Prof Sibanda and Dr Damelin test prep

Question 2

With specific reference to named marine microbes, describe the significance of marine microbes in the context of global climate change?

Marine cyanobacteria (prochlorococcus and synechococcus) and eukaryotic algae/diatoms are oxygenic phototrophs that do photosynthesis. Fix inorganic carbon (CO₂) into organic carbon using sunlight while releasing oxygen. They drive the marine biological carbon pump sequestering CO₂ out of the atmosphere and trapping it in the deep ocean as organic matter reducing global greenhouse warming.

Question 2

With specific reference to named marine microbes, describe the significance of marine microbes in the context of global climate change?

Marine archaea Ammonia oxidizing Thaumarchaeota and marine Euryarchaeota (methanogens and methanotrophs). Thaumarchaeota oxidize ammonia (NH₄⁺) to produce nitrous oxide (N₂O). Methanogens make CH₄ methane and methanotrophs consume it. Methane and nitrous oxide are greenhouse gases with much higher heat trapping capacity than CO₂. By controlling the production and destruction of these gases before they escape the oceans, archaea control the rate of atmospheric heat retention and global climate warming.

Question 2

With specific reference to named marine microbes, describe the significance of marine microbes in the context of global climate change?

Filamentous chemolithotrophic sulfur oxidizers (Thioploca chilae). Live in marine sediments, they store nitrate NO₃^- in cell vacuoles to oxidize toxic hydrogen sulfide H₂S coming from anoxic sediments. By removing toxic hydrogen sulfide, they prevent ocean acidification and toxic dead zones. They preserve sea floor as carbon sink preventing stored organic Carbon from degrading and escaping back into atmosphere as emission.

Question 1

How does microbial diversity influence ecosystem function and stability?

Microbial species diversity is defined by species richness (total number of different species present) and species abundance(relative proportion of each species in the ecosystem). Both are controlled by the types of and quantities of nutrients and physical conditions available in a habitat. Metabolically related microbial populations form guilds that share a common niche. High species richness within a guild provides functional redundancy: environmental stress supresses one species, other taxa within the guild sustain essential biogeochemical cycles (C,N, Fe, S and P). Metabolic cooperation between complementary guilds (syntrophy) allows chemical transformations to occur that single species cannot do alone driving rapid ecosystem recovery and resilience following environmental perturbations.

Why are microbes critical in the cycling of sulfur in anoxic environments, and how does this impact global biogeochemical cycles? (3 marks)

Why are microbes critical in the cycling of sulfur in anoxic environments, and how does this impact global biogeochemical cycles? (3 marks)

In anoxic environments (such as deep lake sediments and waterlogged soils where oxygen is absent), sulfate-reducing bacteria and sulfur-reducing bacteria perform anaerobic respiration. They use sulfate (SO₄^-) or elemental sulfur (S⁰) as terminal electron acceptors along the redox tower to break down organic carbon, producing hydrogen sulfide (H₂S). The produced hydrogen sulfide diffuses upward from anoxic zones toward illuminated oxic-anoxic boundaries. There, it acts as an essential electron donor for anoxygenic phototrophic bacteria (such as Green Sulfur bacteria Chlorobi) to fix carbon dioxide (CO₂) using sunlight without producing oxygen, as well as for chemolithotrophic sulfur-oxidizing mats (such as Thioploca). Microbially mediated sulfur transformations drive global oxidation-reduction (redox) cycles and directly alter the availability of other key elements.Toxic hydrogen sulfide reacts with dissolved heavy metals to precipitate them out as insoluble metal sulfides. Accumulating H₂S and anoxic conditions cause insoluble ferric iron (Fe³⁺) to be reduced to soluble ferrous iron (Fe²⁺), which breaks the bond holding phosphate (PO₄^3-) in sediments and releases it into the water column.

How do environmental factors like temperature and pH shape microbial community composition in soil ecosystems?

How do environmental factors like temperature and pH shape microbial community composition in soil ecosystems?

