Nitrosopumilus

Key takeaways

Nitrosopumilus belongs to biology; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Nitrosopumilus to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Nitrosopumilus from memory before moving on to harder problems.

Reference excerpt

Nitrosopumilus is a genus of archaea. The type species, Nitrosopumilus maritimus, is an extremely common archaeon living in seawater. It is the first member of the Group 1a Nitrososphaerota (formerly Thaumarchaeota) to be isolated in pure culture. Gene sequences suggest that the Group 1a Nitrososphaerota are ubiquitous with the oligotrophic surface ocean and can be found in most non-coastal marine waters around the planet. It is one of the smallest living organisms at 0.2 micrometers in diameter. Cells in the species N. maritimus are shaped like peanuts and can be found both as individuals and in loose aggregates. They oxidize ammonia to nitrite and members of N. maritimus can oxidize ammonia at levels as low as 10 nanomolar, near the limit to sustain its life. Archaea in the species N. maritimus live in oxygen-depleted habitats. Oxygen needed for ammonia oxidation might be produced by novel pathway which generates oxygen and dinitrogen. N. maritimus is thus among other organisms which are able to produce oxygen in the dark. This organism was isolated from sediment in a tropical tank at the Seattle Aquarium by a group led by David Stahl (University of Washington).

Biology

Lipid membranes Populations of N. maritimus are probably the main source of glycerol dialkyl glycerol tetraethers (GDGTs) in the ocean, a compound which constitutes their monolayer lipidic cell membranes as intact polar lipids (IPLs) together with crenarcheol. This membrane structure is thought to maximise proton motive force. The compounds found in the membrane of these organisms, such as GDGTs, IPLs, and crenarcheol, can be useful as biomarkers for the presence of organisms belonging to the Nitrososphaerota group in the water column. These archaea have also been found to change their membrane's composition in relation to temperature (by GDGT cyclization), growth, metabolic status, and, even if less dramatically, to pH.

Cell division All known Archaea use cell division to duplicate. Euryarchaeota and Bacteria use the FtsZ mechanism in cell division, while Thermoproteota divide using the Cdv machinery. However, Nitrososphaerota such as N. maritimus adopts both mechanisms, FtsZ and Cdv. Nevertheless, after further researches, N. maritimus was found to use mainly Cdv proteins rather than FtsZ during cell division. In this case, Cdv is the primary system in cell division for N. maritimus. Therefore, to replicate a genome of 1.645Mb, N. maritimus spends 15 to 18 hours.

Physiology

Genome Ammonia-oxidizing bacteria (AOB) are known to have chemolithoautotrophic growth by using inorganic carbon, N. maritimus, an Ammonia-oxidizing archaea (AOA) use a similar process of growth. While AOB uses Calvin–Bassham–Benson cycle with the CO2-fixing enzyme ribulose bisphosphate carboxylase/oxygenase (RubisCO) as the key enzyme; N. maritimus seems to grow and use an alternative pathway due to the lack of genes and enzymes. Therefore, a variant of the 3-hydroxypropionate/4-hydroxybutyrate is used by N. maritimus to develop autotrophically, which allows its capacity to assimilate inorganic carbon. Using the 3-hydroxypropionate/4-hydroxybutyrate pathway method instead of the Calvin cycle, N. maritimus could provide a growth advantage as the process is more energy-efficient. Due to its originality, N. maritimus plays an essential role in the carbon and nitrogen cycle

Ammonia oxidation The isolation and the sequencing of N. maritimuss genome have allowed to extend the insight into the physiology of the organisms belonging to the Nitrososphaerota group. N. maritimus was the first Archaeon with an ammonia oxidizing metabolism to be studied. This organism is common in the marine environment especially at the bottom of the photic zone where the amount of Ammonium and Iron is enough to support its growth. The physiology of N. maritimus remains unclear under certain aspects. It conserves energy for its vital functions, from the oxidation of Ammonia (NH3) and the reduction of Oxygen (O2), with the formation of Nitrite. CO2 is the carbon source. It is fixed and assimilated by the microorganism through the 3-hydroxypropinate/4-hydroxybutyrate carbon cycle. N. maritimus carries out the first step of Nitrification, by acting in a key role in the Nitrogen cycle along the water column. Since this oxidizing reaction releases just a little amount of energy, the growth of this microorganism is slow. N. maritimus’s genome includes the amoA gene, encoding for the Ammonia Monooxygenase (AMO) enzyme. This latter allows the oxidation of ammonia to hydroxylamine (NH2OH). Instead, the genome lacks the gene encoding for Hydroxylamine Oxidoreductase (HAO) responsible for oxidizing the intermediate (NH2OH) to nitrite. The hydroxylamine is produced as a metabolite, and it is immediately consumed during the metabolic reaction. Other intermediates produced during this metabolic pathway are: the nitric oxide (NO), the nitrous oxide (N2O), the nitoxyl (HNO). These are toxic at high concentration. The enzyme responsible for oxidizing the hydroxylamine to nitrite is not well-known yet. Two hypotheses are suggested for the metabolic pathway of N. maritimus that involve two types of enzymes : the copper-based enzyme (Cu-ME) and the nitrite reductase enzyme (nirK) and its reverse:

In the first one ammonia is oxidized through AMO forming the hydroxylamine; the latter, plus a molecule of nitric oxide, are, in turn, oxidized by a copper-based enzyme (Cu-ME) producing two molecules of nitrite. One of these is reduced to NO by the nitrite reductase (nirK) and goes back to the cu-ME enzyme. An electrons translocation occurs producing a Proton Motive Force (PMF) and allowing ATP synthesis. In the second one ammonia is oxidized through AMO making up the hydroxylamine and then the two enzymes, nirK and Cu-ME, oxidize the hydroxylamine to nitric oxide and this to nitrite. The proper roles and the order at which these enzymes work, have to be clarified. The S-layer of N. maritimus is found to form into multiple layers of channels that allow ammonium (NH+4) cations to flow through. Additionally, nitrous oxide is released by this type of metabolism. It is an important greenhouse gas that likely is produced as result of abiotic denitrification of metabolites.

Taxonomy The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI).

Nitrosopumilus incertae sedis:

… excerpt ends here. Continue reading the full article.

Illustrations

Worked examples

Example 1 — a first encounter with Nitrosopumilus

Start with the simplest possible case. Write down what Nitrosopumilus claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Nitrosopumilus before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Nitrosopumilus ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Nitrosopumilus

In research: Nitrosopumilus appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Nitrosopumilus in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Nitrosopumilus is common in secondary-school and first-year university syllabi. It links to neighbouring topics Archaea genera, Marine microorganisms, Thermoproteota, so understanding it makes those chapters shorter.
In everyday life: Look for Nitrosopumilus outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study Nitrosopumilus in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Nitrosopumilus means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain Nitrosopumilus out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Nitrosopumilus in simple terms?

Nitrosopumilus is a genus of archaea. The type species, Nitrosopumilus maritimus, is an extremely common archaeon living in seawater.

Why does Nitrosopumilus matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Nitrosopumilus?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Nitrosopumilus.