This paper contrasts the natural and anthropogenic controls on the conversion of unreactive N2 to more reactive forms of nitrogen (Nr). A variety of data sets are used to construct global N budgets for 1860 and the early 1990s and to make projections for the global N budget in 2050. Regional N budgets for Asia, North America, and other major regions for the early 1990s, as well as the marine N budget, are presented to highlight the dominant fluxes of nitrogen in each region. Important findings are that human activities increasingly dominate the N budget at the global and at most regional scales, the terrestrial and open ocean N budgets are essentially dis- connected, and the fixed forms of N are accumulating in most environmental reservoirs. The largest uncertainties in our understanding of the N budget at most scales are the rates of natural biological nitrogen fixation, the amount of Nr storage in most environmental reservoirs, and the production rates of N2 by denitrification.

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Nitrogen cycles: past, present, and future

Denitrification is a distinct means of energy conservation, making use of N oxides as terminal electron acceptors for cellular bioenergetics under anaerobic, microaerophilic, and occasionally aerobic conditions. The process is an essential branch of the global N cycle, reversing dinitrogen fixation, and is associated with chemolithotrophic, phototrophic, diazotrophic, or organotrophic metabolism but generally not with obligately anaerobic life. Discovered more than a century ago and believed to be exclusively a bacterial trait, denitrification has now been found in halophilic and hyperthermophilic archaea and in the mitochondria of fungi, raising evolutionarily intriguing vistas. Important advances in the biochemical characterization of denitrification and the underlying genetics have been achieved with Pseudomonas stutzeri, Pseudomonas aeruginosa, Paracoccus denitrificans, Ralstonia eutropha, and Rhodobacter sphaeroides. Pseudomonads represent one of the largest assemblies of the denitrifying bacteria within a single genus, favoring their use as model organisms. Around 50 genes are required within a single bacterium to encode the core structures of the denitrification apparatus. Much of the denitrification process of gram-negative bacteria has been found confined to the periplasm, whereas the topology and enzymology of the gram-positive bacteria are less well established. The activation and enzymatic transformation of N oxides is based on the redox chemistry of Fe, Cu, and Mo. Biochemical breakthroughs have included the X-ray structures of the two types of respiratory nitrite reductases and the isolation of the novel enzymes nitric oxide reductase and nitrous oxide reductase, as well as their structural characterization by indirect spectroscopic means. This revealed unexpected relationships among denitrification enzymes and respiratory oxygen reductases. Denitrification is intimately related to fundamental cellular processes that include primary and secondary transport, protein translocation, cytochrome c biogenesis, anaerobic gene regulation, metalloprotein assembly, and the biosynthesis of the cofactors molybdopterin and heme D1. An important class of regulators for the anaerobic expression of the denitrification apparatus are transcription factors of the greater FNR family. Nitrate and nitric oxide, in addition to being respiratory substrates, have been identified as signaling molecules for the induction of distinct N oxide-metabolizing enzymes.

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Cell biology and molecular basis of denitrification.

A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.

Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA.

Removal of nutrients in various types of constructed wetlands.

Currently available microbiological techniques are not designed to deal with very slowly growing microorganisms. The enrichment and study of such organisms demands a novel experimental approach. In the present investigation, the sequencing batch reactor (SBR) was applied and optimized for the enrichment and quantitative study of a very slowly growing microbial community which oxidizes ammonium anaerobically. The SBR was shown to be a powerful experimental set-up with the following strong points: (1) efficient biomass retention, (2) a homogeneous distribution of substrates, products and biomass aggregates over the reactor, (3) reliable operation for more than 1 year, and (4) stable conditions under substrate-limiting conditions. Together, these points made possible for the first time the determination of several important physiological parameters such as the biomass yield (0.066 ± 0.01 C-mol/mol ammonium), the maximum specific ammonium consumption rate (45 ± 5 nmol/mg protein/min) and the maximum specific growth rate (0.0027 · h−1, doubling time 11 days). In addition, the persisting stable and strongly selective conditions of the SBR led to a high degree of enrichment (74% of the desired microorganism). This study has demonstrated that the SBR is a powerful tool compared to other techniques used in the past. We suggest that the SBR could be used for the enrichment and quantitative study of a large number of slowly growing microorganisms that are currently out of reach for microbiological research.

The sequencing batch reactor as a powerful tool for the study of slowly growing anaerobic ammonium-oxidizing microorganisms

https://repository.tudelft.nl/islandora/object/uuid%3Af359a226-ad83-420a-b20e-fca92bdc2afc/datastream/OBJ/download

Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor

An autotrophic, synthetic medium for the enrichment of anaerobic ammonium-oxidizing (Anammox) micro-organisms was developed This medium contained ammonium and nitrite, as the only electron donor and electron acceptor, respectively, while carbonate was the only carbon source provided Preliminary studies showed that the presence of nitrite and the absence of organic electron donors were essential for Anammox activity The conversion rate of the enrichment culture in a fluidized bed reactor was 3 kg NH4 + m-3 d-1 when fed with 30 mM NH4 + This is equivalent to a specific anaerobic ammonium oxidation rate of 1000-1100 nmol NH4 +h-1 (mg volatile solids)-1 The maximum specific oxidation rate obtained was 1500 nmol NH4 +h-1 (mg volatile solids)-1 Per mol NH4 + oxidized, 0041mol CO2 were incorporated, resulting in a estimated growth rate of 0001 h-1 The main product of the Anammox reaction is N2, but about 10% of the N-feed is converted to NO3 - The overall nitrogen balance gave a ratio of NH4 --conversion to NO2 --conversion and NO3 --production of 1:1-31++006:022+002 During the conversion of NH4 + with NO2 -, no other intermediates or end-products such as hydroxylamine, NO and N2O could be detected Acetylene, phosphate and oxygen were shown to be strong inhibitors of the Anammox activity The dominant type of micro-organism in the enrichment culture was an irregularly shaped cell with an unusual morphology During the enrichment for Anammox micro-organisms on synthetic medium, an increase in ether lipids was observed The colour of the biomass changed from brownish to red, which was accompanied by an increase in the cytochrome content Cytochrome spectra showed a peak at 470 nm gradually increasing in intensity during enrichment

https://repository.tudelft.nl/islandora/object/uuid%3Afd4a0685-4292-4498-911f-9f85302e3291/datastream/OBJ/download

Autotrophic growth of anaerobic ammonium-oxidizing micro-organisms in a fluidized bed reactor

A newly discovered process by which ammonium is converted to dinitrogen gas under anaerobic conditions (the Anammox process) has now been examined in detail. In order to confirm the biological nature of this process, anaerobic batch culture experiments were used. All of the ammonium provided in the medium was oxidized within 9 days. In control experiments with autoclaved or raw wastewater, without added sludge or with added sterilized (either autoclaved or gamma irradiated) sludge, no changes in the ammonium and nitrate concentrations were observed. Chemical reactions could therefore not be responsible for the ammonium conversion. The addition of chloramphenicol, ampicillin, 2,4-dinitrophenol, carbonyl cyanide m-chlorophenyl-hydrazone (CCCP), and mercuric chloride (HgIICl2) completely inhibited the activity of the ammonium-oxidizing sludge. Furthermore, the rate of ammonium oxidation was proportional to the initial amount of sludge used. It was therefore concluded that anaerobic ammonium oxidation was a microbiological process. As the experiments were carried out in an oxygen-free atmosphere, the conversion of ammonium to dinitrogen gas did not even require a trace of O2. That the end product of the reaction was nitrogen gas has been confirmed by using 15NH4+ and 14NO3-. The dominant product was 14-15N2. Only 1.7% of the total labelled nitrogen gas produced was 15-15N2. It is therefore proposed that the N2 produced by the Anammox process is formed from equimolar amounts of NH4+ and NO3-.

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Anaerobic oxidation of ammonium is a biologically mediated process

During studies on the denitrifying mixotroph, Thiosphaera pantotropha, it has been found that this organism is capable of simultaneously utilizing nitrate and oxygen as terminal electron acceptors in respiration. This phenomenon, termed aerobic denitrification, has been found in cultures maintained at dissolved oxygen concentrations up to 90% of air saturation.

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Aerobic denitrification: a controversy revived

Thiosphaera pantotropha is capable of simultaneous heterotrophic nitrification and aerobic denitrification. Consequently, its nitrification potential could not be judged from nitrite accumulation, but was estimated from complete nitrogen balances. The maximum rate of nitrification obtained during these experiments was 93.9 nmol min−1 mg of protein−1. The nitrification rate could be reduced by the provision of nitrate, nitrite, or thiosulfate to the culture medium. Both nitrification and denitrification increased as the dissolved oxygen concentration fell, until a critical level was reached at approximately 25% of air saturation. At this point, the rate of (aerobic) denitrification was equivalent to the anaerobic rate. At this dissolved oxygen concentration, the combined nitrification and denitrification was such that cultures receiving ammonium as their sole source of nitrogen appeared to become oxygen limited and the nitrification rate fell. It appeared that, under carbon-and energy-limited conditions, a high nitrification rate was correlated with a reduced biomass yield. To facilitate experimental design, a working hypothesis for the mechanism behind nitrification and denitrification by T. pantotropha was formulated. This involved the basic assumption that this species has a “bottleneck” in its cytochrome chain to oxygen and that denitrification and nitrification are used to overcome this. The nitrification potential of other heterotrophic nitrifiers has been reconsidered. Several species considered to be “poor” nitrifiers also simultaneously nitrify and denitrify, thus giving a falsely low nitrification potential.

/pdf/simultaneous-nitrification-and-denitrification-in-aerobic-3xm27gi600.pdf

Lesley A. Robertson

Papers

Anaerobic ammonium oxidation discovered in a denitrifying fluidized bed reactor

Autotrophic growth of anaerobic ammonium-oxidizing micro-organisms in a fluidized bed reactor

Anaerobic oxidation of ammonium is a biologically mediated process

Aerobic denitrification: a controversy revived

Simultaneous Nitrification and Denitrification in Aerobic Chemostat Cultures of Thiosphaera pantotropha