My Microbiology Notes

Lect 1 

Introduction to Microbiology

1. Define microbiology and microorganism.

Basic science of understanding microbial life.

Diverse group exist as single cell (unicellular) or cell clusters (multicellular)

2. Briefly explain about the importance of microbes.

a. Maintain balance of environment, nitrogen fixation, photosynthesis (microbial ecology)

b. Manufacture of food and drinks, bioremediation, synthesis of chemical products, biological pest control, normal microbiota

c. Related to life processes, basis of food chain, nutrient cycling

d. Disease, pollution caused by microbes

3. Branches of microbiology.

a. Bacterialogy

b. Mycology(fungus)

c. Parasitology(protozoa, helminth)

d. Immunology

e. Virology

f. Recombinant DNA technology

g. Biotechnology

4. Contributions.

a. Antonie van Leeuwenhoek: first to see bacteria by microscope

b. Louis Pasteur: disproved spontaneous generation, vaccination, pasteurization

c. Robert Koch: germ theory, demonstrates that specific microorganism cause specific disease

Koch's postulates 1844: 1. Suspect pathogenic organism should be present in all cases disease and absent from healthy animals. 2. Suspect organism should be grown in pure culture. 3. Cells from a pure culture of suspect organism should cause disease in healthy animal. 4. Organism should be reisolated and shown to be same as original.

d. Walter & Fannie Hesse: suggested that agar could be used as a solidifying agent

e. Sir Alexander Fleming: discover penicillin

5. Classification.

3 domains: 

a. Bacteria

b. Archae

c. Eukarya: protists, fungi, plants, animals

6. Determine the characteristics.

Bacteria:

Archae:

Fungi:

Protozoa:

Algae:

Virus:

Animal parasites:

7. Application of microbes.

8. Identification methods.

a. Manual biochemical systems (API 20 E system)

b. Mechanised/automated systems

c. Immunological systems

d. Serology: involves reactions of microorganism with specific antibodies. Useful in determining the identity of strains and species, as well as relationships among organism. Slide agglutination, ELISA, western blot

e. Genetics: DNA fingerprinting. Ribotyping. PCR.

Lect 2 Prokaryotic 

Lect 3 Eukaryotic

1. Difference between prokaryotic and eukaryotic cell.

https://microbenotes.com/differences-between-prokaryotes-and-eukaryotes/

2. Similarities between prokaryotic and eukaryotic cell.

Plasma membrane, DNA, cell wall

3. Define prokaryote and eukaryote.

Pro = before

Eu = true

Karyon = nucleus

Prokaryote is a single cell and all are bacteria. Eukaryote is single cell or multicellular.

4. Describe characteristics of prokaryote and eukaryote.

5. Determine the size, shape and arrangement of bacteria.

Size of prokaryote is 0.5 – 3.0 µm, 0.5 – 2.0 µm in diameter and 1.0 – 60 µm in length whereas size of eukaryote is >5 µm.

Shape and arrangement:

6. Determine the structure and function of bacteria.

7. Differentiate between gram positive and gram negative cell wall.

https://microbenotes.com/differences-between-gram-positive-and-gram-negative-bacteria/

8. Determine bacterial flagella arrangement.

https://microbiologyinfo.com/flagella-introduction-types-examples-parts-functions-and-flagella-staining-principal-procedure-and-interpretation/

9. Chemotaxis.

https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_%28Bruslind%29/06%3A_Bacteria_-_Surface_Structures

10. Movement of substances across membrane.

 Form 4 bio unit 3

Eukaryotic cells move substances by forming membrane-enclosed vesicles.

1. Endocytosis: Form by invagination (poking in) and surrounding substances from outside the cell 

2. Exocytosis: Vesicles inside the cell fuse with the plasma membrane and extrude  contents from the cell

3. Define parasite.

organism that lives at the expense of host

pathogens can cause disease

4. Ectoparasite: live on surface (tick, lies)

Endoparasite: live within bodies (protozoa, worms)

5. Obligate parasite: spend at least some of life cycle in or on host

Facultative parasite: free-living, obtain nutrients from host

Permenant parasite: remain in or on host once invaded/spread into it (tapeworms)

Temporary parasite: feed on & then leave host (mosquito)

Accidental parasite: invade organism other than normal host (ticks)

Hyperparasitisim: refer to parasite itself having parasites (malaria)

5. Vector: agents of transmission, transfer parasite to new host

Biological: parasite goes through part of its life cycle (malaria mosquito)

