Overview: Mibi Midterm Notes on Microbial Life | Môn Microbiology - Trường Đại học Quốc tế, Đại học Quốc gia Thành phố Hồ Chí Minh

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Chapter I : OVERVIEW OF MICROBIAL LIFE Microbe in Our Lives
Microbiology: Is the study of microorganisms (or microbes). The overall theme of
the microbiology course is to study the relationship between microbes and our lives.
Microorganisms (Microbes): Any living organism that is either a single cell
(unicellular), a cell cluster, or has no cells at all (acellular). Generally, they are too
small to be seen with the unaided eye, and usually require a microscope to be seen.
The relationship between microbes and our lives involves harmful and beneficial effects
Microorganisms include: - Bacteria
- Fungi (yeasts and molds) - Microscopic algae - Protozoa
- Virus, Viroids, Prions
Microorganisms are Essential for Life on Earth
Microbes have many important and beneficial biological functions: Photosynthesis:
Algae and some bacteria capture energy from sunlight and convert it to food,
forming the basis of the food chain.
Decomposition: Many microbes break down dead and decaying matter and recycle
nutrients that can be used by other organisms.
Nitrogen fixation: Some bacteria can take nitrogen from air and incorporate it into soil.
Digestion: Animals have microorganisms in their digestive tract, that are essential
for digestion and vitamin synthesis.
Medicine: Many antibiotics and other drugs are naturally synthesized by microbes.
Food industry: Many important foods and beverages are made with microbes
(vinegar, pickles, alcoholic beverages, green olives, soy sauce, buttermilk, cheese, yogurt, and bread).
Genetic engineering: Recent advances in gene splicing allow us to design
recombinant microbes that produce important products such as human growth
hormone, insulin, blood clotting factor, human hemoglobin, erythropoietin and monoclonal antibodies.
Medical research: Microbes are well suited for biological and medical research for several reasons: lOMoAR cPSD| 58504431
- Relatively simple and small structures, easy to study
- Genetic material is easily manipulated
- Can grow a large number of cells very quickly and at low cost
- Short generation times make them very useful to study genetic changes
Microbial Relationships • Symbiosis
Many microbes form mutually beneficial relationships with other organisms,
such as gut bacteria aiding in digestion. • Pathogenesis:
Some microbes can cause disease by infecting and harming their host, leading
to the study of microbial pathogens. • Competition:
Microbes also compete for resources and can produce antimicrobial
compounds to outcompete their rivals.
Microbes and the Environment • Nutrient cycling
Microbes play crucial roles in the cycling of essential nutrients like carbon,
nitrogen, and sulfur in ecosystems. • Bioremediation:
Certain microbes can break down pollutants and clean up contaminated
environments, making them valuable for environmental restoration. • Biotechnology:
Microbes are increasingly being harnessed for industrial and medical
applications, such as the production of biofuels and pharmaceuticals. • Climate impact:
Microbial activities can influence global climate patterns, either by producing
or consuming greenhouse gases.
Microbial Interactions With Humans • Gut microbiome
The trillions of microbes living in our digestive system play a key role in maintaining health. • Immune system:
Microbes can both support and challenge our immune defenses, influencing our overall wellbeing. • Infectious diseases: lOMoAR cPSD| 58504431
Some microbes can cause serious illnesses, leading to the study and treatment of microbial pathogens. • Biotechnology:
Microbes are increasingly being harnessed for various industrial and medical applications.
Knowledge of Microorganisms (MOs) •
Today, we understand that MOs are almost everywhere! •
Yet not long ago, before the invention of the microscope, microbes were
unknown to scientists and: o Thousands of people died in devastating
epidemics, the causes of which were not understood.
o Entire families died because vaccinations and antibiotics were not
available to fight infections. •
Therefore, knowledge of MOs allows humans to:
o Prevent disease occurrence o Prevent food spoilage o Led
to aseptic techniques to prevent
contamination in medicine and in microbiology laboratories.
