugation (sex) pili
1).Allows two bacteria to adhere
to each other
3).Provides a pathway for a
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segment of DNA to be
transferred from one cell to the
 Bacterial reproduction
Two types of reproduction (Asexual & Sexual)
Asexual reproduction (binary fission)-very simple
1.The cell increases in size ( metabolism, production of cell parts & energy)
2.A double wall develops across midline of the enlarged cell (DNA duplication).
3.The cell separates into two cells at the midline wall.
4. Each cell is then able to function as a separate entity.
The process of multiplication can be quite rapid. The bacterium E. coli
may double in number every 20 minutes in ideal conditions. If you plot
the graph of population over time, you get an exponential increase
Two daughter cells

1St generation

2nd generation

3rd generation 16
Binary fission
Binary fission begins with
DNA replication.
 The cell elongates, causing the
DNA to separate
The cell wall and plasma
membrane starts growing
transversely from near the middle
of the dividing cell. This
separates the parent cell into two
nearly equal daughter cells, each
having a nuclear body
The cell membrane then
invaginates (grows inwards) and
splits the cell into two daughter
cells, separated by a newly 17grown
cell plate
 Bacterial reproduction
Sexual reproduction (conjugation)
 Bacterial conjugation is the transfer of genetic material between
bacterial cells by direct cell-to-cell contact or by a bridge-like
connection between two cells
 Discovered in 1946 by Joshua Lederberg and Edward Tatum
 The genetic information transferred is often beneficial to the
recipient. Benefits may include antibiotic resistance, xenobiotic
tolerance or the ability to use new metabolites

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 Bacterial reproduction
Sexual reproduction
 .differs somewhat from what we consider sex in eukaryotes. It
involves the plasmid, which has several important characteristics:
 A plasmid is a loop of DNA that can multiply autonomously within
the cell.
 Many plasmids can insert into the DNA of the nucleus, and detach
from it. In doing so, the plasmid may leave part of the plasmid DNA
behind, and take some of the nuclear DNA with it.
 Plasmids can transfer from cell to cell, & cells need not be of the
same bacterial 'species'.
 Reference: Ochman et al (2000) Lateral gene transfer and the nature
of bacterial innovation. Nature 405: 299-304

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 Bacterial Conjugation diagram

1- Donor cell produces pilus. 2- Pilus attaches to recipient cell and brings the two cells
together. 3- The mobile plasmid is nicked and a single strand of DNA is then
transferred to the recipient cell. 4- Both cells synthesize a complementary strand to
produce a double stranded circular plasmid and also reproduce pili; both cells are 20 now
viable
 Bacterial growth curve
Bacterial growth is the division of one bacterium into two daughter cells.
Providing no mutational event occurs the resulting daughter cells are
genetically identical to the original cell. Hence, "local doubling" of the
bacterial population occurs. Both daughter cells from the division do not
necessarily survive. However, if the number surviving exceeds unity on
average, the bacterial population undergoes exponential growth

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Phases of bacterial growth curve
1.Lag phase, bacteria adapt themselves to growth conditions. It is the
period where the individual bacteria are maturing and not yet able to
divide. Synthesis of RNA, enzymes and other molecules occurs -so in
this phase the microorganisms are not dormant.
2.Exponential phase (log phase or the logarithmic phase) is a period
characterized by cell doubling. The number of new bacteria appearing
per unit time is proportional to the present population. If growth is not
limited, doubling will continue at a constant rate so both the number of
cells and the rate of population increase doubles with each consecutive
time period. Exponential growth cannot continue indefinitely, because
the medium is soon depleted of nutrients and enriched with wastes.
3.Stationary phase, growth rate slows as a result of nutrient depletion
and accumulation of toxic products. This phase is reached as the bacteria
begin to exhaust the resources that are available to them. This phase is a
constant value as the rate of bacterial growth is equal to the rate of
bacterial death. 22
4.Death phase, bacteria run out of nutrients and die.
Bacterial colony morphology

