Denitrification is a microbially facilitated process where nitrate (NO3−) is reduced and ultimately produces molecular nitrogen (N2) through a series of intermediate gaseous nitrogen oxide products. Facultative anaerobic bacteria perform denitrification as a type of respiration that reduces oxidized forms of nitrogen in response to the oxidation of an electron donor such as organic matter. The preferred nitrogen electron acceptors in order of most to least thermodynamically favorable include nitrate (NO3−), nitrite (NO2−), nitric oxide (NO), nitrous oxide (N2O) finally resulting in the production of dinitrogen (N2) completing the nitrogen cycle. Denitrifying microbes require a very low oxygen concentration of less than 10%, as well as organic C for energy. Since denitrification can remove NO3−, reducing its leaching to groundwater, it can be strategically used to treat sewage or animal residues of high nitrogen content. Denitrification can leak N2O, which is an ozone-depleting substance and a greenhouse gas that can have a considerable influence on global warming.
The process is performed primarily by heterotrophic bacteria (such as Paracoccus denitrificans and various pseudomonads), although autotrophic denitrifiers have also been identified (e.g., Thiobacillus denitrificans). Denitrifiers are represented in all main phylogenetic groups. Generally several species of bacteria are involved in the complete reduction of nitrate to N2, and more than one enzymatic pathway has been identified in the reduction process.
Direct reduction from nitrate to ammonium, a process known as dissimilatory nitrate reduction to ammonium or DNRA, is also possible for organisms that have the nrf-gene. This is less common than denitrification in most ecosystems as a means of nitrate reduction. Other genes known in microorganisms which denitrify include nir (nitrite reductase) and nos (nitrous oxide reductase) among others; organisms identified as having these genes include Alcaligenes faecalis, Alcaligenes xylosoxidans, many in the genus Pseudomonas, Bradyrhizobium japonicum, and Blastobacter denitrificans.
Denitrification generally proceeds through some combination of the following half reactions, with the enzyme catalyzing the reaction in parentheses:
In nature, denitrification can take place in both terrestrial and marine ecosystems. Typically, denitrification occurs in anoxic environments, where the concentration of dissolved and freely available oxygen is depleted. In these areas, nitrate (NO3−) or nitrite (NO
2−) can be used as a substitute terminal electron acceptor instead of oxygen (O2), a more energetically favourable electron acceptor. Terminal electron acceptor is a compound that gets reduced in the reaction by receiving electrons. Examples of anoxic environments can include soils, groundwater, wetlands, oil reservoirs, poorly ventilated corners of the ocean and seafloor sediments.
Furthermore, denitrification can occur in oxic environments as well. High activity of denitrifers can be observed in the intertidal zones, where the tidal cycles cause fluctuations of oxygen concentration in sandy coastal sediments. For example, the bacterial species Paracoccus denitrificans engages in denitrification under both oxic and anoxic conditions simultaneously. Upon oxygen exposure, the bacteria is able to utilize nitrous oxide reductase, an enzyme that catalyzes the last step of denitrification. Aerobic denitrifiers are mainly Gram-negative bacteria in the phylum Proteobacteria. Enzymes NapAB, NirS, NirK and NosZ are located in the periplasm, a wide space bordered by the cytoplasmic and the outer membrane in Gram-negative bacteria.
Denitrification can lead to a condition called isotopic fractionation in the soil environment. The two stable isotopes of nitrogen, 14N and 15N are both found in the sediment profiles. The lighter isotope of nitrogen, 14N, is preferred during denitrification, leaving the heavier nitrogen isotope, 15N, in the residual matter. This selectivity leads to the enrichment of 14N in the biomass compared to 15N. Moreover, the relative abundance of 14N can be analyzed to distinguish denitrification apart from other processes in nature.
Denitrification is commonly used to remove nitrogen from sewage and municipal wastewater. It is also an instrumental process in constructed wetlands and riparian zones for the prevention of groundwater pollution with nitrate resulting from excessive agricultural or residential fertilizer usage. Wood chip bioreactors have been studied since the 2000s and are effective in removing nitrate from agricultural run off and even manure.
