 | This article'slead sectionmay be too short to adequatelysummarize the key points. Please consider expanding the lead toprovide an accessible overview of all important aspects of the article.(December 2020) |
Microbial metabolism is the means by which amicrobe obtains the energy and nutrients (e.g.carbon) it needs to live and reproduce. Microbes use many different types ofmetabolic 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'secological niche, and often allow for that microbe to be useful inindustrial processes or responsible forbiogeochemical cycles.
All microbial metabolisms can be arranged according to three principles:
1. How the organism obtains carbon for synthesizing cell mass:[1]
2. How the organism obtainsreducing equivalents (hydrogen atoms or electrons) used either in energy conservation or in biosynthetic reactions:
3. How the organism obtains energy for living and growing:
In practice, these terms are almost freely combined. Typical examples are as follows:
Some microbes are heterotrophic (more precisely chemoorganoheterotrophic), using organic compounds as both carbon and energy sources. Heterotrophic microbes live off of nutrients that they scavenge from living hosts (ascommensals orparasites) or find in dead organic matter of all kind (saprophages). Microbial metabolism is the main contribution for the bodily decay of all organisms after death. Manyeukaryotic microorganisms are heterotrophic bypredation orparasitism, properties also found in some bacteria such asBdellovibrio (an intracellular parasite of other bacteria, causing death of its victims) and Myxobacteria such asMyxococcus (predators of other bacteria which are killed and used by cooperating swarms of many single cells of Myxobacteria). Mostpathogenic bacteria can be viewed as heterotrophic parasites of humans or the other eukaryotic species they affect. Heterotrophic microbes are extremely abundant in nature and are responsible for the breakdown of large organicpolymers such ascellulose,chitin orlignin which are generally indigestible to larger animals. Generally, the oxidative breakdown of large polymers to carbon dioxide (mineralization) requires several different organisms, with one breaking down the polymer into its constituent monomers, one able to use the monomers and excreting simpler waste compounds as by-products, and one able to use the excreted wastes. There are many variations on this theme, as different organisms are able to degrade different polymers and secrete different waste products. Some organisms are even able to degrade more recalcitrant compounds such as petroleum compounds or pesticides, making them useful inbioremediation.
Biochemically,prokaryotic heterotrophic metabolism is much more versatile than that of eukaryotic organisms, although many prokaryotes share the most basic metabolic models with eukaryotes, e. g. usingglycolysis (also calledEMP pathway) for sugar metabolism and thecitric acid cycle to degradeacetate, producing energy in the form ofATP and reducing power in the form ofNADH orquinols. These basic pathways are well conserved because they are also involved in biosynthesis of many conserved building blocks needed for cell growth (sometimes in reverse direction). However, manybacteria andarchaea utilize alternative metabolic pathways other than glycolysis and the citric acid cycle. A well-studied example is sugar metabolism via theketo-deoxy-phosphogluconate pathway (also calledED pathway) inPseudomonas. Moreover, there is a third alternative sugar-catabolic pathway used by some bacteria, thepentose phosphate pathway. The metabolic diversity and ability of prokaryotes to use a large variety of organic compounds arises from the much deeper evolutionary history and diversity of prokaryotes, as compared to eukaryotes. It is also noteworthy that themitochondrion, the small membrane-bound intracellular organelle that is the site of eukaryotic oxygen-using energy metabolism, arose from theendosymbiosis of a bacterium related to obligate intracellularRickettsia, and also to plant-associatedRhizobium orAgrobacterium. Therefore, it is not surprising that all mitrochondriate eukaryotes share metabolic properties with thesePseudomonadota. Most microbesrespire (use anelectron transport chain), althoughoxygen is not the onlyterminal electron acceptor that may be used. As discussed below, the use of terminal electron acceptors other than oxygen has important biogeochemical consequences.
