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Microbial metabolism
Microbial metabolism
Microbial metabolism
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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.

Types

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Flow chart to determine the metabolic characteristics of microorganisms
Main article: Primary nutritional groups

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 obtains reducing 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:

Heterotrophic microbial metabolism

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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 (as commensals or parasites) 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. Many eukaryotic microorganisms are heterotrophic by predation or parasitism, properties also found in some bacteria such as Bdellovibrio (an intracellular parasite of other bacteria, causing death of its victims) and Myxobacteria such as Myxococcus (predators of other bacteria which are killed and used by cooperating swarms of many single cells of Myxobacteria). Most pathogenic 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 organic polymers such as cellulose, chitin or lignin 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 in bioremediation.

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. using glycolysis (also called EMP pathway) for sugar metabolism and the citric acid cycle to degrade acetate, producing energy in the form of ATP and reducing power in the form of NADH or quinols. 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, many bacteria and archaea utilize alternative metabolic pathways other than glycolysis and the citric acid cycle. A well-studied example is sugar metabolism via the keto-deoxy-phosphogluconate pathway (also called ED pathway) in Pseudomonas. Moreover, there is a third alternative sugar-catabolic pathway used by some bacteria, the pentose 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 the mitochondrion, the small membrane-bound intracellular organelle that is the site of eukaryotic oxygen-using energy metabolism, arose from the endosymbiosis of a bacterium related to obligate intracellular Rickettsia, and also to plant-associated Rhizobium or Agrobacterium. Therefore, it is not surprising that all mitrochondriate eukaryotes share metabolic properties with these Pseudomonadota. Most microbes respire (use an electron transport chain), although oxygen is not the only terminal electron acceptor that may be used. As discussed below, the use of terminal electron acceptors other than oxygen has important biogeochemical consequences.

Fermentation

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Main article: Fermentation (biochemistry)

Fermentation is a specific type of heterotrophic metabolism that uses organic carbon instead of oxygen as a terminal electron acceptor. This means that these organisms do not use an electron transport chain to oxidize NADH to NAD+
 and therefore must have an alternative method of using this reducing power and maintaining a supply of NAD+
 for the proper functioning of normal metabolic pathways (e.g. glycolysis). As oxygen is not required, fermentative organisms are anaerobic. Many organisms can use fermentation under anaerobic conditions and aerobic respiration when oxygen is present. These organisms are facultative anaerobes. To avoid the overproduction of NADH, obligately fermentative organisms usually do not have a complete citric acid cycle. Instead of using an ATP synthase as in respiration, ATP in fermentative organisms is produced by substrate-level phosphorylation where a phosphate group is transferred from a high-energy organic compound to ADP to form ATP. As a result of the need to produce high energy phosphate-containing organic compounds (generally in the form of Coenzyme A-esters) fermentative organisms use NADH and other cofactors to produce many different reduced metabolic by-products, often including hydrogen gas (H
2). These reduced organic compounds are generally small organic acids and alcohols derived from pyruvate, the end product of glycolysis. Examples include ethanol, acetate, lactate, and butyrate. 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-level phosphorylation. Instead, some organisms are able to couple the oxidation of low-energy organic compounds directly to the formation of a proton motive force or sodium-motive force and therefore ATP synthesis. Examples of these unusual forms of fermentation include succinate fermentation by Propionigenium modestum and oxalate fermentation by Oxalobacter formigenes. These reactions are extremely low-energy yielding. Humans and other higher animals also use fermentation to produce lactate from excess NADH, although this is not the major form of metabolism as it is in fermentative microorganisms.

Special metabolic properties

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Methylotrophy

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Methylotrophy refers to the ability of an organism to use C1-compounds as energy sources. These compounds include methanol, methyl amines, formaldehyde, and formate. Several other less common substrates may also be used for metabolism, all of which lack carbon-carbon bonds. Examples of methylotrophs include the bacteria Methylomonas and Methylobacter. Methanotrophs are a specific type of methylotroph that are also able to use methane (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 enzyme methane monooxygenase. As oxygen is required for this process, all (conventional) methanotrophs are obligate aerobes. Reducing power in the form of quinones 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 the serine pathway (Methylosinus, Methylocystis) or the ribulose 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 of methanogenic Archaea 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, strictly anaerobic Archaea such as Methanococcus, Methanocaldococcus, Methanobacterium, Methanothermus, Methanosarcina, Methanosaeta and Methanopyrus. The biochemistry of methanogenesis is unique in nature in its use of a number of unusual cofactors to sequentially reduce methanogenic substrates to methane, such as coenzyme M and methanofuran.[4] These cofactors are responsible (among other things) for the establishment of a proton 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 as interspecies 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 from acetate (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 the reductive acetyl-CoA pathway to fix CO2 and obtain cellular carbon.

