Week 1: Introduction to microbiology and microbial diversity

Question 1

Define Microbiology.

Answer 1

The study of microorganisms that cannot be seen by the naked eye.

Question 2

What are the main classes of prokaryotes?

Answer 2

Bacteria and Archaea.

Question 3

What are the main classes in Eukaryotes?

Answer 3

Fungi, Algae, Protozoa.

Question 4

Give some examples of how Prokaryotes differ from Eukaryotes.

Answer 4

P: circular DNA, lack double membrane bound organelles, not associated with histones
E: linear DNA, double membrane bound organelles, associated with histones

Question 5

What are examples of non-living entities?

Answer 5

virus, prions

Question 6

What are Prions?

Answer 6

A type of protein that can trigger abnormal protein foldings that cause diseases (eg BSE/’mad cow’ disease)

Question 7

What are the 5 subcategories in microbiology?

Answer 7

virology, bacteriology, mycology, protozoology, phycology (algae)

Question 8

Why is microbiology important? (6 points)

Answer 8

1. To identify zoonotic diseases (eg COVID-19, SARS, ebola…)
2. To identify animal diseases (eg blue tongue, Q fever, foot & mouth disease…)
3. To identify plant diseases
4. To identify emerging infectious diseases as they increase the rate of infection
5. To prevent food spoilage and contamination from humans
6. To identify microbes that cause diseases (eg tuberculosis, leprosy, sepsis, MRSA…)

Question 9

What is emerging infectious diseases (EID)?

Answer 9

Diseases that can increase the rate of infection or threaten to increase in near future

Question 10

What are the sources of EID? (4 points)

Answer 10

1. By unknown/undetected infectious diseases
2. By known agents that have spread to new geological regions/population
3. By previously known agents whose role in specific disease has gone unrecognised (ie mutation/resistance)
4. Re-emergence of agents that have previously declined in the past

Question 11

What are the benefits of microbes? (7 points)

Answer 11

1. Produce food directly (eg mushroom, yoghurt…) or indirectly (eg cheese, kimchi…)
2. Bioremediation: using pollutants as energy to clean the atmosphere
3. Biotechnology: making chemicals (eg biofuels, organic acids…), enzymes, therapeutics (eg drugs, vaccines…), gene therapy (virus vector)
4. Sewer treatment: help re-claim + recycle water and convert organic materials to by-products (eg CO2, NO3-, SO42-, PO43-, H2S, NH3, CH4…)
5. Biological insecticides: prevent damage to agricultural crops and disease transmission
6. Recycle and use vital elements that are in non-accessible states (C, N, S, O, P)
7. Form the basis of the food chain

Question 12

How do certain microbes help indirectly produce meat for food?

Answer 12

Microbes in ruminant guts help break down cellulose to generate proteins (eg muscles…)

Question 13

What are some examples of microbes converting essential elements?

Answer 13

1. Saprobionts convert dead organisms through ammonification, to release CO2 to atm
2. Algae/cyanobacteria for photosynthesis to make carbs and O2
3. Nitrogen0fixing bacteria (eg Rhizobium) convert nitrogen in atm to ammonia
4. oxidation of H2S to S/SO42-

Question 14

What bacteria produce diamond crystals that are toxic to only insects?

Answer 14

Bacillus thuringiensis

Question 15

Why are bacteria ubiquitous?

Answer 15

They are found in almost all niches (hydrothermal vents, volcanos, food, skin, ocean, plants…)

Question 16

Define Microbiome.

Answer 16

Microorganisms exist within a population

Question 17

Define Habitat.

Answer 17

A place for population to live in

Question 18

Define ecosystem.

Answer 18

Existence of microbiome, physical, and chemical constituents

Question 19

What is microbial ecology?

Answer 19

Study of microbes within their natrual habitat

Question 20

What do microbes do within a community?

Answer 20

Interact with:

1. Each other symbiotically (help each other)
2. Each other competitively (kill each other)
3. With their environment (physical & chemical constituents)

Question 21

Using an example, how do some microbes provide a more favourable environment for others to live in?

Answer 21

O2 can be a toxic component for some microbes.

When there are microbes that use O2 as energy - eliminate O2 from atm (become anoxic) - thus favouring anaerobes

Question 22

What is a biofilm?

Answer 22

A layer where microorganisms attach onto each other and to surfaces forming masses

Question 23

What do biofilms do?

Answer 23

Protect microbes; allow microbes to stick to surfaces such as teeth/prosthetics and destroy them

Question 24

What are nutritional groups?

Answer 24

Organisms determined by what nutrients they use to obtain carbon and energy sources

Question 25

What are autotrophs and heterotrophs?

Answer 25

Autotrophs use inorganic carbon compounds to produce more complex molecules - anabolic Chemotrophs use mainly organic carbon to produce energy - catabolic

Question 26

What are chemoautotrophs?

Answer 26

Use inorganic carbon compounds to synthesise organic compounds and energy Usually bacteria/archaea living in hostile environments

Question 27

Give examples of chemoautotrophs.

Answer 27

1. Acidothiobacillus ferrooxidans: convert ferrous (+2) iron to ferric (+3) iron 2. Beggiatoa: convert H2S to S 3. Acidothiobacillus thiooxidans: convert S to SO42- 4. Nitrosomas: convert NH3 to NO2- 5. Nitrobacter: convert NO2- to NO3-

Question 28

What are chemoheterotrophs?

Answer 28

Use macromolecules as C source to produce more complex compounds Usually fungi, most protozoa, and most bacteria

Question 29

Give examples of chemoheterotrophs.

Answer 29

1. Clostridium tetani - Tetanus 2. Samonella typhi - Typhoid 3. Xanthomonas axonopodis - citrus canker in plants 4. Corynebacterium diphtheriae - Diphtheria

Question 30

What are photoautotrophs?

