Introduction to Microbiology

Lecture 1: Introduction to Microbiology

• Microorganisms are too small to be clearly seen by the unaided eye.
• Microorganisms include bacteria, archaea, fungi (yeasts, molds), protozoa, algae, and viruses.
• Microorganisms range in size from ~0.2 µm to several millimeters.
• Microscopes (light or electron) are required for microorganism observation and study.
• Spontaneous Generation: The outdated belief that living organisms could arise from nonliving matter.
• Louis Pasteur disproved spontaneous generation with the swan-neck flask experiment.
• Broth was sterilized (boiled)
• The flask neck trapped microbes/dust from entering.
• No microbial growth occurred unless the neck was broken or tilted.
• Conclusion: Microbes arise from other microbes, not spontaneously.
• Microscopy enabled direct observation of microorganisms.
• Antonie van Leeuwenhoek first saw microorganisms using a single-lens microscope.
• Advanced microscopes enable visualization of:
• Cell morphology, movement, and cell division
• Microscopy provided the foundation for:
• Koch's postulates, cell theory, and germ theory of disease.
• Sterilization: The complete destruction/removal of all living microorganisms.
• Sterilization methods include heat (autoclaving), filtration, radiation, and chemicals.
• Pasteurization: A controlled heating form kills pathogens and reduces spoilage organisms, without sterilization.
• Aseptic Technique involves practices to prevent sterile materials or environments contamination.
• Needed in laboratories, medical settings (surgery, injections), and industrial microbiology.
• Pure Culture: A population of cells comes from a single cell and is free from contamination.
• Pure cultures are key for:
• Studying individual species, identifying pathogens and performing biochemical tests
• Koch's Postulates are used to establish a causal relationship between a microorganism and a disease.
• The microorganism must be present in every case, but absent from healthy individuals.
• The microorganism must be isolated and grown in pure culture.
• The cultured microorganism should cause disease when introduced into a healthy host.
• The microorganism must be re-isolated from the diseased host.
• These postulates provided the foundation for medical microbiology and the identification of many pathogens.
• Martinus Beijerinck and Sergei Winogradsky developed Enrichment Cultures and Microbial Ecology
• Enrichment is using selective media and conditions to favor growth for specific microorganisms.
• Winogradsky column: A layered microbial ecosystem in a column of mud and water, creating diverse microenvironments (aerobic, anaerobic, sulfur-rich, etc.).
• Microbes adapt to and shape their environment.
• Microbial plant interactions include:
• Potato blight: Caused by Phytophthora infestans (a water mold).
• Rust and smut: Caused by fungal pathogens, like Puccinia species.
• Tobacco mosaic virus (TMV): The first virus discovered; causes mottling of tobacco leaves.
• Nitrogen fixation happens when:
• Some bacteria (e.g., Rhizobium) form symbiotic relationships with legumes.
• Convert atmospheric N2 to ammonia (NH3), usable by plants, occurring in root nodules.
• Plant-microbe interactions are critical for agriculture, ecosystem function, and global nitrogen cycling.

Lecture 2: Prokaryotic Cell Structure and Function

Key topics:

• Diversity of prokaryotes in size, shape, and arrangement

• Basic features of a bacterial cell

• Binary fission

• Chemical composition of a bacterial cell

• Components of a bacterial cell: Nucleoid, plasmids, cytoplasm, inclusion bodies, internal membranes, plasma membrane, and cell wall

• The Gram stain differentiates bacteria into Gram-positive and Gram-negative categories

• Structural differences and similarities of Gram-negative and Gram-positive envelopes and qualities the features impart

• Prokaryotes have a variety of sizes, shapes, and arrangements.

• Cocci are spherical and display in chains (Streptococcus) or clusters (Staphylococcus).

• Bacilli are rod-shaped (e.g., E. coli).

• Vibrio are comma-shaped bacteria.

• Spirilla display rigid spiral shape

• Spirochetes display a flexible spiral shape

• Other forms include filamentous, star-shaped, and square (e.g., Haloarcula)

• Typical bacterial size: 0.2–2.0 µm diameter, up to 700 µm in length.

• Example: Thiomargarita namibiensis are measured to be ~750 µm (largest known bacterium)

• High Surface to Volume (S/V) ratio supports:

• Efficient nutrient uptake and rapid diffusion of waste

• Larger bacteria can develop structures such as vacuoles to overcome S/V limitations.

• Diagrams of a bacterial cell should include:

• Nucleoid, plasmids, cytoplasm, inclusion bodies, internal membranes (if present), plasma membrane, and cell wall (Gram-positive vs. Gram-negative).)

• Process of binary fission includes:

• Chromosome replication, cell elongation, septum formation, division into two daughter cells

• Binary fission is an asexual reproduction method for exponential population growth.