Fermentation is a specific type of heterotrophic metabolism that usesorganic carbon instead of oxygen as a terminal electron acceptor. This means that these organisms do not use an electron transport chain to oxidize NADH toNAD+
and therefore must have an alternative method of using this reducing power and maintaining a supply ofNAD+
for the proper functioning of normal metabolic pathways (e.g. glycolysis). As oxygen is not required, fermentative organisms areanaerobic. Many organisms can use fermentation under anaerobic conditions andaerobic respiration when oxygen is present. These organisms arefacultative anaerobes. To avoid the overproduction of NADH,obligately fermentative organisms usually do not have a complete citric acid cycle. Instead of using anATP synthase as inrespiration, ATP in fermentative organisms is produced bysubstrate-level phosphorylation where aphosphate group is transferred from a high-energy organic compound toADP to form ATP. As a result of the need to produce high energy phosphate-containing organic compounds (generally in the form ofCoenzyme A-esters) fermentative organisms use NADH and othercofactors to produce many different reduced metabolic by-products, often includinghydrogen gas (H
2). These reduced organic compounds are generally smallorganic acids andalcohols derived frompyruvate, the end product ofglycolysis. Examples includeethanol,acetate,lactate, andbutyrate. Fermentative organisms are very important industrially and are used to make many different types of food products. The different metabolic end products produced by each specific bacterial species are responsible for the different tastes and properties of each food.
Not all fermentative organisms use substrate-levelphosphorylation. Instead, some organisms are able to couple the oxidation of low-energy organic compounds directly to the formation of aproton motive force orsodium-motive force and thereforeATP synthesis. Examples of these unusual forms of fermentation includesuccinate fermentation byPropionigenium modestum andoxalate fermentation byOxalobacter formigenes. These reactions are extremely low-energy yielding. Humans and other higher animals also use fermentation to producelactate from excess NADH, although this is not the major form of metabolism as it is in fermentative microorganisms.
Methylotrophy refers to the ability of an organism to useC1-compounds as energy sources. These compounds includemethanol,methyl amines,formaldehyde, andformate. Several other less common substrates may also be used for metabolism, all of which lack carbon-carbon bonds. Examples of methylotrophs include the bacteriaMethylomonas andMethylobacter.Methanotrophs are a specific type of methylotroph that are also able to usemethane (CH
4) as a carbon source by oxidizing it sequentially to methanol (CH
3OH), formaldehyde (CH
2O), formate (HCOO−
), and carbon dioxide CO2 initially using the enzymemethane monooxygenase. As oxygen is required for this process, all (conventional) methanotrophs areobligate aerobes. Reducing power in the form ofquinones and NADH is produced during these oxidations to produce a proton motive force and therefore ATP generation. Methylotrophs and methanotrophs are not considered as autotrophic, because they are able to incorporate some of the oxidized methane (or other metabolites) into cellular carbon before it is completely oxidized to CO2 (at the level of formaldehyde), using either theserine pathway (Methylosinus,Methylocystis) or theribulose monophosphate pathway (Methylococcus), depending on the species of methylotroph.
In addition to aerobic methylotrophy, methane can also be oxidized anaerobically. This occurs by a consortium of sulfate-reducing bacteria and relatives ofmethanogenicArchaea working syntrophically (see below). Little is currently known about the biochemistry and ecology of this process.