Answer 30

With light, convert inorganic materials into organic materials for use in cellular functions (eg biosynthesis, respiration) and provide nutrition for others Usually in cyanobacteria, green/purple S bacteria/algae

Question 31

Give examples of photoautotrophs.

Answer 31

1. Cyanobacteria/algae – oxidise H2O to O2 (oxygenic) | 2. Green/purple S bacteria – oxidise H2S to S (anoxygenic)

Question 32

What are photoheterotrophs?

Answer 32

Use light and organic C compounds as C source + energy Usually in green/purple non-S bacteria (usually anoxygenic)

Question 33

Approximately how many years is it that we are seeing such diversity of evolution in microbiology?

Answer 33

~3.8 billion years of evolution

Question 34

What is bacteria?

Answer 34

Microscopic single-celled organisms that lack a true nucleus most abundant group of living organisms Relatively simple – unicellular, no organelle structure, prokaryote Circular DNA/ some with plasmids; Not associated with histones; No introns Swim via flagella; Divide by binary fission, exponential growth; 70S ribosome Peptidoglycan cell walls – stains that help determine their classes Cell membrane with unbranched FA chains attached to glycerol by ester linkages

Question 35

What are different shapes of bacteria?

Answer 35

Coccus, rod, spirochete, spirillum, filamentous

Question 36

What are the different combinations of coccus?

Answer 36

``` Coccus diplococcus (eg Neisseria) Tetracoccus (eg Micrococcus) Sarcina (x8) Staphylococcus (cluster) Streptococcus (linear) ```

Question 37

What are the different combinations of rods?

Answer 37

Single bacillus Diplobacilli Streptobacilli Coccobacillus

Question 38

Out of 11 types of genus Neisseria, which ones are pathogens?

Answer 38

1. Neisseria gonorrhoeae - gonorrhea | 2. Neisseria meningitidis - bacterial meningitis & septicaemia

Question 39

What are archaea?

Answer 39

mostly chemoautotrophs unicellular, no double membrane-bound organelle, no introns, binary division, 1 circular chromosome

Question 40

What are the 3 types of archaea?

Answer 40

1. Methanogens (anaerobes that produce methane) 2. Extreme halophiles (salt-loving) 3. Extreme thermophiles (heat-loving)

Question 41

Who proposed the difference between archaea and bacteria in 1977?

Answer 41

Woese and Fox

Question 42

What are features that archaea contain but not bacteria?

Answer 42

1. unique 70S ribosome 2. histone associated 3. LACK peptidoglycan, and instead, some have psuedopeptidoglycan/S layer 4. membrane composed of branched hydrocarbons attached to glycerol by ETHER bond

Question 43

What are fungi?

Answer 43

Mostly chemoheterotrophs Multilinear chromosome, double membrane-bound organelles, histone associated, 80S ribosome, introns Chitin cell wall made of N- acetylglucosamine (NAG) Unicellular ones are generally oval-shaped (larger than bacteria) – reproduce by forming spores (sexual) or yeast budding (asexual) Multicellular ones contain mycelium and vegetative hyphae (long branches) – they reproduce in different mechanisms

Question 44

What are the different mechanisms multicellular fungi reproduce?

Answer 44

1. hyphal fragmentation (asexual) 2. sporangia spores (asexual) 3. gametangia (sexual)

Question 45

Give an example of a thermally dimorphic fungus.

Answer 45

Blastomyces dermatitidis - causes Blastomycosis It exists as a mold at room temperature in the environment (eg soil containing organic debris) It is a yeast at 37°C in human tissues

Question 46

Why are fungi dimorphic?

Answer 46

Can grow either as mycelium (mould) or yeast (unicellular) – can switch due to environment

Question 47

Give an example of a thermally dimorphic fungus.

Answer 47

Blastomyces dermatitidis - causes Blastomycosis It exists as a mold at room temperature in the environment (eg soil containing organic debris) It is a yeast at 37°C in human tissues

Question 48

What are Protozoa?

Answer 48

Mostly chemoheterotrophs – feed on other microbes Unicellular (2 types): free-living (Paramecium/amoeba) and parasitic (Plasmodium/trypanosoma/giardia) Eukaryotic features: membrane-bound organelles, multi-linear chromosomes, histone associated, introns and exons, 80S ribosomes Lack cell walls

Question 49

What are ways protozoa reproduce asexually?

Answer 49

1. budding 2. binary division 3. schicozony (nucleus divides many times before meiosis)

Question 50

What are ways protozoa reproduce sexually?

Answer 50

1. Fusion of gametes | 2. Produce cyst (eg giardia/entamoeba)

Question 51

How do protozoa move?

Answer 51

Pseudopodia/flagella/cilia

Question 52

What are algae?

Answer 52

Photoautotrophs Oxygenic Photosynthetic machinery derived cyanobacteria – have different pigmentation (red, green, brown…) Eukaryotic features Cellulose cell wall (multicellular/unicellular) – lives in water (fresh/marine/snow) though lacks organs of plants (root/leaves)

Question 53

Compare the cell wall features of each classification.

Answer 53

``` Protozoa - LACK cell wall Archaea - pseudopeptidoglycan/S-layer cell wall Bacteria - peptidoglycan cell wall Fungi - chitin cell wall Algae - cellulose cell wall ```

Question 54

Compare whether organelles are present in each classification.

Answer 54

Bacteria and Archaea = absent Fungi, Algae, Protozoa = present

Question 55

Compare the ribosome size in each classification.

Answer 55

Bacteria and Archaea = 70S | Fungi, Algae, Protozoa = 80S