Physical and chemical factors (such as pH, temperature, water potential, and O₂) act as environmental conditions—physicochemical settings that govern microbial growth rates, enzyme kinetics, and cell structure without being consumed (unlike nutrient resources).Soil pH dictates taxonomic dominance across vertical soil horizons:

• Topsoil (O and A Horizons): Organic-rich surface soils favor fast-growing copiotrophic phyla (Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes).

• Subsoil (B and C Horizons): Acidic, nutrient-poor subsoils select for oligotrophic specialists (Acidobacteria, Verrucomicrobia).

• Cellular Adaptation: Obligate acidophiles (thriving at pH ≤ 3) maintain intracellular pH homeostasis by using specialized membrane lipids and actively pumping protons (H⁺) out of the cell using ATP-driven efflux pumps.

Severe temperature fluctuations (ranging from below -24°C to above 60°C in arid soils) select for extremotolerant communities. In desert soils, surface Biological Soil Crusts (BSCs) dominated by photosynthetic cyanobacteria and filamentous fungi bind soil particles together, prevent erosion, retain moisture, and fix carbon and nitrogen.

Soil acts as a "heterogeneous mosaic of microhabitats". At the millimeter scale, a single soil particle/aggregate exhibits steep oxygen gradients:

• Exterior Surface: Oxic (21% O₂), supporting obligate aerobes.

• Aggregate Core: Completely anoxic (0% O₂), enabling strict anaerobes (such as sulfate reducers and methanogens) to live right next to aerobes inside the exact same soil particle.

What factors regulate microbial diversity in oligotrophic freshwater lakes, and how does this impact nutrient cycling?

What factors regulate microbial diversity in oligotrophic freshwater lakes, and how does this impact nutrient cycling?

• Microbial diversity in oligotrophic (low-nutrient) lakes is regulated by low concentrations of essential inorganic nutrients (primarily limiting phosphorus) combined with high light penetration through clear water.

• Spatiotemporal Nutrient Inputs (1 Mark): High species diversity is sustained by seasonally variable inputs of both endogenous nutrients (produced inside the lake, such as algal exudates, cell lysis, and sediment release) and exogenous nutrients (entering from outside, such as watershed runoff, river inflows, leaf litter, and atmospheric deposition).

• Dominant Lineages (1 Mark): Culture-independent 16S rRNA gene sequencing reveals a diverse community dominated by Betaproteobacteria (versatile heterotrophs and nitrifiers), Actinobacteria (small, free-living oligotrophic specialists), Bacteroidetes (polymer degraders), oxygenic Cyanobacteria, and archaea such as Thaumarchaeota.

• Nutrient Cycling and The Microbial Loop (1 Mark): Heterotrophic bacteria rapidly assimilate low levels of dissolved organic carbon (DOC) released by phytoplankton, converting it into cellular bacterial biomass. Protozoa graze on these bacteria, recycling carbon and energy back into the main food web via the microbial loop.

How does stratification in freshwater lakes impact microbial community structure and biogeochemical cycling? (4 marks)

How does stratification in freshwater lakes impact microbial community structure and biogeochemical cycling? (4 marks)

• Thermal Stratification (1 Mark): Summer solar heating creates density differences that separate temperate lakes into three physical zones across a thermocline barrier:

  1. Epilimnion: Warm, light-rich, well-mixed, oxygen-saturated surface layer.

  2. Thermocline (Metalimnion): Zone of sharp temperature and density change acting as a barrier to mixing.

  3. Hypolimnion: Cold, dense bottom layer cut off from atmospheric oxygen.

• Epilimnion Photosynthesis (1 Mark): Oxygenic phototrophs (phytoplankton: cyanobacteria and algae) perform oxygenic photosynthesis (6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂), fixing carbon and maintaining high oxygen saturation in surface waters.

