Contributions of autotrophic and heterotrophic nitrifiers to soil NO and N2O emissions
01 Jun 1990-Applied and Environmental Microbiology (American Society for Microbiology)-Vol. 56, Iss: 6, pp 1799-1805
TL;DR: The results suggest that chemoautotrophic ammonium-oxidizing bacteria are the predominant source of NO and N(2)O produced during nitrification in soil.
Abstract: Soil emission of gaseous N oxides during nitrification of ammonium represents loss of an available plant nutrient and has an important impact on the chemistry of the atmosphere. We used selective inhibitors and a glucose amendment in a factorial design to determine the relative contributions of autotrophic ammonium oxidizers, autotrophic nitrite oxidizers, and heterotrophic nitrifiers to nitric oxide (NO) and nitrous oxide (N2O) emissions from aerobically incubated soil following the addition of 160 mg of N as ammonium sulfate kg−1. Without added C, peak NO emissions of 4 μg of N kg−1 h−1 were increased to 15 μg of N kg−1 h−1 by the addition of sodium chlorate, a nitrite oxidation inhibitor, but were reduced to 0.01 μg of N kg−1 h−1 in the presence of nitrapyrin [2-chloro-6-(trichloromethyl)-pyridine], an inhibitor of autotrophic ammonium oxidation. Carbon-amended soils had somewhat higher NO emission rates from these three treatments (6, 18, and 0.1 μg of N kg−1 h−1 after treatment with glucose, sodium chlorate, or nitrapyrin, respectively) until the glucose was exhausted but lower rates during the remainder of the incubation. Nitrous oxide emission levels exhibited trends similar to those observed for NO but were about 20 times lower. Periodic soil chemical analyses showed no increase in the nitrate concentration of soil treated with sodium chlorate until after the period of peak NO and N2O emissions; the nitrate concentration of soil treated with nitrapyrin remained unchanged throughout the incubation. These results suggest that chemoautotrophic ammonium-oxidizing bacteria are the predominant source of NO and N2O produced during nitrification in soil.
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TL;DR: It is completely unclear how important microbial diversity is for the control of trace gas flux at the ecosystem level, and different microbial communities may be part of the reason for differences in trace gas metabolism, e.g., effects of nitrogen fertilizers on CH4 uptake by soil; decrease of CH4 production with decreasing temperature.
1,622 citations
TL;DR: The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB.
Abstract: The current perception of evolutionary relationships and the natural diversity of ammonia-oxidizing bacteria (AOB) is mainly based on comparative sequence analyses of their genes encoding the 16S rRNA and the active site polypeptide of the ammonia monooxygenase (AmoA). However, only partial 16S rRNA sequences are available for many AOB species and most AOB have not yet been analyzed on the amoA level. In this study, the 16S rDNA sequence data of 10 Nitrosomonas species and Nitrosococcus mobilis were completed. Furthermore, previously unavailable 16S rRNA sequences were determined for three Nitrosomonas sp. isolates and for the gamma-subclass proteobacterium Nitrosococcus halophilus. These data were used to revaluate the specificities of published oligonucleotide primers and probes for AOB. In addition, partial amoA sequences of 17 AOB, including the above-mentioned 15 AOB, were obtained. Comparative phylogenetic analyses suggested similar but not identical evolutionary relationships of AOB by using 16S rRNA and AmoA as marker molecules, respectively. The presented 16S rRNA and amoA and AmoA sequence data from all recognized AOB species significantly extend the currently used molecular classification schemes for AOB and now provide a more robust phylogenetic framework for molecular diversity inventories of AOB. For 16S rRNA-independent evaluation of AOB species-level diversity in environmental samples, amoA and AmoA sequence similarity threshold values were determined which can be used to tentatively identify novel species based on cloned amoA sequences. Subsequently, 122 amoA sequences were obtained from 11 nitrifying wastewater treatment plants. Phylogenetic analyses of the molecular isolates showed that in all but two plants only nitrosomonads could be detected. Although several of the obtained amoA sequences were only relatively distantly related to known AOB, none of these sequences unequivocally suggested the existence of previously unrecognized species in the wastewater treatment environments examined.
