Nitrogen cycle and other geochemical cycles

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Nitrogen is a major element of living matter and is often present in limiting amounts in ecosystems. In fact, humans frequently add it as ammonium nitrate to crops. It is one of the major players in the eutrophication of biotopes. Its natural cycle consists in the fixation of atmospheric nitrogen N₂, which is a poorly reactive gas, into ammonium that can be used by organisms, followed by the return of nitrogen to the atmosphere via nitrite and nitrate (Figure 357). Ammonium is incorporated into biological molecules by metabolism primarily by forming a complex with glutamate resulting in glutamine. Nitrate can also be transformed back into ammonium using enzymes capable of reducing nitrates and then nitrites, allowing their assimilation. In this cycle, prokaryotes play a major role because eukaryotes are not able to fix atmospheric nitrogen independently of associated symbiotic bacteria, nor are they able to denitrify in N₂. However, in some Bacillariophyta and Haptophyta algae, the nitrogen-fixing cyanobacterium has degenerated enough to be considered an organelle (Box 10). Likewise, it is possible that the Paulinella are endowed with this function via their particular plastids resulting from an independent endosymbiosis (Box 6). On the other hand, the role of eukaryotes in the assimilation of nitrates is very important. Indeed, many eukaryotes have enzymes that convert nitrates into ammonium, including plants but also many protists: Eumycota and Oomycota fungi, Viridiplantae, Phaeophyta or Bacillariophyta algae… Often, the genes encoding these enzymes arrive in the form of a cluster that has been subjected to horizontal transfers, so that closely related species have different abilities to use nitrates as a source of nitrogen (see page 194). Some eukaryotes, including Eumycota, are also able to use nitrate as a final electron acceptor (Table 3). Their contribution to the cycle is poorly understood, but Eumycota are present in anoxic environments such as deep soils, where this type of respiration could be important. More superficial ecosystems, such as coastal sediments or prairie soils, also seem to be the site of this particular respiration. In these ecosystems, Eumycota seem to be the main denitrifiers. However, they do not generate N₂ by their respiration, but NO which is converted into NO₂. These two gases are involved in the greenhouse effect.

The other atomic components of living matter are often present in trace amounts in organisms, except phosphate and sulfur which are components of amino acids, bases or cofactors. In nature, they are most often present as an insoluble mineral in rocks. They are solubilized by physical or chemical erosion processes or by the activity of prokaryotic and eukaryotic microorganisms as well as that of plants. Protists and especially Eumycota have a very important role in this process because they secrete organic acids such as citric, oxalic or gluconic acid which will lower the pH. The activity of saprotrophs in the degradation of lignocellulose will produce humic acids which will also participate in the lowering of pH and make the various nutrients available for assimilation. However, mycorrhizal bacteria have also been shown to actively participate in the acidification process. The Eumycota also have physical activity on rocks. Several species, in particular Ascomycota, including lichens, are endolithic, that is, they have the ability to grow in rock. To do this, they use a combination of chemical effects by producing organic acids but also by exerting pressure in the rock. Their activity results in the fragmentation of the material and its reduction to powder. Lichens, for example, are the first to invade new territories such as newly formed islands or cooled lava flows (Box 27). The activity of endolithic fungi and lichens therefore contributes to erosion and soil formation. In marine environments, endolithic fungi participate in the fragmentation of limestone tests and shells as well as that of coral reefs.

Phosphorus never enters the atmosphere and its cycle is slow. Phosphate typically comes from apatite, a mineral common in igneous rocks. Once dissolved, it enters living matter where it is incorporated into organic molecules or stored in the form of poly-phosphates. Slowly, it is carried towards the oceans where it is often present in limited quantities. Phosphates complex with calcium, magnesium and iron to give various minerals that go into the composition of shells, bones and teeth, but also tests of certain protists, as in Cryptodifflugia which are Tubulinean Amoebozoa, thus returning to the mineral state when the cells die.

Sulfur is present in the atmosphere in various forms via volcanic activity, but also biological. For example, “white tides” of Haptophyta algae are known to produce dimethyl sulfide (Box 26). Atmospheric or mineral sulfur will be converted into sulphate by various abiotic or biotic reactions of prokaryotic origin by chemo-autotrophs. The sulfate is then assimilated and incorporated into the amino acids. Plants and Eumycota once again have a major role in this last stage. Like phosphate, sulphates will then be carried to the oceans, where it is also a limiting element. It returns to the mineral state through various prokaryotic as well as eukaryotic abiotic and biotic activities, such as the production of dimethyl sulfide.

The role of protists in the other cycles is variously known, but it is probable that the Eumycota fungi play an important role in terrestrial ecosystems by participating in the solubilization of rocks and the incorporation of the atoms produced in living matter. In aquatic ecosystems, the production of tests, thecae and other protection reinforced by mineral elements have important roles in the return to mineral forms. For example, Haptophyta coccoliths are major players in the calcium cycle, Bacillariophyta, DictyochophyceaeBacillariophyta or Polycystinea in that of silicon and Acantharea in that of strontium.

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