• Hypolimnion Anoxia and The Redox Tower (1 Mark): Organic matter sinking into the hypolimnion is decomposed by aerobic respirers, depleting oxygen until the bottom water turns anoxic. Anaerobic microbes then consume electron acceptors sequentially along the redox tower based on energy yield:

  • Oxygen Respiration (O₂) → Denitrification (NO₃⁻) → Metal Reduction (Fe³⁺/Mn⁴⁺) → Sulfate Reduction (SO₄²⁻ → H₂S) → Methanogenesis (CO₂ → CH₄)

• Interface Dynamics and Autumn Turnover (1 Mark): At the oxic-anoxic thermocline interface, anoxygenic phototrophs (green sulfur bacteria Chlorobi) use light and upward-diffusing H₂S as an electron donor. In autumn, surface water cools and wind mixes the entire lake (autumn turnover), re-oxygenating deep waters and redistributing accumulated nutrients throughout the water column.

What adaptations allow microbes to survive in nutrient-poor, oligotrophic deep-sea environments and how do they maintain ecosystem function? (4 marks)

What adaptations allow microbes to survive in nutrient-poor, oligotrophic deep-sea environments and how do they maintain ecosystem function? (4 marks)

Extreme Subsurface Stressors (1 Mark): Deep-sea sediments and deep terrestrial subsurface rocks (>3000 m depth) represent extreme anoxic habitats characterized by high hydrostatic pressure, elevated temperatures (>50°C), total darkness, and severe energy/nutrient scarcity.

• Chemolithoautotrophic Energy Base (1 Mark): Lacking sunlight, primary production relies on chemolithoautotrophy—oxidizing inorganic electron donors (H₂, Fe²⁺, reduced sulfur/H₂S) coupled with autotrophic CO₂ fixation. Self-sustaining subsurface taxa such as Desulforudis audaxviator rely on radiolytic H₂, CO₂, SO₄²⁻, and N₂ without requiring any input from solar photosynthesis.

• Cellular and Physiological Adaptations (1 Mark): Microbes adapt through reduced cell sizes (ultramicrobacteria), high-affinity transport systems, mixotrophic metabolic flexibility, ultra-low metabolic rates, and extremely long generation times (spanning decades to centuries).

• Novel Archaeal Lineages (1 Mark): Deep marine environments host unique uncultivated archaea, including the Asgard superphylum (Lokiarchaeota, Thorarchaeota, Odinarchaeota) and DPANN superphylum. Lineages such as Lokiarchaeota are anoxic, mixotrophic organisms that use H₂ and organic carbon to maintain baseline carbon, nitrogen, sulfur, and iron cycling in energy-limited ecosystems.

What is a disease?

Any condition (other than a disability) in which the normal structure or functions of the body are damaged or impaired.

Infectious diseases occur when the above damage is the result of an infection by disease-causing (micro) organisms.

infection

The successful colonization of a host by a microorganism or parasite.

Infections lead to disease, when there is a deviation from the normal structure or functioning of the host, as a result of this colonization.

pathogens

Microorganisms that can cause disease are

Pathogens may be cellular (bacteria, parasites, and fungi) or acellular (viruses, viroids, and prions).

Horizontal Transmission

Infectious diseases can be communicable in that they are spread from one individual to another

Contagiousness.

The ease by which a pathogen spreads. This is largely dictated by the mode of transmission.

Modes of Horizontal Transmission/entry

1. Respiratory tract: aerosols (tiny droplets of liquid containing the virus expelled by an infected individual by coughing, sneezing etc.) are inhaled by individuals. The respiratory tract is ordinarily protected by effective defence mechanisms such as a mucus blanket and ciliary cells that line the nasal cavity and most of the lower respiratory tract. Inhaled viral particles, deposited on this surface are trapped in mucus and carried by ciliary action from the nasal cavity and airways to the pharynx and then swallowed. Particles inhaled directly into the lungs may also be destroyed by alveolar macrophages The respiratory tract is an important entry site of viruses and many bacterial pathogens such as Mycobacterium tuberculosis, Streptococcus pneumonia. Pathogens may stay within the respiratory tract or move to other sites within the body.