Syntrophy

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Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple species to achieve a chemical 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 and butyrate) by organisms such as Syntrophomonas. Alone, the oxidation of butyrate to acetate and hydrogen gas is energetically unfavorable. However, when a hydrogenotrophic (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 the equilibrium 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 eventual mineralization of these compounds. These reactions help prevent the excess sequestration of carbon over geologic time scales, releasing it back to the biosphere in usable forms such as methane and CO2.

Aerobic respiration

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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 as Haiobacterium, Thermoplasma, Sulfolobus and Yymbaculum. Most of the known eukaryotes carry out aerobic metabolism within their mitochondria which is an organelle that had a symbiogenesis origin from prokarya . All aerobic organisms contain oxidases of the cytochrome oxidase super family, but some members of the Pseudomonadota (E. coli and Acetobacter) can also use an unrelated cytochrome bd complex as a respiratory terminal oxidase.[5]

Anaerobic respiration

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While aerobic organisms during respiration use oxygen as a terminal electron acceptor, anaerobic organisms use other electron acceptors. These inorganic compounds release less energy in cellular respiration, which leads to slower growth rates than aerobes. Many facultative 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 of anaerobic respiration are also known.

Denitrification – nitrate as electron acceptor

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Main article: Denitrification

Denitrification is the utilization of nitrate (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 ferric iron (Fe3+
) and some organic electron acceptors. Denitrification involves the stepwise reduction of nitrate to nitrite (NO−
2), nitric oxide (NO), nitrous oxide (N
2O), and dinitrogen (N
2) by the enzymes nitrate 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 or Pseudomonas stutzeri) reduce nitrate completely. Complete denitrification is an environmentally significant process because some intermediates of denitrification (nitric oxide and nitrous oxide) are important greenhouse gases that react with sunlight and ozone to produce nitric acid, a component of acid rain. Denitrification is also important in biological wastewater treatment where it is used to reduce the amount of nitrogen released into the environment thereby reducing eutrophication. Denitrification can be determined via a nitrate reductase test.

Sulfate reduction – sulfate as electron acceptor

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Main article: Sulfate-reducing bacteria

Dissimilatory sulfate reduction is a relatively energetically poor process used by many Gram-negative bacteria found within the Thermodesulfobacteriota, Gram-positive organisms relating to Desulfotomaculum or the archaeon Archaeoglobus. Hydrogen sulfide (H
2S) is produced as a metabolic end product. For sulfate reduction electron donors and energy are needed.

Electron donors

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Many sulfate reducers are organotrophic, using carbon compounds such as lactate and pyruvate (among many others) as electron 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 use phosphite (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]

Energy for reduction

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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 form sulfite (SO2−
3) and AMP. 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 – carbon dioxide as electron acceptor

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Main article: Acetogenesis

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 dioxide reduction 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.

Other inorganic electron acceptors

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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 in electron 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 include Shewanella putrefaciens and Geobacter metallireducens. Since some ferric iron-reducing bacteria (e.g. G. metallireducens) can use toxic hydrocarbons such as toluene as a carbon source, there is significant interest in using these organisms as bioremediation agents in ferric iron-rich contaminated aquifers.

Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms (including the iron-reducing bacteria mentioned above) can use other inorganic ions in anaerobic respiration. While these processes may often be less significant ecologically, they are of considerable interest for bioremediation, especially when heavy metals or radionuclides are used as electron acceptors. Examples include:

Organic terminal electron acceptors

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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 by fish, 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

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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).

Hydrogen oxidation

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Main article: Hydrogen oxidizing bacteria

Many organisms are capable of using hydrogen (H
2) as a source of energy. While several mechanisms of anaerobic hydrogen oxidation 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]

2 H2 + O2 → 2 H2O + energy

In these organisms, hydrogen is oxidized by a membrane-bound hydrogenase causing proton pumping via electron transfer to various quinones and cytochromes. 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 the Calvin cycle. Hydrogen-oxidizing organisms, such as Cupriavidus necator (formerly Ralstonia 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

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Sulfur oxidation involves the oxidation of reduced sulfur compounds (such as sulfide H
2S), inorganic sulfur (S), and thiosulfate (S
2O2−
3) to form sulfuric acid (H
2SO
4). A classic example of a sulfur-oxidizing bacterium is Beggiatoa, a microbe originally described by Sergei Winogradsky, one of the founders of environmental microbiology. Another example is Paracoccus. 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 using reverse electron flow, an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH. Biochemically, reduced sulfur compounds are converted to sulfite (SO2−
3) and subsequently converted to sulfate (SO2−
4) by the enzyme sulfite oxidase.[12] Some organisms, however, accomplish the same oxidation using a reversal of the APS reductase system used by sulfate-reducing bacteria (see above). 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 (Fe2+
) oxidation

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Further information: Acidophiles in acid mine drainage

