Table of Contents
Nitrogen is an essential element for all living things: it is a key component of amino acids (and thus proteins), nucleic acids (DNA and RNA), ATP, and many other biomolecules. Yet, most organisms cannot use the most abundant form of nitrogen on Earth: molecular nitrogen gas $N_2$, which makes up about 78% of the atmosphere. The nitrogen cycle describes how nitrogen is transformed between different chemical forms and moved between the atmosphere, biosphere, hydrosphere, and lithosphere, making it biologically available and then returning it to inert forms.
This chapter focuses on the specific processes and organisms involved in the nitrogen cycle, how these processes are linked, and how human activities have altered the natural nitrogen balance.
Major Nitrogen Pools and Forms
In the nitrogen cycle, nitrogen appears in several oxidation states and chemical forms:
- Atmospheric nitrogen:
- $N_2$ (dinitrogen gas): very stable, triple bond; unavailable to most organisms.
- $N_2O$ (nitrous oxide): trace gas, greenhouse gas, and ozone-depleting substance.
- $NO$ and $NO_2$ (nitric oxide, nitrogen dioxide): components of air pollution; involved in acid rain and ozone chemistry.
- In soils and water (dissolved or bound to particles):
- Ammonia / Ammonium: $NH_3$ and $NH_4^+$ (depending on pH).
- Nitrite: $NO_2^-$.
- Nitrate: $NO_3^-$.
- Organic nitrogen: amino acids, proteins, nucleic acids in living organisms; humus and other organic matter in soil and sediments.
- In rocks and sediments:
- Organic nitrogen buried in sediments.
- Some nitrogen-bearing minerals; these are relatively minor for the active, short-term nitrogen cycle.
The central aspect of the cycle is the conversion between biologically unavailable atmospheric $N_2$ and reactive (biologically available) forms such as ammonium and nitrate.
Key Processes in the Nitrogen Cycle
The nitrogen cycle is driven by several biological and abiotic processes. Each transforms nitrogen from one form to another and is carried out by specific groups of organisms, mainly microbes.
Nitrogen Fixation: From $N_2$ to Ammonium
Nitrogen fixation is the conversion of atmospheric $N_2$ into ammonia $NH_3$ (which in water becomes ammonium $NH_4^+$). This is the essential entry point of atmospheric nitrogen into the biosphere.
The overall reaction for biological nitrogen fixation can be simplified as:
$$
N_2 + 8H^+ + 8e^- + 16 \text{ ATP} \rightarrow 2NH_3 + H_2 + 16 \text{ ADP} + 16P_i
$$
Key points:
- Why fixation is needed:
$N_2$ is chemically very stable due to its triple bond. Breaking it requires a lot of energy and specialized enzymes. - Biological nitrogen fixation:
- Performed by a limited group of prokaryotes (bacteria and archaea) called diazotrophs.
- The key enzyme is nitrogenase, which is highly sensitive to oxygen.
- Diazotrophs can be:
- Free-living in soil or water (e.g., some cyanobacteria, Azotobacter, Clostridium).
- Symbiotic with plants:
- Legume–rhizobium symbioses (e.g., peas, beans, clover, alfalfa with Rhizobium/Bradyrhizobium species).
- Non-legume symbioses (e.g., alder trees with Frankia).
- In symbioses, plants provide carbohydrates and a low-oxygen environment (nodules often contain leghemoglobin to bind oxygen), while bacteria fix nitrogen for the plant as ammonium.
- Abiotic nitrogen fixation:
- Lightning: high energy breaks $N_2$ and $O_2$, forming nitrogen oxides ($NO_x$), which dissolve in rain and are deposited as nitrate $NO_3^-$.
- Industrial fixation (Haber–Bosch process): production of ammonia fertilizer from $N_2$ and $H_2$ under high pressure and temperature using catalysts.
Biological fixation historically dominated the input of reactive nitrogen, but human-made fixation now rivals or exceeds natural rates.
Ammonification (Mineralization): From Organic N to Ammonium
Ammonification, also called nitrogen mineralization, is the conversion of organic nitrogen into ammonia / ammonium.
- Carried out primarily by decomposer microorganisms (various bacteria and fungi) that break down:
- Dead plant and animal material.
- Waste products such as urea, uric acid, and feces.
- During decomposition, nitrogen in proteins, nucleic acids, and other molecules is released as $NH_3$ (and quickly becomes $NH_4^+$ in moist, slightly acidic environments).
This process returns nitrogen from organic forms back to an inorganic, plant-available pool.
Nitrification: From Ammonium to Nitrate
Nitrification is the aerobic, two-step oxidation of ammonium to nitrate, carried out mainly by specialized chemoautotrophic bacteria and archaea:
- Ammonia oxidation:
- $NH_4^+ \rightarrow NO_2^-$
- Typically carried out by ammonia-oxidizing bacteria (AOB) (e.g., Nitrosomonas) or ammonia-oxidizing archaea (AOA).
- Releases energy used by these microbes to fix CO$_2$.