Mechanical: does not go through during transit (flies)

6. Host

Definitive: harbor/shelter parasite while reproduces sexually (malaria mosquito)

Intermediate: harbor during some developmental stages (human)

Resevoir: infected organism that make parasites available for transmission to other hosts

7. Protist

member of the kingdom protista

diverse assortment of organisms

unicellular, eukaryotic

true nuclei and membrane-enclosed organelles

microscopic and vary in diameter from 5um-5mm

Ex: Gonyaulax, Pfiesteria piscida dinoflagelletes, produces red tide and toxin

8. Fungus like protist

water molds (oomyocota) and slime molds (saphrophytes)

same characteristics of fungi and some of animals

water molds, mildews, and plant blights produced flagellated spores called zoospore

slime molds commonly found as glistening, viscous masses of slime on rotting logs, also live in other decaying matter or in soil

Hemitrichia

plasmodial slime molds from a multinucleate, amoeboid mass called plasmodium

cellular slime molds produce pseudoplasmodia, fruiting bodies, and spores with characteristics different from plasmodial slime molds

Dicytostelium discoideum

pseudoplasmodium is a slightly motile aggregation of cells that produces fruiting bodies, which in turn produce spores

9. Protozoa (Animal like protist)

heterophic, mostly unicellular

free-living

some commersal

a.mastigrophan

flagella

free-living

live in symbiotic relationship

Trichonympha

b.sarcodine

uusually amoeboid

move by means of pseupodia, few have flagella

Amoeba proteus

c.apicomplexan

parasitic, immobile

Plasmodium vivax, malaria

sporozoites

merozoites

trophozoites

gametocytes

10. Fungi

diverse group of heterotrophs

mycology

saprophytes digest dead organic matter and wastes

obtain nutrients from tissue

molds and mushroom multicellular, yeasts unicellular

Reproduction:

sexual:

plasmogamy

dikaryotic

karyogamy

asexual: 

involves mitotic cell division 

yeast occurs by budding

11. Helminth:

Flatworm/platyhelminth:

no body cavity

cestoda

termatoda

hermaphroditic(both female and male reproductive organ)

Roundworm/nematodes:

Parasitic helminths

Flukes:

a. tissue flukes:

bile duct, lungs, other tissue

b. blood flukes:

Tapeworms:

a. consist of scolex, or head end with suckers that attach to intestinal wall and a long chain of hermaphroditic proglottids

b. proglottids contain hermaphroditic

c. life cycle:

embryos develop inside eggs and are released from proglottids

proglottids and eggs leave host with faeces

another animal ingests vegetation or water contaminated with eggs and eggs hatch into larvae, which invade the intestinal wall

larvae can develop into cysticercus (bladder worm), or form a cyst

cyst can enlarge and develop many tapeworm heads within it (hydatid cyst) and if animal eats flesh containing this, each scolex can develop into new tapeworm

Adult roundworms of the intestine:

a. most that parasitize human live much of their life cycle in digestive tract

b. Usually enter body by ingestion with food or water, but some penerate skin (hookworm)

c. life cycle shows considerable variation

Roundworm larvae:

12. Arthropod:

a. Arachnid:

wood tick

Dermacentor andersoni

4 pairs legs, 2 body regions: cephalothorax, abdomen

b. Insect:

housefly, Aedes mosquito, flea

Musca domestica

Ctentocephalidis canis

carry microbes on itself

c. Crustacean:

generally aquatic arthropods

typically have a pair of appendages associated with each segment

appendages include: mouthparts, claws, walking legs, appendages aid in swimming or copulation 

Lect 4

Microscopy and staining

1. Leeuwenhoek's microscope

2. Principle of microscopy.

Microscopy is the technology of making very small things visible to the human eye. Mili=one thousandth 10^-3, Micro=one millionth 10^-6, Nano=one billionth 10^-9.

3.Relative sizes of objects

4.Properties of light

a.wavelength: 

length of  a light ray

lambda

equal to distance btwn 2 adjacent crests or troughs of a wave

b. Resolution:

ability to see 2 items as separate and discrete units

5. Electromagnetic spectrum

only a narrow range of wavelengths, those of visible and uv light are used in light microscopy

the shorter wavelength used, the greater the resolution that can be attained

Resolving Power(RP): in numerical measure of resolution that can be obtained with lens

Numerical Aperture(NA): a mathematical expression relating to extent that light is concentrated by the condenser lens and collected by objective

the smaller the distance btwn objects that can be distinguished, the greater the resolving power of the lens.

