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39 results for “ammonia oxidation”
Seasonal Distribution of Ammonia-Oxidizing Archaea and Ammonia-Oxidation Rates in the South Atlantic Bight from April to November 2014
Previous work in nearshore waters of the Georgia USA coast has demonstrated mid-summer peaks in the abundance of Thaumarchaeota (blooms with 100 to 1,000-fold increases) accompanied by spikes in nitrite concentration. These studies were performed at one location, so the areal extent of the bloom is unknown, nor has it been demonstrated conclusively that it develops in inshore waters. We collected data on rates of ammonia oxidation and the distribution of Thaumarchaeota, ammonia-oxidizing Betaproteobacteria (AOB), nitrite-oxidizing Nitrospina and environmental variables during 6 cruises aboard the UNOLS vessel R/V Savannah from April to November 2014 on transects of the South Atlantic Bight to evaluate the areal extent and timing of the bloom. This data set includes measurements of Chlorophyll-a concentration, PAR attenuation coefficient, oxygen concenrations, temperature, salinity and nitogenous nutrient concentrations (nitrite, nitrite + nitrate, ammonium, urea), and estimates of Archaea, bacteria and diatom gene concentration based on quantitative PCR.
Coupling between Sediment and Water Column Populations of Ammonia Oxidizing Thaumarchaeota in the Duplin River near Sapelo Island, Georgia
Populations of nitrifying organisms in the water column at Marsh Landing display a midsummer peak in the abundance of ammonia oxidizing Archaea (AOA) at the site, coinciding with a peak in nitrite concentration. Marsh Landing is at the mouth of the Duplin River, a dead-end tidal channel that drains an extensive area of salt marsh. While the lower Duplin River at Marsh Landing exchanges tidally with Doboy Sound and thus South Atlantic Bight (SAB) coastal waters, water in its upper reaches has a residence time of weeks. The work reported here had two goals: 1) test the hypothesis that the surrounding salt marsh is the source of nitrifiers seen in water samples taken at Marsh Landing; and 2) compare the seasonal dynamics of nitrifiers in surficial sediments with those in the water column. We sampled 6 stations along the ~20 km length of the Duplin River. We collected surface water samples (~0.20 m) at low- to mid-tide, monthly from April-December 2014. Sediment samples (top 1 cm) were collected at the same time from unvegetated creek bank at 2 locations on the Duplin River and from 4 locations spanning the creek bank-to-upland gradient of the saltmarsh accessible from the Teal Boardwalk. The abundance of ammonia oxidizing Archaea, Marine Group 1 Archaea (Thaumarchaeota), ammonia oxidizing Betaproteobacteria (AOB), Bacteria and Nitrospina, a nitrite oxidizing bacterium, were determined by quantitative PCR (qPCR) of DNA extracted from the samples. This data set contains the abundance estimates from April to December 2014 for sediment and water column samples, with corresponding water quality measurements (temperature, salinity and nitrogenous nutrient concentrations).
