Differential contributions of ammonia oxidizers and nitrite oxidizers to nitrification in four paddy soils

Ammonia oxidation to nitrite and its subsequent oxidation to nitrate provides energy to the two populations of nitrifying chemoautotrophs in the energy-starved dark ocean, driving a coupling between reduced inorganic nitrogen (N) pools and production of new organic carbon (C) in the dark ocean. However, the relationship between the flux of new C production and the fluxes of N of the two steps of oxidation remains unclear. Here, we show that, despite orders-of-magnitude difference in cell abundances between ammonia oxidizers and nitrite oxidizers, the two populations sustain similar bulk N-oxidation rates throughout the deep waters with similarly high affinities for ammonia and nitrite under increasing substrate limitation, thus maintaining overall homeostasis in the oceanic nitrification pathway. Our observations confirm the theoretical predictions of a redox-informed ecosystem model. Using balances from this model, we suggest that consistently low ammonia and nitrite concentrations are maintained when the two populations have similarly high substrate affinities and their loss rates are proportional to their maximum growth rates. The stoichiometric relations between the fluxes of C and N indicate a threefold to fourfold higher C-fixation efficiency per mole of N oxidized by ammonia oxidizers compared to nitrite oxidizers due to nearly identical apparent energetic requirements for C fixation of the two populations. We estimate that the rate of chemoautotrophic C fixation amounts to ∼1 × 1013to ∼2 × 1013mol of C per year globally through the flux of ∼1 × 1014to ∼2 × 1014mol of N per year of the two steps of oxidation throughout the dark ocean.

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Nitrite oxidation inhibition by hydroxylamine: experimental and model evaluation

Water Science & Technology ◽

10.2166/wst.2004.0388 ◽

2004 ◽

Vol 50 (6) ◽

pp. 295-304 ◽

Cited By ~ 12

Author(s):

P. (Lek) Noophan ◽

L.A. Figueroa ◽

J. Munakata-Marr

Keyword(s):

Oxidation Rate ◽

Biological Nitrogen Removal ◽

Ammonia Oxidizers ◽

Batch Experiments ◽

Nitrite Oxidation ◽

Ph Values ◽

Initial Ph ◽

Nitrogen Concentrations ◽

Biological Nitrogen ◽

Nitrite Oxidizers

A proposed approach for biological nitrogen removal significantly reduces cost by reducing biomass production and carbon requirements via inhibition of nitrite oxidation (NO2− to NO3−). Batch experiments were conducted to examine the effect of hydroxylamine (HM) on nitrite oxidizers, ammonia oxidizers, and nitrite reducers. Hydroxylamine effect experiments were done at initial pH values of 7.4-8.4, nitrogen concentrations of 100 mg N/L, biomass concentrations of 100-400 mg VSS/L and HM dosages up to 43 mg/L. Nitrite oxidizer activity was completely inhibited by HM at dosages of 7.0 and 8.9 mg/L for pH values of 8.4 and 7.6, respectively. Relatively low HM concentrations (0.35-5.5 mg/L) can be used to completely inhibit nitrite oxidation, but do not significantly affect ammonia oxidizers and nitrite reducers. A model developed to describe the effect of pH on nitrite oxidation rate fits the data well (R2 = 0.89) with values for Vmax of 0.372 (mg N/mg VSS-hr), pH* of 7.72, and the inhibition constant Kh of 0.154. Incorporation of HM inhibition into the model provided a good fit to relative nitrite oxidation rate as a function of undissociated HM concentration (R2 = 0.80, Vmax = 0.028 mg N/mg VSS-hr, pH* = 7.89, Kh * 0.302, a * 0.195, and Ki = 0.277 mg/L).

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Changes in Diversity and Functional Gene Abundances of Microbial Communities Involved in Nitrogen Fixation, Nitrification, and Denitrification in a Tidal Wetland versus Paddy Soils Cultivated for Different Time Periods

Applied and Environmental Microbiology ◽

10.1128/aem.01751-10 ◽

2011 ◽

Vol 77 (17) ◽

pp. 6109-6116 ◽

Cited By ~ 68

Author(s):

Andrea Bannert ◽

Kristina Kleineidam ◽

Livia Wissing ◽

Cornelia Mueller-Niggemann ◽

Vanessa Vogelsang ◽

...

Keyword(s):

Nitrogen Fixation ◽

Species Richness ◽

Microbial Biomass ◽

Rice Cultivation ◽

Paddy Soils ◽

Tidal Wetlands ◽

Tidal Wetland ◽

Ammonia Oxidizers ◽

Relative Species Richness ◽

Nitrification And Denitrification

ABSTRACTIn many areas of China, tidal wetlands have been converted into agricultural land for rice cultivation. However, the consequences of land use changes for soil microbial communities are poorly understood. Therefore, we investigated bacterial and archaeal communities involved in inorganic nitrogen turnover (nitrogen fixation, nitrification, and denitrification) based on abundances and relative species richness of the corresponding functional genes along a soil chronosequence ranging between 50 and 2,000 years of paddy soil management compared to findings for a tidal wetland. Changes in abundance and diversity of the functional groups could be observed, reflecting the different chemical and physical properties of the soils, which changed in terms of soil development. The tidal wetland was characterized by a low microbial biomass and relatively high abundances of ammonia-oxidizing microbes. Conversion of the tidal wetlands into paddy soils was followed by a significant increase in microbial biomass. Fifty years of paddy management resulted in a higher abundance of nitrogen-fixing microbes than was found in the tidal wetland, whereas dominant genes of nitrification and denitrification in the paddy soils showed no differences. With ongoing rice cultivation, copy numbers of archaeal ammonia oxidizers did not change, while that of their bacterial counterparts declined. ThenirKgene, coding for nitrite reductase, increased with rice cultivation time and dominated its functionally redundant counterpart,nirS, at all sites under investigation. Relative species richness showed significant differences between all soils with the exception of the archaeal ammonia oxidizers in the paddy soils cultivated for 100 and 300 years. In general, changes in diversity patterns were more pronounced than those in functional gene abundances.