Naming and Classifying Microorganisms •
Linnaeus established the system of scientific nomenclature (naming) of organisms in 1735. •
Latin was the language traditionally used by scholars. •
Today, microorganism names originate from four different sources. • Descriptive:
Ex: Staphylococcus aureus (grape-like cluster of spheres, golden in color) Scientist’s names:
Ex: Escherichia coli (Theodor Esherich) •
Listeria (Joseph Lister) Geographic places:
Ex: Legionella longbeachiae (Long Beach, California, US)
Pseudomonas fairmontensis (Fairmont Park, Pennsylvania, US) Organizations:
Ex: Afipia felis (Air force Institute of Pathology) •
Bilophila wadsworthia (VA Wadsworth Medical Center in Los Angles) Rules of Nomenclature Use binary names: lOMoAR cPSD| 58504431
Binary names consisting of a generic name and a species epithet
(e.g., Escherichia coli), must be used for all microorganisms. Name of
categories at or above the genus level may be used alone, but species and
subspecies names (species names) may not. Never use a species name alone! When to Capitalize:
The genus name (and above) is always capitalized, the species name is never
capitalized, e.g. Bacillus anthracis. • When to Italicize:
Name of all taxa (kingdom, phyla, classes, orders, families, genera, species
and subspecies) are printed in italics and should be underlined of handwritten;
strain designations and number are not. If all surrounding text is italic, then
the binary name would be non-italic (roman typeface) or underlined (e.g. A
common cause of diarrhea is E.coli 0157, a gran negative bacillus). • When to use Initials:
A specific must be preceded by a generic name written out in full the first time
it is used in a paper. Thereafter, the generic name should be abbreviated to the
initial capital letter (e.g. E.coli), provided there can be no confusion with other
genera used in the paper. Be careful with the “S” words: Salmonella, Shigella,
Serratia, Staphylococcus, Streptococcus, etc. • Common names:
Common names should be in lowercase roman type, non-italic (e.g.
streptococcus, brucella). However, when referring to the actual genus name
(or above) always capitalize and italicize. •
Subspecies and serovars:
For Salmonella, genus, species and subspecies names should be rendered in
standard form: Salmonella enterica at first use, S.enterica thereafter;
Salmonella enterica subsp. arizonae at first use, S.
enterica subsp. Arizonae thereafter. •
Abbreviations for species:
Use “sp.” for a particular species, “spp.” for several species (“spp” stands for
“species plural”). These abbreviations are not italicized; e.g. Clostridium sp. or Clostridium spp. • Plural forms:
o Plural of genus is genera o Plural of species (sp.) is
species (spp.) o Plural of medium is media o Plural of
fungus is fungi o Plural of streptococcus is streptococci
o Plural of bacillus is bacilli o Plural of bacterium is
bacteria o Plural of alga is algae lOMoAR cPSD| 58504431
o Plural of protozoan is protozoa Microbial Genomics • DNA sequencing
Advances in DNA sequencing technologies have enabled the study of
microbial genomes in unprecedented detail. • Genome assembly:
Researchers can now piece together the complete genetic blueprints of various
microbes, revealing their evolutionary histories and metabolic capabilities. • Metagenomics:
By analyzing the collective genomes of entire microbial communities,
scientists can better understand the ecological roles and interactions of these microscopic life forms.
CHAPTER II : CELL STRUCTURE AND FUNCTION IN BACTERIA AND ARCHAEA Microbial Size •
Bacteria are typically 1/10 the size of eukaryotic cells, measuring
approximately 1 micron (1um) in diameter. lOMoAR cPSD| 58504431 •
Viruses are even smaller, with many being only 100 nanometers (nm) in diameter. •
Microorganisms can only be observed under a microscope. Classification •
Old: Five-Kingdom Systems o Monera, Protists, Plants, Fungi, Animals •
New: Three Domains (Woese, 1980) o Reflects a greater understanding of
evolution and molecular evidence. o Prokaryote: Bacteria o Prokaryote: Archaebacteria o Eukaryotes Protists Plants Fungi Animals lOMoAR cPSD| 58504431
Domain Bacteria, Archaea, Eukarya
The three-domain system is a more recent classification system that is based on the
differences in the ribosomal RNA (rRNA) genes of organisms. It is considered a
more accurate representation of evolutionary relationships among living organisms.
Archaea can only be observed under a microscope 1. Microbial Size: lOMoAR cPSD| 58504431 •
Bacteria are typically 1/10 the size of eukaryotic cells, measuring about 1 micron (1µm) in diameter. •
Viruses are even smaller, with many only 100 nanometers (nm) in diameter.