1,085 citations
TL;DR: Volume 62, no. 6, p. 2157, Table 1: the sequence for probe Nso1225, 5(prm1)-CGCGATTGTATTACGTGTGTGA-3( prm1), should read 5(PRm1-CGCCATTGTattACGT GTGA- 3(prM1).
Abstract: A hierarchical set of five 16S rRNA-targeted oligonucleotide DNA probes for phylogenetically defined groups of autotrophic ammonia- and nitrite-oxidizing bacteria was developed for environmental and determinative studies. Hybridization conditions were established for each probe by using temperature dissociation profiles of target and closely related nontarget organisms to document specificity. Environmental application was demonstrated by quantitative slot blot hybridization and whole-cell hybridization of nitrifying activated sludge and biofilm samples. Results obtained with both techniques suggested the occurrence of novel populations of ammonia oxidizers. In situ hybridization experiments revealed that Nitrobacter and Nitrosomonas species occurred in clusters and frequently were in contact with each other within sludge flocs.
934 citations
Cites background from "Contributions of autotrophic and he..."
...Although nitrifying bacteria are central to the global nitrogen cycle, they contribute to pollution problems through oxidation of ammonia fertilizers to nitrite and nitrate in water supplies, the production of greenhouse gases (NO) (6, 29), and biodeterioration of building materials (20)....
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TL;DR: The data suggest that denitrification and N2 fixation are not genetic traits of most of the uncultured bacteria.
Abstract: Isolated soil DNA from an oak-hornbeam forest close to Cologne, Germany, was suitable for PCR amplification of gene segments coding for the 16S rRNA and nitrogenase reductase (NifH), nitrous oxide reductase (NosZ), cytochrome cd1-containing nitrite reductase (NirS), and Cu-containing nitrite reductase (NirK) of denitrification. For each gene segment, diverse PCR products were characterized by cloning and sequencing. None of the 16S rRNA gene sequences was identical to any deposited in the data banks, and therefore each of them belonged to a noncharacterized bacterium. In contrast, the analyzed clones of nifH gave only a few different sequences, which occurred many times, indicating a low level of species richness in the N2-fixing bacterial population in this soil. Identical nifH sequences were also detected in PCR amplification products of DNA of a soil approximately 600 km distant from the Cologne area. Whereas biodiversity was high in the case of nosZ, only a few different sequences were obtained with nirK. With respect to nirS, cloning and sequencing of the PCR products revealed that many false gene segments had been amplified with DNA from soil but not from cultured bacteria. With the 16S rRNA gene data, many sequences of uncultured bacteria belonging to the Acidobacterium phylum and actinomycetes showed up in the PCR products when isolated DNA was used as the template, whereas sequences obtained for nifH and for the denitrification genes were closely related to those of the proteobacteria. Although in such an experimental approach one has to cope with the enormous biodiversity in soils and only a few PCR products can be selected at random, the data suggest that denitrification and N2 fixation are not genetic traits of most of the uncultured bacteria.
526 citations
Cites background from "Contributions of autotrophic and he..."
...Both gases are formed in soils as side products in nitrification by either autotrophic or heterotrophic nitrifiers (42)....
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TL;DR: In this article, it was shown that Nitrosomonas europaea contributes significantly to the production of N2O in soils treated with ammonium or ammonium-yielding fertilizers such as urea.
Abstract: Research to identify sources of nitrous oxide (N2O) in soils has indicated that most, if not all, of the N2O evolved from soils is produced by biological processes and that little, if any, is produced by chemical processes such as chemodenitrification. Early workers assumed that denitrification was the only biological process responsible for N2O production in soils and that essentially all of the N2O evolved from soils was produced through reduction of nitrate by denitrifying microorganisms under anaerobic conditions. It is now well established, however, that nitrifying microorganisms contribute significantly to emissions of N2O from soils and that most of the N2O evolved from aerobic soils treated with ammonium or ammonium-yielding fertilizers such as urea is produced during oxidation of ammonium to nitrate by these microorganisms. Support for the conclusion that chemoautotrophic nitrifiers such as Nitrosomonas europaea contribute significantly to production of N2O in soils treated with N fertilizers has been provided by studies showing that N2O emissions from such soils can be greatly reduced through addition of nitrification inhibitors such as nitrapyrin, which retard oxidation of ammonium by chemoautotrophic nitrifiers but do not retard reduction of nitrate by denitrifying microorganisms.