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 Bacterial genetics-DNA
 Deoxyribonucleic acid or DNA, is a nucleic acid that contains the genetic
instructions used in the development and functioning of all living organisms
(except RNA viruses).
 The main role of DNA molecules is the long-term storage of information. DNA is
often compared to a set of blueprints, like a recipe or a code, since it contains the
instructions needed to construct other components of cells, such as proteins and
RNA molecules.
 The DNA segments that carry this genetic information are called genes, but other
DNA sequences have structural purposes, or are involved in regulating the use of
this genetic information.
 DNA consists of two long polymers (run in opposite directions to each other and
are therefore anti-parallel ) of simple units called nucleotides, with backbones
made of sugars and phosphate groups.
 Attached to each sugar is one of four types of molecules called bases. It is the
sequence of these four bases along the backbone that encodes information (read
using the genetic code) which specifies the sequence of the amino acids within
proteins.
 Within cells, DNA is organized into long structures called chromosomes. These
chromosomes are duplicated before cells divide, in a process called DNA 24
A section of DNA
The bases lie horizontally between the two
spiraling strands
Components of DNA
A. 2- deoxyribose sugar
B. Phosphate group (PO4)
C. Nitrogen (N) bases
–1. Pyrimidines
 Thymine
 Cytosine
–2. Purines
 Adenine
 Guanine
Pairing of nitrogen bases
Pairing of N bases is specific
a. Adenine to thymine - 2 “weak” hydrogen
(H) bonds
b. Guanine to cytosine - 3 “weak” H bonds
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 Genetic code
•The genetic code is the set of rules by which information encoded
in genetic material (DNA or mRNA sequences) is translated into
proteins (amino acid sequences) by living cells.
• The code defines a mapping between tri-nucleotide sequences,
called codons, and amino acids.
•A triplet codon in a nucleic acid sequence specifies a single amino
acid and is called the genetic code
•Start codons Translation starts with a chain initiation codon (start
codon). The most common start codon is AUG which is read as
methionine or, in bacteria, as formylmethionine. (GUG" or "UUG”
stop codons
•The three stop codons have been given names: UAG is amber,
UGA is opal (sometimes also called umber), and UAA is ochre. “.
Stop codons are also called "termination" or "nonsense" codons and
they signal release of the nascent polypeptide from the ribosome

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 Central dogma

The central dogma of molecular biology was first articulated by Francis Crick in
1958
The central dogma deals with the detailed residue-by-residue transfer of sequential
information.
It states that information cannot be transferred back from protein to either protein or
nucleic acid (once information gets into protein, it can't flow back to nucleic acid)
27
 DNA replication, transcription, & translation
DNA replication
As the final step in the Central Dogma, to transmit the genetic
information between parents and progeny, the DNA must be
replicated faithfully. Replication is carried out by a complex group
of proteins that unwind the super helix, unwind the double-stranded
DNA helix, and, using DNA polymerase and its associated
proteins, copy or replicate the master template itself so the cycle
can repeat DNA → RNA → protein in a new generation of cells or
organisms
Transcription
Transcription is the process by which the information contained in
a section of DNA is transferred to a newly assembled piece of
messenger RNA (mRNA). It is facilitated by RNA polymerase and
transcription factors.
Translation
Translation is the process by which mature mRNA information is
converted into amino acid (protein) mRNA finds its way to a
ribosome, where it is translated.. The mRNA is read by the
ribosome as triplet codons
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 Gene regulation-A typical operon

In genetics, an operon is a functioning unit of genomic material containing a cluster

of genes under the control of a single regulatory signal or promoter[
 The genes are transcribed together into an mRNA strand and either translated
together in the cytoplasm, or undergo trans-splicing to create mRNAs that are
translated separately, i.e. several strands of mRNA that each encode a single gene
product.
The result of this is that the genes contained in the operon are either expressed
together or not at all
 Several genes must be both co-transcribed and co-regulated to define an operon.
Examples of operons
1.The lac operon 29

2.The trp operon

 The lac operon

The lac operon is an operon required for the transport and metabolism of lactose in
Escherichia coli and some other enteric bacteria
 It consists of three adjacent structural genes, lacZ, lacY and lacA
 The lac operon is regulated by several factors including the availability of glucose
and of lactose.
Gene regulation of the lac operon was the first complex genetic regulatory
mechanism to be elucidated and is one of the foremost examples of prokaryotic gene
regulation.