• Chemical composition of a bacterial cell is:

• Protein (~55%), RNA (~20%), DNA (~3%), Polysaccharides (~5%), Lipids (~9%), Small molecules, ions (~8%)

• Water (wet weight) is ~70% of total weight

• Nucleoid: The region contains the bacterial chromosome (usually circular).

• Lacks a membrane-bound but is associated with nucleoid-associated proteins (NAPs).

• Plasmids: Small, circular DNA that encodes accessory genes (e.g., antibiotic resistance).

• They can be transferred between bacteria via conjugation.

• Cytoplasm:

• An aqueous matrix with enzymes, ribosomes, solutes and the site of metabolism and biosynthesis.

• Inclusion Bodies:

• Storage granules stores in forms of Carbon (glycogen, PHB); Phosphate: volutin (Sulfur granules, gas vesicles, magnetosomes)

• Internal Membranes are specialized membranes in some bacteria:

• Thylakoids for photosynthesis (cyanobacteria), respiratory or metabolic roles in nitrifiers and methanotrophs.

• Plasma (Cytoplasmic) Membrane:

• Phospholipid bilayer with proteins

• Selectively permeable barrier

• Located where energy production (electron transport chain, ATP synthesis) and involves nutrient transfer and signal sensing.

• Cell Wall: Maintains shape, prevents osmotic lysis, composed of peptidoglycan.

• Differences form the basis for Gram staining

• Gram staining differentiates bacteria into Gram-positive and Gram-negative based on cell wall structure:

• Crystal violet is the primary stain and both cell types turn purple.

• Gram's iodine forms crystal violet-iodine complex.

• Alcohol/acetone decolorizes Gram-positive cells (retains crystal violet) and Gram-negative cells (loses dye/becomes colorless).

• Safranin counterstain:

• Gram-negative and Gram-positive appear pink/red and remains purple

• Components and Properties of Gram-Positive vs. Gram-Negative Cell Walls:

• Feature and properties for each are:

• Peptidoglycan layer(Thick vs. Thin)

• Teichoic acids(Present vs. Absent)

• Outer membrane(Absent vs. Present)

• Periplasmic space(Narrow or Absent vs. Present)

• Antibiotic sensitivity(Sensitive vs. Resistant)

• Stain color(retains crystal violet vs. retains safranin)

• Gram-negative outer membrane acts as a permeability barrier, contributing to antibiotic resistance and immune evasion.

Lecture 3: Bacterial Cell Envelopes and Specialized Structures

• Explain the functions of periplasm, cell wall, and outer membrane

• Describe the cell walls of Mycobacteria, Archaea, and Bacteria

• Describe the chemical composition of peptidoglycan, teichoic acids, mycolic acids, and lipopolysaccharide (LPS)

• Explain the structure and function of capsules, slime layers, pili, and flagella

• Describe the alternate cell structures: endospores and conidiospores

• Explain the steps in endospore sporulation

• Periplasm: The space between the inner (plasma) membrane and outer membrane in Gram-negative bacteria. Functions

• Nutrient acquisition (e.g., binding proteins for sugars and amino acids)

• Peptidoglycan biosynthesis

• Protein folding and assembly via chaperones

• Stress response

• Involved in the assembly of pili and flagella

• The Cell Wall provides structural strength, maintains cell shape, and prevents osmotic lysis.

• In Gram-positive bacteria it has a thick peptidoglycan layer, contains teichoic acids (wall teichoic acids and lipoteichoic acids) and is involved in cell division and acts as an anchor for surface proteins

• The Outer Membrane is only in Gram-negative bacteria

• Asymmetric lipid bilayer: inner leaflet = phospholipids, outer leaflet = lipopolysaccharide (LPS) Functions

• Selective permeability barrier and secretes proteins

• Houses porins (channels for small molecules)

• Provides protection from toxins, antibiotics, and host defenses

• Cell Walls of Mycobacteria, Archaea, and Bacteria:

• Mycobacteria- Complex cell wall with mycolic acids of a waxy, hydrophobic structure

• Archaea- lack true peptidoglycan but may have S-layers and Pseudomurein to help adapt to extreme environments (thermophiles, halophiles, acidophiles)

• Bacteria- there are either Gram-positive or Gram-negative, and contain cross-linked peptidoglycan

• Chemical Composition of Cell Envelope Components:

• Peptidoglycan (PG)- Polymer of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM)

• Gram-positive often has peptide interbridges in cross-links in S. aureus

• Teichoic Acids found in Gram-positive walls helps attach Peptidoglycan

• Lipopolysaccharide (LPS) is only found in Gram-positive outer membrane

• It is structural integrity that triggers immune responses in the host (endotoxin)