Ferrous iron is a soluble form of iron that is stable at extremely low pHs or under anaerobic conditions. Under aerobic, moderate pH conditions ferrous iron is oxidized spontaneously to the ferric (Fe3+
) form and is hydrolyzed abiotically to insoluble ferric hydroxide (Fe(OH)
3). There are three distinct types of ferrous iron-oxidizing microbes. The first are acidophiles, such as the bacteria Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans, as well as the archaeon Ferroplasma. These microbes oxidize iron in environments that have a very low pH and are important in acid mine drainage. The second type of microbes oxidize ferrous iron at near-neutral pH. These micro-organisms (for example Gallionella ferruginea, Leptothrix ochracea, or Mariprofundus ferrooxydans) live at the oxic-anoxic interfaces and are microaerophiles. The third type of iron-oxidizing microbes are anaerobic photosynthetic bacteria such as Rhodopseudomonas,[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 enzyme rusticyanin 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

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Nitrification is the process by which ammonia (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 to hydroxylamine (NH
2OH) by the enzyme ammonia monooxygenase in the cytoplasm, followed by the oxidation of hydroxylamine to nitrite by the enzyme hydroxylamine oxidoreductase in the periplasm.

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 enzyme nitrite 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 genus Nitrospira is capable of complete nitrification (Comammox).[14][15]

Anammox

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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 the Planctomycetota (e.g. "Candidatus Brocadia 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 in industrial 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]

Manganese oxidation

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In July 2020 researchers report the discovery of chemolithoautotrophic bacterial culture that feeds on the metal manganese after performing unrelated experiments and named its bacterial species Candidatus Manganitrophus noduliformans and Ramlibacter lithotrophicus.[19][20][21]

Phototrophy

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Main article: Phototrophic prokaryotes

Many microbes (phototrophs) are capable of using light as a source of energy to produce ATP and organic compounds such as carbohydrates, lipids, and proteins. Of these, algae are particularly significant because they are oxygenic, using water as an electron donor for electron transfer during photosynthesis.[22] Phototrophic bacteria are found in the phyla "Cyanobacteria", Chlorobiota, Pseudomonadota, Chloroflexota, and Bacillota.[23] Along with plants these microbes are responsible for all biological generation of oxygen gas on Earth. Because chloroplasts were derived from a lineage of the Cyanobacteria, the general principles of metabolism in these endosymbionts 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, while anoxygenic photosynthetic bacteria belong to the purple bacteria (Pseudomonadota), green sulfur bacteria (e.g., Chlorobium), green non-sulfur bacteria (e.g., Chloroflexus), or the heliobacteria (Low %G+C Gram positives). In addition to these organisms, some microbes (e.g. the Archaeon Halobacterium or the bacterium Roseobacter, among others) can utilize light to produce energy using the enzyme bacteriorhodopsin, 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 their photosynthetic reaction centers within a membrane, which may be invaginations of the cytoplasmic membrane (Pseudomonadota), thylakoid membranes ("Cyanobacteria"), specialized antenna structures called chlorosomes (Green sulfur and non-sulfur bacteria), or the cytoplasmic membrane itself (heliobacteria). Different photosynthetic bacteria also contain different photosynthetic pigments, such as chlorophylls and carotenoids, allowing them to take advantage of different portions of the electromagnetic spectrum and thereby inhabit different niches. 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 the Z 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 protein ferredoxin, 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 fixation

[edit]
Main article: Nitrogen fixation

Nitrogen is an element required for growth by all biological systems. While extremely common (80% by volume) in the atmosphere, dinitrogen gas (N
2) is generally biologically inaccessible due to its high activation 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 between legumes 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 enzyme nitrogenase, 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:

  • heterocyst formation (cyanobacteria e.g. Anabaena) where one cell does not photosynthesize but instead fixes nitrogen for its neighbors which in turn provide it with energy
  • root nodule symbioses (e.g. Rhizobium) with plants that supply oxygen to the bacteria bound to molecules of leghaemoglobin
  • anaerobic lifestyle (e.g. Clostridium pasteurianum)
  • very fast metabolism (e.g. Azotobacter vinelandii)

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 per N
2 fixed) and due to the extreme sensitivity of the nitrogenase to oxygen.

See also

[edit]

References

[edit]

Further reading

[edit]
Revisions and contributorsEdit on WikipediaRead on Wikipedia

Microbial metabolism

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Microbial metabolism refers to the ensemble of biochemical reactions occurring within microorganisms—such as , , and fungi—that enable the acquisition of , the synthesis of cellular components, and adaptation to diverse environmental conditions. These processes are broadly divided into , which breaks down organic substrates like carbohydrates, proteins, and to release via pathways such as , the tricarboxylic acid (TCA) cycle, and electron transport chains, and , which utilizes that to build macromolecules including nucleic acids, proteins, and cell walls. This metabolic framework is governed by balances, notably involving NAD+/NADH ratios, and allows microbes to thrive in extreme habitats ranging from deep-sea vents to the human gut. The diversity of microbial metabolism is remarkable, encompassing aerobic respiration, anaerobic fermentation, photosynthesis, and chemolithotrophy, which collectively drive global biogeochemical cycles like carbon, , and transformations. For instance, heterotrophic microbes degrade complex polymers through specialized pathways such as the Entner-Doudoroff route or , while autotrophs fix CO₂ via the Calvin-Benson-Bassham cycle or reverse TCA cycle to support in ecosystems. This versatility not only facilitates microbial survival under scarcity or but also enables interspecies interactions, such as cross-feeding in communities where one organism's becomes another's . Ecologically and biotechnologically, microbial metabolism plays a pivotal role in processes like , where certain metabolize pollutants such as hydrocarbons, and in sustainable production of biofuels and pharmaceuticals through engineered pathways that enhance yields of compounds like polyketides or fatty acids. In human , gut microbiota metabolism influences nutrient absorption and immune function, with over 1,000 species contributing to the breakdown of dietary fibers into . Advances in have further illuminated these networks, revealing regulatory mechanisms like post-translational modifications that fine-tune fluxes in response to environmental cues.

