Nitrification in sediments

Lipschultz et al. (1985) documented the light inhibition of NH3 oxidation in the Delaware River and concluded that this effect influenced the spatial distribution of nitrification in the estuary. Depending on their depth, light is not usually a problem for nitrification in sediments. In shallow sediments, light may have an indirect positive effect on nitrification rates by increasing photosynthesis, and thus increasing oxygen supply to the sediments (Lorenzen et al., 1998). 

Nitrifying bacteria are traditionally considered to be obligate aerobes they require molecular oxygen for reactions in the N oxidation pathways and for respiration. They are reputed to be microaerophiles, however, who thrive best under relatively low oxygen conditions. Microaerophily may be important in interface environments such as the sediment water interface and in the oxygen minimum zones of the ocean. The role of oxygen in sedimentary nitrification and coupled nitrification/ denitrification is discussed above in the section on nitrification in sediments. 

Rysgaard-Petersen, N., Rysgaard, S., Nielsen, L. P., and Revsbech, N. P. (1994). Diurnal variation of denitrification and nitrification in sediments colonized by benthic microphytes. Limnol. Oceanogr. 39, 573-579. 

Henriksen, K., 1980. Measurement of in situ rates of nitrification in sediment. Microbial Ecology, 6 329-337. 

Continuous Multicomponent Distillation Column 501 Gas Separation by Membrane Permeation 475 Transport of Heavy Metals in Water and Sediment 565 Residence Time Distribution Studies 381 Nitrification in a Fluidised Bed Reactor 547 Conversion of Nitrobenzene to Aniline 329 Non-Ideal Stirred-Tank Reactor 374 Oscillating Tank Reactor Behaviour 290 Oxidation Reaction in an Aerated Tank 250 Classic Streeter-Phelps Oxygen Sag Curves 569 Auto-Refrigerated Reactor 295 Batch Reactor of Luyben 253 Reversible Reaction with Temperature Effects 305 Reversible Reaction with Variable Heat Capacities 299 Reaction with Integrated Extraction of Inhibitory Product 280... 

Seventeen genera of facultative anaerobic bacteria (e.g., Pseudomonas and Bacillus) can perform denitrification under anaerobic or low-oxygen conditions, where they use NO3- as an electron acceptor during anaerobic respiration (Jaffe, 2000). In fact, in many estuaries, denitrification is limited by the availability of NC>3 (Koike and Sprensen, 1988 Cornwell et al., 1999). Sources of NC>3 and NC>2 for denitrification are from diffusive inputs from the overlying water column and nitrification in the sediments (Jenkins and Kemp, 1984). The activity of other bacterial processes under anoxic conditions has been shown to affect the activity of denitrifying bacteria. For example, SO42- reduction occurs in anoxic sediments whereby SC>42 is reduced to sulfide (Morse et al., 1992)—more... 

Figure 10.15 Major pathways of the N cycle in sediments (a), as a function of redox conditions in bottom waters and sediments (b). Both diffusive and advective processes strongly control the distribution of O and N compounds which ultimately affect the coupling between nitrification and denitrification. (Modified from Jprgensen and Boudreau, 2001.)...

Carini, S., Orcutt, B.N., and Joye, S.B. (2003) Interactions between methane oxidation and nitrification in coastal sediments. Geomicrobiol. J. 20, 355-374. 

Henriksen, K., and Kemp, W.M. (1988) Nitrification in estuarine and coastal marine sediments. In Nitrogen Cycling in Coastal Marine Environments. SCOPE (Blackburn, T.H., and Sprensen, J., eds.), pp. 207-249, John Wiley, New York. 

Joye, S.B., and Hollibaugh, J.T (1995) Sulfide inhibition of nitrification influences nitrogen regeneration in sediments. Science 270, 623-625. 

Rysgaard, S., Risgaard-Petersen, Sloth, N.P., Jensen, K., and Nielsen, L.P. (1994) Oxygen regulation of nitrification and denitrification in sediments. Lirnnol. Oceanogr. 39, 1634-1652. 

In some cases, the effects of complex environmental mixtures could be accounted for in terms of concentration-additive effects of a few chemicals. In sediments of the German river Spittelwasser, which were contaminated by chemical industries in its vicinity, around 10 chemicals of a cocktail of several hundred compounds were found to explain the toxicity of the complex mixture to different aquatic organisms (Brack et al. 1999). The complex mixture of chemicals contained in motorway runoff proved toxic to a crustacean species (Gammarus pulex). Boxall and Maltby (1997) identified 3 polycyclic aromatic hydrocarbons (PAHs) as the cause of this toxicity. Subsequent laboratory experiments with reconstituted mixtures revealed that the toxicity of motorway runoff could indeed be traced to the combined concentration-additive effects of the 3 PAHs. Svenson et al. (2000) identified 4 fatty acids and 2 monoterpenes to be responsible for the inhibitory effects on the nitrification activity of the bacteria Nitrobacter in wastewater from a plant for drying wood-derived fuel. The toxicity of the synthetic mixture composed of 6 dominant toxicants agreed well with the toxicity of the original sample. 

