Diazotroph
Encyclopedia
Diazotrophs are bacteria
and archaea
that fix
atmospheric nitrogen
gas into a more usable form such as ammonia
.
A diazotroph is an organism that is able to grow without external sources of fixed nitrogen. Examples of organisms that do this are rhizobia
and Frankia
(in symbiosis) and Azospirillum. All diazotrophs contain iron-molybdenum nitrogenase
systems. Two of the most studied systems are those of Klebsiella pneumoniae
and Azotobacter vinelandii
. These systems are used because of their genetic tractability and their fast growth.
but also a couple of Archaea
). Even within a species that can fix nitrogen there may be strains that do not fix nitrogen. Fixation is shut off when other sources of nitrogen are available, and, for many species, when oxygen is at high partial pressure. Bacteria have different ways of dealing with the debilitating effects of oxygen on nitrogenases, listed below.
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
and archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
that fix
Nitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
atmospheric nitrogen
Nitrogen
Nitrogen is a chemical element that has the symbol N, atomic number of 7 and atomic mass 14.00674 u. Elemental nitrogen is a colorless, odorless, tasteless, and mostly inert diatomic gas at standard conditions, constituting 78.08% by volume of Earth's atmosphere...
gas into a more usable form such as ammonia
Ammonia
Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...
.
A diazotroph is an organism that is able to grow without external sources of fixed nitrogen. Examples of organisms that do this are rhizobia
Rhizobia
Rhizobia are soil bacteria that fix nitrogen after becoming established inside root nodules of legumes . Rhizobia require a plant host; they cannot independently fix nitrogen...
and Frankia
Frankia
Frankia is a genus of nitrogen fixing, filamentous bacteria that live in symbiosis with actinorhizal plants, similar to the Rhizobia bacteria that are found in the root nodules of legumes in the Fabaceae family. Bacteria of this genus also form root nodules.The genus Frankia was originally named by...
(in symbiosis) and Azospirillum. All diazotrophs contain iron-molybdenum nitrogenase
Nitrogenase
Nitrogenases are enzymes used by some organisms to fix atmospheric nitrogen gas . It is the only known family of enzymes that accomplish this process. Dinitrogen is quite inert because of the strength of its N-N triple bond...
systems. Two of the most studied systems are those of Klebsiella pneumoniae
Klebsiella pneumoniae
Klebsiella pneumoniae is a Gram-negative, non-motile, encapsulated, lactose fermenting, facultative anaerobic, rod shaped bacterium found in the normal flora of the mouth, skin, and intestines....
and Azotobacter vinelandii
Azotobacter vinelandii
Azotobacter vinelandii is diazotroph that can fix nitrogen while grown aerobically. It is a genetically tractable system that is used to study nitrogen fixation...
. These systems are used because of their genetic tractability and their fast growth.
Types of diazotrophs
Diazotrophs are scattered across bacterial taxonomic groups (mostly in the BacteriaBacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
but also a couple of Archaea
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
). Even within a species that can fix nitrogen there may be strains that do not fix nitrogen. Fixation is shut off when other sources of nitrogen are available, and, for many species, when oxygen is at high partial pressure. Bacteria have different ways of dealing with the debilitating effects of oxygen on nitrogenases, listed below.
Free-living diazotrophs
- Anaerobes—these are obligate anaerobes that cannot tolerate oxygen even if they are not fixing nitrogen. They live in habitats low in oxygen, such as soils and decaying vegetable matter. ClostridiumClostridiumClostridium is a genus of Gram-positive bacteria, belonging to the Firmicutes. They are obligate anaerobes capable of producing endospores. Individual cells are rod-shaped, which gives them their name, from the Greek kloster or spindle...
is an example. Sulphate-reducing bacteria are important in ocean sediments (e.g. DesulfovibrioDesulfovibrioDesulfovibrio is a genus of Gram negative sulfate-reducing bacteria. Some species of Desulfovibrio are capable of transduction. Desulfovibrio species are commonly found in aquatic environments with high levels of organic material, as well as in water-logged soils, and form major community members...