RP=𝝺/2(NA)

6. Properties of light: light & object

a. reflection: 

if the light strikes an object and bounces back (giving the object colour)

b. transmission:

the passage of light through an object

c. absorption:

the light rays neither pass through nor bounce off an object but are taken up by the object

d. refraction:

bending of light as it passes from1 medium to another different density

bending gives rise to angle of refraction(degree)

index of refraction: meausre of speed at which light passes through the material

e. diffraction

7. Light microscopy

refers to the use of any kind of microscope that uses visible light to make specimens observable

magnification: objective*ocular(10x)

monocular and binocular

parfocal: specimen will remain very nearly in focus as microscopist increases or decreases the magnification

ocular micrometer: for measuring objects viewed

a. Bright-field and Dark-field

b. Phase Contrast

c. Differentiatial Interference Contrast/Normaski

d. Fluorescence

e. Confocal

f. Digital

8. Electron microscopy

use of beam of electrons

electromagnets rather than glass lenses to focus the beam

produce electron micrographs with great detail

a. Transmission electron

b. Scanning electron

Freeze-fracturing&freeze-etching

9. Techniques of light microscopy

a. Wet mounts:

A drop of medium containing organisms is placed on slide and used to view living microorganisms

b. Smears:

Microorganisms are spread onto the surface of a glass slide and used to view destroyed organisms

c. Heat fixation: 

destroys the organisms, causes organism to adhere to slide, and alters organism to accept stains (dyes)

d. Hanging drop/mortality technique

10. Principles of staining

a. Stain or dye: A molecule that can bind to a cellular structure and give it color (contrast) 

1. Cationic or Basic Dyes

2. Anionic or Acidic Dyes

b. Simple stain: makes use of a single dye and reveals basic cell shapes and arrangements 

c. Differential stain: makes use of two or more dyes and distinguishes between organisms based on structural differences

Gram positive bacteria stain violet due to the presence of a thick layer of peptidoglycan in their cell walls, which retains the crystal violet these cells are stained with. Alternatively, Gram negative bacteria stain red, which is attributed to a thinner peptidoglycan wall, which does not retain the crystal violet during the decoloring process.

Lect 5

Growth and Culturing of bacteria

1. Briefly explain about growth and cell division.

Growth:

a. the increase in the number of cells (cell size and cell mass), which occurs by cell division

b. Mother parent cell doubles in size 

c. Divides into two daughter cells

d. Spectrometer  can be used to measure bacterial growth by determining the degree of light transmission through the cultures

Cell division:

a. Binary fission (equal cell division): A cell duplicates its components and divides into 2 cells 

Septum: A partition that grows between 2 daughter cells and they separate at this location 

b. Budding (unequal cell division): A small, new cell develops from surface of exisiting cell and subsequently separates from parent cell

2. Determine the phases of growth/bacterial growth curve.

a. The lag phase

• Binary fission

• metabolically active, not increase significantly in no.

• Grow in size, synthesize enzymes DNA RNA, incorporate molecules from medium

• ATP energy

• Adapt new environment, grow condition

b. The logarithmic/exponential phase

• Adapt to medium

• Occurs exponential rate

• Divide most rapid rate

• Regular, genetically determined interval/ generation time

Synchronous growth: A hypothetical situation in which the number of cells in a culture would increase in a stair-step pattern, dividing together at the same rate 

Non-synchronous growth: A natural situation in which an actual culture has cell dividing at one rate and other cells dividing at a slightly slower rate

c. The stationary phase

• Cell division decreases to a point that new cells are produced at same rate as old cell die.  

• The number of live cells stays constant. No Bacterial growth.

d. The death/decline phase

• Condition in the medium become less and less supportive of cell division

• Cell lose their ability to divide and thus die

• Number of live cells decreases at a logarithmic rate, as lack nutrients

• forms spores, preserve themselves to grow again

3. Serial dilution.

• dilute the original bacterial culture before you transfer known volume of culture onto agar plate 

• decrease concentration to achieve countable culture 

• Pour plate: made by first adding 1.0ml of diluted culture to 9ml of molten agar, colonies on surface 

• Spread plate: made by adding 0.1ml of  diluted culture to  surface of solid medium, some colonies on surface, many below