2. Conjunctival route: Ebola virus, Staphylococcus, Chlamydia trachomatis (via flies or human contact.

3. Oral/Faecal route: Vibrio cholera, Shigella, Salmonella

Mechanical routes of transmission:

Injection of the virus via dirty syringes, contaminated medical equipment (iatrogenic infections), puncture wounds from dirty objects

Route through the skin

Pathogens can replicate in the skin to produce local lesions , after entry through minor abrasions or burns e.g. HPV, Staphylococcus aureus or Pseudomonas aeruginosa. An efficient way by which pathogens are introduced through the skin is by the bite of an arthropod vector, such as a mosquito, tick or sandfly (examples: Yellow fever virus (mosquitoes) , leishmaniasis (sand fly) , Lyme disease, Borrelia burgdorferi, Rocky mountain spotted fever Rickettsia rickettsia (ticks).

Sexually transmitted infections

HIV-1, HSV-2, Neisseria gonorrhoea, Syphilis (Treponema pallidum).

Urine

Lassa fever (a haemorrhagic fever virus spread though human exposure to rat urine and droppings.

zoonosis

From animals to humans, such as rabies.

Plague (Yersinia pestis)

nosocomial diseases

Diseases acquired in hospital settings

Pathogens are spread via contaminated hospital equipment, bed sheets, poor hygiene practises and often easily infect patients with weakened immune systems or wounds from surgical procedures.

Nosocomial infections are often antibiotic resistant.

Acinetobacter baumannii

Vertical transmission

The transfer of a virus from a mother to her baby/foetus.

This occurs with many viruses, including HIV-1 and German measles (rubella virus)

Syphilis (bacterial disease)

Noncommunicable infectious disease

Not spread from person to person

Tetanus, caused by Clostridium tetani

Legionnaires disease, caused by Legionella pneumophila.

General types of infections

1. Acute infections

2. Subclinical

3. Persistent/chronic

4. Latent

5. Slowly Progressive disease

Acute infections

A sudden or rapid onset of disease, which can be resolved quickly by robust innate immune responses exerted by the host or, instead, may kill the host e.g. Influenza, scarlet fever (Streptococcus pyogenes).

Subclinical

An infection resulting in no detectible signs of the disease, ie: no symptoms of infection, although infected individuals can be infectious e.g. HIV-1, Syphilis Typhoid in some carriers (the famous case of Typhoid Mary)

Persistent/chronic

An infection that is not cleared by the host and remains active and in equilibrium with the hosts immune system. HCV, Leprosy (mycobacterium leprae).

Latent

A ‘dormant’ or inactive viral infection that may become productive under the appropriate conditions. Varicella Zoster, HSV 1,2. HIV-1, and Syphilis.

Slowly Progressive disease

A disease that ultimately causes irreversible damage to the host, this includes HIV-1 or Syphilis, Lyme Disease.

Primary pathogen

Causes disease in the host, regardless of the immune or health status of the host. An example of this would be Vibrio cholera

Opportunistic pathogen

Causes disease in the compromised host, where protective barriers, immune function or normal flora are sub-optimal or lacking.

Situations that compromise the host’s defences. E.g. Clostridium difficile.

pathogenicity

The ability of an organisms to cause disease

Virulence

The degree to which an organism is pathogenic (ability of organism to cause disease).

measure at how effective a pathogen is at causing disease also determines the severity of the disease;

less virulent organisms tend to cause less severe disease while

increased virulence results in greater disease severity and greater mortality.

ID50

Median infectious dose

The ID50 is the number of pathogen cells or virions required to cause active infection in 50% of inoculated animals

LD50

Median Lethal dose

The number of pathogenic cells, virions, or amount of toxin required to kill 50% of infected animals

Virulence Attenuation

Attenuation

• The decrease or loss of virulence

• When pathogens are kept in laboratory culture rather than isolated from diseased animals, their virulence often decreases or may be completely lost.

• used in production of viral vaccines.

• Example: The Edmonston strain of the measles virus, the Sabin polio vaccine.

Pathogens cause disease by successfully carrying out four steps

1) Contact

2) Adhesion

3) Invasion

4) Infection

local infection

confined to a small area of the body, typically near the portal of entry. e.g. a boil (Staphylococcus aureus infection).

