Ammonium assimilation

In Table 5.4 the contributions of the individual weathering reactions were assigned and combined in such a way as to yield the concentrations of Ca2+, Mg2+, Na+, K+, and H+ measured in these lakes the amounts of silicic acid and aluminum hydroxide produced and the hydrogen ions consumed were calculated stoichiometrically from the quantity of minerals assumed to have reacted. Corrections must be made for biological processes, such as ammonium assimilation and nitrification and the uptake of silicic acid by diatoms. Some of the H4Si04 was apparently lost by adsorption on aluminum hydroxide and Fe(III)(hydr)oxides, but the extent of these reactions was difficult to assess. 

Nitrogen transformations such as nitrate assimilation, denitrification, and decomposition (eqs 10-12) contribute to alkalinity by consuming H+. In contrast, both ammonium assimilation and nitrification (eqs 13 and 14) consume alkalinity via the production of H +. 

All plants contain a PEPCase enzyme which, among other likely roles (Vidal et al., 1986), serves to replenish tricarboxylic acid cycle intermediates that are consumed during ammonium assimilation (Latzko Kelly, 1983). The role of this enzyme, other than its presumed housekeeping function, has not been studied in any detail and its activity is probably not controlled by environmental factors. Isoforms of PEPCase have been observed in many plants (C3, C4 and CAM) for example, in rice five isoforms have been detected immunologically and in most plants two to four bands that react with anti-PEPCase antibodies are found (Matsuoka Hata, 1987). It is not clear how these isoforms arise, e.g. by post-translational modification of one form, or whether all of these forms are products of different genes. The housekeeping-type PEPCase enzyme, concerned with anaplerotic functions, is distinct from other PEPCase enzymes that function in plants with C4 and CAM metabolism (see below). 

Reynolds, P.H.S., Boland, M.J., McNaughton, G.S., More, R.D. Jones, W.T. (1990). Induction of ammonium assimilation leguminous roots compared with nodules using split root system. Physiologia Plantarum 79, 359-67. 

Bruggeman, F. J. Boogerd, F. C. Wester-hoff, H. V. The multifarious short-term regulation of ammonium assimilation of Escherichia coli dissection using an in sil-ico replica. FEBSJ 2005, 272 1965-1985. 

Figure 5.2 Depth distribution of ammonia oxidation rate (VNH4) and ammonium assimilation rate (VPN) in the surface layer in Monterey Bay, CA. Dataware obtained from N-NH4 tracer incubations at simulated in situ light intensities. (FromWard 2005)...

Ward, B. B. (1985). Light and substrate concentration relationships with marine ammonium assimilation and oxidation rates. Mar. Chem. 16, 301—316. 

Le Corre, P., Wafar, M., Helguen, S. L., and Maguer, J. P. (1996). Ammonium assimilation and regeneration by size-fractionated plankton in permanendy well-mixed temperate waters. /. Plankton Res. 18(3), 355-370. 

Zehr, J. P., and Falkowski, P. G. (1988). Pathway of ammonium assimilation in a marine diatom determined with the radiotracer N-13. J. Phycol. 24, 588-591. 

Summons, R. E., Boag, T. S., and Osmond, C. B. (1986). The effect of ammonium on photosynthesis and the pathway of ammonium assimilation in Gymnodinium microadriaticum in vitro and in symbiosis with tridacnid clams and corals proceedings of the royal society of London. Ser. B Biol. Sci. 227(1247), 147-159. 

Ahmad, I., and HeUebust, J. A. (1988). Enzymology of ammonium assimilation in three green flageUates. New Phytol. 109, 415—421. 

Rees, T., Grant, C., Harmens, H., and Taylor, R. (1998). Measuring rates of ammonium assimilation in marine algae Use of the protonophore carbonyl cyanide m-chlorophenylhydrazone to distinguish between uptake and assimilation. J. Phycol. 34, 264—272. 

