Several environmental factors that might control nitrification in various ecosystems have already been mentioned. They include the kinds of things that affect biological processes in general, as well as those particular to the metabolism of nitrifiers: temperature, salinity, light, organic matter concentrations, substrate (ammonium and nitrite) concentrations, pH, and oxygen concentration. A few of the interesting and unique interactions of nitrifiers with their environment are explored below.
Salinity and temperature do not appear to set any unusual constraints on the range of conditions under which nitrification can occur, and different kinds of nitri-fiers appear to have adapted to the wide range of these variables found on Earth. The mechanism by which salinity affects nitrification is not known, but it is clear that salinity is an important determinant of the community composition of nitrifying microbes, if not the net rate of nitrification; that is, different kinds of nitrifiers are adapted to different salinity levels, but nitrification occurs under high as well as low salinity and depends on the presence of different species. Nevertheless, it can be shown that salinity dramatically affects the rate of nitrification, when salinity changes are imposed in an experiment with natural assemblages. Ionic strength effects related to the sorption and availability of ammonium are not sufficient to explain the effects of salinity, suggesting that direct physiological responses are also involved.
AOB and NOB require molecular oxygen for their metabolism and thus are restricted to oxic environments.
Nonetheless, they seem to prefer and to do quite well under very low oxygen conditions, displaying a micro-aerophilic lifestyle. Under these conditions, AOB tend to produce higher quantities of N2O, relative to nitrite. Although not well known, it is assumed that AOA use essentially the same pathway as do AOB, and thus are likely obligate aerobes as well. Anammox organisms, in contrast, are strictly anaerobic, and while oxygen apparently does not kill them, it does inhibit their activity. Thus, oxygen concentration, in the bulk water of aquatic environments and in the interstices of sediments and soils, is likely a very important variable for regulation of micro-bial activities and the resulting distribution of nitrogen-cycling processes.
All of the nitrifying microorganisms are predominantly autotrophs, that is, they fix their own carbon from CO2, and thus do not rely on a supply of organic matter for nutrition. This means that they are not in competition with heterotrophs for the utilization of organic substrates, but rather that they exploit a different niche. This niche involves certain 'sacrifices', in terms of slower growth rates (see Units of Selection). These forms of autotrophic growth are also quite inefficient, due to the low energy yield of the transformations involved. Thus nitrifiers process large amounts of nitrogen in order to obtain the energy required for CO2 fixation. The molar ratio of N oxidized to C fixed has been estimated at 35-100 for conventional nitrifiers, ensuring that their metabolism has a very large effect on the nitrogen cycle, but very little influence on the carbon cycle, where photo-synthetic autotrophs are overwhelmingly important.
Light inhibition of nitrifiers is suspected as a mechanism for the formation of the primary nitrite maximum (see above) and it is easily demonstrated in culture that both AOB and NOB are sensitive to light. The light sensitivity of AOA has not been investigated. The basis for the light sensitivity of AOB and NOB is assumed to be damage to the many cytochromes that are involved in the energy transduction pathways of nitrification.
Any transformation that involves the production or consumption of hydrogen ions is pH sensitive, and ammonia oxidation is no exception (see Acidification). Oxidation of ammonia by AOB and AOA results in the acidification of the medium. Low pH eventually inhibits AOB in culture, and activity can be restored by pH adjustment. It is unlikely that pH is an important controlling variable in the ocean, even in sediments, but pH could be very important in regulation of nitrification in acid soils. While nitrification generally occurs in acid soils, it has proven difficult to obtain acidophilic nitrifiers in culture, leading to speculation about the importance of heterotrophic nitrification in this system. It is now known that many of the kinds of nitrifying bacteria that can be identified by their gene sequences in the natural environment, are not in fact represented in culture collections.
Thus it is quite possible that acidophilic autotrophic nitrifiers exist but are resistant to cultivation.
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