Some of these bacteria are aerobic, others are anaerobic; some are phototrophic, others are chemotrophic i. Although there is great physiological and phylogenetic diversity among the organisms that carry out nitrogen fixation, they all have a similar enzyme complex called nitrogenase that catalyzes the reduction of N 2 to NH 3 ammonia , which can be used as a genetic marker to identify the potential for nitrogen fixation.
One of the characteristics of nitrogenase is that the enzyme complex is very sensitive to oxygen and is deactivated in its presence.
This presents an interesting dilemma for aerobic nitrogen-fixers and particularly for aerobic nitrogen-fixers that are also photosynthetic since they actually produce oxygen. Over time, nitrogen-fixers have evolved different ways to protect their nitrogenase from oxygen.
For example, some cyanobacteria have structures called heterocysts that provide a low-oxygen environment for the enzyme and serves as the site where all the nitrogen fixation occurs in these organisms. Other photosynthetic nitrogen-fixers fix nitrogen only at night when their photosystems are dormant and are not producing oxygen. Genes for nitrogenase are globally distributed and have been found in many aerobic habitats e.
The broad distribution of nitrogen-fixing genes suggests that nitrogen-fixing organisms display a very broad range of environmental conditions, as might be expected for a process that is critical to the survival of all life on Earth.
Nitrification is the process that converts ammonia to nitrite and then to nitrate and is another important step in the global nitrogen cycle. Most nitrification occurs aerobically and is carried out exclusively by prokaryotes.
There are two distinct steps of nitrification that are carried out by distinct types of microorganisms. The first step is the oxidation of ammonia to nitrite, which is carried out by microbes known as ammonia-oxidizers. Aerobic ammonia oxidizers convert ammonia to nitrite via the intermediate hydroxylamine, a process that requires two different enzymes, ammonia monooxygenase and hydroxylamine oxidoreductase Figure 4. The process generates a very small amount of energy relative to many other types of metabolism; as a result, nitrosofiers are notoriously very slow growers.
Additionally, aerobic ammonia oxidizers are also autotrophs, fixing carbon dioxide to produce organic carbon, much like photosynthetic organisms, but using ammonia as the energy source instead of light.
Figure 4: Chemical reactions of ammonia oxidation carried out by bacteria Reaction 1 converts ammonia to the intermediate, hydroxylamine, and is catalyzed by the enzyme ammonia monooxygenase.
Reaction 2 converts hydroxylamine to nitrite and is catalyzed by the enyzmer hydroxylamine oxidoreductase. Unlike nitrogen fixation that is carried out by many different kinds of microbes, ammonia oxidation is less broadly distributed among prokaryotes. Until recently, it was thought that all ammonia oxidation was carried out by only a few types of bacteria in the genera Nitrosomonas , Nitrosospira , and Nitrosococcus.
However, in an archaeon was discovered that could also oxidize ammonia Koenneke et al. Since their discovery, ammonia-oxidizing Archaea have often been found to outnumber the ammonia-oxidizing Bacteria in many habitats.
In the past several years, ammonia-oxidizing Archaea have been found to be abundant in oceans, soils, and salt marshes, suggesting an important role in the nitrogen cycle for these newly-discovered organisms. Currently, only one ammonia-oxidizing archaeon has been grown in pure culture, Nitrosopumilus maritimus , so our understanding of their physiological diversity is limited.
This step is carried out by a completely separate group of prokaryotes, known as nitrite-oxidizing Bacteria. Some of the genera involved in nitrite oxidation include Nitrospira , Nitrobacter , Nitrococcus , and Nitrospina. Similar to ammonia oxidizers, the energy generated from the oxidation of nitrite to nitrate is very small, and thus growth yields are very low.
In fact, ammonia- and nitrite-oxidizers must oxidize many molecules of ammonia or nitrite in order to fix a single molecule of CO 2. For complete nitrification, both ammonia oxidation and nitrite oxidation must occur. Ammonia-oxidizers and nitrite-oxidizers are ubiquitous in aerobic environments. They have been extensively studied in natural environments such as soils, estuaries, lakes, and open-ocean environments.
