Lecture 3 + 4

Question 1

What Elements Make Up Bacterial Biomass?

Answer 1

96% of bacterial cell dry mass:

Composed of: C, H, N, O, P, S (CHNOPS)

Key 3 elements:

Carbon (C) – backbone of all organic molecules

Nitrogen (N) – proteins, nucleic acids

Phosphorus (P) – nucleotides, membranes (phospholipids)

Remaining 4%:

Trace elements & metal ions:

E.g. Na⁺, K⁺, Cl⁻, Mg²⁺, Fe²⁺/Fe³⁺, Zn, Cu

Essential as enzyme cofactors, osmotic balance, and electron carriers

Question 2

Carbon Acquisition Strategies

Answer 2

Autotrophs:

Use inorganic carbon (CO₂) and fix it into organic compounds

Example: Cyanobacteria (photosynthetic, CO₂ → glucose)

Heterotrophs:

Use organic carbon sources

Often simple sugars, or complex organic molecules (e.g. by gliding bacteria)

Question 3

Nitrogen Acquisition

Answer 3

Assimilation:

Incorporate NH₄⁺ or NO₃⁻ into biomass

Most bacteria use this method

Nitrogen fixation:

Convert atmospheric N₂ into NH₄⁺ using nitrogenase

Energetically expensive but essential in nitrogen-poor environments

Question 4

Phosphorus Acquisition

Answer 4

Assimilate inorganic phosphate (PO₄³⁻)

Required for DNA/RNA, ATP, phospholipids

Question 5

Bacterial Input/Output Schematic

Answer 5

Inputs:
Carbon source (organic/inorganic)

Energy source (light or chemicals)

Electron donor (reduced compound)

Electron acceptor (oxidised compound)

Inorganic nutrients

Outputs:
Excreted carbon

Spent energy source

Oxidised electron donor

Reduced electron acceptor

Question 6

Metabolic classifications: Phototrophs

Answer 6

Energy source: light

Question 7

Metabolic classifications: Chemotrophs

Answer 7

Chemical energy

Question 8

Metabolic classifications: Organotrophs

Answer 8

Organic e⁻ donors

Question 9

Metabolic classifications: Lithotrophs

Answer 9

Inorganic e⁻ donors

Question 10

Metabolic classifications: Autotrophs

Answer 10

Inorganic carbon (CO₂)

Question 11

Metabolic classifications: Heterotrophs

Answer 11

Organic carbon

Question 12

What is a guild

Answer 12

A group of bacteria (often across genera) that exploit similar substrates/environmental niches

Three categories:

Aerobic habitat

Aerobic–anaerobic interface

Anaerobic habitat

Question 13

Guild types: Aerobic Habitat: Guild A

Answer 13

Guild A: Aerobic Decomposers
Carbon, energy, and electron source: Dissolved Organic Carbon (DOC)

Metabolism: Aerobic respiration

Function: mineralise DOC to CO₂

Core genus: Pseudomonas

Question 14

Guild types: Aerobic habitat: Guild B

Answer 14

Guild B: Gliding Bacteria
Carbon, energy, and electron source: Particulate Organic Carbon (POC)

Metabolism: Aerobic degradation of macromolecules

True decomposers — break down large polymers into DOC (e.g., cellulose, chitin, pectin, keratin; some can degrade agar)

Further mineralise DOC into CO₂

Core genus: Cytophaga

Question 15

Guild types: Aerobic–Anaerobic Border: Guild C

Answer 15

Guild C: Nitrifying Bacteria

Carbon source: CO₂ (autotrophic)

Energy and electron source: Inorganic nitrogen compounds

Metabolism: Chemolithoautotrophy

NH₄⁺ → NO₂⁻ (by Nitrosomonas)

NO₂⁻ → NO₃⁻ (by Nitrobacter)

Question 16

Guild types: Aerobic–Anaerobic Border: Guild D

Answer 16

Guild D: Colourless Sulphur Bacteria

Carbon source: CO₂ (autotrophic)

Energy and electron source: Reduced sulphur compounds (e.g., H₂S, S⁰, thiosulphate)

Metabolism: Chemolithoautotrophy – aerobic

Function:

Oxidise sulphur compounds to generate energy

Some also oxidise iron and participate in metal leaching

Notable genera: Thiobacillus

Question 17

Guild types: Anaerobic: Guild E

Answer 17

Guild E: Sulphate-reducing bacteria
Carbon, energy, and electron source: DOC (heterotrophic)

Electron acceptor: Sulfate (SO₄²⁻) or elemental sulphur (S⁰)

Metabolism: Anaerobic respiration via dissimilatory sulphate reduction

Function:

Use SO₄²⁻ as a terminal electron acceptor → produce H₂S

Core genera: Desulfovibrio (SO42-) and Desulfuromonas (S)

Question 18

Guild types: Anaerobic: Guild F

Answer 18

Guild F: Green & Purple Sulphur Bacteria
Photoautotrophs

Carbon source: CO₂ (autotrophic)

Energy source: Infrared light

Electron donor: Hydrogen sulphide (H₂S)

Metabolism: Anoxygenic photosynthesis (no O₂ produced)

Purple:
Bacteriochlorophyll a and b
store S⁰ inside cells
Chromatium, Thiospirillum