Electronic Supporting Information for Catalytic Ammonia Oxidation to Dinitrogen by a Nickel Complex
<p>The dataset provides electronic supporting information in the format of XYZ molecular files, formatted Gaussian checkpoint files, and cube files for atomic spin density distributions for selected complexes obtained while investigating the catalytic mechanism of ammonia oxidation to dinitrogen using a N-heterocyclic carbene containing nickelocene complex.</p> <p>The level of theory used for all calculations is omega-B97xD with def2TZVP basis set. All calculations were performed using the Gaussian16 suite of programmes.</p> <p><strong>Model Set 1</strong> contains the metal free compounds and were used to calculate the overall thermodynamics of the ammonia oxidation reaction.</p> <p><strong>Model Set 2</strong> corresponds to the most truncated, in vacuo optimized structures.</p> <p><strong>Model Set 3</strong> comprises from non-truncated, realistic structures embedded in polarizable continuum model of benzene.</p> <p> </p>
Data from: Biological controls over the abundances of terrestrial ammonia oxidizers
<blockquote> <p>Aim: Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the primary agents for nitrification, converting ammonia (NH4+) into nitrate (NO3-) and modulating plant nitrogen (N) utilization and terrestrial N retention. However, there is still lack of a unifying framework describing the patterns of global AOA and AOB distribution. In particular, biotic interactions are rarely integrated into any of the conceptual models.<br> Location: World-wide.<br> Time period: 2005-2016.<br> Major taxa studied: Ammonia-oxidizing archaea and ammonia-oxidizing bacteria. <br> Methods: A meta-analysis and synthesis was conducted to obtain a general picture of global AOA and AOB distribution and identify the primary driving factors. A microcosm experiment was then conducted to assess effects of relative carbon to nitrogen availability for heterotrophic microbes on AOA and AOB in two distinct soils. A mesocosm experiment was further carried out to characterize the effects of plant roots and their arbuscular mycorrhizal fungi (AMF) on AOA and AOB abundances using hyphae- or root-ingrowth techniques. <br> Results: Our meta-analysis showed that soil carbon to nitrogen (C/N) ratios explained the most variance in AOA and AOB abundances, although soil pH had a significant effect. Experimental results demonstrated that high cellulose and mineral N inputs increased total microbial biomass and microbial activities, but inhibited AOA and AOB, suggesting microbial inhibition of AOA and AOB. Also, AMF and roots suppressed AOA and AOB, respectively. <br> Main conclusions: Our study provided convincing evidence illustrating that relative carbon to nitrogen availability can dominate the abundances of AOA and AOB. Our experimental results further validated that biotic competitions among plants, heterotrophic microbes and ammonia oxidizers for substrate N predominantly control AOA and AOB abundances. Together, these findings provide new insights into the role of abiotic and biotic factors in modulating terrestrial AOA and AOB abundances and their potential applications for management of nitrification in an increasing reactive N world.</p> </blockquote>
Potential contributions of ammonia-oxidizing microorganisms to the distributions of nitrous oxide in the northern Bering Sea
<ul> <li> <p>Basic GHGs data for the Bering Sea in CHINARE2016</p> </li> </ul>
Data from: Global evaluation of inhibitor impacts on ammonia and nitrous oxide emissions from agricultural soils: A meta-analysis
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Data from: Biological controls over the abundances of terrestrial ammonia oxidizers
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Nitrogen isotope fractionation during archaeal ammonia oxidation: coupled estimates from measurements of residual ammonium and accumulated nitrite