- Nitrite oxidation:
- $NO_2^- \rightarrow NO_3^-$
- Performed by nitrite-oxidizing bacteria (NOB) (e.g., Nitrobacter, Nitrospira).
Both steps can be summarized as:
$$
NH_4^+ \rightarrow NO_2^- \rightarrow NO_3^-
$$
Important features:
- Requires oxygen: nitrification is most active in well-aerated soils and oxygenated water.
- Environmental effects:
- Produces nitrate, which is highly soluble and can be easily taken up by plants, but also easily leached into groundwater.
- Intermediate and side reactions can release nitrous oxide ($N_2O$), a potent greenhouse gas.
Assimilation: Uptake of Inorganic Nitrogen by Organisms
Assimilation is the incorporation of inorganic nitrogen into organic molecules by plants, algae, and many microbes.
- In plants and many autotrophs:
- Nitrate or ammonium is taken up from soil water (or water in aquatic environments) through transport proteins.
- Nitrate is first reduced to ammonium inside the organism:
- $NO_3^- \rightarrow NO_2^- \rightarrow NH_4^+$.
- The resulting ammonium is incorporated into amino acids (e.g., glutamine, glutamate).
- In heterotrophs (animals, many microbes):
- Most obtain nitrogen by eating organic nitrogen (proteins, nucleic acids) already synthesized by autotrophs or other organisms.
- Animals rarely assimilate nitrate directly; they rely on ingested organic nitrogen.
Assimilation transfers reactive inorganic nitrogen into organic biomass, linking inorganic pools with living organisms.
Denitrification: Returning Nitrogen to the Atmosphere
Denitrification is the process by which certain microbes convert nitrate and nitrite back into gaseous forms, mainly $N_2$ and $N_2O$, thus closing the nitrogen cycle.
Overall, a simplified sequence is:
$$
NO_3^- \rightarrow NO_2^- \rightarrow NO \rightarrow N_2O \rightarrow N_2
$$
Key aspects:
- Performed by facultative anaerobic bacteria (e.g., Pseudomonas, Paracoccus) and some archaea and fungi.
- Occurs under low-oxygen or anoxic conditions, such as:
- Waterlogged soils.
- Sediments in lakes, rivers, wetlands, and oceans.
- Micro-sites in soil aggregates where oxygen diffusion is limited.
- Nitrate or nitrite serve as alternative electron acceptors in respiration when oxygen is scarce, allowing microbes to gain energy.
Ecological significance:
- Denitrification removes reactive nitrogen from soil and water, returning it to the atmosphere as $N_2$.
- It is a key loss pathway for nitrate from ecosystems, counterbalancing nitrogen fixation and atmospheric deposition.
- Incomplete denitrification can release substantial amounts of $N_2O$, contributing to climate change and stratospheric ozone depletion.
Anammox and Other Specialized Processes
In addition to the classical steps, there are specialized microbial pathways that play important roles, especially in aquatic and sedimentary environments:
- Anammox (anaerobic ammonium oxidation):
- Reaction (simplified):
$$
NH_4^+ + NO_2^- \rightarrow N_2 + 2H_2O
$$
- Carried out by specialized bacteria in the phylum Planctomycetes.
- Occurs in anoxic, yet nitrate/nitrite-rich environments such as:
- Oxygen minimum zones in the ocean.
- Anoxic sediments.
- Wastewater treatment reactors.
- An important pathway for the removal of fixed nitrogen from aquatic systems, bypassing some steps of classical nitrification–denitrification.
- Dissimilatory nitrate reduction to ammonium (DNRA):
- $NO_3^- \rightarrow NO_2^- \rightarrow NH_4^+$.
- Occurs under low-oxygen conditions when microbes use nitrate to gain energy but retain nitrogen in reduced form ($NH_4^+$) rather than releasing it as $N_2$.
- Helps retain nitrogen within ecosystems instead of losing it to the atmosphere.
These pathways refine the view of the nitrogen cycle from a simple loop to a network of parallel and intersecting microbially mediated processes.
Nitrogen Cycle in Terrestrial and Aquatic Ecosystems
The basic processes are similar everywhere, but their balance and importance differ between land and water.
Terrestrial Ecosystems (Soils and Plants)
In soils, the main features include:
- Inputs:
- Biological nitrogen fixation by free-living and symbiotic microbes.
- Deposition of nitrate and ammonium from the atmosphere (both natural and human-derived).
- Application of synthetic nitrogen fertilizers in agricultural systems.
- Transformations:
- Ammonification of organic matter from plant litter, dead organisms, and wastes.
- Nitrification in aerated soil layers, producing nitrate.
- Assimilation by plant roots of ammonium and nitrate.
- Immobilization of inorganic nitrogen into microbial biomass and soil organic matter.
- Losses:
- Denitrification in anoxic microsites or waterlogged soils, releasing $N_2$ and $N_2O$.
- Leaching of nitrate into deeper soil layers and groundwater.