• External cell structures:

• The capsule is a well-organized, tightly bound extracellular layer that is typically composed of polysaccharides, Functions:

• Protection from phagocytosis, prevents desiccation, and promotes adherence to surfaces

• The Slime Layer is diffuse and loosely attached and is also polysaccharide-rich Functions include: -Gliding motility

• The Pili (Fimbriae) is short with thin hair-like appendages; Peritrichous or polar Functions:

• Adhesion to surfaces, twitching/gliding motility, and/or DNA transfer

• Flageela, is a long helical structure responsible for motility rotates like a propeller Functions:

• Used in Monotrichous (single), Lophotrichous (tuft at one end), Amphitrichous (one at each end), Peritrichous (all over)

• Alternative Structures: Endsopores and Conidiospores

• Endospores are a dormant resistant structures produced by some Gram-Positive Bacteria

• Conidospores are formed by Streptomyces and are resistant to desiccation, but not heat

• Endopspores consists of Asymmetric cell division, Forming cell division, Cortex synthesis, Endospore maturation

Lecture 4: Bacterial Growth and Culture Methods

• Chemical composition of bacterial cells
• Major factors required for bacterial growth and cultivation
• Types and compositions of culture media

Bacterial cultivation is essential for:

• Studying microbial physiology and genetics, Identifying pathogens, Producing antibiotics and industrial enzymes, Observing metabolism and testing drugs

Chemical composition of bacterial cells that are primarily:

• Water (~70% of cell weight), Dry weight includes: Proteins (most abundant macromolecule), RNA, DNA, Lipids, Polysaccharides, and Small molecules (ions, cofactors, metabolites)
• Requires sources of carbon, energy, electrons, Nitrogen, Phosphorus, Sulfur, and Growth factors

Bacteria uptake 4 primary methods to transport nutrients across the plasma membrane:

• Passive diffusion through movement from high to low concentration.
• Facilitated diffusion uses carrier proteins.
• Active transport requires energy and Moves substances against concentration gradient.
• Group translocation chemically modifies substances during transport.

Microbial growth has been affected by oxygen Requirement:

• Obligate aerobes (require oxygen); Facultative anaerobes (grow with or without oxygen); Obligate anaerobes (cannot tolerate oxygen) Aerotolerant anaerobes: indifferent to oxygen; Microaerophiles: require low oxygen levels; Oxygen can be toxic and need ROS

Temperature preferences have been determined between:

• Psychrophiles: <15°C (cold-loving); Mesophiles: 20–45°C (most pathogens); Thermophiles: 45–80°C (hot springs); Hyperthermophiles: >80°C (extreme heat) Temperature affects enzyme function and membrane fluidity.

Bacteria are cultured in liquid(broth) or solid(agar) media that are :

• Defined (synthetic) media requires an exact chemical composition that helps is used to study nutritional requirements
• Complex media contains unknown quantities of nutrients
• Selective media inhibits growth for some microbes that helps others ex: MacConkey agar
• Differential media distinguishes on biological traits.
• Selective/Differential media combines both properties and
• Enriched media contains additional nutrients for fastidious organisms

Lecture 5: Bacterial Growth and Population Dynamics

• Understand the difference between individual cell growth and population growth
• Understand the key phases of bacterial population growth
• Know the various methods for measuring bacterial growth
• Recognize real-world applications of understanding bacterial growth

Cell growth has increased in size and biomass of an individual cell

• Population has had an increased number of bacterial cells over time Binary fission: One cell divides into two identical daughter cells

Bacterial growth in batch culture follows a pattern of 5 phases:

• Lag phase has cells metabolically active but not dividing; New environment adaptation
• Exponential (log) phase exhibits rapid cell division where the population doubles at constant rate
• Stationary phase is when the growth rate slows and levels off that ends in division = cell death
• Death phase exhibits cells begin to die at an exponential rate and irreversible loss of viability
• Long-term stationary phase is when a small subpopulation survives through slow metabolism

Growth in nature isn't ideal due to its fluctuating and competing.

• Biofilms dominate in microbial life when encased in polymeric substances

Measuring Bacterial Growth happens through the following methods:

• Microscopic cell counts via counting chamber;

• Flow cytometry where the measures granularity, fluorescens, and etc...

