In a single spoonful of soil from a milpa live more bacteria than there are people in all of Mexico. They are the oldest, most numerous, and most metabolically versatile organisms on Earth: there are bacteria that breathe sulfur, that make oxygen, that live at 110 °C, or that survive in saturated brines. Even in the pools of Cuatro Ciénegas, Coahuila, there are microbial communities that resemble those of billions of years ago. To understand microbial life, we have to start with its cell.
The prokaryotic cell
Under the microscope, a stained cheek cell shows a dark, well-defined nucleus, while the bacteria in yogurt look uniform, with no visible internal compartments. Where do they keep their genetic material if they have no nucleus?
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State three structural differences between a bacterial prokaryotic cell and a eukaryotic cell, and explain the functional consequence of each one.
State three structural differences between a bacterial prokaryotic cell and a eukaryotic cell, and explain the functional consequence of each one.
Well-known examples: Streptococcus pyogenes (cocci in chains, the cause of strep throat), Escherichia coli (bacillus), Vibrio cholerae (vibrio, the one that causes cholera), and Spirillum (spirillum).
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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…
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.
If you immerse a red blood cell in distilled water, it swells until it bursts because of osmosis. A freshwater bacterium does not burst: what structure withstands that enormous internal osmotic pressure?
Bacterial metabolism and ecological role
A tortilla, a ray of sunlight, or a rock with sulfur can be "food" for different bacteria. It all depends on where they get their energy and carbon.
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Bacterial metabolism is very diverse. Describe photoautotrophic, chemoautotrophic, and heterotrophic types: where each obtains energy and carbon from, and give an…
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…
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.
In summer, some reservoirs and lakes in Mexico turn green and smell bad. What organism is responsible, and why does it appear just then?
Cyanobacteria carry out oxygenic photosynthesis, like plants, but they are prokaryotes. Some, in addition, fix nitrogen with the enzyme nitrogenase. There is a biochemical problem: nitrogenase is inactivated by oxygen, and photosynthesis produces oxygen.
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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…
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.
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.
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.
If you dig into the mud of a lake or of a canal in Xochimilco, the surface layer is light and the lower ones are dark and smell like rotten eggs. The microbes change with depth: what decides who lives where?
All respiration passes electrons from a donor (organic matter, NADH) to a final acceptor. The more positive the redox potential $E'$ of the acceptor, the more energy is released per electron and the more ATP the cell can make.
Final acceptor
Product
Approximate $E'$ (V)
Who uses it
$\mathrm{O_2}$
$\mathrm{H_2O}$
$+0.82$
aerobes
$\mathrm{NO_3^-}$
$\mathrm{N_2}$
$+0.75$
denitrifiers
$\mathrm{SO_4^{2-}}$
$\mathrm{H_2S}$
$-0.22$
sulfate reducers
$\mathrm{CO_2}$
$\mathrm{CH_4}$
$-0.24$
methanogenic archaea
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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…
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.
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.
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.
In the intestine of a healthy person live trillions of bacteria, and almost all of them are harmless or useful. Why can a bacterium that was there without causing anything suddenly make the patient sick?
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A hospitalized patient receiving clindamycin (a broad-spectrum antibiotic) for three weeks develops severe diarrhea due to a Clostridioides difficile infection. This…
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.
a) Justify this clinical scenario using precisely the ecological concepts of ecological niche, competitive exclusion, and colonization resistance.
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.
In the late 1970s, Carl Woese compared ribosomal RNA sequences and discovered that microbes from hydrothermal vents differed more from Escherichia coli than the latter did from a plant. How can two organisms that look identical under the microscope be such different lineages?
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Many archaebacteria are extremophiles (thermophiles, halophiles, acidophiles). Describe which environments they colonise, what biochemical adaptations allow them to live…
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…
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.
Bacteria usually reproduce by binary fission (each cell divides into two identical ones), but they can acquire DNA without reproducing. Transformation takes up free DNA from the environment; transduction carries it by means of bacteriophages (viruses of bacteria); conjugation transfers DNA, often plasmids, through contact between cells.
Back to the beginning: bacteria are prokaryotes, with no nucleus and no membrane-bound organelles, and yet they dominate the Earth because of their metabolism, their speed, and their ability to exchange genes. Their DNA floats in the nucleoid and they function in soil, water, the gut, and even in extreme pools like those of Cuatro Ciénegas.
Let's practice! 3 medium exercises in this section