Domains 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 sterilization 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 hemolysis) 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, wastewater treatment 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 "recognize" each other to establish the association.

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.

Many archaebacteria are extremophiles (thermophiles, halophiles, acidophiles). Describe which environments they colonize, 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 organization), which photosynthesis they perform (oxygenic) and what historical role they played in the Earth's atmosphere.

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.