These microscopic organisms require a microscope for observation. 2. Classification:
The three-domain system, proposed by Carl Woese, is the current accepted
classification system for living organisms. It distinguishes between bacteria,
archaea, and eukaryotes, acknowledging their unique evolutionary histories and molecular differences.
3. Archaea: A Unique Domain: •
Archaea are prokaryotic cells, meaning they lack a nucleus and other membrane-bound organelles. •
They have a unique cell wall structure that is different from bacteria. •
Archaea thrive in extreme environments, often found in hot springs, salt lakes, and acidic conditions. •
Key features of archaea: o Plasma membrane: associated with lipids or glycerol o 70S ribosomes o 16S rRNA
o Cell wall without peptidoglycan o Histone-like proteins associated
with DNA o No true nucleus (nucleoid in the cytoplasm) o No membrane-bound organelles
4. Bacteria: A Diverse Group: •
Bacteria are also prokaryotic cells. •
They exhibit a variety of shapes, including rod-shaped (bacilli), spherical
(cocci), and spiral-shaped (spirilla). • Key features of bacteria:
o 70S ribosomes o Cell wall with peptidoglycan o Circular chromosome, naked DNA
5. Bacterial Structures: •
Flagella: Long, whip-like appendages that help bacteria move. They come in
various arrangements, including monotrichous (single flagellum),
peritrichous (multiple flagella covering the surface), and lophotrichous
(multiple flagella at one end). Flagella are powered by a proton motive force. lOMoAR cPSD| 58504431 •
Pili: Short, hair-like structures that help bacteria adhere to surfaces and
exchange genetic material during conjugation. •
Fimbriae: Smaller, hair-like structures that also assist with adhesion and can
contribute to biofilm formation. •
Capsule: A protective, well-organized layer of polysaccharide that surrounds
the cell wall and protects the bacteria from phagocytosis and desiccation. •
Slime layer: A diffuse, less organized layer of polysaccharide that also
provides protection and can contribute to biofilm formation. •
Glycocalyx: A general term for a protective covering that surrounds the cell
membrane and can be composed of polysaccharide units, proteins, or both. •
Endospores: Highly resistant, dormant structures formed by certain bacteria
to survive harsh conditions. They have a thick cell wall and are highly resistant
to heat, chemicals, and radiation. Endospores are important for bacterial
survival and can cause diseases like tetanus, anthrax, botulism, and gangrene.
6. Bacterial Cell Wall: •
Peptidoglycan: A unique molecule found in bacterial cell walls that provides
rigidity and shape. It is composed of sugars (glycans) and amino acids (peptides). •
Gram-positive bacteria: Have a thick layer of peptidoglycan, making them
appear purple under a Gram stain. •
Gram-negative bacteria: Have a thinner layer of peptidoglycan that is
sandwiched between an inner cell membrane and an outer membrane, which
contains lipopolysaccharides. They appear pink-red under a Gram stain.
7. Other Bacterial Structures: •
Nucleoid: The region within the cytoplasm where the circular DNA is located. •
Ribosomes: Essential for protein synthesis, they have a 70S structure in prokaryotes. •
Plasmids: Small, circular DNA molecules that carry extra genes. They are
often involved in antibiotic resistance, toxin production, and other functions. •
Inclusion bodies: Store nutrients and help bacteria survive under harsh conditions.
8. The Actin Cytoskeleton:
This plays a role in maintaining the shape of some bacteria.
9. Prokaryotic Fission: lOMoAR cPSD| 58504431
This is the process of cell division in prokaryotes, where one cell divides into
two identical daughter cells.
10. The Main Differences Between Bacteria, Archaea, and Eukaryotes: Feature Eukaryotes Bacteria Archaea Nucleus Present Absent Absent Chromosome Linear Circular Circular Ribosomes 80S (cytoplasmic) 70S 70S Organelles Present Absent Absent Cell
wall Varies, often with Peptidoglycan Varies, different composition cellulose or chitin from bacteria
First amino acid in Methionine N-formyl Methionine protein synthesis methionine
11. Prokaryotic Metabolism: •
Prokaryotes can obtain energy and nutrients through a variety of mechanisms,
including: o Photoautotrophy: Using light to convert carbon dioxide into organic compounds.
o Chemoautotrophy: Using inorganic chemicals for energy. o
Heterotrophy: Obtaining nutrients from organic compounds produced by other organisms.