Methanogenesis is the biological production of methane. It is carried out by methanogens, strictlyanaerobic Archaea such asMethanococcus,Methanocaldococcus,Methanobacterium,Methanothermus,Methanosarcina,Methanosaeta andMethanopyrus. The biochemistry of methanogenesis is unique in nature in its use of a number of unusualcofactors to sequentially reduce methanogenic substrates to methane, such ascoenzyme M andmethanofuran.[4] These cofactors are responsible (among other things) for the establishment of aproton gradient across the outer membrane thereby driving ATP synthesis. Several types of methanogenesis occur, differing in the starting compounds oxidized. Some methanogens reduce carbon dioxide (CO2) to methane (CH
4) using electrons (most often) from hydrogen gas (H
2) chemolithoautotrophically. These methanogens can often be found in environments containing fermentative organisms. The tight association of methanogens and fermentative bacteria can be considered to be syntrophic (see below) because the methanogens, which rely on the fermentors for hydrogen, relieve feedback inhibition of the fermentors by the build-up of excess hydrogen that would otherwise inhibit their growth. This type of syntrophic relationship is specifically known asinterspecies hydrogen transfer. A second group of methanogens use methanol (CH
3OH) as a substrate for methanogenesis. These are chemoorganotrophic, but still autotrophic in using CO2 as only carbon source. The biochemistry of this process is quite different from that of the carbon dioxide-reducing methanogens. Lastly, a third group of methanogens produce both methane and carbon dioxide fromacetate (CH
3COO−
) with the acetate being split between the two carbons. These acetate-cleaving organisms are the only chemoorganoheterotrophic methanogens. All autotrophic methanogens use a variation of thereductive acetyl-CoA pathway to fix CO2 and obtain cellular carbon.
Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple species to achieve achemical reaction that, on its own, would be energetically unfavorable. The best studied example of this process is the oxidation of fermentative end products (such as acetate,ethanol andbutyrate) by organisms such asSyntrophomonas. Alone, the oxidation of butyrate to acetate and hydrogen gas is energetically unfavorable. However, when ahydrogenotrophic (hydrogen-using) methanogen is present the use of the hydrogen gas will significantly lower the concentration of hydrogen (down to 10−5 atm) and thereby shift theequilibrium of the butyrate oxidation reaction under standard conditions (ΔGº') to non-standard conditions (ΔG'). Because the concentration of one product is lowered, the reaction is "pulled" towards the products and shifted towards net energetically favorable conditions (for butyrate oxidation: ΔGº'= +48.2 kJ/mol, but ΔG' = -8.9 kJ/mol at 10−5 atm hydrogen and even lower if also the initially produced acetate is further metabolized by methanogens). Conversely, the available free energy from methanogenesis is lowered from ΔGº'= -131 kJ/mol under standard conditions to ΔG' = -17 kJ/mol at 10−5 atm hydrogen. This is an example of intraspecies hydrogen transfer. In this way, low energy-yielding carbon sources can be used by a consortium of organisms to achieve further degradation and eventualmineralization of these compounds. These reactions help prevent the excesssequestration of carbon over geologic time scales, releasing it back to the biosphere in usable forms such as methane and CO2.
Aerobic metabolism occurs in Bacteria, Archaea and Eucarya. Although most bacterial species are anaerobic, many are facultative or obligate aerobes. The majority of archaeal species live in extreme environments that are often highly anaerobic. There are, however, several cases of aerobic archaea such asHaiobacterium,Thermoplasma,Sulfolobus andYymbaculum. Most of the known eukaryotes carry out aerobic metabolism within theirmitochondria which is an organelle that had asymbiogenesis origin fromprokarya . Allaerobic organisms containoxidases of thecytochrome oxidase super family, but some members of the Pseudomonadota (E. coli andAcetobacter) can also use an unrelated cytochrome bd complex as a respiratory terminal oxidase.[5]
Whileaerobic organisms during respiration use oxygen as aterminal electron acceptor,anaerobic organisms use other electron acceptors. These inorganic compounds release less energy incellular respiration, which leads to slower growth rates than aerobes. Manyfacultative anaerobes can use either oxygen or alternative terminal electron acceptors for respiration depending on the environmental conditions.
Most respiring anaerobes are heterotrophs, although some do live autotrophically. All of the processes described below are dissimilative, meaning that they are used during energy production and not to provide nutrients for the cell (assimilative). Assimilative pathways for many forms ofanaerobic respiration are also known.
