Bacteria and Archaea

State three structural differences between a bacterial prokaryotic cell and a eukaryotic cell, and explain the functional consequence of each one.

Look at the bacteria in the diagram (A to F). Classify them according to their shape (coccus, bacillus, spirillum, or vibrio) and, where applicable, according to their arrangement (diplococci, streptococci, staphylococci), giving a well-known example where possible.

Explain what the bacterial cell wall is (peptidoglycan) and what the Gram stain consists of: which two major groups it distinguishes (Gram-positive and Gram-negative) and why it is so useful for choosing a treatment.

1. a) Name three external structures that a bacterium can have.
2. b) Explain the main function of each of them.

What is an endospore? Explain how it forms, what extraordinary resistance it has (heat, desiccation, disinfectants) and why it complicates sterilisation in medicine and in canned food (examples: tetanus, botulism).

Biofilms are bacterial communities adhered to a surface and wrapped in a matrix. Explain where they form (dental plaque, catheters, pipes, river stones), why they are much more resistant to antibiotics and disinfectants than free bacteria, and what problems they cause in hospitals.

Selective and differential media are used in the laboratory. Explain what each type is with an example (MacConkey agar selects Gram-negative bacteria and distinguishes lactose fermenters; blood agar reveals haemolysis) and what information they provide when identifying an unknown bacterium.

Bacterial metabolism is very diverse. Describe photoautotrophic, chemoautotrophic, and heterotrophic types: where each obtains energy and carbon from, and give an example of a bacterium or environment for each type.

Distinguish between a strict aerobic bacterium, a strict anaerobic one and a facultative anaerobic one, and associate each type with an environment (the soil surface, the bottom of a deep wound, the digestive tract).

Explain the essential role of bacteria in the nitrogen and carbon cycles (fixation, nitrification, denitrification, and decomposition) and reason what would happen to ecosystems if they disappeared.

Methanogenic archaebacteria produce methane. Explain where they live (the rumen of herbivores, the bottoms of marshes and rice paddies, sewage plants), what they feed on, and why their metabolism concerns both the climate (methane as a greenhouse gas) and energy (biogas).

Bacterial symbiosis goes far beyond the human gut. Describe one specific example — the luminous bacteria of the squid (Vibrio fischeri) or the Rhizobium nodules in legumes — explaining what each partner contributes and how they "recognise" each other to establish the association.

In an aquatic sediment, the stratification of redox potential (E') with depth is analyzed. Measurements indicate that at 2 cm from the surface, dissolved O₂ is depleted, at 6 cm NO_3^- completely disappears, and starting from 15 cm, a constant emission of CH_4 begins to be detected.

1. a) Justify, in terms of redox potential difference (\\Delta E') and ATP synthesis yield via oxidative phosphorylation, why denitrifying bacteria colonize and dominate the layer immediately below that of obligate aerobes, displacing methanogenic archaea to deeper layers.
2. b) Reasonedly predict what will happen to the methane emission rate and to the active population of methanogens if a concentrated solution of sodium nitrate (NaNO_3) is artificially injected into the deep anoxic sediment.

A hospitalized patient receiving clindamycin (a broad-spectrum antibiotic) for three weeks develops severe diarrhea due to a Clostridioides difficile infection. This bacterium was present in their intestine before starting the treatment, but accounted for less than 0.1 % of the microbial community and caused no symptoms. After several lines of drugs fail, a fecal microbiota transplant (FMT) from a healthy donor is performed, successfully eradicating the infection within 48 hours.

1. a) Justify this clinical scenario using precisely the ecological concepts of ecological niche, competitive exclusion, and colonization resistance.
2. b) Design a simple experiment using axenic (germ-free) laboratory mice that allows discerning whether the curative factor of the fecal transplant lies in the direct physical competition exerted by viable bacteria or in heat-stable protective metabolites dissolved in the donor's stool filtrate.

During a warm summer, a reservoir receives a discharge rich in phosphorus that causes the water's nitrogen:phosphorus (N:P) ratio to plummet. A few weeks later, a dense greenish layer forms on the surface dominated by filamentous cyanobacteria with heterocysts, and tests detect dangerous levels of microcystins.