In some wastewater treatment plants, compounds such as methanol, ethanol, acetate, glycerin, or proprietary products are added to the wastewater to provide a carbon and electron source for denitrifying bacteria. The microbial ecology of such engineered denitrification processes is determined by the nature of the electron donor and the process operating conditions. Denitrification processes are also used in the treatment of industrial wastewater. Many denitrifying bioreactor types and designs are available commercially for the industrial applications, including Electro-Biochemical Reactors (EBRs), membrane bioreactors (MBRs), and moving bed bioreactors (MBBRs).
Aerobic denitrification, conducted by aerobic denitrifiers, may offer the potential to eliminate the need for separate tanks and reduce sludge yield. There are less stringent alkalinity requirements because alkalinity generated during denitrification can partly compensate for the alkalinity consumption in nitrification.
It is possible to encounter DNRA when your source of carbon is a fermentable substrate, as glucose, so if you wanna avoid DNRA use a non fermentable substrateCS1 maint: Multiple names: authors list (link)
Aerobic denitrification or co-respiration the simultaneous use of both oxygen (O2) and nitrate (NO3−) as oxidizing agents, performed by various genera of microorganisms. This process differs from anaerobic denitrification not only in its insensitivity to the presence of oxygen, but also in that it has a higher potential to create the harmful byproduct nitrous oxide.Nitrogen, acting as an oxidant, is therefore reduced in a succession of four reactions performed by the enzymes nitrate, nitrite, nitric-oxide, and nitrous oxide reductases. The pathway ultimately yields reduced molecular nitrogen (N2), as well as, when the reaction does not reach completion, the intermediate species nitrous oxide (N2O). A simple denitrification reaction proceeds as:
NO3− → NO2− → NO → N2O → N2 (g)The respiration reaction which utilizes oxygen as the oxidant is:
C6H12O6 (aq) + 6O2 (g) → 6CO2 (g) + 6H2OClassically, it was thought that denitrification would not occur in the presence of oxygen since there seems to be no energetic advantage to using nitrate as an oxidant when oxygen is available. Experiments have since proven that denitrifiers are often facultative anaerobes and that aerobic denitrification does indeed occur in a broad range of microbial organisms with varying levels of productivity, usually lower productivity than results from purely aerobic respiration. The advantages of being able to perform denitrification in the presence of oxygen are uncertain, though it is possible that the ability to adapt to changes in oxygen levels plays a role. Aerobic denitrification may be found in environments where fluctuating oxygen concentrations and reduced carbon are available. The relative harsh environment inspires the potential of denitrifiers to degrade toxic nitrate or nitrate under an aerobic atmosphere. Aerobic denitrifiers tend to work efficiently at 25 ~ 37°C and pH 7 ~ 8, when dissolved oxygen concentration is 3 ~ 5 mg/L and C/N load ratio is 5 ~ 10.Anaerobic respiration
Anaerobic respiration is respiration using electron acceptors other than molecular oxygen (O2). Although oxygen is not the final electron acceptor, the process still uses a respiratory electron transport chain.In aerobic organisms undergoing respiration, electrons are shuttled to an electron transport chain, and the final electron acceptor is oxygen. Molecular oxygen is a highly oxidizing agent and, therefore, is an excellent electron acceptor. In anaerobes, other less-oxidizing substances such as sulphate (SO42−), nitrate (NO3−), sulphur (S), or fumarate are used. These terminal electron acceptors have smaller reduction potentials than O2, meaning that less energy is released per oxidized molecule. Therefore, generally speaking, anaerobic respiration is less efficient than aerobic.Beaver dam
Beaver dams or beaver impoundments are dams built by beavers to provide ponds as protection against predators such as coyotes, wolves, and bears, and to provide easy access to food during winter. These structures modify the natural environment in such a way that the overall ecosystem builds upon the change, making beavers a keystone species. Beavers work at night and are prolific builders, carrying mud and stones with their fore-paws and timber between their teeth.Betaproteobacteria