Denitrification is the utilization ofnitrate (NO−
3) as a terminal electron acceptor. It is a widespread process that is used by many members of the Pseudomonadota. Many facultative anaerobes use denitrification because nitrate, like oxygen, has a high reduction potential. Many denitrifying bacteria can also use ferriciron (Fe3+
) and some organicelectron acceptors. Denitrification involves the stepwise reduction of nitrate tonitrite (NO−
2),nitric oxide (NO),nitrous oxide (N
2O), and dinitrogen (N
2) by the enzymesnitrate reductase,nitrite reductase, nitric oxide reductase, and nitrous oxide reductase, respectively. Protons are transported across the membrane by the initial NADH reductase, quinones, and nitrous oxide reductase to produce the electrochemical gradient critical for respiration. Some organisms (e.g.E. coli) only produce nitrate reductase and therefore can accomplish only the first reduction leading to the accumulation of nitrite. Others (e.g.Paracoccus denitrificans orPseudomonas stutzeri) reduce nitrate completely. Complete denitrification is an environmentally significant process because some intermediates of denitrification (nitric oxide and nitrous oxide) are importantgreenhouse gases that react withsunlight andozone to produce nitric acid, a component ofacid rain. Denitrification is also important in biologicalwastewater treatment where it is used to reduce the amount of nitrogen released into the environment thereby reducingeutrophication. Denitrification can be determined via anitrate reductase test.
Dissimilatory sulfate reduction is a relatively energetically poor process used by many Gram-negative bacteria found within theThermodesulfobacteriota, Gram-positive organisms relating toDesulfotomaculum or the archaeonArchaeoglobus.Hydrogen sulfide (H
2S) is produced as a metabolic end product. For sulfate reduction electron donors and energy are needed.
Many sulfate reducers are organotrophic, using carbon compounds such as lactate and pyruvate (among many others) aselectron donors,[6] while others are lithotrophic, using hydrogen gas (H
2) as an electron donor.[7] Some unusual autotrophic sulfate-reducing bacteria (e.g.Desulfotignum phosphitoxidans) can usephosphite (HPO−
3) as an electron donor[8] whereas others (e.g.Desulfovibrio sulfodismutans,Desulfocapsa thiozymogenes,Desulfocapsa sulfoexigens) are capable of sulfur disproportionation (splitting one compound into two different compounds, in this case an electron donor and an electron acceptor) using elemental sulfur (S0), sulfite (SO2−
3), and thiosulfate (S
2O2−
3) to produce both hydrogen sulfide (H
2S) and sulfate (SO2−
4).[9]
All sulfate-reducing organisms are strict anaerobes. Because sulfate is energetically stable, before it can be metabolized it must first be activated by adenylation to form APS (adenosine 5'-phosphosulfate) thereby consuming ATP. The APS is then reduced by the enzyme APS reductase to formsulfite (SO2−
3) andAMP. In organisms that use carbon compounds as electron donors, the ATP consumed is accounted for by fermentation of the carbon substrate. The hydrogen produced during fermentation is actually what drives respiration during sulfate reduction.
Acetogenesis is a type of microbial metabolism that uses hydrogen (H
2) as an electron donor and carbon dioxide (CO2) as an electron acceptor to produce acetate, the same electron donors and acceptors used in methanogenesis (see above). Bacteria that can autotrophically synthesize acetate are called homoacetogens. Carbon dioxidereduction in all homoacetogens occurs by the acetyl-CoA pathway. This pathway is also used for carbon fixation by autotrophic sulfate-reducing bacteria and hydrogenotrophic methanogens. Often homoacetogens can also be fermentative, using the hydrogen and carbon dioxide produced as a result of fermentation to produce acetate, which is secreted as an end product.
Ferric iron (Fe3+
) is a widespread anaerobic terminal electron acceptor both for autotrophic and heterotrophic organisms. Electron flow in these organisms is similar to those inelectron transport, ending in oxygen or nitrate, except that in ferric iron-reducing organisms the final enzyme in this system is a ferric iron reductase. Model organisms includeShewanella putrefaciens andGeobacter metallireducens. Since some ferric iron-reducing bacteria (e.g.G. metallireducens) can use toxichydrocarbons such astoluene as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron-rich contaminatedaquifers.
Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms (including the iron-reducing bacteria mentioned above) can use otherinorganic ions in anaerobic respiration. While these processes may often be less significant ecologically, they are of considerable interest for bioremediation, especially whenheavy metals orradionuclides are used as electron acceptors. Examples include:
A number of organisms, instead of using inorganic compounds as terminal electron acceptors, are able to use organic compounds to accept electrons from respiration. Examples include:
TMAO is a chemical commonly produced byfish, and when reduced to TMA produces a strong odor. DMSO is a common marine and freshwater chemical which is also odiferous when reduced to DMS. Reductive dechlorination is the process by which chlorinated organic compounds are reduced to form their non-chlorinated endproducts. As chlorinated organic compounds are often important (and difficult to degrade) environmental pollutants, reductive dechlorination is an important process in bioremediation.
Chemolithotrophy is a type of metabolism where energy is obtained from the oxidation of inorganic compounds. Most chemolithotrophic organisms are also autotrophic. There are two major objectives to chemolithotrophy: the generation of energy (ATP) and the generation of reducing power (NADH).
Many organisms are capable of using hydrogen (H
2) as a source of energy. While several mechanisms of anaerobic hydrogenoxidation have been mentioned previously (e.g. sulfate reducing- and acetogenic bacteria), the chemical energy of hydrogen can be used in the aerobic Knallgas reaction:[10]
In these organisms, hydrogen is oxidized by a membrane-boundhydrogenase causing proton pumping via electron transfer to various quinones andcytochromes. In many organisms, a second cytoplasmic hydrogenase is used to generate reducing power in the form of NADH, which is subsequently used to fix carbon dioxide via theCalvin cycle. Hydrogen-oxidizing organisms, such asCupriavidus necator (formerlyRalstonia eutropha), often inhabit oxic-anoxic interfaces in nature to take advantage of the hydrogen produced by anaerobic fermentative organisms while still maintaining a supply of oxygen.[11]
Sulfur oxidation involves the oxidation of reduced sulfur compounds (such as sulfideH
2S), inorganic sulfur (S), and thiosulfate (S
2O2−
3) to formsulfuric acid (H
2SO
4). A classic example of a sulfur-oxidizing bacterium isBeggiatoa, a microbe originally described bySergei Winogradsky, one of the founders ofenvironmental microbiology. Another example isParacoccus. Generally, the oxidation of sulfide occurs in stages, with inorganic sulfur being stored either inside or outside of the cell until needed. This two step process occurs because energetically sulfide is a better electron donor than inorganic sulfur or thiosulfate, allowing for a greater number of protons to be translocated across the membrane. Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle usingreverse electron flow, an energy-requiring process that pushes the electrons against theirthermodynamic gradient to produce NADH. Biochemically, reduced sulfur compounds are converted to sulfite (SO2−
3) and subsequently converted to sulfate (SO2−
4) by the enzymesulfite oxidase.[12] Some organisms, however, accomplish the same oxidation using a reversal of the APS reductase system used by sulfate-reducing bacteria (seeabove). In all cases the energy liberated is transferred to the electron transport chain for ATP and NADH production.[12] In addition to aerobic sulfur oxidation, some organisms (e.g.Thiobacillus denitrificans) use nitrate (NO−
3) as a terminal electron acceptor and therefore grow anaerobically.
Ferrous iron is a soluble form of iron that is stable at extremely lowpHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric (Fe3+
) form and is hydrolyzed abiotically to insolubleferric hydroxide (Fe(OH)
3). There are three distinct types of ferrous iron-oxidizing microbes. The first areacidophiles, such as the bacteriaAcidithiobacillus ferrooxidans andLeptospirillum ferrooxidans, as well as thearchaeonFerroplasma. These microbes oxidize iron in environments that have a very low pH and are important inacid mine drainage. The second type of microbes oxidize ferrous iron at near-neutral pH. These micro-organisms (for exampleGallionella ferruginea,Leptothrix ochracea, orMariprofundus ferrooxydans) live at the oxic-anoxic interfaces and are microaerophiles. The third type of iron-oxidizing microbes are anaerobic photosynthetic bacteria such asRhodopseudomonas,[13] which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation. Biochemically, aerobic iron oxidation is a very energetically poor process which therefore requires large amounts of iron to be oxidized by the enzymerusticyanin to facilitate the formation of proton motive force. Like sulfur oxidation, reverse electron flow must be used to form the NADH used for carbon dioxide fixation via the Calvin cycle.