12. Genetic Variation in Bacteria: •
Mutations: Errors in DNA replication lead to mutations, which can provide bacteria with new traits. •
Genetic recombination: Bacteria can exchange genetic information through
mechanisms like conjugation (direct transfer of DNA through pili),
transduction (transfer of DNA through a virus), and transformation (uptake of DNA from the environment). 13. Gram Staining:
This staining technique differentiates between gram-positive and
gramnegative bacteria based on their cell wall structure. o Gram-positive:
Bacteria with a thick peptidoglycan layer will stain purple.
o Gram-negative: Bacteria with a thin layer of peptidoglycan and an outer membrane will stain pink-red. lOMoAR cPSD| 58504431
CHAPTER III : MICROBIAL NUTRITION, LABORATORY
CULTURE AND METABOLISM OF MICROORGANISMS
Nutritional Categories of Microorganisms Based on Carbon Source •
Autotrophs: Obtain carbon from inorganic sources, such as carbon dioxide (CO2). •
Photoautotrophs: Use sunlight as an energy source to convert CO2 into
organic compounds (e.g., plants, algae, cyanobacteria). •
Chemoautotrophs: Obtain energy from inorganic chemicals, like hydrogen
sulfide or methane, to fix CO2 (e.g., some bacteria and archaea). •
Heterotrophs: Obtain carbon from organic compounds produced by other organisms. •
Saprophytes: Decompose dead organic matter (e.g., most bacteria and fungi). •
Parasites: Obtain nutrients from a living host (e.g., many bacteria, viruses, and protozoa). Based on Energy Source •
Phototrophs: Obtain energy from sunlight. •
Chemotrophs: Obtain energy from the oxidation of chemical compounds.
o Chemoorganotrophs: Obtain energy from organic compounds (e.g., most bacteria and fungi). lOMoAR cPSD| 58504431
o Chemolithotrophs: Obtain energy from inorganic compounds (e.g., some bacteria and archaea). Combined Categories •
Photoheterotrophs: Obtain energy from sunlight and carbon from organic
compounds (e.g., some bacteria and algae). •
Chemolithoheterotrophs: Obtain energy from inorganic compounds and
carbon from organic compounds (e.g., some bacteria).
Biochemical Components of Cells • Water: 80% of wet weight •
Dry weight o Protein: 40-70% o Nucleic acid: 13-34% o Lipid: 10-15% o
Also monomers, intermediates and inorganic ions Micronutrients
Micronutrients, also known as trace elements, are essential elements that cells
require in small quantities for optimal growth and function. While these elements
are present in trace amounts, their absence or deficiency can have significant
consequences for cellular processes. 1. Iron (Fe):
- Component of hemoglobin and myoglobin involved in oxygen transport -
Essential for many enzymes, including those involved in energ metabolism 2. Zinc (Zn):
- Involved in numerous enzymatic reactions, including those related to DNA
synthesis, protein synthesis, and immune function.
- Essential for the structure and function of many proteins 3. Copper (Cu):
- Cofactor for many enzymes, including those involved in energy production,
iron metabolism, and connective tissue synthesis.
- Antioxidant properties, protecting cells from oxidative damage 4. Manganese (Mn):
- Involved in various enzymatic reactions, including those related to
carbohydrate metabolism, energy production, and bone formation 2. Selenium (Se):
- Antioxidant properties, protecting cells from oxidative damage.
- Essential component of the enzyme glutathione peroxidase, which helps
neutralize harmful free radicals 3. Molybdenum (Mo): lOMoAR cPSD| 58504431
- Cofactor for several enzymes involved in nitrogen metabolism, sulfur
metabolism, and detoxification Vitamins • Vitamin B12:
o Essential for DNA synthesis, red blood cell production, and nerve function.
o Found primarily in animal products. • Vitamin D:
o Regulates calcium and phosphorus absorption, essential for bone health.
o Can be synthesized by the body from sunlight. •
Vitamin K: o Essential for blood clotting and bone health.
o Found in green leafy vegetables and produced by intestinal bacteria.
The specific micronutrients required by cells can vary depending on the
organism, its environment, and its metabolic needs. Deficiencies in
micronutrients can lead to a variety of health problems, including
anemia, impaired growth and development, and weakened immune function. Macronutrients
Macronutrients are essential elements that cells require in relatively large quantities
for their growth, development, and function. Unlike micronutrients, which are
needed in trace amounts, macronutrients form the building blocks of cellular
structures and participate in numerous metabolic processes.
