Assimilatory processes

Ammonia is oxidized in nature to nitrate via several intermediates in the process of nitrification. Nitrate may be reduced to nitrite by either a dissimilatory or an assimilatory process. Nitrite may be assimilated into the cell via reduction to ammonia, or it may be reduced by microorganisms to N20 and N2 in denitrification. A major part of the total nitrogen in this pathway is lost to the atmosphere. However, in turn, atmospheric dinitrogen is converted to ammonia by various bacteria in nitrogen fixation. 

While this formally may follow assimilatory (to NH3) or dissimilatory (to N2) pathways, it is becoming clear that a number of non-denitrifiers are also able to produce dinitrogen monoxide by reduction of nitrite.1513,1514 Furthermore, reduction of nitrite to ammonia by one pathway (the NADPH-sulfite reductase) does not appear to be an assimilatory process, but rather one in which catabolic reducing equivalents are removed. 

Subareal plants use atmospheric (gaseous) C02 (C02(g)) as their photosynthetic carbon source, which has a mean 813C value of c— 7%o. Subaquatic plants use the dissolved (aqueous) C02 (C02(aq)), which is at one end of the series of equilibria shown in Eqn 3.8. Both these assimilatory processes are accompanied by isotopic fractionations, as discussed in Section 5.8.2. In marine environments there are also C isotopic fractionations associated with the formation of calcium carbonate tests (using bicarbonate) by some organisms that for formation of calcite is different from that for aragonite. The overall fractionation, caicjee co2(aq) s l31 6 and temperature dependent (Fig. 5.55 Mook et al. 1974 Morse Mackenzie 1990), primarily because of the equilibrium between dissolved C02 and bicarbonate... 

With whole-cell studies, we have unfortunately been unable to elucidate the [ N]ammonia uptake mechanism. The incomplete inhibition of assimilatory processes both by mutation and by inhibitors is the major obstacle. Vahd transport studies require that the accumulated substrate be unmodified by subsequent metabolism. However, these preliminary experiments have yielded interesting conclusions about the... 

Assimilatory Processes Building the Essential Molecules of Life... 

Nitrogen uptake that results in the formation of new biomolecules is termed an assimilation process, such as assimilatory nitrogen reduction. The processes that result in the release of DIN into seawater are referred to as dissimilations, such as dissimi-latory nitrogen reduction. An example of the latter is denitrification, in which nitrate and nitrite obtained from seawater serve as electron acceptors to enable the oxidation of organic matter. This causes the nitrate and nitrite to be transformed into reduced species, such as N2O and N2, which are released back into seawater. 

The biogeochemical cycling of nitrogen is very much controlled by redox reactions. This perspective is presented in Figure 24.3 for the redox reactions that take place in the water column and sediments. The major pathways of reduction are nitrogen fixation, assimilatory nitrogen reduction, and denitrification. The major oxidation processes are nitrification and anaerobic ammonium oxidation (anammox). Each of these is described next in further detail. 

This process is commonly referred to as assimilatory nitrogen (nitrate or nitrite) reduction. The electrons for these reductions are supplied by half-cell oxidations involving NADPH/NADP" and NADH/NAD" (Table 7.11). All of these reactions and membrane transport processes are mediated by enzymes that are specific to the DIN species. Considerable variation exists among the phytoplankton species in their ability to produce the necessary enzymes. Since marine phytoplankton are often nitrogen limited, the quantity and type of DIN available in the water column can greatly influence overall phytoplankton abundance and species diversity. 

Assimilatory nitrate reduetion The reduction of nitrate to organic nitrogen compounds that constitute the tissues of marine organisms. Plankton and some bacteria assimilate nitrogen via this process. 