30
 Structure of the Operon
• lacZ encodes β-galactosidase (LacZ): An intracellular enzyme that
cleaves the disaccharide lactose into glucose and galactose.
• lacY encodes β-galactoside permease (LacY)- a membrane-bound
transport protein that pumps lactose into the cell.
• lacA encodes β-galactoside transacetylase (LacA)- an enzyme that
transfers an acetyl group from acetyl-CoA to β-galactosides.
• Specific control of the lac genes depends on the availability of the
substrate lactose to the bacterium.
• The proteins are not produced by the bacterium when lactose is
unavailable as a carbon source.
• The lac genes are organized into an operon; they are oriented in the
same direction immediately adjacent on the chromosome and are co-
transcribed into a single polycistronic mRNA molecule.

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 Transfer of genetic material
Common properties of transfer:
 Transfer is unidirectional - donor cell → recipient cell
 Fragment of DNA is transferred
Three methods by which genetic material is transferred in bacteria.
Transformation-Viable bacteria absorb “naked” fragments of DNA
released from dead bacteria
Transduction-Transduction is the process by which DNA is transferred
from one bacterium to another by a virus (bacteriophage)
Conjugation-Bacterial conjugation is the transfer of genetic material
between bacterial cells by direct cell-to-cell contact or by a bridge-
like connection between two cells
a. Occurs amongst bacteria with sex pili
b. Bridge formed between cells by pilus
c. Fragment of DNA (plasmid) transferred from one bacterial cell
32
(donor) to another bacterial cell (recipient)
Bacterial Conjugation

33
 Bacteria in Nature
1.Decomposers
– Bacteria play a critical role in nature by recycling dead
organisms
– Nutrients in dead organisms can then be reused, instead of
accumulating
– Require the right mix of the following variables for maximum
decomposition to occur:
• Temperature
• Gas availability for terminal electron accepting (O2 is the
best)
• Water
– Widely used by humans to process dead materials to get rid of
them or to recycle them
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 Bacteria in Nature
2. Nitrogen Fixation
– Bacteria play a critical role in nature bringing “new” nitrogen
into the biosphere
– Lots of N2 gas in the atmosphere, but very few organisms can
capture it for use
– Certain bacterial species can “fix” the N2 into NH3 (ammonia)
or other nitrogen compounds
– Once “fixed” the nitrogen can be used by other organisms
– Legumes – plants that harbor nitrogen fixing bacteria in root
nodules
• These root nodules are functionally equal to having
fertilizer factory in your roots
35
 Bacteria in Nature
3. Bacteria and Disease
– Not all bacteria cause disease, but some do. These few “bad” bugs
give bacteria the group name of “germs”
– Pathogen – disease causing agent
– Two general ways a pathogen can operate:
• Break down tissues for food (ex. Tuberculosis)
• Release toxins that harm the host (ex. Food poisoning)
– Many bacteria can be killed or kept in check with antibiotics or
vaccines
• However, there is a rising problem with bacteria that are
resistant to our drugs (Imagine that! A bacterium that doesn’t
want to die).