Nitrification is the process by whichammonia (NH
3) is converted to nitrate (NO−
3). Nitrification is actually the net result of two distinct processes: oxidation of ammonia to nitrite (NO−
2) by nitrosifying bacteria (e.g.Nitrosomonas) and oxidation of nitrite to nitrate by the nitrite-oxidizing bacteria (e.g.Nitrobacter). Both of these processes are extremely energetically poor leading to very slow growth rates for both types of organisms. Biochemically, ammonia oxidation occurs by the stepwise oxidation of ammonia tohydroxylamine (NH
2OH) by the enzymeammonia monooxygenase in thecytoplasm, followed by the oxidation of hydroxylamine to nitrite by the enzymehydroxylamine oxidoreductase in theperiplasm.
Electron and proton cycling are very complex but as a net result only one proton is translocated across the membrane per molecule of ammonia oxidized. Nitrite oxidation is much simpler, with nitrite being oxidized by the enzymenitrite oxidoreductase coupled to proton translocation by a very short electron transport chain, again leading to very low growth rates for these organisms. Oxygen is required in both ammonia and nitrite oxidation, meaning that both nitrosifying and nitrite-oxidizing bacteria are aerobes. As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.
In 2015, two groups independently showed the microbial genusNitrospira is capable of complete nitrification (Comammox).[14][15]
Anammox stands for anaerobic ammonia oxidation and the organisms responsible were relatively recently discovered, in the late 1990s.[16] This form of metabolism occurs in members of thePlanctomycetota (e.g. "CandidatusBrocadia anammoxidans") and involves the coupling of ammonia oxidation to nitrite reduction. As oxygen is not required for this process, these organisms are strict anaerobes.Hydrazine (N
2H
4 – rocket fuel) is produced as an intermediate during anammox metabolism. To deal with the high toxicity of hydrazine, anammox bacteria contain a hydrazine-containing intracellular organelle called the anammoxasome, surrounded by highly compact (and unusual)ladderane lipid membrane. These lipids are unique in nature, as is the use of hydrazine as a metabolic intermediate. Anammox organisms are autotrophs although the mechanism for carbon dioxide fixation is unclear. Because of this property, these organisms could be used to remove nitrogen inindustrial wastewater treatment processes.[17] Anammox has also been shown to have widespread occurrence in anaerobic aquatic systems and has been speculated to account for approximately 50% of nitrogen gas production in the ocean.[18]
In July 2020 researchers report the discovery ofchemolithoautotrophic bacterial culture thatfeeds on the metalmanganese after performing unrelated experiments and named its bacterial speciesCandidatus Manganitrophus noduliformans andRamlibacter lithotrophicus.[19][20][21]
Many microbes (phototrophs) are capable of using light as a source of energy to produceATP andorganic compounds such ascarbohydrates,lipids, andproteins. Of these,algae are particularly significant because they are oxygenic, using water as anelectron donor for electron transfer during photosynthesis.[22] Phototrophic bacteria are found in the phyla "Cyanobacteria",Chlorobiota,Pseudomonadota,Chloroflexota, andBacillota.[23] Along with plants these microbes are responsible for all biological generation of oxygen gas onEarth. Becausechloroplasts were derived from a lineage of the Cyanobacteria, the general principles of metabolism in theseendosymbionts can also be applied to chloroplasts.[24] In addition to oxygenic photosynthesis, many bacteria can also photosynthesize anaerobically, typically using sulfide (H
2S) as an electron donor to produce sulfate. Inorganic sulfur (S
0), thiosulfate (S
2O2−
3) and ferrous iron (Fe2+