The pathogen is largely contained to this small location.

urinary tract infections confined to the bladder

pneumonia confined to the lungs.

focal infection

localized pathogen, or the toxins it produces, can spread to a secondary location

systemic infection

The pathogen spreads throughout the body of the organism

infection by Yersinia pestis

primary infection

initial infection caused by one pathogen

secondary infection

by another pathogen after primary infection

Mechanisms of viral spread in the host

• Viruses may remain localized to the body surface through which they entered (i.e., skin, respiratory tract, intestine, genital tract, or conjunctiva.

• Or they may cause generalized infections, which are usually associated with viremia (virus in the blood stream) and subsequent localization in particular organs.

• Viruses, such as papilloma viruses (which cause warts) replicate in skin epithelia and spread occurs through the infection of neighbouring cells.

• Cells that infect mucosal epithelial cells rapidly spread through a similar process, examples include rotaviruses and coronaviruses, adenoviruses.

• Many viruses will move from a localised site of infection and disseminate within the host, firstly though the lymphatic system and from there into the blood stream and to other tissues/organs.

• The lymphatic system is a complex network of tissues, organs and vessels in vertebrates that is part of the immune system, and complementary to the circulatory system. Lymph nodes, lymphoid organs (e.g. spleen, thymus), lymphoid tissues such as bone marrow make up this system

Microbial adherence

Adherence

enhanced ability of microbes to attach to host tissues. It is necessary, but not sufficient, to start disease.

Adhesins are glycoproteins or lipoproteins found on the pathogen’s surface that enable it to bind to host cells

Heparan sulfate (a glycosamino glycan) serves as an attachment factor for many viruses, therefore these receptors have low specificity.

Capsules

bacterial capsule forms a thick hydrated polysaccharide-based (or sometimes peptide/polysaccharide-based) coating outside the plasma membrane and cell wall and serves two important functions in bacterial pathogenicity:

The capsule is both sticky and contains specific receptors to facilitate attachment on host tissues.

Capsules, found in encapsulated strains of Streptococcus pneumoniae, protect the bacteria from ingestion by phagocytic cells

Fimbriae, Pili, and Flagella

Colonization

The growth of microorganisms after they’ve gained access to host tissues.

Biofilms

• A hydrogel composed of polysaccharides, proteins, lipids and DNA that comprises a consortium of bacteria/microorganisms that adhere to one another within the gel matrix.

• Bacteria within biofilms are physiologically distinct from planktonic cells. They are more protected, exhibit ‘communal’ behaviour.

• They undergo a phenotypic shift and express/regulate different sets of proteins.

• Opportunistic pathogens such as Pseudomonas aeruginosa commonly form biofilms on hospital equipment and on damaged tissue surfaces such as burn wounds.

• dental plaque on teeth

Invasion

• The dissemination of a pathogen throughout local tissues or the body.

• Pathogens may produce exoenzymes or toxins, which serve as virulence factors that allow them to colonize and damage host tissues as they spread deeper into the body.

• Pathogens may also produce virulence factors that protect them against immune system defences.

• A pathogen’s specific virulence factors determine the degree of tissue damage that occurs

Exoenzymes

• Virulence factors that facilitate invasiveness.

• Invasiveness often requires a pathogen to break down host tissues in order to gain access to deeper or distal tissues.

• This is often done with enzymes e.g.

• Hyaluronidase breaks down host tissues.

• Coagulase and streptokinase manipulate clotting.

• Coagulase forms clots

• streptokinase breaks them down.

Toxins

• Pathogens can produce toxins used to damage tissues, facilitate invasion and damage the host’s defence mechanisms. This is called toxigenicity.

• Exotoxins- produced and excreted by living pathogens.

• Endotoxins- Lipopolysaccharides, components of the cell walls of gram –ve bacteria that are released from dead bacteria or those undergoing division.