36
 Bacteria in Nature
4. Human Uses of Bacteria
I. Many food products are made or modified through the
action of microorganisms. Cheese, yogurt, buttermilk,
sour cream, pickles, chocolate, tofu, etc.
II. Bacteria can also be used in industry to clean up toxic waste
and to help recover gold
III. Bacteria can also be used to make medicines
IV. “Bio-prospecting” – looking an industrially important
biological products

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 The nitrogen cycle
1. Nitrogen is required for all organisms to live and grow
because it is the essential component of DNA, RNA, and
protein.
2. However, most organisms cannot use atmospheric
nitrogen, the largest reservoir hence N limiting factor
3. The nitrogen cycle is the set of biogeochemical processes
by which nitrogen undergoes chemical reactions, changes
form, and moves through different reservoirs on earth,
including living organisms
4. The five processes in the nitrogen cycle -fixation, uptake,
mineralization, nitrification, and denitrification -are all
driven by microorganisms. 38
 The nitrogen cycle

Yellow-human sources of nitrogen to the environment

Red-microbial transformations of nitrogen
Blue-physical forces acting on nitrogen 39
Green-natural, non-microbial processes affecting form and fate of nitrogen
The nitrogen cycle

40
 Processes in nitrogen cycle-Nitrogen
fixation
 (N2 NH4+) Nitrogen fixation is the process where N2 is converted
to ammonium, essential because it is the only way that organisms
can attain nitrogen directly from the atmosphere
 Certain bacteria (genus Rhizobium) are the only organisms that fix
nitrogen through metabolic processes
 Nitrogen fixing bacteria often form symbiotic relationships with host
legume family plants (e.g. beans, peas, and clover)
 In this relationship, nitrogen fixing bacteria inhabit legume root
nodules (Figure 2) and receive carbohydrates and a favorable
environment from their host plant in exchange for some of the
nitrogen they fix

Rhizobium nodule
41
 Processes in nitrogen cycle-Nitrogen fixation
 There are also nitrogen fixing bacteria that exist without plant hosts,
known as free-living nitrogen fixers. In aquatic environments, blue-
green algae ( a bacteria called cyanobacteria) is an important free-
living nitrogen fixer.
 In addition to nitrogen fixing bacteria, high-energy natural events such
as lightning, forest fires, and even hot lava flows can cause the fixation
of smaller, but significant amounts of nitrogen
 The high energy of these natural phenomena can break the triple bonds
of N2 molecules, making individual N atoms available for chemical
transformation with oxygen to nitrogen oxide and nitrates
 Within the last century, humans have become as important a source of
fixed nitrogen as all natural sources combined. Burning fossil fuels,
using synthetic nitrogen fertilizers, and cultivation of legumes all fix
nitrogen. Through these activities, humans have more than doubled the
amount of fixed nitrogen that is pumped into the biosphere every year
42
Processes in nitrogen cycle-Nitrogen uptake
(NH4+ Organic N )The ammonia produced by nitrogen fixing bacteria is
usually quickly incorporated into protein and other organic nitrogen
compounds, either by a host plant, the bacteria itself, or another soil
organism.
Processes in nitrogen cycle-Nitrogen mineralization
(Organic N NH4+) After nitrogen is incorporated into organic matter, it
is often converted back into inorganic nitrogen by a process called
nitrogen mineralization, otherwise known as decay.
When organisms die, decomposers (such as bacteria and fungi)
consume the organic matter and lead to the process of decomposition.
During this process, a significant amount of the nitrogen contained within
the dead organism is converted to ammonium. Once in the form of
ammonium, nitrogen is available for use by plants or for further
transformation into nitrate (NO3-) through the process called nitrification.
43
 Processes in nitrogen cycle-Nitrification
 (NH4+ NO3-) Some of the ammonium produced by decomposition is
converted to nitrate via a process called nitrification. The bacteria that
carry out this reaction gain energy from it.
 Nitrification requires the presence of oxygen, so nitrification can
happen only in oxygen-rich environments like circulating or flowing
waters and the very surface layers of soils and sediments.
 The process of nitrification has some important consequences.
Ammonium ions are positively charged and therefore stick to
negatively charged clay particles and soil organic matter preventing
ammonium nitrogen from being washed out of soil (or leached) by
rainfall.
 In contrast, the negatively charged nitrate ion is not held by soil
particles and so can be washed down the soil profile, leading to
decreased soil fertility and nitrate enrichment of downstream surface
and ground waters. 44