However, ammonia- and nitrite-oxidizers also play a very important role in wastewater treatment facilities by removing potentially harmful levels of ammonium that could lead to the pollution of the receiving waters. Much research has focused on how to maintain stable populations of these important microbes in wastewater treatment plants.
Additionally, ammonia- and nitrite-oxidizers help to maintain healthy aquaria by facilitating the removal of potentially toxic ammonium excreted in fish urine. Traditionally, all nitrification was thought to be carried out under aerobic conditions, but recently a new type of ammonia oxidation occurring under anoxic conditions was discovered Strous et al.
Anammox anaerobic ammonia oxidation is carried out by prokaryotes belonging to the Planctomycetes phylum of Bacteria. The first described anammox bacterium was Brocadia anammoxidans. Anammox bacteria oxidize ammonia by using nitrite as the electron acceptor to produce gaseous nitrogen Figure 6.
Anammox bacteria were first discovered in anoxic bioreactors of wasterwater treatment plants but have since been found in a variety of aquatic systems, including low-oxygen zones of the ocean, coastal and estuarine sediments, mangroves, and freshwater lakes.
In some areas of the ocean, the anammox process is considered to be responsible for a significant loss of nitrogen Kuypers et al. However, Ward et al. Whether anammox or denitrification is responsible for most nitrogen loss in the ocean, it is clear that anammox represents an important process in the global nitrogen cycle. Denitrification is the process that converts nitrate to nitrogen gas, thus removing bioavailable nitrogen and returning it to the atmosphere.
Dinitrogen gas N 2 is the ultimate end product of denitrification, but other intermediate gaseous forms of nitrogen exist Figure 7. Some of these gases, such as nitrous oxide N 2 O , are considered greenhouse gasses, reacting with ozone and contributing to air pollution. Figure 7: Reactions involved in denitrification Reaction 1 represents the steps of reducing nitrate to dinitrogen gas. Reaction 2 represents the complete redox reaction of denitrification.
Unlike nitrification, denitrification is an anaerobic process, occurring mostly in soils and sediments and anoxic zones in lakes and oceans. Similar to nitrogen fixation, denitrification is carried out by a diverse group of prokaryotes, and there is recent evidence that some eukaryotes are also capable of denitrification Risgaard-Petersen et al.
Some denitrifying bacteria include species in the genera Bacillus , Paracoccus , and Pseudomonas. Denitrifiers are chemoorganotrophs and thus must also be supplied with some form of organic carbon. Denitrification is important in that it removes fixed nitrogen i.
This is particularly important in agriculture where the loss of nitrates in fertilizer is detrimental and costly. However, denitrification in wastewater treatment plays a very beneficial role by removing unwanted nitrates from the wastewater effluent, thereby reducing the chances that the water discharged from the treatment plants will cause undesirable consequences e. When an organism excretes waste or dies, the nitrogen in its tissues is in the form of organic nitrogen e. Various fungi and prokaryotes then decompose the tissue and release inorganic nitrogen back into the ecosystem as ammonia in the process known as ammonification.
The ammonia then becomes available for uptake by plants and other microorganisms for growth. Many human activities have a significant impact on the nitrogen cycle. Burning fossil fuels, application of nitrogen-based fertilizers, and other activities can dramatically increase the amount of biologically available nitrogen in an ecosystem.
And because nitrogen availability often limits the primary productivity of many ecosystems, large changes in the availability of nitrogen can lead to severe alterations of the nitrogen cycle in both aquatic and terrestrial ecosystems. Industrial nitrogen fixation has increased exponentially since the s, and human activity has doubled the amount of global nitrogen fixation Vitousek et al.
In terrestrial ecosystems, the addition of nitrogen can lead to nutrient imbalance in trees, changes in forest health, and declines in biodiversity. With increased nitrogen availability there is often a change in carbon storage, thus impacting more processes than just the nitrogen cycle.