Introduction

Definition and scope

Microbial metabolism comprises the ensemble of enzymatic reactions within microorganisms that facilitate the acquisition of energy, primarily in the form of adenosine triphosphate (ATP), reducing equivalents such as nicotinamide adenine dinucleotide phosphate (NADPH), and essential building blocks for biomass synthesis. These reactions integrate catabolic pathways, which break down substrates to release energy, and anabolic processes that construct cellular components from simpler precursors. The scope of microbial metabolism extends across prokaryotes, including and , as well as unicellular eukaryotes such as fungi and , reflecting the biochemical unity of despite phylogenetic diversity. In contrast to multicellular organisms, which often exhibit specialized, stable metabolic networks, microbial metabolism emphasizes rapid adaptability to fluctuating environmental conditions, enabling survival in extreme habitats from deep-sea vents to acidic soils. This adaptability is underscored by metabolic rates with population doubling times spanning from under 10 minutes in optimal laboratory conditions to several days in natural settings. Historically, foundational insights emerged in the through Louis Pasteur's demonstrations of as an anaerobic microbial process, and in the early via Otto Warburg's elucidation of aerobic respiration mechanisms, including the role of respiratory enzymes in oxygen-dependent energy production. The vast diversity of microbial metabolism is exemplified by estimates of over 10^{12} species of , , and microscopic fungi, each potentially employing unique strategies for nutrient acquisition and energy conservation. Central to these processes are reactions that maintain the balance between oxidation for energy yield and reduction for biosynthetic needs.

Ecological and applied significance

Microbial metabolism plays a central role in driving global biogeochemical cycles, particularly those of , , and , which are essential for maintaining Earth's . In the , photosynthetic microbes, including and , contribute approximately 50% of global , fixing vast amounts of CO₂ into and supporting higher trophic levels. Through , microbes recycle the majority of —typically 80-85% via respiration—preventing accumulation of dead and releasing nutrients back into ecosystems. In marine environments, microbial respiration alone consumes around 50-60 Gt of carbon per year, influencing atmospheric CO₂ levels and chemistry. Microbes also dominate the nitrogen cycle by fixing atmospheric N₂ into bioavailable forms, with global biological nitrogen fixation estimated at 100-200 Tg N per year in marine systems alone, complementing terrestrial inputs of up to 140 Tg N per year. In the sulfur cycle, diverse microbial communities perform key transformations, such as sulfate reduction and oxidation, which regulate sulfur availability and mitigate toxic sulfide accumulation in sediments and soils. These processes collectively sustain nutrient flows, with microbial autotrophy accounting for about half of Earth's primary productivity and decomposition ensuring nutrient recycling across ecosystems. The applied significance of microbial metabolism spans , , and industry. In , hydrocarbon-degrading , such as those in the genera Alcanivorax and , naturally break down oil spills, as demonstrated in the and incidents, reducing environmental persistence of pollutants. Fermentative like Clostridium species enable production by converting into and through anaerobic metabolism, offering sustainable alternatives to fossil fuels. In pharmaceuticals, species produce over 70% of clinically used antibiotics, such as and , via specialized secondary metabolic pathways that yield bioactive compounds. Food production benefits from , including Lactobacillus bulgaricus and , which ferment into during manufacture, enhancing flavor, texture, and shelf life while providing health effects. Emerging applications in leverage CRISPR-Cas9 to engineer microbial metabolisms, such as modifying for efficient production of chemicals like and biofuels, with advancements in the 2020s enabling scalable, pathway-optimized strains for industrial synthesis.