Betaproteobacteria are a class of gram-negative bacteria, and one of the eight classes of the phylum Proteobacteria.The Betaproteobacteria are a class comprising over 75 genera and 400 species of bacteria. Together, the Betaproteobacteria represent a broad variety of metabolic strategies and occupy diverse environments from obligate pathogens living within host organisms to oligotrophic groundwater ecosystems. Whilst most members of the Betaproteobacteria are heterotrophic, deriving both their carbon and electrons from organocarbon sources, some are photoheterotrophic, deriving energy from light and carbon from organocarbon sources. Other genera are autotrophic, deriving their carbon from bicarbonate or carbon dioxide and their electrons from reduced inorganic ions such as nitrite, ammonium, thiosulfate or sulfide - many of these chemolithoautotrophic Betaproteobacteria are economically important, with roles in maintaining soil pH and in elementary cycling. Other economically important members of the Betaproteobacteria are able to use nitrate as their terminal electron acceptor and can be used industrially to remove nitrate from wastewater by denitrification. A number of Betaproteobacteria are diazotrophs, meaning that they can fix molecular nitrogen from the air as their nitrogen source for growth - this is important to the farming industry as it is a primary means of ammonium levels in soils rising without the presence of leguminous plants.Cattle urine patches
Urine patches in cattle pastures generate large concentrations of the greenhouse gas nitrous oxide through nitrification and denitrification processes in urine-contaminated soils. Over the past few decades, the cattle population has increased more rapidly than the human population. Between the years 2000 and 2050, the cattle population is expected to increase from 1.5 billion to 2.6 billion. When large populations of cattle are packed into pastures, excessive amounts of urine soak into soils. This increases the rate at which nitrification and denitrification occur and produce nitrous oxide. Currently, nitrous oxide is one of the single most important ozone-depleting emissions and is expected to remain the largest throughout the 21st century.Constructed wetland
A constructed wetland (CW) is an artificial wetland to treat municipal or industrial wastewater, greywater or stormwater runoff. It may also be designed for land reclamation after mining, or as a mitigation step for natural areas lost to land development.
Constructed wetlands are engineered systems that use natural functions vegetation, soil, and organisms to treat wastewater. Depending on the type of wastewater the design of the constructed wetland has to be adjusted accordingly. Constructed wetlands have been used to treat both centralized and on-site wastewater. Primary treatment is recommended when there is a large amount of suspended solids or soluble organic matter (measured as BOD and COD).Similarly to natural wetlands, constructed wetlands also act as a biofilter and/or can remove a range of pollutants (such as organic matter, nutrients, pathogens, heavy metals) from the water. Constructed wetlands are a sanitation technology that have not been designed specifically for pathogen removal, but instead, have been designed to remove other water quality constituents such as suspended solids, organic matter and nutrients (nitrogen and phosphorus). All types of pathogens (i.e., bacteria, viruses, protozoan and helminths) are expected to be removed to some extent in a constructed wetland. Subsurface wetland provide greater pathogen removal than surface wetlands.There are two main types of constructed wetlands: subsurface flow and surface flow constructed wetlands. The planted vegetation plays an important role in contaminant removal. The filter bed, consisting usually of sand and gravel, has an equally important role to play. Some constructed wetlands may also serve as a habitat for native and migratory wildlife, although that is not their main purpose. Subsurface flow constructed wetlands are designed to have either horizontal flow or vertical flow of water through the gravel and sand bed. Vertical flow systems have a smaller space requirement than horizontal flow systems.Denitrifying bacteria
Denitrifying bacteria are a diverse group of bacteria that encompass many different phyla. This group of bacteria, together with denitrifying fungi and archaea, is capable of performing denitrification as part of the nitrogen cycle. They metabolise nitrogenous compounds using various enzymes, turning nitrogen oxides back to nitrogen gas or nitrous oxide.Detritivore
Detritivores, also known as detrivores, detritophages, detritus feeders, or detritus eaters, are heterotrophs that obtain nutrients by consuming detritus (decomposing plant and animal parts as well as faeces). There are many kinds of invertebrates, vertebrates and plants that carry out coprophagy. By doing so, all these detritivores contribute to decomposition and the nutrient cycles. They should be distinguished from other decomposers, such as many species of bacteria, fungi and protists, which are unable to ingest discrete lumps of matter, but instead live by absorbing and metabolizing on a molecular scale (saprotrophic nutrition). However, the terms detritivore and decomposer are often used interchangeably.