4. Standard plate counts.

• method to measure bacterial growth 

• Agar plate: A petri dish containing a nutrient medium solidified with agar

5. Direct microscopic counts.

• method to measure bacterial growth

• Petroff-Hausser counting chamber

• Bacterial suspension is introduced onto chamber with a calibrated pipette 

• Microorganisms are counted in specific calibrated areas 

• No./V is calculated using an appropriate formula

6. Most probable number (MPN).

• For coliforms from faeces (has lactose), e. coli, river water

• method to estimate number of cells

• Used when samples contain too few organisms to give reliable measures of population size by standard plate count 

• Series of progressively greater dilutions

• Typical MPN test consists of five tubes of each of three volumes (e.g. 10, 1, and 0.1ml) (10ml 5 cloudy=+ve, 1ml 2 +ve, 0.1ml all -ve )

#Positive carbohydrate fermentation test , Yellow(+acid), Durham tube clear above (+gas), not all bacteria capable of fermentation, peptone broth phenol red indicator and sugar indicator

https://www.youtube.com/results?search_query=Positive+carbohydrate+fermentation+test+microbe

#Turbidity, or a cloudy appearance, is an indicator of bacterial growth in urine in the tube on the left(e.g. secchi's disc)#spectrophotometer

7. Determine the factors affecting bacterial growth.

a. Physical:

. pH

• Optimum pH: the pH at which the microorganism grows best (e.g. pH 7) 

• According to their tolerance for acidity/alkalinity, bacteria are classified as: 

1. Acidophiles (acid-loving): grow best at pH 0.1-5.4 

2. Neutrophiles: grow best at pH 5.4 to 8.0

3. Alkaliphiles (base-loving): grow best at pH 7.0-11.5

. Temperature

• Obligate: organism must have specified environmental condition 

• Facultative: organism is able to adjust to and tolerate environmental condition, but can also live in other conditions 

• According to their growth temperature range, bacteria can be classified as: 

1. psychrophiles: 15-20°C (flavobacterium)

2. Mesophiles: 25-40°C (Escherichia)

3. Thermophiles:50-60°C (Thermus)

. O2 concentration

• Aerobes: require oxygen to grow

• Obligate aerobes: must have free oxygen for aerobic respiration (e.g. Pseudomonas) 细菌在上

• Anaerobes: do not require oxygen to grow

• Obligate anaerobes: killed by free oxygen (e.g. Bacteroides) 细菌在下

• Microaerophiles: grow best in presence of small amount of free oxygen 细菌在中

• Capnophiles: carbon-dioxide loving organisms that thrive under conditions of low oxygen 

• Facultative anaerobes: carry on aerobic metabolism when oxygen is present, but shift to anaerobic metabolism when oxygen is absent 细菌可独自生存

• Aerotolerant anaerobes: can survive in the presence of oxygen but do not use it in their metabolism

. Hydrostatic Pressure

• Water in oceans and lakes exerts pressure exerted by standing water, in proportion to its depth 

• Pressure doubles with every 10 meter increase in depth 

• Barophiles: bacteria that live at high pressures, but die if left in laboratory at  standard atmospheric pressure

. Osmotic Pressure

• Environments that contain dissolved substances exert osmotic pressure, and pressure can exceed that exerted by dissolved substances in cells 

• Hyperosmotic environments: cells lose water and undergo plasmolysis (shrinking of cell) 

• Hypoosmotic environment: cells gain water and swell and burst

. Halophiles

• Salt-loving organisms which require moderate to large quantities of salt (NaCl) 

• Membrane transport systems actively transport sodium ions out of cells and concentrate  potassium ions inside 

• Why do halophiles require sodium?

1. Cells need sodium to maintain a high intracellular potassium concentration for enzymatic function 

2. Cells need sodium to maintain the integrity of their cell walls

• Nonhalophiles, moderate halophiles, extreme halophiles (halobacterium)

. Moisture

Bound water & free water

. Radiation

b. Nutritional/biochemical:

. Carbon sources

. Nitrogen sources

. Sulfur and phosphorus

. Trace elements (e.g. copper, iron, zinc, and cobalt) 

. Vitamins (e.g. folic acid, vitamin B- 12, vitamin K)

8. Determine the locations of enzymes.

• Exoenzymes: production of enzymes that are released through cell or plasma membrane 

• Extracellular enzymes: usually produced by gram-positive rods, which act in the medium around the organism 

• Periplasmic enzymes: usually produced by gram-negative organisms, which act in the periplasmic space