1. a) Justify why nitrogen-fixing cyanobacteria displace eukaryotic microalgae when the N:P ratio drops drastically. Explain what fundamental biochemical incompatibility the heterocyst resolves and what structural and metabolic adaptations it exhibits to achieve this.
2. b) Paradoxically, despite cyanobacteria carrying out oxygenic photosynthesis, reservoir technicians record massive fish mortality due to anoxia in the intermediate and bottom layers. Deduce the ecological and biochemical causes of this oxygen collapse throughout the water column.

A biotechnology team searches for bacterial enzymes capable of hydrolyzing PET plastic at 70 °C from volcanic soil samples. When plating soil dilutions on Petri dishes with nutrient agar and incubating them at 70 °C, they obtain only two bacterial colonies that do not degrade the plastic. However, upon extracting and sequencing total environmental DNA (metagenomics) from a single gram of that soil, they discover more than 300 distinct bacterial taxa, among them sequences homologous to PETase genes.

1. a) Justify two ecophysiological causes that explain the inability of the vast majority of these soil bacteria to form colonies on conventional laboratory plates ("the great plate count anomaly").
2. b) Design a strategy based on functional metagenomics (library construction and screening in model organisms such as Escherichia coli) that allows identifying and producing the PET-degrading enzyme without the need to isolate or culture the original thermophilic bacterium in the laboratory.

In a metallic sulphide mine, two areas are analysed: a pyrite (FeS_2) waste dump compacted and sealed against air, and another identical waste dump that is porous, moist, and exposed to weathering. The water draining from this second dump has a pH of 1.7 and a high concentration of ferric ions (Fe^3+) and sulphate, due to the action of Acidithiobacillus ferrooxidans.

1. a) Deduce the role that A. ferrooxidans plays as a biogeochemical catalyst: explain which chemical species it oxidises, what the final electron acceptor is, and why its metabolism acidifies the medium so sharply. Classify its metabolic type according to its carbon and energy source.
2. b) A mining company uses bioreactors with A. ferrooxidans to leach low-grade chalcopyrite (bioleaching), while the River Basin Authority reports the mine for acid mine drainage from the open waste dump. Chemically justify why the same microbial process constitutes a clean and profitable biotechnology in one context, but an ecotoxicological catastrophe for river ecosystems in the other.

Many archaebacteria are extremophiles (thermophiles, halophiles, acidophiles). Describe which environments they colonise, what biochemical adaptations allow them to live there, and why studying them is relevant to hypotheses about the origin of life.

State two molecular differences between eubacteria and archaebacteria (for example in the cell wall or membrane lipids) and explain why they are classified into different domains.

Cyanobacteria were called "blue algae" for centuries. Explain why that name was incorrect (prokaryotic organisation), which photosynthesis they perform (oxygenic) and what historical role they played in the Earth's atmosphere.

For decades, the red and extremely acidic waters (average pH of 2.2) of the River Avoca (Co. Wicklow) were considered to be exclusively the result of historical mining. However, deep boreholes from the MARTE project revealed that the acidity is of biogenic origin and that living consortia of chemolithotrophic bacteria inhabit the anoxic subsurface.

1. a) If the intracellular environment of Leptospirillum ferrooxidans must be maintained at a near-neutral pH (6.5 to 7.0) so that its macromolecules do not denature, justify what adaptations in its membrane potential or in its transmembrane active transport systems allow it to prevent the massive passive influx of H^+ protons from the external medium.
2. b) The Mars mission rover detected mineral formations of jarosite (hydrated basic potassium and iron sulphate) and hematite on the Martian surface. Justify why the River Avoca is used as a terrestrial analogue of Mars and reason what astrobiology deduces about the past hydrosphere of Mars and what subsurface biosignatures we should look for.

What are plasmids? Explain what type of genes they usually carry (antibiotic resistance, toxins) and why their ability to pass from one bacterium to another worries doctors.