Detritivores are an important aspect of many ecosystems. They can live on any type of soil with an organic component, including marine ecosystems, where they are termed interchangeably with bottom feeders.
Typical detritivorous animals include millipedes, springtails, woodlice, dung flies, slugs, many terrestrial worms, sea stars, sea cucumbers, fiddler crabs, and some sedentary polychaetes such as worms of the family Terebellidae).
Scavengers are not typically thought to be detritivores, as they generally eat large quantities of organic matter, but both detritivores and scavengers are the same type of cases of consumer-resource systems. The consumption of wood, whether alive or dead, is known as xylophagy. Τhe activity of animals feeding only on dead wood is called sapro-xylophagy and those animals, sapro-xylophagous. It is a good source of manure.Dissimilatory nitrate reduction to ammonium
Dissimilatory nitrate reduction to ammonium (DNRA), also known as nitrate/nitrite ammonification, is the result of anaerobic respiration by chemoorganoheterotrophic microbes using nitrate (NO3−) as an electron acceptor for respiration. In anaerobic conditions microbes which undertake DNRA oxidise organic matter and use nitrate (rather than oxygen) as an electron acceptor, reducing it to nitrite, then ammonium (NO3−→NO2−→NH4+).Dissimilatory nitrate reduction to ammonium is more common in prokaryotes but may also occur in eukaryotic microorganisms. DNRA is a component of the terrestrial and oceanic nitrogen cycle. Unlike denitrification, it acts to conserve bioavailable nitrogen in the system, producing soluble ammonium rather than unreactive dinitrogen gas.Human impact on the nitrogen cycle
Human impact on the nitrogen cycle is diverse. Agricultural and industrial nitrogen (N) inputs to the environment currently exceed inputs from natural N fixation. As a consequence of anthropogenic inputs, the global nitrogen cycle (Fig. 1) has been significantly altered over the past century. Global atmospheric nitrous oxide (N2O) mole fractions have increased from a pre-industrial value of ~270 nmol/mol to ~319 nmol/mol in 2005. Human activities account for over one-third of N2O emissions, most of which are due to the agricultural sector. This article is intended to give a brief review of the history of anthropogenic N inputs, and reported impacts of nitrogen inputs on selected terrestrial and aquatic ecosystems.Microbial metabolism
Microbial metabolism is the means by which a microbe obtains the energy and nutrients (e.g. carbon) it needs to live and reproduce. Microbes use many different types of metabolic strategies and species can often be differentiated from each other based on metabolic characteristics. The specific metabolic properties of a microbe are the major factors in determining that microbe's ecological niche, and often allow for that microbe to be useful in industrial processes or responsible for biogeochemical cycles.Nitrite reductase (NO-forming)
In enzymology, a nitrite reductase (NO-forming) (EC 188.8.131.52) is an enzyme that catalyzes the chemical reaction
nitric oxide + H2O + ferricytochrome c ⇌ nitrite + ferrocytochrome c + 2 H+The 3 substrates of this enzyme are nitric oxide, H2O, and ferricytochrome c, whereas its 3 products are nitrite, ferrocytochrome c, and H+.
This enzyme belongs to the family of oxidoreductases, specifically those acting on other nitrogenous compounds as donors with a cytochrome as acceptor. The systematic name of this enzyme class is nitric-oxide:ferricytochrome-c oxidoreductase. Other names in common use include cd-cytochrome nitrite reductase, [nitrite reductase (cytochrome)] [misleading, see comments.], cytochrome c-551:O2, NO2+ oxidoreductase, cytochrome cd, cytochrome cd1, hydroxylamine (acceptor) reductase, methyl viologen-nitrite reductase, nitrite reductase (cytochrome, and NO-forming). This enzyme participates in nitrogen metabolism. It has 3 cofactors: FAD, Iron, and Copper.Nitrogen cycle
The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmosphere, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmosphere nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.