9. Sporulation.

• The formation of endospores, occurs in Bacillus (in rice), Clostridium (food in tin) and a few other gram- positive genera 

• Protective or survival mechanism, not a means of reproduction 

• As endospore formation begins, DNA is replicated and forms a long, compact, axial nucleoid

Vegetative cycle: binary fission

10. Culturing bacteria.

. Problems: 

A pure culture of a single species is needed to study an organism’s  characteristics & A medium must be found that will support growth of the desired organism 

• Pure culture: a culture that contains only a single species of organism

Streak plate method (e.g. serratia marcescens)

11. Determine types of culture media.

• Natural Media: In nature, many species of microorganisms grow together in oceans, lakes, and soil and on living or dead organic matter 

• Synthetic medium: A medium prepared in the laboratory from material of precise or reasonably well-defined composition 

• Complex medium: contains reasonably familiar material but varies slightly in chemical  composition from batch to batch (e.g. peptone, a product of enzyme digestion of proteins)

12. Commonly used media.

• Yeast Extract

• Casein Hydrolysate

• Serum

• Blood agar

• Chocolate agar

13. Selective, Differential, and Enrichment Media.

• Selective medium: encourages growth of some organisms but suppresses (some die) growth of others (e.g. antibiotics) (EMB, HE agar) 

• Differential medium: contains a constituent that causes an observable change (e.g.  MacConkey agar, EMB) 

• Enrichment medium: contains special nutrients that allow growth of a particular organism that might not otherwise be present in sufficient numbers to allow it to be isolated and identified

-CHROM agar (e.g. candida plate), candle jars culture

- To culture obligate anaerobes, all molecular oxygen must be removed and kept out of medium. Agar plates are incubated in sealed jars containing chemical substances that remove oxygen and generate carbon dioxide or water (gas pack)

-anaerobic transfer

14. Preserved Cultures.

• To avoid risk of contamination and to reduce mutation rate, stock culture organisms should be kept in a preserved culture, a culture in which organisms are maintained in a dormant state 

1. Lyophilization

2. Frozen at -70°C

3. Refrigeration

• Reference culture (type culture): a preserved culture that maintains the organisms with characteristics as originally defined

Lect 6

Microbial metabolism

1. Define metabolism, anabolism and catabolism.

 Metabolism :

All chemical reactions that occur within a cell 

the sum of Catabolism and Anabolism

 Catabolism :

break down a  substrate and capture energy 

reactions that release energy by breaking complex molecules into simpler ones that can be reused as building blocks

 Anabolism :

synthesis of more complex compounds  and use of energy

reactions that require energy to synthesize complex molecules from simpler ones 

-Oxidation: the loss or removal of electrons

-Reduction: the gain of electrons

2.  Describe about energy.

•  Necessary for most cellular activities, produced by oxidation and reduction 

• Adenosine Triphosphate (ATP)

A) Energy currency for all living things

B) Composed of an adenine, ribose, and 3 PO4 -

C) Energy is stored in the high-energy phosphate bonds and released when they are broken

ATP to ADP + P (releases energy)

ADP + P to ATP (requires energy)

3. Groups of microorganism by energy capture and how they obtain carbon

 Autotrophy : use carbon dioxide to synthesize organic molecules 植物

Carbon source: inorganic CO2

Self-feeder

- Photoautotrophs: obtain energy from light

Green sulfur bacteria

Purple sulfur bacteria

Cyanobacteria

Algae

- Chemoautotrophs: obtain energy from oxidizing simple inorganic substances 

Iron, sulfur, hydrogen, nitrifying bacteria

Archaeobacteria

 Heterotrophy : get their carbon from ready-made organic molecules 人动物

Carbon source: organic compounds

Other-feeder

- Photoheterotrophs: obtain chemical energy from light

Purple nonsulfur bacteria

Green nonsulfur bacteria

- Chemoheterotrophs: obtain energy from breaking down ready-made organic compounds

All protozoan, fungi, animals

Most bacteria

4. Metabolic pathway

 Glycolysis, fermentation, aerobic respiration, and photosynthesis each consist of a series of chemical reaction 

 The product of one reaction serves as the substrate for the next: A->B->C->D 

 Such chain of reactions is called a metabolic pathway

 Catabolic pathways capture energy in a form cells can use

 Anabolic pathways make the complex molecules that form structure of cells, enzymes, and molecules that control cells