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Nitrosomonas Nm143-like ammonia oxidizers and Nitrospira marina-like nitrite oxidizers dominate the nitrifier community in a marine aquaculture biofilm

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2007.00418.x ◽

2008 ◽

Vol 63 (2) ◽

pp. 192-204 ◽

Cited By ~ 87

Author(s):

BÃ¤rbel U. Foesel ◽

Armin Gieseke ◽

Carsten Schwermer ◽

Peter Stief ◽

Liat Koch ◽

...

Keyword(s):

Ammonia Oxidizers ◽

Marine Aquaculture ◽

Nitrite Oxidizers

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Numbers, activities, and diversity of autotrophic ammonia-oxidizing bacteria in a freshwater, eutrophic lake sediment

Canadian Journal of Microbiology ◽

10.1139/m91-143 ◽

1991 ◽

Vol 37 (11) ◽

pp. 828-833 ◽

Cited By ~ 46

Author(s):

W. T. Smorczewski ◽

E. L. Schmidt

Keyword(s):

Lake Sediment ◽

Environmental Changes ◽

Ammonia Oxidation ◽

Eutrophic Lake ◽

Ammonia Oxidizer ◽

Most Probable Number ◽

Ammonia Oxidizing Bacteria ◽

Ammonia Oxidizers ◽

Probable Number ◽

Nitrite Oxidizers

The microbiological and chemical potential for ammonia oxidation in a freshwater, eutrophic lake sediment was examined in relation to environmental changes caused by seasonal, dimictic circulation. Poulations of both ammonia and nitrite oxidizers as estimated by most probable number (MPN) were sustained throughout extended anaerobic summer intervals, with nitrite oxidizers outnumbering ammonia oxidizers by a factor ranging from 3.0 to 8.1. Ammonia oxidation potential on a per cell basis was affected by seasonal changes and was seen to decrease as oxygen was removed from the sediments. Pure-culture isolations from a positive MPN tube inoculated with oxygenated sediment and representing a single point in a seasonal cycle produced ammonia-oxidizing strains belonging to the genus Nitrosospira. These strains did not react with known ammonia-oxidizer serotypes and, therefore, extend the serological diversity of this group of bacteria. An immunofluorescence analysis of MPN tubes from sediment collected during a period of lake stratification revealed progressive changes in the diversity of the ammonia-oxidizer population. The genera Nitrosomonas, Nitrosolobus, and Nitrosospira, including the novel serotype of Nitrosospira isolated from the sediment a year earlier, were found to coexist in well-oxygenated sediment. This diversity was seen to disappear, with Nistrosomonas surviving, as anaerobic conditions persisted. Key words: ammonia oxidizers, lake sediments, nitrifiers, nitrification.

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Nitrification in sequencing biofilm batch reactors: lessons from molecular approaches

Water Science & Technology ◽

10.2166/wst.2001.0113 ◽

2001 ◽

Vol 43 (3) ◽

pp. 9-18 ◽

Cited By ~ 81

Author(s):

H. Daims ◽

U. Purkhold ◽

L. Bjerrum ◽

E. Arnold ◽

P. A. Wilderer ◽

...

Keyword(s):

Laser Scanning ◽

Amoa Gene ◽

Laser Scanning Microscopy ◽

Confocal Laser ◽

Molecular Evidence ◽

Organic Substrates ◽

Gene Fragment ◽

Ammonia Oxidizers ◽

Oxidation Rates ◽

Nitrite Oxidizers

The nitrifying microbial diversity and population structure of a sequencing biofilm batch reactor receiving sewage with high ammonia and salt concentrations (SBBR 1) was analyzed by the full-cycle rRNA approach. The diversity of ammonia-oxidizers in this reactor was additionally investigated using comparative sequence analysis of a gene fragment of the ammonia monooxygenase (amoA), which represents a key enzyme of all ammonia-oxidizers. Despite the “extreme” conditions in the reactor, a surprisingly high diversity of ammonia- and nitrite-oxidizers was observed to occur within the biofilm. In addition, molecular evidence for the existence of novel ammonia-oxidizers is presented. Quantification of ammonia- and nitrite-oxidizers in the biofilm by Fluorescent In situ Hybridization (FISH) and digital image analysis revealed that ammonia-oxidizers occurred in higher cell numbers and occupied a considerably larger share of the total biovolume than nitrite-oxidizing bacteria. In addition, ammonia oxidation rates per cell were calculated for different WWTPs following the quantification of ammonia-oxidizers by competitive PCR of an amoA gene fragment. The morphology of nitrite-oxidizing, unculturable Nitrospira-like bacteria was studied using FISH, confocal laser scanning microscopy (CLSM) and three-dimensional visualization. Thereby, a complex network of microchannels and cavities was detected within microcolonies of Nitrospira-like bacteria. Microautoradiography combined with FISH was applied to investigate the ability of these organisms to use CO2 as carbon source and to take up other organic substrates under varying conditions. Implications of the obtained results for fundamental understanding of the microbial ecology of nitrifiers as well as for future improvement of nutrient removal in wastewater treatment plants (WWTPs) are discussed.

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