Here are some key macronutrients and their roles in cells: 1. Carbon (C):
- The backbone of organic molecules, including carbohydrates, lipids, proteins, and nucleic acids
- Essential for energy production and cellular structure 2. Hydrogen (H):
- Component of water and organic molecules.
- Involved in energy metabolism and maintaining cellular pH 3. Oxygen (O):
- Essential for respiration and energy production..
- Component of water and organic molecules 4. Nitrogen (N):
- Found in proteins, nucleic acids, and other organic compounds lOMoAR cPSD| 58504431
- Essential for growth and development 5. Phosphorus (P):
- Component of nucleic acids, phospholipids, and ATP (energy currency).
- Involved in bone and tooth formation. 6. Sulfur (S):
- Found in amino acids, proteins, and vitamins
- Essential for protein structure and function 7. Potassium (K):
- Maintains intracellular fluid balance and nerve function.
- Involved in protein synthesis and energy metabolism 8. Sodium (Na)
- Maintains extracellular fluid balance and nerve function
- Involved in nutrient absorption and waste removal 9. Calcium (Ca):
- Essential for bone and tooth formation.
- Involved in muscle contraction, blood clotting, and nerve function. 10.Magnesium (Mg):
- Cofactor for many enzymes involved in energy production, protein
synthesis, and muscle function
While these are the primary macronutrients, other elements may also be required by
cells in smaller amounts, depending on the organism and its environment.
Deficiencies in macronutrients can lead to various health problems, including
impaired growth, weakened immune function, and muscle weakness. Uptake of Nutrients
Bacteria have evolved various mechanisms to efficiently acquire the nutrients they
need from their environment. These mechanisms can be broadly categorized into: 1. Passive transport:
- Simple Diffusion: Nutrients move from a higher concentration to a
lower concentration across the cell membrane. This is suitable for small, uncharged molecules.
- Facilitated Diffusion: Requires a membrane protein (carrier or channel
protein) to transport molecules across the membrane, even against a
concentration gradient. This is used for larger or charged molecules. 2. Active Transport
- Primary Active Transport: Uses energy directly from ATP hydrolysis
to transport molecules against a concentration gradient. lOMoAR cPSD| 58504431
Examples include the sodium-potassium pump and proton pumps.
- Secondary Active Transport: Uses the energy stored in an
electrochemical gradient (often created by primary active transport) to
transport other molecules. This can be symport (moving molecules in
the same direction) or antiport (moving molecules in opposite directions).
ABC (ATP-binding cassette) transport systems •
ABC (ATP-binding cassette) transport systems: A large family of
membrane proteins found in all living organisms, including bacteria. They are
crucial for the uptake and efflux (transport out) of various molecules. •
Structure and Function:
o Periplasmic Binding Protein (PBP): Binds to the specific molecule to
be transported in the periplasmic space (the space between the inner and
outer membranes in Gram-negative bacteria). o Membrane Fusion
Protein (MFP): Interacts with the PBP and the ABC transporter. o
ABC Transporter: Consists of two transmembrane domains and two
nucleotide-binding domains (NBDs). The NBDs bind and hydrolyze
ATP to provide the energy needed for transport. •
Types of ABC Transport Systems:
o Importer systems: Transport molecules into the cell, crucial for
acquiring nutrients. o Exporter systems: Transport molecules out of
the cell, involved in toxin efflux, antibiotic resistance, and protein secretion. • Key components:
o Periplasmic Binding Protein (PBP): Binds to the specific molecule to be transported.
o Membrane Fusion Protein (MFP): Connects the PBP to the ABC transporter.
o ABC Transporter: Consists of two transmembrane domains and two
nucleotide-binding domains (NBDs). The NBDs bind and hydrolyze
ATP to provide energy for transport. The Process:
1. PBP binding: The PBP binds to the molecule to be transported in the periplasmic space.
2. MFP interaction: The PBP-molecule complex interacts with the MFP.
3. ABC transporter binding: The ABC transporter binds to the complex and hydrolyzes ATP. lOMoAR cPSD| 58504431
4. Transport: The energy from ATP hydrolysis is used to transport the molecule across the membrane. •
Examples of ABC Transport Systems:
o Maltose transporter: A classic example of an importer system that
transports maltose into the cell.
o Multidrug efflux pumps: Exporter systems that pump out a wide range
of antibiotics and toxic compounds, contributing to antibiotic resistance. •
Importance of ABC Transport Systems:
o Essential for survival: ABC transport systems are essential for
bacterial survival by allowing them to acquire nutrients and eliminate toxic substances.
o Drug resistance: Overexpression of efflux pumps can contribute to antibiotic resistance.
o Virulence: Some bacteria use ABC transport systems to secrete
virulence factors that help them cause disease.