<p>The naturally occurring nitrogen (N) isotopes, <sup>15</sup>N and <sup>14</sup>N, exhibit different reaction rates during many microbial N transformation processes, which results in N isotope fractionation. Such isotope effects are critical parameters for interpreting natural stable isotope abundances as proxies for biological process rates in the environment across scales. The kinetic isotope effect of ammonia oxidation (AO) to nitrite (NO<sub>2</sub><sup>-</sup>), performed by ammonia-oxidizing archaea (AOA) and bacteria (AOB), is generally ascribed to the enzyme ammonia monooxygenase (AMO), which catalyzes the first step in this process. However, the kinetic isotope effect of AMO, or ε<sub><i>AMO</i></sub><span><span> </span></span>, has been typically determined based on isotope kinetics during product formation (cumulative product, NO<sub>2</sub><sup>-</sup>) alone, which may have overestimated ε<sub><i>AMO</i></sub><span><span> </span></span> due to possible accumulation of chemical intermediates and alternative sinks of ammonia/ammonium (NH<sub>3</sub>/NH<sub>4</sub><sup>+</sup>). Here, we analyzed <sup>15</sup>N isotope fractionation during archaeal ammonia oxidation based on both isotopic changes in residual substrate (RS, <span>NH<sub>4</sub><sup>+</sup></span>) and cumulative product (CP, NO<sub>2</sub><sup>-</sup>) pools in pure cultures of the soil strain <i>Nitrososphaera viennensis</i> EN76, and in highly enriched cultures of the marine strain <i>Nitrosopumilus adriaticus</i> NF5, under non-limiting substrate conditions. We obtained ε<sub><i>AMO</i></sub><span><span> </span></span> values of 31.9-33.1‰ for both strains based on RS (<span>δ<sup>15</sup>NH<sub>4</sub><sup>+</sup>), and show that </span>estimates based on CP (δ<sup>15</sup>NO<sub>2</sub><sup>-</sup>) give larger isotope fractionation factors by 6-8‰. Complementary analyses showed that, at the end of the growth period, microbial biomass was <sup>15</sup>N-enriched<span> (10.1</span>‰),<span> whereas </span>nitrous oxide (N<sub>2</sub>O) was highly <sup>15</sup>N depleted (-38.1‰) relative to the initial substrate. Although we did not determine the isotope effect of <span>NH<sub>4</sub><sup>+</sup> </span>assimilation (biomass formation) and N<sub>2</sub>O production by AOA, our results nevertheless show that the discrepancy between ε<sub><i>AMO</i></sub><span><span> </span></span> estimates based on RS and CP might have derived from incorporation of <sup>15</sup>N-enriched residual NH<sub>4</sub><sup>+</sup> after AMO reaction into microbial biomass, and that N<sub>2</sub>O production did not affect isotope fractionation estimates significantly.</p>
Data from: Exotic invasive plants increase productivity, abundance of ammonia-oxidizing bacteria, and nitrogen availability in intermountain grasslands
1. Exotic plant invasion is often associated with dramatic increases in above-ground net primary productivity and soil nitrogen. However, most evidence for these increases comes from correlative studies of single species, leaving open the question of whether invasive plants drive these processes and if they are consistent among invaders. 2. We combined field surveys and measurements within experimental plantings to examine how plant productivity, soil nitrogen, and the abundance of ammonia-oxidizing bacteria (AOB) change in response to invasions by four exotic species. 3. The relationship between plant productivity and soil nitrate differed among native and invasive species, suggesting a fundamental disparity in the effects of natives and invaders on ecosystem processes. In field surveys, dense patches of all invasive species had higher abundances of AOB than native-dominated sites. Three of the four invasive species had higher productivity, soil nitrate concentrations, and rates of potential nitrification as compared to nearby native-dominated communities. In our experimental plantings we found that two invasive species drove increases in soil nitrate and one invader caused increased productivity after a single season. 4. Synthesis:Our results highlight the importance of the N-cycling soil microbial community in how exotic invasive plants alter ecosystem function and show that shifts in function can occur rapidly.
Evolution of ammonia-oxidizing archaea related to global events
<p>Ammonia-oxidizing archaea (AOA) are chemolithoautotrophs that dominate nitrification in today's low ammonium ocean, playing critical roles in the global nitrogen cycle, alongside ammonia-oxidizing bacteria (AOB) that favor higher ammonium environments. Nitrification may have occurred soon after the origin of oxygenic photosynthesis and provided fundamental nutrients for the emergence of eukaryotic organisms in the Proterozoic; however, the timing of biological evidence remains unclear. Here we show using phylogenetic models that AOA occurred ~1,165 (1,928-880) Mya in a terrestrial geothermal environment, ~652 (767-554) Mya in low temperature soil niches, and ~509 (629-412) Mya in aquatic environments. AOA originated in marine settings around 362 (478-274) Mya, which was followed by the rapid diversification of shallow- and deep- subgroups around 315 (478-207) Mya and 309 (460-207) Mya, respectively, leading to today's domination of AOA in global oceans. The radiation of thermophilic AOA into mesophilic terrestrial soil may have been triggered by the 'snowball Earth' events of the Cryogenian Period and their 'hothouse Earth' aftermaths. The radiation of AOA into the deep ocean had to await the persistent oxygenation of the deep ocean that was associated with the rise of land plants. Our genetic analyses integrated with a geochemical data and a modeling framework offers an intriguing linkage between microbial evolution and the belated oxygenation of the deep ocean in the Paleozoic Era.</p>