5. Enzymes

 In general, chemical reactions that release energy can occur without input of energy 

 The oxidation of glucose releases energy, but the reaction does not occur without an input of energy 

 Activation energy: the energy required to start such a reaction 

 Enzymes lower the activation energy so reactions can occur at mild temperatures in living cells

 Provide a surface on which reactions take place

 Active site: the area on the enzyme surface where the enzyme forms a loose association with the substrate 

 Substrate: the substance on which the enzyme acts

 Enzyme-substrate complex: formed when the substrate molecule collides with the active site of its enzyme 

Key&lock hypothesis

 Enzymes generally have a high degree of specificity

 Endoenzymes(intracellular) /exoenzymes (extracellular)

6. Properties of coenzymes and cofactors

 Many enzymes can catalyze a reaction only if substances called coenzymes, or cofactors are present 

 Apoenzyme: protein portion of such enzymes

 Holoenzyme: nonprotein coenzyme or cofactor that is active when combined with apoenzyme 

 Coenzyme: nonprotein organic molecule bound to or loosely associated with an enzyme 

 Cofactor: an inorganic ion (e.g. magnesium, zinc) that often improve the fit of an enzyme with its substrate

Energy transfer by carrier molecules: Carrier molecules such as cytochromes (cyt) and some coenzymes carry energy in the form of electrons in many biochemical reactions. Coenzymes such as FAD carry whole hydrogen atoms (electrons together with protons); NAD carries one hydrogen atom and one “naked” electron

When coenzymes are reduced, they increase in energy; when they are oxidized, they decrease in energy

7. Anaerobic Metabolism:

a. Glycolysis:

 Glycolysis (Embden-Meyerhof pathway): is the metabolic pathway used by most autotrophic and heterotrophic organisms to begin breakdown of glucose 

 Does not require oxygen, but can occur in presence or absence of oxygen 

 Phosphorylation: the addition of a phosphate group to a molecule, often from ATP and generally increases the molecule’s energy

Four Important Events Occur in the Glycolytic Pathway:

• Substrate level phosphorylation: the transfer of phosphate groups from ATPs to glucose 

• Breaking of a six- carbon molecule (glucose) into two three-carbon molecules 

• The transfer of two electrons to the coenzyme NAD 

• The capture of energy in ATP

b. Fermentation:

 One process by which pyruvate is subsequently metabolized in the absence of oxygen 

 The result of the need to recycle the limited amount of NAD by passing the electrons of reduced NAD to other molecules 

 Homolactic acid fermentation: pyruvate is converted directly to lactic acid, using electrons from reduced NAD 

 Alcoholic fermentation: carbon dioxide is released from pyruvate to form acetaldehyde, which is reduced to  ethanol

# Mixed acid fermentation: pyruvic acid to acetic acid, succinct acid, ethyl alcohol, CO2, H2

Propionic fermentation: pyruvic acid to propionic acid, acetic acid, CO2

Butane diol fermentation: pyruvic acid to butane diol & CO2 

Butyric-butylic fermentation: butyric acid, butanol, isopropyl alcohol, acetone, CO2

#A positive (yellow) mannitol-fermentation test. This test distinguishes the pathogenic Staphylococcus aureus.

#End products

Ethanol and carbon dioxide are produced from alcohol fermentation (ethanol fermentation). They are produced by fungi, notably by yeast.

Lactic acids are produced from homolactic acid fermentation. They are produced by Streptococcus and some species of Lactobacillus and bacillus.

Lactic acid, acetic acid, formic acid, acetoin, 2,3-butylene glycol, ethanol, and carbon dioxide are produced from heterolactic acid fermentation. They are produced by Enterobacter, Aeromonas, and Bacillus polymyxa.

Propionic acid, acetic acid, succinic acid, and carbon dioxide are produced from Propionic acid fermentation. They are produced by Clostridium propionicum, Propionicum, Corynebacterium diphtheriae, Neisseria, Veillonella, and Micromonospora.

Lactic acid, acetic acid, formic acid, succinic acid, Hydrogen, ethanol, and carbon dioxide are produced from Mixed acid fermentation. They are produced by E. coli, Salmonella, Shigella, and Proteus.

Butanol, butyric acid, acetone, isopropanol, acetic acid, hydrogen, ethanol, and carbon dioxide are produced from Butanol-Butyric Acid fermentation. They are produced by Butyribacterium, Zymosarcina maxima and Clostridium.