Fundamental concepts

Catabolism and energy conservation

refers to the metabolic processes in microorganisms that involve the oxidative breakdown of complex organic and inorganic compounds into simpler molecules, thereby releasing energy stored in chemical bonds. This degradation primarily occurs through reactions where substrates serve as electron donors, contrasting with , which utilizes energy to synthesize macromolecules from simpler precursors. Energy from catabolic reactions is conserved mainly through two mechanisms: and . In , ATP is generated directly by the transfer of a high-energy phosphate group from an intermediate substrate to ADP during enzymatic reactions, a process common in anaerobic conditions. , on the other hand, couples the energy from electron transport to the creation of a proton motive force across the membrane, which drives ATP synthesis via , enabling higher energy yields in aerobic or alternative respiration scenarios. A general representation of catabolic redox processes is the oxidation of an electron donor, such as glucose, by an acceptor like oxygen, producing oxidized products and ATP: C6H12O6+6O2→6CO2+6H2O+∼30 ATP\mathrm{C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \sim 30\ ATP} Respiration achieves approximately 40% efficiency in capturing the free energy of substrate oxidation into ATP, far surpassing the roughly 2% efficiency of , which relies solely on . Universal electron carriers, including NAD⁺/NADH and FAD/FADH₂, play a critical role in by shuttling electrons from donors to acceptors, facilitating oxidation steps and maintaining intracellular balance essential for continued metabolic flux. These coenzymes accept electrons and protons during the breakdown of substrates, becoming reduced forms (NADH and FADH₂), which then donate them to downstream processes like the .

Anabolism and biosynthesis

, also known as , encompasses the metabolic pathways in microorganisms that assemble complex cellular components from simpler precursors, powered by ATP and reducing equivalents like NADPH. These processes are vital for microbial growth, enabling the construction of macromolecules essential for cell structure, function, and replication, including proteins, nucleic acids, , and . In such as , anabolic routes typically draw carbon skeletons and energy from central catabolic intermediates, ensuring coordinated progression from nutrient uptake to formation. Prominent anabolic pathways involve the synthesis of from glycolytic or tricarboxylic acid cycle intermediates; for example, pyruvate serves as a starting point for non-essential like via with glutamate, while branched-chain such as derive from pyruvate through acetolactate formation. biosynthesis proceeds de novo through and pathways, where (PRPP) reacts with or aspartate, incorporating and requiring multiple ATP-dependent phosphorylations to form AMP or UMP, which are then converted to DNA and RNA precursors. Lipid biosynthesis initiates with the ATP-dependent of to , followed by iterative condensation and reduction cycles in the complex to produce acyl chains for phospholipids. Many anabolic reactions are reductive, necessitating NADPH as the ; in facultative anaerobes like E. coli, the oxidative generates NADPH via and 6-phosphogluconate dehydrogenase, yielding up to 2 NADPH per glucose molecule oxidized to ribulose-5-phosphate. In anaerobic or photosynthetic microbes, ferredoxin-NADP⁺ reductases transfer electrons from to NADP⁺, providing an alternative NADPH source for reductive steps in and . These NADPH pools support the high reducing power demands of without interfering with NADH-dependent . Anabolism imposes significant energetic demands, with approximately 20-25 ATP equivalents required on average per for precursor synthesis in E. coli, plus about 4 ATP for (tRNA charging, elongation, and ). In exponentially growing bacterial cells, a large portion of catabolically generated ATP is allocated to anabolic processes, highlighting the resource-intensive nature of assembly and the need for efficient energy partitioning. Regulation of anabolic pathways ensures and adaptation, primarily through allosteric mechanisms where pathway end products inhibit upstream enzymes—for instance, allosterically represses deaminase in the route—and systems that modulate in dense populations by altering via autoinducer signals, thereby balancing catabolic flux with anabolic output.

Metabolic classification

Energy sources: phototrophy versus chemotrophy

Microbial metabolism is fundamentally classified based on energy acquisition strategies, with phototrophy and chemotrophy representing the primary modes by which microorganisms harness for growth and . Phototrophs derive directly from , while chemotrophs obtain it through the oxidation of chemical compounds. This distinction influences their ecological niches, with phototrophs dominating illuminated environments and chemotrophs thriving in diverse, often dark habitats. Phototrophy involves the capture of energy by specialized pigments embedded in membrane-bound structures, converting photons into primarily in the form of ATP via . In oxygenic phototrophs such as , chlorophyll a absorbs in the , driving electron transport that splits to produce oxygen as a byproduct. Anoxygenic phototrophs, including like Rhodobacter species, utilize bacteriochlorophylls that absorb in the range, allowing energy capture in low-light or anaerobic conditions without . These pigments are organized in antenna complexes and reaction centers, achieving high quantum efficiencies (typically >95%) for excitation transfer and charge separation, though overall photosynthetic energy conversion efficiencies range from 1% to 10% due to losses in light absorption, fluorescence, and downstream metabolism. Examples include such as Synechocystis, which form extensive blooms in aquatic ecosystems and contribute significantly to global oxygen production. In contrast, chemotrophy relies on reactions where electrons from donor molecules are transferred to acceptors, generating a proton motive force for ATP synthesis through or . This mode is subdivided into chemoorganotrophy, where organic compounds like glucose serve as electron donors (common in heterotrophic bacteria such as ), and chemolithotrophy, where inorganic substrates like or ferrous iron are oxidized. A representative chemolithotroph is Thiobacillus thiooxidans, which derives energy from compounds in acidic environments, enabling growth in extreme conditions like mine drainage sites. Chemotrophs exhibit broad metabolic versatility, adapting to varied electron donors and acceptors across aerobic and anaerobic settings. Comparatively, phototrophy yields high ATP output under optimal light conditions—up to 3 ATP per electron pair in cyclic photophosphorylation—but demands intricate spatial organization, such as thylakoid membranes in , to segregate electron transport components and prevent wasteful recombination. This structural complexity enhances efficiency but limits adaptability to fluctuating light. Chemotrophy, while potentially generating more ATP per reaction in high-substrate scenarios (e.g., 30-38 ATP from complete glucose oxidation in aerobes), is constrained by the availability and concentration of chemical substrates, often resulting in lower yields in nutrient-poor environments. Globally, microbial phototrophs, particularly and eukaryotic , drive approximately 40-50% of primary productivity, underscoring their role in carbon fixation and sustaining food webs.