With M. gryphiswaldense, Schuler and Bauerlein (1996) recorded an Fe uptake rate from Fe " citrate of 0.86 nmol min mg dry weight and suggested that the major portion of Fe is taken up in an energy-dependent process possibly by a reductive step (Schuler, 1999). Fukumori et al. (1997) proposed that the dissimilatory nitrite reductase of M. magnetotacticum may function as an Fe" oxidizing enzyme. Later, Fuko-mori (2000) suggested an Fe "quinate complex as the source of Fe which is subsequently reduced in the cell in a microaerobic environment at about neutral pH by the iron reductase NADH (an assimilatory enzyme). 

As noted in Section 62.1.9.6, reduction of nitrate may occur by assimilatory or dissimilatory pathways. In the former case, the nitrate produced is reduced further to ammonia, which is incorporated into the cell. In the latter case, nitrate is reduced anaerobically to nitrite, serving as an electron acceptor in the respiration of facultative or a few obligate anaerobic bacteria. The example of Escherichia coli has been considered in Section 62.1.13.4.3. This process is usually terminated at nitrite, which accumulates around the cells, but may proceed further1511 as nitrite-linked respiration in the process of denitrification. 

The potentials found for nitrate reductases [96] vary with the role of the particular enzyme. Assimilatory nitrate reductase, found in plants, algae, and fungi, is involved in the first step in nitrogen assimilation and has a molybdenum center that operates at around 0 mV. Respiratory (dissimilatory) nitrate reductase, utilized by bacteria in energy yielding processes, has a molybdenum center that operates at around +200 mV [97,98],... 

Figure 10.5 Major processes involved in the biogeochemical cycling of N in estuaries and the coastal ocean (1) biological N2 fixation (2) ammonia assimilation (3) nitrification (4) assimilatory NC>3 reduction (5) ammonification or N remineralization (6) ammonium oxidation (speculative at this time) (7) denitrification and dissimilatory NO3 reduction to NH4+ and (8) assimilation of dissolved organic nitrogen (DON). (Modified from Libes, 1992.)...

This reaction is of particular interest inasmuch ns it constitutes nature s method of replenishing the free oxygen content of the atmosphere. The ollioiency of the process is evident when, to quote an example of medium assimilatory activity, it is remembered that one square metre of sunllower leaf can effect the decomposition of some to grams of carbon dioxide, and the simultaneous evolution of 30 grams of oxygen in one summer day of 15 hours duration. 

Nitrate in the soil environment, therefore, can undergo two distinct biochemical processes (1) assimilatory, where N03 is used to produced protein, and (2) dissimila-tory, where NOa is used to produce energy for microbes. The rate at which the latter process occurs depends indirectly on 02 availability, or Eh, and directly on available moisture, organic carbon content, and pH. The optimum pH is around neutral and the... 

A heterogeneous group of microorganisms, including many bacterial, fungal, and algal species, are capable of assimilatory nitrate reduction, a process that reduces nitrate and nitrite to ammonia, which can be subsequently incorporated into amino acids. 

In contrast to the specialized dissimilatory sulfate reducers, many organisms (humans as well) are capable of assimilatory sulfate reduction. This process, which requires chemical energy in the form of ATP and a series of transfer reactions, can occur anaerobically and aerobically. It produces low concentrations of hydrogen sulfide that are immediately incorporated into organic compounds. Many microbes, plants, and animals have such a metabolic ability. 

In contrast to zinc, the crucial role of Fe in the bioenergetics of carbon (C) and N metabolism is well recognized (e.g., Morel et al., 1991 Sunda, 1989). Substantial amounts of Fe are required in both photosynthetic and respiratory electron transport chains (e.g., Raven, 1988), the synthesis of chlorophyll (Chereskin and Castelfranco, 1982), and the assimilation ofNOj. Theoretical calculations based on Fe utilization efficiencies and cellular metabolic Fe demands, predict that phytoplankton growing on NOJ require 60% more Fe than those growing on NH (Raven, 1988, 1990), and greater cellular Fe requirements for NO growth have indeed been demonstrated for laboratory cultures of diatoms (Maldonado and Price, 1996). The extra Fe is needed to reduce NO to NH4 before it can be incorporated into amino acids. This process requires the assimilatory enzymes nitrate reductase (requires one... 

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