In agricultural systems, fertilizers are used extensively to increase plant production, but unused nitrogen, usually in the form of nitrate, can leach out of the soil, enter streams and rivers, and ultimately make its way into our drinking water. The process of making synthetic fertilizers for use in agriculture by causing N 2 to react with H 2 , known as the Haber-Bosch process, has increased significantly over the past several decades.
Much of the nitrogen applied to agricultural and urban areas ultimately enters rivers and nearshore coastal systems. In nearshore marine systems, increases in nitrogen can often lead to anoxia no oxygen or hypoxia low oxygen , altered biodiversity, changes in food-web structure, and general habitat degradation.
One common consequence of increased nitrogen is an increase in harmful algal blooms Howarth Toxic blooms of certain types of dinoflagellates have been associated with high fish and shellfish mortality in some areas. Even without such economically catastrophic effects, the addition of nitrogen can lead to changes in biodiversity and species composition that may lead to changes in overall ecosystem function.
Some have even suggested that alterations to the nitrogen cycle may lead to an increased risk of parasitic and infectious diseases among humans and wildlife Johnson et al.
Additionally, increases in nitrogen in aquatic systems can lead to increased acidification in freshwater ecosystems. Nitrogen is arguably the most important nutrient in regulating primary productivity and species diversity in both aquatic and terrestrial ecosystems Vitousek et al. Microbially-driven processes such as nitrogen fixation, nitrification, and denitrification, constitute the bulk of nitrogen transformations, and play a critical role in the fate of nitrogen in the Earth's ecosystems.
However, as human populations continue to increase, the consequences of human activities continue to threaten our resources and have already significantly altered the global nitrogen cycle. Galloway, J. Year Consequences of population growth and development on deposition of oxidized nitrogen. Ambio 23 , — Howarth, R. Coastal nitrogen pollution: a review of sources and trends globally and regionally.
Harmful Algae 8 , 14— Johnson, P. Linking environmental nutrient enrichment and disease emergence in humans and wildlife. Ecological Applications 20 , 16—29 Koenneke, M. Isolation of an autotrophic ammonia-oxidizing marine archaeon.
Nature , — Kuypers, M. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium oxidation. Risgaard-Petersen, N.
Evidence for complete denitrification in a benthic foraminifer. Nature , 93—96 Strous, M. Missing lithotroph identified as new planctomycete. Vitousek, P. Human alteration of the global nitrogen cycle: sources and consequences. Ecological Applications 7 , — Towards an ecological understanding of biological nitrogen fixation.
Biogeochemistry 57 , 1—45 Ward, B. Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature , 78—81 Introduction to the Basic Drivers of Climate. During the conversion of nitrogen cyano bacteria will first convert nitrogen into ammonia and ammonium, during the nitrogen fixation process. Plants can use ammonia as a nitrogen source.
Aerobic bacteria use oxygen to convert these compounds. Nitrosomonas bacteria first convert nitrogen gas to nitrite NO 2 - and subsequently nitrobacter convert nitrite to nitrate NO 3 - , a plant nutrient. Animals cannot absorb nitrates directly. They receive their nutrient supplies by consuming plants or plant-consuming animals.
When nitrogen nutrients have served their purpose in plants and animals, specialized decomposing bacteria will start a process called ammonification , to convert them back into ammonia and water-soluble ammonium salts.
After the nutrients are converted back into ammonia, anaerobic bacteria will convert them back into nitrogen gas, during a process called denitrification. The whole process starts over after release. A schematic representation of the nitrogen cycle is shown here: Nitrogen as a limiting factor Although the nitrogen conversion processes often occurs and large quantities of plant nutrients are produced, nitrogen is often a limiting factor for plant growth.
Water flowing across the soil causes this error. Nitrogen nutrients are water-soluble and as a result they are easily drained away, so that they are no longer available for plants. The annamox reaction In researchers at the Gist-Brocades in Delft, The Netherlands, discovered a new reaction to be added to the nitrogen cycle; the so-called annamox reaction.
This is now found to occur in the Black Sea, as well.
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