Figure 12 Major reduction-oxidation reactions involving nitrogen. The reactions are numbered as follows (1) mineralization, (2) ammonium assimilation, (3) nitrification, (4) assimilatory or dissimilatory nitrate reduction, (5) ammonium oxidation, (6) nitrite oxidation, (7) assimilatory or dissimilatory nitrate reduction, (8) assimilatory or dissimilatory nitrite reduction, (9) denitrification, (10) chemodenitrification, (11) anaerobic ammonium oxidation, and (12) dinitrogen fixation (after Capone, 1991) (reproduced by permission of ASM Press from Microbial Production and Consumption of Greenhouse Gases Methane, Nitrogen Oxides, and Halomethanes, 1991).

Figure 28. Hypothetical anaerobic nitrogen cycle based on the following thermodynamically permissible reactions (1) ammonium oxidation to dinitrogen by carbon dioxide,. sulfate or ferric iron (no evidence at present, possibly kinetically limited) (2) dinitrogen fixation by various organic and inorganic reductants (known) (3) ammonium oxidation by nitrite or nitrate producing dinitrogen (known) (4) denitrification (known) (5) nitrite or nitrate respiration (known) (6) ferric iron oxidation of ammonium to nitrite or nitrate (no evidence at present) (7) nitrate assimilation (known) (8) ammonium assimilation and di.s,similation (known) (Fenchel etai, 1998).

G. Dohler, T. Buchmann (1995). Effects of UV-A and UV-B irradiance on pigments and 15N-ammonium assimilation of the haptophycean Pavlova. J. Plant Physiol, 146, 29-34. 

Fig. 3.17 Summary of the nitrogen cycle (oxidation states of nitrogen shown in parentheses). Ammonium assimilation and ammonification can occur in oxic and anoxic environments, as can nitrogen fixation (although the most prolific bacteria are aerobes).

Debouba, M., Maaroufi-Dghimi, H., Suzuki, A., Ghorbel, M.H., and Gouia, H. (2007). Changes in growth and activity of enzymes involved in nitrate reduction and ammonium assimilation in tomato seedlings in response to NaCl stress. Ann. Bot. (London) 99, 1143-1151. 

Figure 3 Schematic diagram of the processes and pools central to the internal cycling of N in the ocean. The isotope effects shown here are based on laboratory studies. Dashed arrows represent assimilation of dissolved species into particulate matter, and solid arrows represent remineralization. Complete consumption of the ammonium pool by assimilation in the surface ocean or by nitrification in the ocean interior causes the relatively high isotope effects associated with these processes to have little effect on N isotope dynamics. However, in regions where ammonium assimilation and nitrification co-occur, their isotope effects will impact the <5 N of their respective products, PN and nitrate. In nitrification, ammonia (NHs), rather than the protonated form ammonium (NH4 ), is oxidized. However, ammonium is the dominant species in seawater, and there is isotope discrimination in the ammonium-ammonia interconversion. Thus, the isotope effects for ammonia oxidation given here and elsewhere in the text refer specifically to consumption of ammonium. The processes surrounding DON production and utilization are not well understood from an isotopic perspective but are thought to play an important role in N cycling.

Ammonium is normally exchanged with protons to balance charge in passing through each cell membrane, so that each ammonium absorbed and assimilated by chloroplasts has half the alkaline effect of each nitrite assimilation. When taken together, the processes of nitrite and ammonium assimilation might therefore be of a similar order in terms of alkaline effect as the acidic effect of oxygenase activity of Rubisco,... 

A literature search revealed that the distribution of the enzymes of nitrate assimilation had been determined in one case and was apparently as predicted by the theory. Nitrate and nitrite reductases were shown by isolation of mesophyll and bundle-sheath protoplasts to be predominantly in mesophyll cells. In addition, the enzymes of ammonium assimilation (glutamine synthetase and glutamate synthase) were also found mainly in these cells (see Edwards and Huber, ref. 9), rather than in the Kranz cells. No conclusions were drawn about the significance of such a distribution. 

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