8. Aerobic Metabolism: Respiration

 Fermentation yields small amount of ATP

• Partial oxidation of carbon atoms

• Reduction potential difference between electron donor and acceptor is small (electron tower)  

 Respiration (aerobic or anaerobic):

• Substrate molecules are completely oxidized to C02

• Farhigher yield of ATP 

• The Krebs Cycle

9. Electron Transport and Oxidative Phosphorylation 

 Electron transport: the process leading to the transfer of electrons from substrate to  oxygen 

 Oxidative phosphorylation: energy-releasing dehydrogenation reactions captured in high- energy bonds as Pi , combines with ADP to  form ATP

The electron transport chain modeled as a waterfall:

• As the electrons are passed from carrier to carrier in the chain, they decrease in energy, and some of the energy they lose is harnessed to make ATP

The Electron Transport Chain

 Through a series of oxidation-reduction reactions, the electron transport chain performs two basic functions: 

• Accepting electrons from an electron donor and transferring them to an electron acceptor 

• Conserving for ATP synthesis some of the energy released during the electron transfer

10. Chemiosmosis

 Electrons for the hydrogen atoms removed from the reactions of the Krebs cycle are transferred through the electron transport system 

 Electron transport creates the H potential  across the membrane 

 ATP is produced by proton motive force (pmf) by allowing H  across the membrane 

ATP provide energy for flagellar rotation

 Combination of hydrogen/electron  carriers

11. Anaerobic Respiration

 Electron acceptors other than oxygen are used, such as: 

- Inorganic oxygen-containing molecules eg. Nitrate (N0 3 - ), Sulfate (S04 2- ), Ferric iron (Fe 3+), Carbonate  (C03 2- ), and Perchlorate (Cl0 4 - ) 

 Less energy is released

 Permits microorganisms to respire in anoxic environments

#Final electron acceptor

Aerobic respiration(O2), anaerobic respiration(inorganic molecule), and fermentation(organic molecule e.g.pyruvic acid) have different final electron acceptors

12. Metabolism

Fat Metabolism

 Most microorganisms, like most animals, can obtain energy from lipids : 

• Fats are hydrolyzed to glycerol and three fatty acids 

• Glycerol is metabolized by glycolysis

• The fatty acids are broken down into 2-carbon pieces by beta-oxidation

Protein Metabolism

 Proteins can be metabolized for energy

 They are first hydrolyzed into individual amino acids by proteolytic enzymes 

 Amino acids are deaminated/amino acid catabolism

 These molecules enter glycolysis, fermentation or the Kreb’s cycle

Carbohydrate Metabolism

• Glycolysis and Kreb cycle occur

• Electron Transport

• Acetyl-CoA 

13. Phototrophy

 There are two types of photosynthesis in microorganisms: 

• Form similar to plant photosynthesis (evolution of oxygen) – Cyanobacteria and  algae

• Bacterial photosynthesis – phototrophic purple sulfur bacteria

Photosynthesis - conversion of light energy from the sun into chemical energy 

 Chemical energy is used to reduce CO2 to sugar  (CH2O)  

 Carbon Fixation - recycling of carbon in the environment  

 Photosynthesis

◦ Green Plants

◦ Algae

◦ Cyanobacteria

14. Chemoautotrophy

 Energy generation involves inorganic rather than organic chemicals 

 Electron donors are inorganic chemicals such as hydrogen sulfide, hydrogen gas, ferrous iron (Fe2+), and ammonia (NH3) 

 Aerobic respiration but an inorganic energy source 

 Most chemolithotrophs use carbon dioxide as a carbon source (autotrophs)

15. Bioluminescence

 The ability of an organism to emit light, appears to have evolved as a by-product of aerobic metabolism 

 Bacteria of the genera Photobacterium and Achromobacter, fireflies, glowworms, and certain marine organisms living at great depths in the ocean exhibit bioluminescence 

 Many light-emitting organisms have the enzyme luciferase, along with other components of the electron transport system

16. Metabolism & Identification of Microbes API-20E 

 The API-20E test is used to ID Gram-negative enteric bacilli- shaped bacteria from the family. 

 Some microbes can metabolize certain molecules while others can’t.  

 When molecules are metabolized, specific waste products are  created. 

 From identification of metabolic capabilities, we can zero in on  identification of genus and  species.

https://microbiologyinfo.com/api-20e-test/

https://www.youtube.com/results?search_query=MICROBIAL+Anaerobic+Metabolism+animation