The nitrogen cycle

2018 ◽  
Author(s):  
David L. Kirchman
Keyword(s):  
Nitrous Oxide ◽  
Nitrogen Fixation ◽  
Nitrogen Cycle ◽  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
Ammonium Nitrogen ◽  
Gas Production ◽  
Ammonia Oxidizing Bacteria ◽  
Nitrogen Gas ◽  
Chemolithoautotrophic Bacteria

Nitrogen is required for the biosynthesis of many cellular components and can take on many oxidation states, ranging from −3 to +5. Consequently, nitrogen compounds can act as either electron donors (chemolithotrophy) or electron acceptors (anaerobic respiration). The nitrogen cycle starts with nitrogen fixation, the reduction of nitrogen gas to ammonium. Nitrogen fixation is carried out only by prokaryotes, mainly some cyanobacteria and heterotrophic bacteria. The ammonium resulting from nitrogen fixation is quickly used by many organisms for biosynthesis, being preferred over nitrate as a nitrogen source. It is also oxidized aerobically by chemolithoautotrophic bacteria and archaea during the first step of nitrification. The second step, nitrite oxidation, is carried out by other bacteria not involved in ammonia oxidation, resulting in the formation of nitrate. Some bacteria are capable of carrying out both steps (“comammox”). This nitrate can then be reduced to nitrogen gas or nitrous oxide during denitrification. It can be reduced to ammonium, a process called “dissimilatory nitrate reduction to ammonium.” Nitrogen gas is also released by anaerobic oxidation of ammonium (“anammox”) which is carried out by bacteria in the Planctomycetes phylum. The theoretical contribution of anammox to total nitrogen gas release is 29%, but the actual contribution varies greatly. Another gas in the nitrogen cycle, nitrous oxide, is a greenhouse gas produced by ammonia-oxidizing bacteria and archaea. The available data indicate that the global nitrogen cycle is in balance, with losses from nitrogen gas production equaling gains via nitrogen fixation. But excess nitrogen from fertilizers is contributing to local imbalances and several environmental problems in drinking waters, reservoirs, lakes, and coastal oceans.

scholarly journals Measurements of nitrite production in and around the primary nitrite maximum in the central California Current

2013 ◽  
Vol 10 (11) ◽  
pp. 7395-7410 ◽  
Author(s):  
A. E. Santoro ◽  
C. M. Sakamoto ◽  
J. M. Smith ◽  
J. N. Plant ◽  
A. L. Gehman ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
California Current ◽  
Euphotic Zone ◽  
Ammonia Oxidizing Bacteria ◽  
Central California ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Production ◽  
Nh3 Oxidation

Abstract. Nitrite (NO2−) is a substrate for both oxidative and reductive microbial metabolism. NO2− accumulates at the base of the euphotic zone in oxygenated, stratified open-ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2− production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria and archaea as well as assimilatory nitrate (NO3−) reduction by phytoplankton and heterotrophic bacteria. Measurements of NH3 oxidation and NO3− reduction to NO2− were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2− production in the PNM. Sensitive (< 10 nmol L−1), precise measurements of [NH4+] and [NO2−] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2− producing process, with rates of NH3 oxidation to NO2− of up to 31 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2− production from NO3− was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2− production from NO3− were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2− production agreed with production determined from 15N bottle incubations within the PNM, but a modeled net biological sink for NO2− just below the PNM was not captured in the incubations. Residence time estimates of NO2− within the PNM ranged from 18 to 470 days at the mesotrophic station and was 40 days at the oligotrophic station. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

scholarly journals Performance and microbial community of the CANON process in a sequencing batch membrane bioreactor with elevated COD/N ratios

2020 ◽  
Vol 81 (1) ◽  
pp. 138-147
Author(s):  
Xiaoling Zhang ◽  
Xincong Liu ◽  
Meng Zhang
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Nitrogen Removal ◽  
Membrane Bioreactor ◽  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
Removal Rate ◽  
Ammonia Oxidizing Bacteria ◽  
Anaerobic Ammonia Oxidation ◽  
Canon Process