514 citations
References
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01 Jan 1982
2,974 citations
01 Jan 1977
TL;DR: In terms of the global fluxes between aerial and terrestrial-aquatic systems, the simplified nitrogen cycle can be envisioned as a triangle where the only biologically reversible reaction occurs between ammonium and nitrate.
Abstract: The transformations of nitrogenous compounds by soil bacteria have beenstudied for over a century. In terms of the global fluxes between aerial and terrestrial-aquatic systems, the simplified nitrogen cycle can be envisioned as a triangle where the only biologically reversible reaction occurs between ammonium and nitrate. The reverse reactions of dinitrogen fixation or denitrification by biological means do not occur in nature. Hence, the reductive process of denitrification, defined as the reduction of nitrate or nitrite to gaseous nitrogen (usually N2), is intimately associated with the oxidative process of nitrification.
870 citations
TL;DR: The cycle of nitrogen oxides in the troposphere from both global and regional perspectives is discussed in this article, where estimates for the rate of removal of NOx based on recent atmospheric and precipitation chemistry data are consistent with global source strengths derived here.
Abstract: The cycle of nitrogen oxides in the troposphere is discussed from both global and regional perspectives. Global sources for NO(x) are estimated to be of magnitude 50 (+ or - 25) x 10 to the 12th gm N/yr. Nitrogen oxides are derived from combustion of fossil fuels (40 percent) and biomass burning (25 percent) with the balance from lightning and microbial activity in soils. Estimates for the rate of removal of NOx based on recent atmospheric and precipitation chemistry data are consistent with global source strengths derived here. Industrial and agricultural activities provide approximately two thirds of the global source for NOx. In North America, sources from combustion of fossil fuels exceed natural sources by a factor of 3-13. Wet deposition removes about one third of the combustion source of NOx over North America, while dry deposition removes a similar amount. The balance is exported from the continent. Deposition of nitrate in precipitation over eastern Canada and the western Atlantic is clearly influenced by sources of NOx in the eastern United States.
768 citations
TL;DR: The results support the view that nitrification is an important source of N(2)O in the environment and that nitrite-oxidizing bacteria (Nitrobacter sp.) and the dinoflagellate Exuviaella sp.
Abstract: Pure cultures of the marine ammonium-oxidizing bacterium Nitrosomonas sp. were grown in the laboratory at oxygen partial pressures between 0.005 and 0.2 atm (0.18 to 7 mg/liter). Low oxygen conditions induced a marked decrease in the rate for production of NO2-, from 3.6 × 10−10 to 0.5 × 10−10 mmol of NO2- per cell per day. In contrast, evolution of N2O increased from 1 × 10−12 to 4.3 × 10−12 mmol of N per cell per day. The yield of N2O relative to NO2- increased from 0.3% to nearly 10% (moles of N in N2O per mole of NO2-) as the oxygen level was reduced, although bacterial growth rates changed by less than 30%. Nitrifying bacteria from the genera Nitrosomonas, Nitrosolobus, Nitrosospira, and Nitrosococcus exhibited similar yields of N2O at atmospheric oxygen levels. Nitrite-oxidizing bacteria (Nitrobacter sp.) and the dinoflagellate Exuviaella sp. did not produce detectable quantities of N2O during growth. The results support the view that nitrification is an important source of N2O in the environment.
759 citations
TL;DR: In this paper, the authors present a characterization of the trace gases, taking into account the observed abundances, known sources, and sinks in the present-day atmosphere, and their potentials for climate changes.
Abstract: It is pointed out that the release of chemicals into the atmosphere has grown greatly over the last 50 years. Contributed to the observed perturbations of trace chemicals in the atmosphere have an increased reliance on synthetic chemicals, deforestation, biomass burning, and fossil fuel combustion. As trace chemicals modify the radiation energy of the earth-atmosphere system, the considered developments can produce an alteration of the earth's climate. One of the major objectives of the present study is related to the characterization of the trace gases, taking into account the observed abundances, known sources, and sinks in the present-day atmosphere. Other objectives include an estimate of the future concentration of trace gases, an inference of the preindustrial concentrations of trace gases, and an estimate of the radiative effects of the trace gases and their potentials for climate changes. 103 references.
747 citations