), and some Archean methanogens fix nitrogen in muds and animal intestines. - Facultative anaerobes—these species can grow either with or without oxygen, but they only fix nitrogen anaerobically. Often, they respire oxygen as rapidly as it is supplied, keeping the amount of free oxygen low. Examples include Klebsiella pneumoniaeKlebsiella pneumoniaeKlebsiella pneumoniae is a Gram-negative, non-motile, encapsulated, lactose fermenting, facultative anaerobic, rod shaped bacterium found in the normal flora of the mouth, skin, and intestines....
, Bacillus polymyxa, Bacillus macerans, and Escherichia intermedia. - Aerobes—these species require oxygen to grow, yet their nitrogenase is still debilitated if exposed to oxygen. Azotobacter vinelandiiAzotobacter vinelandiiAzotobacter vinelandii is diazotroph that can fix nitrogen while grown aerobically. It is a genetically tractable system that is used to study nitrogen fixation...
is the most studied of these organisms. It uses very high respiration rates, and protective compounds, to prevent oxygen damage. Many other species also reduce the oxygen levels in this way, but with lower respiration rates and lower oxygen tolerance. - Oxygenic photosynthetic bacteria generate oxygen as a by-product of photosynthesisPhotosynthesisPhotosynthesis is a chemical process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight. Photosynthesis occurs in plants, algae, and many species of bacteria, but not in archaea. Photosynthetic organisms are called photoautotrophs, since they can...
, yet some are able to fix nitrogen as well. These are colonial bacteria that have specialized cells (heterocystHeterocystHeterocysts are specialized nitrogen-fixing cells formed by some filamentous cyanobacteria, such as Nostoc punctiforme, Cylindrospermum stagnale and Anabaena sphaerica, during nitrogen starvation. They fix nitrogen from dinitrogen in the air using the enzyme nitrogenase, in order to provide the...
s) that lack the oxygen generating steps of photosynthesis. Examples are Anabaena cylindrica and Nostoc commune. Other cyanobacteria lack heterocysts and can fix nitrogen only in low light and oxygen levels (e.g. Plectonema). - Anoxygenic photosynthetic bacteria do not generate oxygen during photosynthesis, having only a single photosystem which cannot split water. Nitrogenase is expressed under nitrogen limitation. Normally, the expression is regulated via negative feedback from the produced ammonium ion but in the absence of N2, the product is not formed, and the by-product H2 continues unabated [Biohydrogen]. Example species: Rhodobacter sphaeroides, Rhodopseudomonas palustris, Rhodobacter capsulatus.
Symbiotic diazotrophs
- RhizobiaRhizobiaRhizobia are soil bacteria that fix nitrogen after becoming established inside root nodules of legumes . Rhizobia require a plant host; they cannot independently fix nitrogen...
-- these are the species that associate with legumes, plants of the FabaceaeFabaceaeThe Fabaceae or Leguminosae, commonly known as the legume, pea, or bean family, is a large and economically important family of flowering plants. The group is the third largest land plant family, behind only the Orchidaceae and Asteraceae, with 730 genera and over 19,400 species...
family. Oxygen is bound to leghemoglobin in the root nodules that house the bacterial symbionts, and supplied at a rate that will not harm the nitrogenase. - FrankiaFrankiaFrankia is a genus of nitrogen fixing, filamentous bacteria that live in symbiosis with actinorhizal plants, similar to the Rhizobia bacteria that are found in the root nodules of legumes in the Fabaceae family. Bacteria of this genus also form root nodules.The genus Frankia was originally named by...