Abstract In this study, the effects of elevated chemical oxygen demand/nitrogen (COD/N) ratios on nitrogen removal, production and composition of the extracellular polymer substances (EPS) and microbial community of a completely autotrophic nitrogen removal via nitrite (CANON) process were studied in a sequencing batch membrane bioreactor (SBMBR). The whole experiment was divided into two stages: the CANON stage (without organic matter in influent) and the simultaneous partial nitrification, anaerobic ammonia oxidation and denitrification (SNAD) stage (with organic matter in influent). When the inflow ammonia nitrogen was 420 mg/L and the COD/N ratio was no higher than 0.8, the addition of COD was helpful to the CANON process; the total nitrogen removal efficiency (TNE) was improved from approximately 65% to more than 75%, and the nitrogen removal rate (NRR) was improved from approximately 0.255 kgN/(m3·d) to approximately 0.278 kgN/(m3•d), while the TNE decreased to 60%, and the NRR decreased to 0.236 kgN/(m3•d) when the COD/N ratio was elevated to 1.0. For the EPS, the amounts of soluble EPS (SEPS) and loosely bound EPS (LB-EPS) were both higher in the CANON stage than in the SNAD stage, while the amount of tightly bound EPS (TB-EPS) in the SNAD stage was significantly higher due to the proliferation of heterotrophic bacteria. The metagenome sequencing technique was used to analyse the microbial community in the SBMBR. The results showed that the addition of COD altered the structure of the bacterial community in the SBMBR. The amounts of Candidatus ‘Anammoxoglobus’ of anaerobic ammonia oxidation bacteria (AAOB) and Nitrosomonas of ammonia oxidizing bacteria (AOB) both decreased significantly, and Nitrospira of nitrite oxidizing bacteria (NOB) was always in the reactor, although the amount changed slightly. A proliferation of denitrifiers related to the genera of Thauera, Dokdonella and Azospira was found in the SBMBR.

scholarly journals Quantification of Key Genes Steering the Microbial Nitrogen Cycle in the Rhizosphere of Sorghum Cultivars in Tropical Agroecosystems

2009 ◽  
Vol 75 (15) ◽  
pp. 4993-5000 ◽  
Author(s):  
Brigitte Hai ◽  
Ndeye Hélène Diallo ◽  
Saidou Sall ◽  
Felix Haesler ◽  
Kristina Schauss ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Nitrogen Cycle ◽  
Plant Development ◽  
Water Availability ◽  
Management Practices ◽  
Ammonia Oxidation ◽  
Organic Fertilizers ◽  
Ammonia Oxidizing Bacteria ◽  
Development Stages ◽  
The Impact

ABSTRACT The effect of agricultural management practices on geochemical cycles in moderate ecosystems is by far better understood than in semiarid regions, where fertilizer availability and climatic conditions are less favorable. We studied the impact of different fertilizer regimens in an agricultural long-term observatory in Burkina Faso at three different plant development stages (early leaf development, flowering, and senescence) of sorghum cultivars. Using real-time PCR, we investigated functional microbial communities involved in key processes of the nitrogen cycle (nitrogen fixation, ammonia oxidation, and denitrification) in the rhizosphere. The results indicate that fertilizer treatments and plant development stages combined with environmental factors affected the abundance of the targeted functional genes in the rhizosphere. While nitrogen-fixing populations dominated the investigated communities when organic fertilizers (manure and straw) were applied, their numbers were comparatively reduced in urea-treated plots. In contrast, ammonia-oxidizing bacteria (AOB) increased not only in absolute numbers but also in relation to the other bacterial groups investigated in the urea-amended plots. Ammonia-oxidizing archaea exhibited higher numbers compared to AOB independent of fertilizer application. Similarly, denitrifiers were also more abundant in the urea-treated plots. Our data imply as well that, more than in moderate regions, water availability might shape microbial communities in the rhizosphere, since low gene abundance data were obtained for all tested genes at the flowering stage, when water availability was very limited.