Carbon sources: autotrophy versus heterotrophy

Microbial metabolism is fundamentally distinguished by the source of carbon used for biomass synthesis, with heterotrophy and autotrophy representing the primary strategies for acquiring this essential building block. Heterotrophic microbes obtain carbon from pre-formed organic compounds, such as sugars, , and other biomolecules produced by other organisms, which they assimilate through catabolic processes to generate energy and biosynthetic precursors. This mode is prevalent among and that decompose organic matter in soils, sediments, and aquatic environments, as well as parasitic forms that derive carbon from host cells. In contrast, autotrophic microbes fix inorganic carbon, primarily (CO₂), into organic molecules, requiring substantial energy input to drive the reductive assimilation reactions. Autotrophy encompasses two main subtypes based on the energy source harnessed for CO₂ fixation: photoautotrophy and chemoautotrophy. Photoautotrophs, such as , utilize light energy captured through photosynthetic pigments to power carbon fixation, often via the Calvin-Benson cycle, enabling them to thrive in illuminated environments like oceans and freshwater systems. Chemoautotrophs, including many like nitrifying organisms and sulfur-oxidizers, derive energy from the oxidation of inorganic chemicals (chemolithotrophy) to fix CO₂, predominating in dark or energy-limited habitats such as deep-sea vents and subsurface soils. These autotrophs integrate carbon fixation with energy-generating processes that align with their environmental niches, as detailed in discussions of phototrophy and chemotrophy. In terms of metabolic integration, heterotrophs typically couple carbon acquisition to respiration or pathways, breaking down organic substrates via or the tricarboxylic acid cycle to yield ATP and reducing equivalents for . Autotrophs, however, link CO₂ fixation to phototrophic or chemolithotrophic mechanisms, where the energy harvested supports the energetically costly reduction of CO₂ to carbohydrates and other biomolecules. This distinction underscores the complementary roles of heterotrophs in recycling organic carbon and autotrophs in within microbial communities. Although autotrophic microbes constitute only about 5-10% of prokaryotic cells globally—for instance, roughly 8% in the upper —they drive a disproportionate share of carbon cycling, fixing approximately 50 Gt of carbon per year through processes like marine phytoplankton . Many microbes exhibit mixotrophy, a hybrid strategy that combines autotrophy and heterotrophy to opportunistically exploit both inorganic and organic carbon sources, enhancing resilience in fluctuating environments such as stratified columns or nutrient-variable soils. This flexibility allows mixotrophs to balance energy demands and carbon availability, contributing to stability and turnover.

Electron donors and acceptors

In microbial metabolism, electron donors serve as the reducing agents that provide s for energy-generating reactions. These donors are classified into organic and inorganic categories based on their chemical nature and standard reduction potentials (E°'), which indicate their tendency to donate electrons. Organic electron donors, such as glucose (C₆H₁₂O₆ / CO₂ couple, E°' ≈ -0.43 V), are commonly utilized by heterotrophic microbes and yield moderate energy when oxidized. Inorganic electron donors, including (2H⁺ / H₂, E°' = -0.41 V) and (S / HS⁻, E°' = -0.27 V), are employed by chemolithotrophs and often support autotrophic growth due to their highly negative potentials, facilitating to carriers like NAD⁺. Electron acceptors, acting as oxidizing agents, receive these electrons and determine the overall energy yield through their more positive E°' values. Oxygen (½O₂ / H₂O, E°' = +0.82 V) is the most favorable aerobic acceptor, enabling high-energy respiration in oxic environments. Anaerobic acceptors include nitrate (NO₃⁻ / ½N₂, E°' = +0.74 V) for denitrification, sulfate (SO₄²⁻ / HS⁻, E°' = -0.22 V) for sulfate reduction, and carbon dioxide (CO₂ / CH₄, E°' = -0.25 V) in methanogenesis, each with progressively lower potentials that limit energy conservation. The redox tower organizes these couples by decreasing E°', illustrating the thermodynamic favorability of electron flow from donors (negative E°') to acceptors (positive E°'). The free energy change (ΔG) for such transfers is given by the equation: ΔG=−nFΔE\Delta G = -n F \Delta E where nn is the number of electrons transferred, FF is the Faraday constant (96.485 kJ/V·mol), and ΔE\Delta E is the difference in E°' between acceptor and donor. A larger positive ΔE\Delta E releases more energy, supporting greater ATP synthesis via oxidative phosphorylation; for instance, the high ΔE\Delta E with O₂ yields approximately 3 ATP per 2 electrons transferred, compared to about 1 ATP per 2 electrons in CO₂-dependent methanogenesis. Microbial metabolic versatility is exemplified by the ability to utilize over 20 distinct electron acceptors, allowing adaptation to diverse conditions. Facultative anaerobes, such as and , flexibly switch between O₂ and alternatives like NO₃⁻ or fumarate depending on availability, while obligate anaerobes like Geobacter sulfurreducens exclusively employ low-potential acceptors such as Fe(III) or . This adaptability underpins microbial roles in global biogeochemical cycles.