- Erosion and runoff carrying particulate organic nitrogen and dissolved inorganic nitrogen into water bodies.
The balance of these processes strongly influences soil fertility, plant productivity, and pollution of groundwater and surface waters.
Aquatic Ecosystems (Freshwaters, Oceans, Wetlands)
In aquatic systems:
- Inputs:
- Riverine inflow of nitrate, ammonium, and organic nitrogen from land.
- Direct atmospheric deposition of reactive nitrogen.
- Biological nitrogen fixation by cyanobacteria and some heterotrophic bacteria.
- Internal cycling:
- Ammonification of organic nitrogen in the water column and sediments.
- Nitrification mainly in oxygenated layers (surface waters, sediment–water interfaces).
- Assimilation by phytoplankton, algae, and aquatic plants.
- Sinking of organic matter and subsequent decomposition in deeper waters and sediments.
- Losses:
- Denitrification and anammox in anoxic sediments and oxygen minimum zones.
- Burial of organic nitrogen in sediments over long timescales.
Wetlands, estuaries, and coastal zones often act as filters, where denitrification and anammox remove excess nitrate from water before it enters open oceans, although overloading can overwhelm this function.
Human Impacts on the Nitrogen Cycle
Human activities have dramatically altered the global nitrogen cycle, especially over the last century.
Industrial and Agricultural Nitrogen Fixation
- The Haber–Bosch process produces large quantities of ammonia for fertilizers, explosives, and chemicals.
- Combined with increased planting of nitrogen-fixing crops (legumes), this has roughly doubled the rate of nitrogen fixation compared with pre-industrial times.
- Excess fertilizer nitrogen can:
- Accumulate in soils.
- Leach as nitrate into groundwater and surface waters.
- Run off into rivers, lakes, and coastal seas.
Fossil Fuel Combustion and NOx Emissions
- Burning fossil fuels releases nitrogen oxides ($NO_x$) into the atmosphere:
- Contribute to smog and ozone formation in the lower atmosphere.
- Lead to acid deposition (acid rain) when transformed into nitric acid.
- Deposit nitrate on land and water, adding to nitrogen inputs far from emission sources.
Environmental Consequences of Altered Nitrogen Fluxes
Key consequences include:
- Eutrophication:
- Excess nitrogen (often with phosphorus) stimulates algal blooms in lakes, rivers, and coastal waters.
- Decomposition of algal biomass consumes oxygen, leading to hypoxic or anoxic “dead zones” that cannot support many animals (e.g., in the Gulf of Mexico, Baltic Sea).
- Loss of biodiversity:
- Nitrogen-enriched conditions can favor fast-growing, nitrophilous plants over species adapted to low-nutrient conditions.
- Plant community changes cascade to insects, fungi, and other organisms.
- Greenhouse gas emissions:
- Increased nitrification and denitrification lead to higher emissions of nitrous oxide ($N_2O$):
- A greenhouse gas with a much higher warming potential than CO$_2$ (per molecule).
- Also contributes to stratospheric ozone depletion.
- Human health impacts:
- High nitrate concentrations in drinking water can be harmful, particularly for infants (risk of methemoglobinemia or “blue baby syndrome”).
- $NO_x$ and derived pollutants can exacerbate respiratory problems.
Managing and Restoring the Nitrogen Cycle
Various strategies aim to reduce disruptive nitrogen fluxes and restore a more sustainable nitrogen balance:
- Improved fertilizer management:
- Matching nitrogen application to crop needs (precision agriculture) to reduce surplus.
- Use of slow-release fertilizers and nitrification inhibitors to limit leaching and $N_2O$ emissions.
- Enhancing biological nitrogen use efficiency:
- Crop rotations with legumes to supply biologically fixed nitrogen.
- Breeding or engineering crops for better nitrogen uptake and utilization.
- Restoration of natural filters:
- Protecting and restoring wetlands and riparian zones that remove nitrate by denitrification.
- Maintaining healthy soils with high organic matter and microbial diversity.
- Reducing emissions of NOx:
- Cleaner combustion technologies.
- Catalytic converters in vehicles.
- Transition to low- or zero-emission energy sources.
These measures aim to balance the benefits of reactive nitrogen for food production with protecting ecosystems, climate, and human health.
Summary of the Nitrogen Cycle
The nitrogen cycle is a complex web of biological and chemical processes that:
- Converts inert atmospheric $N_2$ into reactive forms usable by organisms (nitrogen fixation).
- Transfers nitrogen through food webs via assimilation and consumption.
- Returns nitrogen to inorganic forms by decomposition and ammonification.
- Transforms ammonium into nitrate in oxygenated environments (nitrification).
- Removes reactive nitrogen from ecosystems by converting it back to gas (denitrification, anammox).
- Is strongly influenced and, in many regions, profoundly altered by human activities.
Understanding the nitrogen cycle is crucial for managing ecosystems, maintaining agricultural productivity, and addressing global environmental issues such as eutrophication, climate change, and air and water pollution.