Green:
Bacteriochlorophyll c, d, e
deposit S⁰ outside cells
Prosthecochloris, Pelodictyon

Question 19

Guild types: Anaerobic: Guild G

Answer 19

Guild G: Methanogenic Archaea

Metabolic type: Chemolithoautotrophic

Carbon source: CO₂ or simple organics

Energy and electron source: Hydrogen (H₂) or small organic compounds

Metabolism: Strictly anaerobic
→ Methanogenesis — unique to Archaea

Function:

Final step in anaerobic degradation of organic matter

Produce methane (CH₄) as the end product

Notable genera:

Methanobacterium,

Question 20

Bacterial Flatulence and VOCs

Answer 20

Main gases: CO₂, CH₄, H₂, N₂

Odorless: CH₄, H₂

Smelly: H₂S (sulfur)

VOCs (volatile organic compounds): Alcohols, alkenes – give odor

VOCs can signal health/disease changes (biomarkers).

Question 21

Disease definition

Answer 21

Pathological condition due to infection or dysfunction

Question 22

Infection definition

Answer 22

Entry & multiplication of microbes in the host

Question 23

Pathogenicity definition

Answer 23

Ability to cause disease

Question 24

Virulence definition

Answer 24

Degree of pathogenicity

Question 25

ID₅₀

Answer 25

ID₅₀ = Infectious dose for 50% of hosts Minimum number of bacteria needed to cause infection. Low ID = high virulence

Question 26

Virulence factos

Answer 26

Virulence factors = tools bacteria use to invade, survive, and damage hosts. These can include: Toxins (kill or harm cells) Adhesins (help attach to host surfaces) Capsules (protect from immune attack) Enzymes (break down host barriers) Carrying virulence genes costs the bacteria energy and resources. So, more virulence = heavier metabolic load.

Question 27

Primary pathogens

Answer 27

Cause disease in healthy individuals. Have strong virulence factors.

Question 28

Oppurtunistic pathogens

Answer 28

Opportunistic Pathogens are the microorganisms that are ordinarily in contact with the host and cause disease when the host's resistance is low (many)

Question 29

What must a pathogen do to cause infection?

Answer 29

Have a natural reservoir Be transmitted to a host Penetrate the host's natural barriers Colonise a sterile site Outcompete existing microbes (on a surface already colonised by good/harmless microbes) Join or form a biofilm ➤ Biofilms = sticky communities of bacteria on surfaces (e.g., teeth, catheters). Bacteria are safer in biofilms — harder to remove and more drug-resistant. .

Question 30

Non- human reservoirs

Answer 30

Soil and water: Legionella pneumophila — causes Legionnaire’s disease (can grow in water tanks, shower heads). Fomites (non-living surfaces): Towels, surgical tools, door handles. Often carry Staphylococcus aureus, including MRSA (methicillin-resistant strains).

Question 31

Human Reservoirs:

Answer 31

Locations: Skin, nose, mouth, eyes, ears Urogenital tract: vagina, urethra, seminal vesicles Digestive tract: anus, rectum Mammary glands

Question 32

Transmission Routes

Answer 32

Aerosol Inhalation of droplets from coughs, sneezes, or mist (e.g., from a shower head). Direct contact Touching people, sexual contact, contaminated food/water, or inanimate objects (fomites). Vector-borne Transmission via insects: ticks (Lyme disease), fleas (plague), mosquitoes (malaria), lice (Rickettsia).

Question 33

What Happens When a Bacterium Enters the Body? Step 1: First Contact

Answer 33

These are moist surfaces connected to the outside world, such as: Mouth Nose Lungs GI tract Urogenital tract Eyes (conjunctiva)

Question 34

Step 2: Avoiding Being Flushed Out

Answer 34

Mucosal surfaces have defences like: Saliva (mouth) Mucus + cilia (lungs, nose) Urine flow (urethra) Peristalsis (gut movement) ➡️ To survive here, bacteria must attach firmly to the surface and resist being washed away.

Question 35

Step 3: Forming or Joining a Biofilm

Answer 35

Bacteria form sticky layers (biofilms) to anchor themselves. Biofilms protect them from: Antibiotics Immune system Physical forces (flushing)

Question 36

The Skin – A Barrier to Infection

Answer 36

Normally impenetrable unless: Broken (cuts, surgery) Damaged (burns, eczema) When damaged: Normal flora (friendly bacteria) can turn pathogenic — these are called pathobionts. Weakened skin lets in external pathogens (e.g., Staphylococcus aureus).

Question 37

Normal Human Flora (a.k.a. Commensals)

Answer 37

You carry >10¹⁴ bacteria on/in your body — that's more than your human cells! Most of them: Don't cause disease Live in biofilms on surfaces (skin, gut, mouth) Are adapted to different conditions: Acidic (e.g., stomach) Anaerobic (e.g., large intestine) Aerobic (e.g., skin)

Question 38

Why Do Pathogens Struggle to Invade Normal Human Flora

Answer 38

Existing bacteria outcompete them for: Nutrients Space Commensals may produce antimicrobials to defend their turf. But Infection Can Still Happen If: Normal flora is disrupted: Injury (wound) Antibiotics (wipe out friendly bacteria) The pathogen has powerful virulence factors: Toxins, adhesion proteins, enzymes that kill off or displace normal flora