• Viable cell counts can be expressed to be colony-forming and requires incubations

• Turbidity where masses can be measured and detected

• Chemostats maintain bacterial cultures in the exponential phase by continuous supply of nutrient and removal of waste

  • Application for antibiotic and enzyme production

Lecture 6: Control of Microorganisms

• Differentiate between sterilization and disinfection
• Describe the pattern of microbial death and the significance of the decimal reduction time (D value)
• Identify the factors that influence the effectiveness of antimicrobial agents
• Understand and compare the advantages, disadvantages, and uses of physical and chemical methods of microbial control

Key Terms Definitions:

• Sterilization (desotrys living organisms)
• Disinfection (Kills, inhibits, or removes disease-causing microorganisms):
• Disinfectant (non-living surface to remove pathogens)
• Sanitisation (reduction to safe pathogens)
• Antiseptics (living tissue to inhibit damage); Aseptic Technique(washing to prevent contamination)

Principles of Microbial Death:

• Is exponential/logarithmic: Constant or not all microbes die at once -Decimal Reduction Time where you assess the efficiency of how sterilisation occues

Effect of Antimicrobial Activity are determined by the following and are affected by:

• Population Size; Population composition; Concentration of agent; Duration of Exposure; Temperature; pH; Presence of organic matter
• Physical Methods of Microbial Control contains:
  • Method,Mechanism, and Application Method; Mechanism, Applictions/Notes
  • Moist is protein denaturation
  • Dry Oxidizes cell components -low temperature inhibits growth -tempRadiation Damages DNA -Filtration physically removes the pathogen.

Chemical Agents function as disinfectants and require sterilisation

Lecture 7: Microbial Bioenergetics and ATP Generation

• Explain how cells trap and use energy to perform work
• Understand the role of ATP as the cell's major energy currency
• Describe and interrelate key processes and concepts including: Substrate-level phosphorylation and oxidative phosphorylation, Exergonic, endergonic, and fueling reactions

Cells trap and obtain energy through chemical and cellular work Adenosine Triphosphate stores energy, its synthesised in catabolism and used in anabolic

• Different ways from the direct transfer of phosphate substrate-level phosphorylation(SLP) and the energy from ETC(Oxidative Phosphorylation)

• Exergonic generates and needs ATP to form and is catalysed to synthesise cells and etc

• Exergonic, Endergonic, and Fueling Reactions are dependent on certain conditions

• Redox recations requires Redox Potential which produces electron donors

• Electrons are transported and the energy pump and is used for nutrient transport and motility

• Enzymes reduce biological processes and must follow conditions

Lecture 8: Microbial Metabolism – Catabolism, Respiration, and Fermentation

• Develop a broad understanding of microbial metabolism
• Explain the major processes involved in catabolism
• Understand how ATP formation is linked to metabolic pathways
• Describe and compare aerobic respiration and fermentation in microbes

Metabolism involves the Breakdown as catabolism and biosynthesis as anabolism

• Heterotrophs utilise carbon and are diverse ATP generatation has 8 mechanisms

• glycolysis generates pathways to follow through

• Oxidation of pyruvate happens through the tricarboxylic acid cycle

ATP will be formed through aeriobic and anaerobic

Lecture 9: Anabolism and Regulation of Metabolism

• Basic features and principles of anabolism

• Relation between anabolism and catabolism

• Precursors for biosynthesis and their metabolic origins

• Mechanisms to understand microbial regulation

• Anabolism involves with proteins and lipids used to store energy for growth

• Cells are build with precursor metabolites and are carbon for skelton

• Catabolism is the breakdown of molecules

• Cells regular to ensure efficiency through 3 mayor regulatory methods -Metabolic channelling, Enzyme expressions, Post-Trasnlation

Lecture 10: Taxonomy, Domains of Life, and Microbial Diversity

• Taxonomy is used to classify and identify Organisms
• Compare Cellular Structures and characteristics of Bacteria for understanding the system
• Endosymbiotic helped to see the evolutary origin
• Viruses are the protists. -Nonproteobacteria bacteria. -Aerobic Photosynthesis for example

Lecture 11: Gram-Positive Bacteria – Firmicutes and Actinobacteriota

• Gram-positive bacteria is where genus and specie is classified

• Description of bacteria is determined by the morphology and diseases of the relevance.

• List some morphologically similar genera with the correct spelling

• Low g vs high c is determined through firm and acitobacteriota bacteria

• Clostridium causes gas gangrene and acts upon the endotoxins

Lecture 12 – Gram-Negative Bacteria

• Arrangement of Gram-Negative Bacteria includes the following

• Nonportebacteria; Proteobacteria

• Understanding key factors include the morphology with its habitat.

• Non-Proteobacetria is photosynthetic

• Spirochaetota has key to know if they are helical

• Baccillovibrionalta are used to bacteria

• Alpha

• Gamma

Lecture 13 – Archaea

• Discovery and Classification of Archaea
• Their unique features compared to Bacteria and Eukarya
• Major ecological groups and representative genera
• General features and evolutary history are needed to understand taxonomy
• key ecological types and the charscterics of major generas must be identified Archaea must be studied in-depth where they originate