Nitrous oxide production by lithotrophic ammonia-oxidizing bacteria and implications for engineered nitrogen-removal systems

2011 ◽  
Vol 39 (6) ◽  
pp. 1832-1837 ◽  
Author(s):  
Kartik Chandran ◽  
Lisa Y. Stein ◽  
Martin G. Klotz ◽  
Mark C.M. van Loosdrecht
Keyword(s):  
Nitrous Oxide ◽  
Nitrogen Removal ◽  
Ammonia Oxidation ◽  
Wastewater Treatment Plants ◽  
N2o Emissions ◽  
Ammonia Oxidizing Bacteria ◽  
N2o Production ◽  
Nitrogen Emissions ◽  
Greenhouse Gas Inventories ◽  
Nitrogen Concentrations

Chemolithoautotrophic AOB (ammonia-oxidizing bacteria) form a crucial component in microbial nitrogen cycling in both natural and engineered systems. Under specific conditions, including transitions from anoxic to oxic conditions and/or excessive ammonia loading, and the presence of high nitrite (NO2−) concentrations, these bacteria are also documented to produce nitric oxide (NO) and nitrous oxide (N2O) gases. Essentially, ammonia oxidation in the presence of non-limiting substrate concentrations (ammonia and O2) is associated with N2O production. An exceptional scenario that leads to such conditions is the periodical switch between anoxic and oxic conditions, which is rather common in engineered nitrogen-removal systems. In particular, the recovery from, rather than imposition of, anoxic conditions has been demonstrated to result in N2O production. However, applied engineering perspectives, so far, have largely ignored the contribution of nitrification to N2O emissions in greenhouse gas inventories from wastewater-treatment plants. Recent field-scale measurements have revealed that nitrification-related N2O emissions are generally far higher than emissions assigned to heterotrophic denitrification. In the present paper, the metabolic pathways, which could potentially contribute to NO and N2O production by AOB have been conceptually reconstructed under conditions especially relevant to engineered nitrogen-removal systems. Taken together, the reconstructed pathways, field- and laboratory-scale results suggest that engineering designs that achieve low effluent aqueous nitrogen concentrations also minimize gaseous nitrogen emissions.

scholarly journals Pertumbuhan Bakteri Anaerobic Ammonia Oxidation (Anammox) Pada Salinitas 2 dan 9 Persen

2018 ◽  
Vol 9 (2) ◽  
pp. 55-62
Author(s):  
Wijanarka Wijanarka ◽  
Sudarno Sudarno ◽  
Novi A. Pratama
Keyword(s):  
Waste Water ◽  
Environmental Effect ◽  
Ammonia Oxidation ◽  
Ammonium Nitrogen ◽  
Anammox Bacteria ◽  
Nitrogen Gas ◽  
Selective Media ◽  
Gram Staining ◽  
Anaerobic Ammonia Oxidation ◽  
Anammox Process

When ammonia in waste water is lost inappropriately, it  will raise an adverse environmental effect for the aquatic cycle. Anammox, anaerobic ammonia oxidation, is a novel process in which nitrite is used as an electron acceptor in the conversion of ammonium to nitrogen gas. The anammox process removes ammonium in the autrotrophic system by leaving little biomass. This study aims to analyze the effect of salinity on the growth of anammox bacteria. The samples used were from the brackish water sediments of the East Flood Canal River of Semarang. The isolation was done by gram staining and the bacteria were inoculated on media with different salinity concentration and the growth was measured using spectrophotometer. The results showed that anammox bacteria had a higher growth rate of 3% (control) when it was grown on a medium with a concentration of 9%. Anammox bacteria grown on anammox selective media showed that the bacteria were able to adapt to environments with different salinity concentrations of 2% and 9%. Key words: anammox, ammonium, nitrogen, anammox bacteria.

Competition of Ammonia-Oxidizing Archaea and Bacteria from Freshwater Environments

2021 ◽  
Author(s):  
Elizabeth French ◽  
Jessica A. Kozlowski ◽  
Annette Bollmann
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
Ammonia Oxidizer ◽  
Ammonium Concentration ◽  
Natural Environments ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Batch Cultures ◽  
Freshwater Systems ◽  
Ammonia Oxidizing Archaea