Fermentation

Mechanisms of substrate-level phosphorylation

Substrate-level phosphorylation is a fundamental mechanism in microbial metabolism whereby ATP is synthesized directly from a high-energy phosphorylated intermediate and an ADP molecule, without the involvement of an or membrane-bound processes. This process occurs during and certain fermentation pathways, where enzymes transfer a phosphate group from substrates like 1,3-bisphosphoglycerate or phosphoenolpyruvate to ADP, forming ATP. For instance, in the conversion of phosphoenolpyruvate to pyruvate, the enzyme catalyzes the reaction: phosphoenolpyruvate + ADP → pyruvate + ATP. This direct phosphorylation contrasts with , which relies on proton gradients across membranes to drive ATP synthesis. In fermentation, the net energy yield from is typically low, exemplified by the alcoholic fermentation equation in yeasts: C₆H₁₂O₆ → 2 CH₃CH₂OH + 2 CO₂ + 2 ATP, where the two ATP molecules are generated per glucose through the . This yield arises from two substrate-level phosphorylation steps in : one at the reaction and another at . The process is oxygen-independent, enabling anaerobic microbes to generate energy when respiratory options are unavailable. Substrate-level phosphorylation is considered an ancient metabolic mechanism, likely originating in primordial conditions lacking oxygen, and it is conserved across all three domains of life—, , and Eukarya—suggesting its role in early evolutionary metabolism. Genomic and phylogenetic evidence suggests that glycolytic enzymes involved in this phosphorylation predate the . Despite its universality, substrate-level phosphorylation has inherent limitations, producing only about 2 ATP per glucose compared to over 30 ATP in aerobic respiration, which restricts microbial growth rates and production in anaerobic environments. Additionally, the accumulation of reduced end products, such as lactate or , can inhibit enzymes and lower the substrate's , further constraining the process efficiency.

Major fermentation pathways and products

Fermentation pathways in heterotrophic microbes enable the regeneration of NAD⁺ under anaerobic conditions, producing a variety of end-products while generating limited ATP via . One of the most prominent is , where glucose is converted to two molecules of lactate and two ATP through the Embden-Meyerhof-Parnas (EMP) pathway in homofermentative such as species. In this process, pyruvate is reduced to lactate by , ensuring efficient energy extraction with nearly 90% of the carbon from glucose directed to lactate. Heterolactic fermentation, observed in certain and related genera like , diverges after the via phosphoketolase, yielding lactate, ethanol, CO₂, and ATP at a lower efficiency of about 1 ATP per glucose. Alcoholic fermentation represents another key pathway, primarily in yeasts like and bacteria such as , where glucose is metabolized to two and two CO₂ molecules, along with two ATP. In S. cerevisiae, this occurs through the EMP pathway followed by and activity, achieving near-theoretical yields under industrial conditions. Z. mobilis employs the Entner-Doudoroff pathway instead of EMP, yet maintains comparable efficiency and is noted for its high tolerance, making it a model for bioethanol production. Several other fermentation pathways diversify microbial metabolism, producing distinct acids and gases. fermentation, characteristic of species like C. butyricum, converts glucose to butyrate, , CO₂, and H₂, with yields of approximately 0.4–0.8 g butyrate per g glucose and net 2–3 ATP. This involves the pathway, where two units condense to form acetoacetyl-CoA, ultimately reduced to butyrate. fermentation in species, such as P. acidipropionici, utilizes the Wood-Werkman cycle to produce propionate, , and CO₂ from lactate or sugars, with propionate yields up to 0.6 g/g substrate and succinate as an intermediate. Mixed-acid fermentation, prevalent in enteric bacteria like , generates a of , , lactate, succinate, and from glucose, with often decomposing to H₂ and CO₂; this pathway supports growth under microaerophilic conditions and yields about 2 ATP per glucose. Archaea also perform fermentation, such as the production of acetate from sugars in species like Thermococcus, highlighting the pathway's universality across domains. Microbial fermentation exhibits vast diversity, with numerous pathways adapted to specific ecological niches and substrates across , , and eukaryotes, enabling the production of numerous distinct organic compounds as end-products. This metabolic versatility underpins industrial applications, including biofuels like from Z. mobilis and S. cerevisiae (yielding up to 100 g/L in optimized fermenters) and solvents such as from via the acetone-butanol-ethanol process. Lactic and propionic acids are also commercially fermented for food preservatives, bioplastics, and pharmaceuticals, with global production exceeding 1 million tons annually for alone. Regulation of these pathways is tightly linked to environmental cues, particularly sensitivity, which influences activity and product yields; for instance, optimal for Lactobacillus homofermentation is 5.5–6.5, below which lactate accumulation inhibits growth. In pathways like butyric fermentation, H₂ production serves as a valve, with yields up to 2 mol H₂ per mol glucose in Clostridium, but excess H₂ can shift metabolism toward reduced products like to maintain balance.