The nitrogen cycle is of particular interest to ecologists because nitrogen availability can affect the rate of key ecosystem processes, including primary production and decomposition. Human activities such as fossil fuel combustion, use of artificial nitrogen fertilizers, and release of nitrogen in wastewater have dramatically altered the global nitrogen cycle. Human modification of global nitrogen cycle can negatively affect the natural environment system and also human health.Nitrous-oxide reductase
In enzymology, a nitrous oxide reductase also known as nitrogen:acceptor oxidoreductase (N2O-forming) is an enzyme that catalyzes the final step in bacterial denitrification, the reduction of nitrous oxide to dinitrogen.
N2O + 2 reduced cytochome c ⇌ N2 + H2O + 2 cytochrome cIt plays a critical role in preventing release of a potent greenhouse gas into the atmosphere.Refugium (fishkeeping)
In fishkeeping, a refugium is an appendage to a marine, brackish, or freshwater fish tank that shares the same water supply. It is a separate sump, connected to the main show tank. It is a "refugium" in the sense that it permits organisms to be maintained that would not survive in the main system, whether food animals, anaerobic denitrifying bacteria, or photosynthesizers. For some applications water flow is limited in order to protect plants or animals that require slow flow. The refugium light cycle can be operated opposite to the main tank, in order to keep total system pH more stable (due to the uptake of acid-forming CO2 by photosynthesis occurring in the refugium during its "daylight" hours). One volume guideline for a refugium is 1:10 main tank volume.
A refugium may be used for one or more purposes such as denitrification, nutrient export, plankton production, circulation, surface agitation to improve oxygen exchange with the atmosphere or even aesthetic purposes.Simultaneous nitrification–denitrification
Simultaneous nitrification–denitrification (SNdN) is a wastewater treatment process. Microbial simultaneous nitrification-denitrification is the conversion of the ammonium ion to nitrogen gas in a single bioreactor. The process is dependent on floc characteristics, reaction kinetics, mass loading of readily biodegradable chemical oxygen demand, rbCOD, and the dissolved oxygen, DO, concentrationSoil biology
Soil biology is the study of microbial and faunal activity and ecology in soil.
Soil life, soil biota, soil fauna, or edaphon is a collective term that encompasses all organisms that spend a significant portion of their life cycle within a soil profile, or at the soil-litter interface.
These organisms include earthworms, nematodes, protozoa, fungi, bacteria, different arthropods, as well as some reptiles (such as snakes), and species of burrowing mammals like gophers, moles and prairie dogs. Soil biology plays a vital role in determining many soil characteristics. The decomposition of organic matter by soil organisms has an immense influence on soil fertility, plant growth, soil structure, and carbon storage. As a relatively new science, much remains unknown about soil biology and its effect on soil ecosystems.Syed Wajih Ahmad Naqvi
Syed Wajih Ahmad Naqvi is an Indian marine scientist and the former director of the National Institute of Oceanography. His work has concentrated in oceanic water chemistry, biogeochemistry, and chemical interrelations with living organisms. He has also performed research on freshwater ecosystems. He was the Chief Indian Scientist of LOHAFEX, an Ocean Iron Fertilization experiment jointly planned by the Council of Scientific Industrial Research (CSIR), India, and Helmholtz Foundation, Germany.Waterlogging (agriculture)
Waterlogging refers to the saturation of soil with water. Soil may be regarded as waterlogged when it is nearly saturated with water much of the time such that its air phase is restricted and anaerobic conditions prevail. In extreme cases of prolonged waterlogging, anaerobiosis occurs, the roots of mesophytes suffer, and the subsurface reducing atmosphere leads to such processes as denitrification, methanogenesis, and the reduction of iron and manganese oxides.In agriculture, various crops need air (specifically, oxygen) to a greater or lesser depth in the soil. Waterlogging of the soil stops air getting in. How near the water table must be to the surface for the ground to be classed as waterlogged, varies with the purpose in view. A crop's demand for freedom from waterlogging may vary between seasons of the year, as with the growing of rice (Oryza sativa).
In irrigated agricultural land, waterlogging is often accompanied by soil salinity as waterlogged soils prevent leaching of the salts imported by the irrigation water.
From a gardening point of view, waterlogging is the process whereby the soil blocks off all water and is so hard it stops air getting in and it stops oxygen from getting in.