s -- much less is known about these 'actinorhizal' nitrogen fixers. The bacteria also infect the roots leading to the formation of nodules. Actinorhizal nodules consist of several lobes, each lobe has a similar structure as a lateral root. Frankia is able to colonize the cortical tissue of nodules where it fixes nitrogen. Actinorhizal plants and Frankias also produce hemoglobins, but their role is less well established than for rhizobia. Although at first it appeared that they inhabit sets of unrelated plants (alderAlderAlder is the common name of a genus of flowering plants belonging to the birch family . The genus comprises about 30 species of monoecious trees and shrubs, few reaching large size, distributed throughout the North Temperate Zone and in the Americas along the Andes southwards to...
s, Australian pines, California lilacCeanothusCeanothus L. is a genus of about 50–60 species of shrubs or small trees in the buckthorn family Rhamnaceae. The genus is confined to North America, the center of its distribution in California, with some species in the eastern United States and southeast Canada, and others extending as far south...
, bog myrtle, bitterbrushPurshiaPurshia is a small genus of 5-8 species of flowering plants in the family Rosaceae, native to western North America, where they grow in dry climates from southeast British Columbia in Canada south throughout the western United States to northern Mexico. The classification of Purshia within the...
, DryasDryas (plant)Dryas is a genus of dwarf perennial herbaceous plants in the rose family Rosaceae, native to the arctic and alpine regions of Europe, Asia and North America. The genus is named after the Greek nymph Dryas. The classification of Dryas within the Rosaceae has been unclear...
), revisions to the phylogeny of angiosperms show a close relatedness of these species and the legumes. These footnotes suggest the ontogeny of these replicates rather than the phylogeny. In other words, an ancient gene (from before the angiosperms and gymnosperms diverged) that is unused in most species was reawakened and reused in these species. - Cyanobacteria -- there are also symbiotic cyanobacteria. Some associate with fungi as lichenLichenLichens are composite organisms consisting of a symbiotic organism composed of a fungus with a photosynthetic partner , usually either a green alga or cyanobacterium...
s, with liverwortMarchantiophytaThe Marchantiophyta are a division of bryophyte plants commonly referred to as hepatics or liverworts. Like other bryophytes, they have a gametophyte-dominant life cycle, in which cells of the plant carry only a single set of genetic information....
s, with a fernFernA fern is any one of a group of about 12,000 species of plants belonging to the botanical group known as Pteridophyta. Unlike mosses, they have xylem and phloem . They have stems, leaves, and roots like other vascular plants...
, and with a cycadCycadCycads are seed plants typically characterized by a stout and woody trunk with a crown of large, hard and stiff, evergreen leaves. They usually have pinnate leaves. The individual plants are either all male or all female . Cycads vary in size from having a trunk that is only a few centimeters...
. These do not form nodules (indeed most of the plants do not have roots). Heterocysts exclude the oxygen, as discussed above. The fern association is important agriculturally: the water fern Azolla harbouring AnabaenaAnabaenaAnabaena is a genus of filamentous cyanobacteria that exists as plankton. It is known for its nitrogen fixing abilities, and they form symbiotic relationships with certain plants, such as the mosquito fern. They are one of four genera of cyanobacteria that produce neurotoxins, which are harmful to...
is an important green manure for riceRiceRice is the seed of the monocot plants Oryza sativa or Oryza glaberrima . As a cereal grain, it is the most important staple food for a large part of the world's human population, especially in East Asia, Southeast Asia, South Asia, the Middle East, and the West Indies...
culture. - Association with animals—although diazotrophs have been found in many animal guts, there is usually sufficient ammonia present to suppress nitrogen fixation. TermiteTermiteTermites are a group of eusocial insects that, until recently, were classified at the taxonomic rank of order Isoptera , but are now accepted as the epifamily Termitoidae, of the cockroach order Blattodea...
s on a low nitrogen diet allow for some fixation, but the contribution to the termite's nitrogen supply is negligible. ShipwormShipwormShipworms are not worms at all, but rather a group of unusual saltwater clams with very small shells, notorious for boring into wooden structures that are immersed in sea water, such as piers, docks and wooden ships...
s may be the only species that derive significant benefit from their gut symbionts.