Exercises: Eubacteria and archaebacteria

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

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.

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.

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.

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.

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.

In an aquatic sediment, the stratification of redox potential (E') with depth is analyzed. Measurements indicate that at 2 cm from the surface, dissolved O_2 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.