Uniport, Symport, and Antiport in Bacteria •
Secondary active transport: These systems use the energy stored in an
electrochemical gradient (often created by primary active transport) to
transport other molecules. They can be: o Uniport: A single molecule is
transported across the membrane in one direction.
o Symport: Two or more molecules are transported across the membrane in the same direction.
o Antiport: Two or more molecules are transported across the membrane in opposite directions. •
In bacteria, these transport systems are essential for: o Nutrient uptake:
Acquiring nutrients from the environment. o Waste removal: Excreting
waste products. o Maintaining intracellular pH: Regulating the pH of the cell's internal environment.
o Signaling: Communicating with the environment. • Key features:
o Uniport: A single molecule is transported across the membrane in one direction.
o Symport: Two or more molecules are transported across the membrane in the same direction.
o Antiport: Two or more molecules are transported across the membrane in opposite directions. lOMoAR cPSD| 58504431 • The image illustrates:
o Uniport: A single molecule (e.g., glucose) is transported from outside
the cell to inside the cell using the energy stored in a proton gradient.
o Symport: Two molecules (e.g., lactose and a proton) are transported
simultaneously from outside the cell to inside the cell, using the energy
of the proton gradient. o Antiport: Two molecules (e.g., sodium and
potassium ions) are transported in opposite directions across the
membrane, using the energy of a sodium gradient. Uptake of nutrients •
Group Translocation: A unique mechanism used by bacteria to
simultaneously transport and chemically modify nutrients. This process
involves a series of membrane proteins that work together to phosphorylate
or add other chemical groups to the nutrient as it enters the cell. •
Group Translocation via PTS (Phosphoenolpyruvate-dependent
phosphotransferase system): This system is a key mechanism used by
bacteria to acquire and modify sugars efficiently.
Group Translocation via PTS Key features of PTS:
o Energy source: PEP, a high-energy compound generated during
glycolysis, provides the energy for transport and phosphorylation.
o Multi-protein system: PTS involves a series of proteins located in the
cytoplasm and the cell membrane, working together to transfer the
phosphate group from PEP to the sugar being transported. o
Phosphorylation: As the sugar is transported across the membrane, it
is phosphorylated, preventing its efflux (movement out) and preparing it for further metabolism. • Advantages of PTS:
o Efficient energy coupling: PTS couples transport and phosphorylation
in a single step. o Regulation of sugar uptake: PTS can be regulated
to control the uptake of different sugars based on their availability.
o Prevention of sugar efflux: The phosphorylation of sugars prevents
their leakage back out of the cell. Uptake of nutrients •
Iron uptake: Iron is an essential micronutrient for most bacteria, but it is often
present in low concentrations and in insoluble forms in the environment.
Bacteria have evolved strategies to acquire iron efficiently. lOMoAR cPSD| 58504431 •
Siderophores: Low-molecular-weight chelating agents produced by bacteria
to bind to ferric iron (Fe³ ) with high affinity.⁺ •
Types of siderophores: There are different types, including hydroxamates,
catecholates, and mixed-type siderophores. •
Iron acquisition: Bacteria secrete siderophores into the environment, where
they bind to ferric iron. The siderophore-iron complex is then transported back into the bacterial cell. •
TonB-dependent transporters: Membrane protein complexes responsible
for the uptake of siderophore-bound iron into the bacterial cell. •
Energy source: TonB, an inner membrane protein, harnesses the proton
motive force to provide the energy needed for iron transport. • Iron utilization:
o Reduction: Once inside the cell, ferric iron (Fe³ ) is reduced to ⁺ ferrous
iron (Fe² ) by reductases.⁺
o Incorporation: Ferrous iron is then incorporated into iron-containing
proteins, such as cytochromes, iron-sulfur proteins, and ferritin. Iron regulation • Iron regulation:
o Fur protein: Bacteria use the Fur (ferric uptake regulator) protein to
regulate iron uptake. When iron levels are high, Fur binds to DNA and
represses the expression of genes involved in iron acquisition.