In the environment, nutrients are rarely available in constant supply. Therefore, microorganisms require strategies to compete for limiting nutrients. In freshwater systems, ammonia-oxidizing archaea (AOA) and bacteria (AOB) compete with heterotrophic bacteria, photosynthetic microorganisms, and each other for ammonium, which AOA and AOB utilize as their sole source of energy and nitrogen. We investigated the competition between highly enriched cultures of an AOA (AOA-AC1) and an AOB (AOB-G5-7) for ammonium. Based on the amoA gene, the newly enriched archaeal ammonia oxidizer in AOA-AC1 was closely related to Nitrosotenuis spp. and the bacterial ammonia oxidizer in AOB-G5-7, Nitrosomonas sp. Is79, belonged to the Nitrosomonas oligotropha group ( Nitrosomonas cluster 6a). Growth experiments in batch cultures showed that AOB-G5-7 had higher growth rates than AOA-AC1 at higher ammonium concentrations. During chemostat competition experiments under ammonium-limiting conditions, AOA-AC1 dominated the cultures, while AOB-G5-7 decreased in abundance. In batch cultures, the outcome of the competition between AOA and AOB was determined by the initial ammonium concentrations. AOA-AC1 was the dominant ammonia oxidizer at an initial ammonium concentration of 50 μM and AOB-G5-7 at 500 μM. These findings indicate that, during direct competition, AOA-AC1 was able to use ammonium that was unavailable to AOB-G5-7, while AOB-G5-7 dominated at higher ammonium concentrations. The results are in strong accordance with environmental survey data suggesting that AOA are mainly responsible for ammonia oxidation under more oligotrophic conditions, whereas AOB dominate under eutrophic conditions. Importance Nitrification is an important process in the global nitrogen cycle. The first step - ammonia oxidation to nitrite – can be carried out by Ammonia-oxidizing Archaea (AOA) and Ammonia-oxidizing Bacteria (AOB). In many natural environments, these ammonia oxidizers coexist. Therefore, it is important to understand the population dynamics in response to increasing ammonium concentrations. Here, we study the competition between AOA and AOB enriched from freshwater systems. The results demonstrate that AOA are more abundant in systems with low ammonium availabilities and AOB when the ammonium availability increases. These results will help to predict potential shifts in community composition of ammonia oxidizers in the environment due to changes in ammonium availability.

Effect of plant growth and form of nitrogen fertilizer on denitrification from four South Australian soils

Soil Research ◽  
1972 ◽  
Vol 10 (2) ◽  
pp. 183 ◽  
Author(s):  
RC Stefanson
Keyword(s):  
Nitrous Oxide ◽  
Plant Growth ◽  
Soil Nitrogen ◽  
Nitrate Nitrogen ◽  
Ammonium Nitrogen ◽  
Soil Nitrate ◽  
Calcareous Sand ◽  
Nitrogen Gas ◽  
Brown Soil ◽  
Growth Chambers

In measuring losses of volatile nitrogen in sealed growth chambers, four major wheat-growing soils were used, namely, a mallisol, a red-brown earth, a calcareous sand, and a grey-brown soil of heavy texture. The rate of loss varied from 1 to 15 mg nitrogen/(kg soil/week) when nitrate nitrogen was applied to the soil; when ammonium nitrogen was used, losses were 1-4 mg nitrogen/(kg soil/week) over a 6-week period. The major component of these losses was nitrogen gas with lesser quantities of nitrous oxide. Both gases were produced by biological denitrification of soil nitrate. This was confirmed with an incubation experiment which used a portion of the same samples of soil. When nitrate nitrogen was applied to the soil, denitrification was increased by increasing soil water content and plant growth. These effects were greatest in the heavy textured soils. The application of ammonium nitrogen to the red-brown earth, mallisol, and grey-brown soil of heavy texture reduced the losses of soil nitrogen as nitrogen gas and nitrous oxide. Considerable losses of soil nitrogen were recorded for the calcareous sand when ammonium nitrogen was applied. Plant growth did not affect the losses of soil nitrogen from those soils receiving ammonium nitrogen.

scholarly journals Measurements of nitrite production and nitrite-producing organisms in and around the primary nitrite maximum in the central California Current