) can also be used by some organisms. Phylogenetically, all oxygenic photosynthetic bacteria are Cyanobacteria, whileanoxygenic photosynthetic bacteria belong to the purple bacteria (Pseudomonadota),green sulfur bacteria (e.g.,Chlorobium),green non-sulfur bacteria (e.g.,Chloroflexus), or theheliobacteria (Low %G+C Gram positives). In addition to these organisms, some microbes (e.g. the ArchaeonHalobacterium or the bacteriumRoseobacter, among others) can utilize light to produce energy using the enzymebacteriorhodopsin, a light-driven proton pump. However, there are no known Archaea that carry out photosynthesis.[23]
As befits the large diversity of photosynthetic bacteria, there are many different mechanisms by which light is converted into energy for metabolism. All photosynthetic organisms locate theirphotosynthetic reaction centers within a membrane, which may be invaginations of thecytoplasmic membrane (Pseudomonadota),thylakoid membranes ("Cyanobacteria"), specialized antenna structures calledchlorosomes (Green sulfur and non-sulfur bacteria), or the cytoplasmic membrane itself (heliobacteria). Different photosynthetic bacteria also contain different photosynthetic pigments, such aschlorophylls andcarotenoids, allowing them to take advantage of different portions of theelectromagnetic spectrum and thereby inhabit differentniches. Some groups of organisms contain more specialized light-harvesting structures (e.g.phycobilisomes in Cyanobacteria and chlorosomes in Green sulfur and non-sulfur bacteria), allowing for increased efficiency in light utilization.
Biochemically, anoxygenic photosynthesis is very different from oxygenic photosynthesis. Cyanobacteria (and by extension, chloroplasts) use theZ scheme of electron flow in which electrons eventually are used to form NADH. Two different reaction centers (photosystems) are used and proton motive force is generated both by using cyclic electron flow and the quinone pool. In anoxygenic photosynthetic bacteria, electron flow is cyclic, with all electrons used in photosynthesis eventually being transferred back to the single reaction center. A proton motive force is generated using only the quinone pool. In heliobacteria, Green sulfur, and Green non-sulfur bacteria, NADH is formed using the proteinferredoxin, an energetically favorable reaction. In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center. In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase.
Most photosynthetic microbes are autotrophic, fixing carbon dioxide via the Calvin cycle. Some photosynthetic bacteria (e.g.Chloroflexus) are photoheterotrophs, meaning that they use organic carbon compounds as a carbon source for growth. Some photosynthetic organisms also fix nitrogen (see below).
Nitrogen is an element required for growth by all biological systems. While extremely common (80% by volume) in theatmosphere, dinitrogen gas (N
2) is generally biologically inaccessible due to its highactivation energy. Throughout all of nature, only specialized bacteria and Archaea are capable of nitrogen fixation, converting dinitrogen gas into ammonia (NH
3), which is easily assimilated by all organisms.[25] These prokaryotes, therefore, are very important ecologically and are often essential for the survival of entire ecosystems. This is especially true in the ocean, where nitrogen-fixing cyanobacteria are often the only sources of fixed nitrogen, and in soils, where specialized symbioses exist betweenlegumes and their nitrogen-fixing partners to provide the nitrogen needed by these plants for growth.
Nitrogen fixation can be found distributed throughout nearly all bacterial lineages and physiological classes but is not a universal property. Because the enzymenitrogenase, responsible for nitrogen fixation, is very sensitive to oxygen which will inhibit it irreversibly, all nitrogen-fixing organisms must possess some mechanism to keep the concentration of oxygen low. Examples include:
The production and activity of nitrogenases is very highly regulated, both because nitrogen fixation is an extremely energetically expensive process (16–24 ATP are used perN
2 fixed) and due to the extreme sensitivity of the nitrogenase to oxygen.
{{cite book}}:|journal= ignored (help)