o RhlR protein: In some bacteria, such as Pseudomonas aeruginosa, the
RhlR protein can also regulate iron uptake in response to quorum sensing signals. •
Key features of iron uptake:
o Siderophore: A small molecule secreted by the bacterium to bind to ferric iron.
o TonB-dependent transporter: A protein complex that transports the
siderophore-iron complex into the cell.
o Reductase: An enzyme that reduces ferric iron to ferrous iron.
o Iron-containing proteins: Proteins that incorporate ferrous iron.
Oxygen Requirements of Bacteria •
Oxygen Requirements of Bacteria: Bacteria have different requirements for
oxygen, which impacts their survival and growth. •
Obligate aerobes: These bacteria require oxygen to survive and grow. They
use oxygen as the final electron acceptor in the electron transport chain to lOMoAR cPSD| 58504431
produce energy. o Example: Pseudomonas aeruginosa is a common obligate
aerobe found in soil, water, and the human body. •
Obligate anaerobes: These bacteria are killed by the presence of oxygen.
They use other molecules, such as sulfate or nitrate, as final electron acceptors
in their metabolism. o Example: Clostridium tetani is an obligate anaerobe that causes tetanus. •
Facultative anaerobes: These bacteria can grow with or without oxygen. In
the presence of oxygen, they will use aerobic respiration. In the absence of
oxygen, they can switch to fermentation. o Example: Staphylococcus aureus
is a facultative anaerobe commonly found on human skin. •
Microaerophiles: These bacteria require oxygen to survive, but at a lower
concentration than what is found in the atmosphere. Too much oxygen can be
toxic to them. o Example: Helicobacter pylori is a microaerophile that causes stomach ulcers.
Laboratory culturing of bacteria •
Laboratory Culturing of Bacteria: This involves creating controlled
conditions to promote bacterial growth and proliferation. It is a fundamental
technique in microbiology with wide-ranging applications. •
Microbial culture: A method of multiplying microorganisms by letting them
reproduce in predetermined culture media under controlled laboratory conditions. • Purpose of culturing:
o Isolation of bacteria o Maintenance of stock cultures o Estimate
viable counts o Test for antibiotic sensitivity o Create antigens for laboratory use
o Certain genetic studies and manipulations of the cells also need that
bacteria to be cultured in vitro
o Culturing on solid media is another convenient way of separating bacteria in mixture •
Essential Components of Bacterial Culture:
o Medium: A nutrient-rich substance that provides bacteria with the
necessary nutrients for growth. o Inoculum: A sample of bacteria that
is introduced into the medium to start the culture.
o Incubation: The process of placing the culture in a controlled
environment with appropriate temperature, humidity, and sometimes carbon dioxide levels. lOMoAR cPSD| 58504431 Pure culture •
Pure culture: A culture that contains only a single type of microorganism.
This is essential for studying the characteristics and properties of a specific microbe without interference. •
Importance of pure cultures:
o Research: Studying the physiology, genetics, and behavior of microorganisms.
o Medical microbiology: Diagnosing infections and testing antibiotic susceptibility.
o Industrial microbiology: Producing useful products, such as
antibiotics, enzymes, and fermented foods.
Maintaining pure cultures: •
Maintaining pure cultures:
o Aseptic techniques: Strict procedures are used to prevent
contamination. o Proper storage: Cultures should be stored under
conditions that maintain their viability. Agar •
Agar: A polysaccharide extracted from marine algae used to solidify a
specific nutrient solution. It is not easily degraded by bacteria, is heatresistant
(can be sterilized), and remains solid once solidified.
Classification based on consistency
Culture media classification:
o Solid media: Contains a solidifying agent (e.g., agar or gelatin) and has a firm texture.
o Liquid media: Does not contain a solidifying agent. o Semisolid
media: Contains a low concentration of solidifying agent.
Classification of Culture Media •
Classification based on chemical composition:
o Simple media: Simple media such as peptone water, nutrient agar can
support most non-fastidious bacteria.
o Complex media: Contain special ingredients for growth.
o Synthetic media: Prepared with known concentrations of pure chemicals.
Classification based on functions