2013 ◽  
Vol 10 (3) ◽  
pp. 5803-5840 ◽  
Author(s):  
A. E. Santoro ◽  
C. M. Sakamoto ◽  
J. M. Smith ◽  
J. N. Plant ◽  
A. L. Gehman ◽  
...  
Keyword(s):  
Ammonia Oxidation ◽  
Heterotrophic Bacteria ◽  
California Current ◽  
Euphotic Zone ◽  
Ammonia Oxidizing Bacteria ◽  
Central California ◽  
Oxidation Rates ◽  
Ammonia Oxidizing Archaea ◽  
Nitrite Production ◽  
Nh3 Oxidation

Abstract. Nitrite (NO2–) is a substrate for both oxidative and reductive microbial metabolism. NO2– accumulates at the base of the euphotic zone in oxygenated, stratified open ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2– production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria or archaea and assimilatory nitrate (NO3–) reduction by phytoplankton or heterotrophic bacteria. Measurements of NH3 oxidation and NO3– reduction to NO2– were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2– production in the PNM. Sensitive (< 10 nmol L−1), high-resolution measurements of [NH4+] and [NO2–] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2– producing process with rates of NH3 oxidation of up to 50 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2– production from NO3– was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2– production from NO3– were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2– profiles supported direct rate measurements of a net biological sink for NO2– just below the PNM. Residence time estimates of NO2– within the PNM were similar at the mesotrophic and oligotrophic stations and ranged from 150–205 d. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

Enzymology and ecology of the nitrogen cycle

2011 ◽  
Vol 39 (1) ◽  
pp. 175-178 ◽  
Author(s):  
Rosa María Martínez-Espinosa ◽  
Jeffrey A. Cole ◽  
David J. Richardson ◽  
Nicholas J. Watmough
Keyword(s):  
Nitrogen Fixation ◽  
Nitrogen Cycle ◽  
Ammonia Oxidation ◽  
Nitrate Assimilation ◽  
Redox Processes ◽  
Chemical Forms ◽  
Anaerobic Ammonia Oxidation ◽  
Ecological Aspects ◽  
Micro Organisms ◽  
Global Nitrogen Cycle

The nitrogen cycle describes the processes through which nitrogen is converted between its various chemical forms. These transformations involve both biological and abiotic redox processes. The principal processes involved in the nitrogen cycle are nitrogen fixation, nitrification, nitrate assimilation, respiratory reduction of nitrate to ammonia, anaerobic ammonia oxidation (anammox) and denitrification. All of these are carried out by micro-organisms, including bacteria, archaea and some specialized fungi. In the present article, we provide a brief introduction to both the biochemical and ecological aspects of these processes and consider how human activity over the last 100 years has changed the historic balance of the global nitrogen cycle.

scholarly journals Phanerozoic radiation of ammonia oxidizing bacteria

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
L. M. Ward ◽  
D. T. Johnston ◽  
P. M. Shih
Keyword(s):  
Nitrogen Cycle ◽  
Ammonia Oxidation ◽  
Deep Ocean ◽  
Nitrogen Isotope ◽  
Ammonia Oxidizing Bacteria ◽  
Crown Group ◽  
Geologic Time ◽  
Absolute Requirement ◽  
Isotope Record ◽  
Late Evolution

AbstractThe modern nitrogen cycle consists of a web of microbially mediated redox transformations. Among the most crucial reactions in this cycle is the oxidation of ammonia to nitrite, an obligately aerobic process performed by a limited number of lineages of bacteria (AOB) and archaea (AOA). As this process has an absolute requirement for O2, the timing of its evolution—especially as it relates to the Great Oxygenation Event ~ 2.3 billion years ago—remains contested and is pivotal to our understanding of nutrient cycles. To estimate the antiquity of bacterial ammonia oxidation, we performed phylogenetic and molecular clock analyses of AOB. Surprisingly, bacterial ammonia oxidation appears quite young, with crown group clades having originated during Neoproterozoic time (or later) with major radiations occurring during Paleozoic time. These results place the evolution of AOB broadly coincident with the pervasive oxygenation of the deep ocean. The late evolution AOB challenges earlier interpretations of the ancient nitrogen isotope record, predicts a more substantial role for AOA during Precambrian time, and may have implications for understanding of the size and structure of the biogeochemical nitrogen cycle through geologic time.

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