Exotoxins

1. A-B toxins – specific cellular targets

2. Cytolytic toxins –Membrane disrupting

3. Superantigens toxins – Cause immune overactivation

A-B exotoxins

• These are intracellular targeting toxins that consist of an A component, the ‘active’ component, and B, the binding component, which facilitates binding to the cell surface and entry of the A component.

• The B component, like a viral receptor, is responsible for the cellular specificity of the toxin and mediates the initial attachment of the toxin to specific cell surface receptors.

• Once the A-B toxin binds to the host cell, it is brought into the cell by endocytosis and entrapped in a vacuole.

• The A and B subunits separate as the vacuole acidifies.

• The A subunit then enters the cell cytoplasm and interferes with the specific internal cellular function that it targets.

• The Diphtheria Toxin

Cytolytic Exotoxins

• These work by degrading cytoplasmic membrane integrity, causing cell lysis and death or forming pores in the cytoplasmic membrane causing an increase in membrane permeability

• Toxins that lyse red blood cells are called hemolysins.

• Staphylococcal α-toxin kills nucleated cells and lyses erythrocytes.

• Cytolysins from Acinetobacter sp. target immune cells such as macrophages.

Superantigen toxins

• Superantigens cause an overstimulation and therefore dysregulation of the immune system.

• Often the result of localized infection, but with systemic effects.

• Gram-positive bacteria, Staphylococcus aureus and Streptococcus pyogenes are major producers of exotoxin superantigens

• Super antigens work by over-activating T-lymphocytes, they are the most powerful T cell mitogens ever discovered! A mitogen is a factor that promotes cell proliferation.

• They function by crosslinking the MHC-II Antigen Presenting Receptor and the T-cell receptor, resulting in T-cell activation.

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Endotoxins

• lipopolysaccharide (LPS) found on the outer membrane of gram-negative bacteria

• Gram-negative bacterial pathogens release endotoxin either when the cell dies, from disintegrating cell walls are when cells proliferate through fission.

• The lipid component of endotoxin, lipid A, is responsible for the toxic properties of the LPS molecule.

• Lipid A is relatively conserved across different genera of gram-negative bacteria; therefore, the toxic properties of lipid A are similar regardless of the gram-negative pathogen.

• Lipid A triggers the immune system’s inflammatory response, which is usually beneficial.

Siderophores/iron transporters

• Iron is an essential element is many essential biological processes such as electron transfer, the TCA cycle, nitrogen metabolism etc…

• In the host organism, iron is not freely available: complexed to storage proteins or bound to proteins/metal complexes such as heme, transferrin, ferritin etc.

• Siderophores are essential virulence factors produced by Gram positive and negative pathogens.

• They are high-affinity iron chelating molecules produced in response to iron deficiency. Pathogen virulence is directly proportional to siderophore production.

Examples of siderophores

• Siderophores are involved in many functions such a biofilm formation and they also exhibit direct toxicity towards mitochondria.

• Siderophores are used to deliver antibiotics (Trojan horse strategy) to resistant bacteria via membrane transporters.

Tuberculosis

Tuberculosis

• A respiratory disease, primarily of the lungs although it can also manifest in the brain, spine, kidneys

• The disease starts by the inhalation of M. tuberculosis into the lung alveoli.

• The mycobacterium is phagocytosed by resident macrophages with the alveoli.

• The bacterium is potentially killed by this process or survives within the specialised endosomes in which they were phagocytosed, called phagosomes.

• M. tuberculosis is able to reproduce inside the macrophage

• The primary site of infection in the lungs is known as the Ghon focus,

• Typically, infected macrophages attract other cells and immune cells (macrophages, epithelioid cells, T lymphocytes, B lymphocytes, and fibroblasts) which aggregate about the infected focus to form and aggregate called a granuloma.

• This structure prevents the bacterium from accessing lung tissue and prevents dissemination but also protects it from immune targeting.

• Bacteria in the granuloma become dormant but may be reactivated and reestablish infections in distal sites. The granulomas areusually filled with dead cells that will eventually form cavities. These can be seen by X-Ray.

• Tissue destruction and necrosis are often balanced by healing and fibrosis.