Ammonia oxidation and urea oxidation in Chesapeake Bay and in the global ocean
<p>Two datasets are included in this submission. One dataset contains newly meausured ammonia oxidation, urea oxidation, nitrous oxide production from ammonium and urea in Chesapeake Bay, one of the largest estuaries in the world. The other dataset contains compiled observations of ammonia oxidation, urea oxidation, qPCR analysis of amoA and ureC gene abundance in the global ocean from previous studies. </p> <p><span>Tang, W.</span>, <span>C. Hexter</span>, <span>R. Dai</span>, et al. <span>2025</span>. “ <span>Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production</span>.” <em>Environmental Microbiology</em> <span>27</span>, no. <span>10</span>: e70187. <a href="https://doi.org/10.1111/1462-2920.70187">https://doi.org/10.1111/1462-2920.70187</a>.</p>
Top-down control of ammonia oxidizers in the North Pacific
<p>necessary data and programs for the submitted manuscript</p>
Dataset,MATLAB Programs, and supported model of "Top-down control of ammonia oxidizers by grazing in the North Pacific"
<p>Dataset,MATLAB Programs, and supported model of "Top-down control of ammonia oxidizers by grazing in the North Pacific". For the detailed information, see in the paper "Top-down control of ammonia oxidizers by grazing in the North Pacific".</p>
Top-down control of ammonia oxidizers in the North Pacific
<p>Dataset and Matlab programs in the submitted "Top-down control of ammonia oxidizers by grazing in the North Pacific ".</p>
Table. Effects of sea animal colonization on the coupling between dynamics and activity of soil ammonia-oxidizing bacteria and archaea in maritime Antarctica.
<p> In this study, we chose active seal colony tundra soils (STS), penguin colony soil (PTS) and its adjacent penguin-lacking tundra soils (PLS), tundra marsh soils (MS), and background tundra soils (BS), to investigate the effects of sea animal colonization on the abundance, activity and diversity of AOA and AOB in maritime Antarctica. </p>
Data from: Vascular plants mediate the effects of aridity and soil properties on ammonia-oxidizing bacteria and archaea
An integrated perspective of the most important factors driving the abundance of ammonia-oxidizing bacteria (AOB) and archaea (AOA) in natural ecosystems is lacking, especially in drylands. We evaluated how different climatic, abiotic, and nutrient-related factors determine AOA and AOB abundance in bare and vegetated microsites from grasslands throughout the Mediterranean Basin. We found a strong negative relationship between the abundance of AOA genes and soil fertility (availability of C, N, and P). Aridity and other abiotic factors (pH, sand content, and electrical conductivity) were more important than soil fertility in modulating the AOA/AOB ratio. AOB were more abundant under vegetated microsites, while AOA, highly resistant to stressful conditions, were more abundant in bare ground areas. These results suggest that AOA may carry out nitrification in less fertile microsites, while AOB predominate under more fertile conditions. Our results indicate that the influence of aridity and pH on the relative dominance of AOA and AOB genes is ultimately determined by local-scale environmental changes promoted by perennial vegetation. Thus, in spatially heterogeneous ecosystems such as drylands, there is a mutual exclusion and niche division between these microorganisms, suggesting that they may be functionally complementary.
Nitrogen isotope fractionation during archaeal ammonia oxidation: coupled estimates from measurements of residual ammonium and accumulated nitrite
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Evolution of ammonia-oxidizing archaea related to global events
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Comparing the impacts of an invasive grass on nitrogen cycling and ammonia-oxidizing Prokaryotes in high-nitrogen forests, open fields, and wetlands
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Data from: Macroecological patterns of archaeal ammonia oxidizers in the Atlantic Ocean
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