Inhibitor approaches similar to those described earher for water samples have been used in sediments (Henricksen et ah, 1981 MUler et ah, 1993). The methyl-fluoride and difluoromethane methods (Cafifey and MUler, 1995 MUler et al., 1993) seem particularly promising because the gases can diffuse thoroughly into the core with minimal disturbance of microzones and gradients. These NH4 oxidation inhibitors are added to cores and the accumulation of NH4+ over time is assumed to represent the net rate of nitrification. Other processes that consume NH4+ would lead to an underestimate of the rate. De Bie et al. (2002) found that both... 

The approach is most useful in water samples because complete mixing of the tracer is possible. In sediments, rate measurements are constrained by the inhomogeneous nature of the sample and the dependence of rates on the structure of the environment. In this situation, fluxes between overlying water and sediment cores can be analyzed to obtain areal rates. In conjunction with tracer addition, estimates of nitrification rates can be obtained from the dilution ofN02 or N03 in the overlying water due to its production in the sediments (Capone et ai, 1992). The isotope pairing method for measurement of denitrification (Nielsen, 1992 Rysgaard et ai, 1993) is essentially an isotope dilution approach from which both nitrification and denitrification rates can be calculated. 

Even if rate measurements in sediments are made using whole core incubations, e.g., when the inhibitor is a gas, it is still difficult to obtain a depth distribution of the rate (usually, an areal rate is obtained). A sophisticated measurement and model based system that avoids direct rate measurements has been used to overcome this problem. Microelectrodes, which have very high vertical resolution, are used to measure the fine scale distribution of oxygen and NOs" in freshwater sediments. By assuming that the observed vertical gradients represent a steady state condition, reaction-diffusion models can then be used to estimate the rates of nitrification, denitrification and aerobic respiration and to compute the location of the rate processes in relation to the chemical profiles (e.g., Binnerup et ai, 1992 Jensen et ai, 1994 Meyer et ai, 2001 Rysgaard et ai, 1994). Recent advances and details of the microelectrode approach can be found in the Chapter by Joye and Anderson (this volume). 

Rysgaard et al. (1999) tested the effect of salinity on nitrification in a Danish estuary to determine whether the increased desorption of NH4+ from sediments was responsible for the decreasing nitrification rates at high salinity. They concluded that salinity influenced nitrification rates independently of NH4+ concentrations and suggested that some physiological factor must be involved. 

There is abundant evidence from culture studies that both AOB and NOB are photosensitive. It is a high priority to investigate the photosensitivity of AOA. Even if aU nitrifiers exhibit photoinhibiton in some form, however, the direct and indirect ecological imphcations of this physiology for the rates and distributions of nitrification in the environment are not easily predicted. Dissolved organic matter in seawater, as well as turbidity due to sediments or phytoplankton, might aU provide photoprotection in surface waters, and regulation of nitrification by other factors discussed in this section may be much more important in many environments. 

Bianchi, M., Fehatra, Treguer, P., Vincendeau, M. A., and Morvan, J. (1997). Nitrification rates, ammonium and nitrate distribution in upper layers of the water column and in sediments of the Indian sector of the Southern Ocean. Deep-Sea Research 44, 1017—1032. 

Binnerup, S.J., Jensen, K., Revsbech, N. P., Jensen, M. H., and Sorensen, J. (1992). Denitrification, dissimilatory reduction of nitrate to ammonium, and nitrification in a bioturbated estuarine sediment as measured with N-15 and microsensor techniques. Applied and Environmental Microbiology 58, 303-313. 

DoUhopf, S. L., Hyun,. H., Smith, A. C., Adams, H.., O Brien, S., and Kostka,. E. (2005). Quantification of ammonia-oxidizing bacteria and factors controfling nitrification in salt marsh sediments. Applied and Environmental Microbiology 71, 240-246. 

Mortimer, R. J. G., Krom, M. D., Harris, S. J., Hayes, P. J., Davies, I. M., Davison, W., and Zhang, H. (2002). Evidence for suboxic nitrification in recent marine sediments. Marine Ecology-Progress Series 236, 31-35. 

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