Respiration

Aerobic respiration

Aerobic respiration in microorganisms is a highly efficient catabolic process that utilizes molecular oxygen (O₂) as the terminal in the (ETC), enabling the complete oxidation of organic substrates to generate substantial ATP through . This pathway predominates in and facultative aerobes, where in the breaks down glucose to pyruvate, yielding a net of 2 ATP and 2 NADH per glucose . Pyruvate is then decarboxylated to in the , which enters the tricarboxylic acid (TCA) cycle, producing additional NADH, FADH₂, and 2 ATP via per glucose. The electrons from NADH and FADH₂ are transferred through the ETC embedded in the , consisting of four main complexes (I–IV) linked by mobile carriers such as ubiquinone and . Complex I () oxidizes NADH and pumps protons across the ; complex II () feeds electrons from FADH₂; complex III (cytochrome bc₁) and complex IV () further transfer electrons to O₂, forming water while establishing a . This drives (complex V) to produce ATP via . Key components include ubiquinone, which shuttles electrons between complexes I/II and III, and (e.g., b, c, a) that facilitate in complexes III and IV. The overall equation for the aerobic oxidation of glucose in microbes is C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + energy, with a theoretical ATP yield of approximately 30–38 molecules per glucose, depending on the efficiency of proton pumping and shuttle systems; for instance, the (ATP produced per oxygen atom reduced) is about 2.5 for NADH oxidation. This high yield contrasts with fermentation's 2 ATP per glucose, allowing aerobes to achieve faster growth rates and higher biomass. In microbial examples, , a facultative anaerobe, shifts to aerobic respiration when O₂ is available, employing a branched ETC with alternative oxidases for flexibility in varying oxygen levels. Similarly, relies on aerobic respiration for optimal growth, utilizing cytochrome oxidases adapted for high O₂ affinity in oxygen-rich environments, though it can tolerate microaerobic niches via regulated ETC components. These adaptations enable colonization of diverse habitats, from to host tissues. Aerobic respiration captures about 34% of the free energy from glucose oxidation as ATP, with the remainder dissipated as , underscoring its thermodynamic compared to anaerobic processes. However, the reduction of O₂ generates (ROS) like and as byproducts, which microbes mitigate through enzymes such as catalases that decompose H₂O₂ to and O₂, preventing oxidative to cellular components.

Anaerobic respiration

Anaerobic respiration in microorganisms involves the use of an (ETC) to transfer electrons from organic or inorganic donors to alternative terminal electron acceptors other than molecular oxygen, generating a proton motive force across the membrane for ATP synthesis via . The core components of the ETC, including dehydrogenases, quinones, and , are analogous to those in aerobic respiration, but the chain terminates with specialized reductases, such as for (NO₃⁻) or sulfite reductase for (SO₃²⁻), which reduce the acceptor to products like or . Although the proton motive force is maintained, the overall difference (ΔE) is lower due to the weaker oxidizing power of these acceptors compared to O₂, resulting in fewer protons translocated per and thus reduced efficiency. The energy yield from anaerobic respiration is substantially lower than that of aerobic processes, typically producing 4–26 ATP molecules per glucose molecule oxidized, in contrast to approximately 30 ATP from aerobic respiration under similar conditions. This variation depends on the terminal acceptor's redox potential; for instance, nitrate respiration yields approximately 20-26 ATP per glucose, while sulfate (SO₄²⁻) reduction provides only about 2–4 ATP because of its more negative reduction potential, limiting proton pumping sites in the ETC. These yields reflect the thermodynamic constraints, where the free energy change (ΔG) per electron transfer is smaller, but still far superior to the 2 ATP from fermentation alone. Anaerobic respiration predominates in oxygen-depleted habitats, including anoxic sediments, stratified water columns, wetlands, and the gastrointestinal tracts of animals, where alternative electron acceptors accumulate from abiotic or biotic processes. Obligate anaerobes, such as sulfate-reducing bacteria in the genus Desulfovibrio, exemplify adaptation to these environments, using sulfate as an acceptor in marine and freshwater sediments or host guts to derive energy from organic matter oxidation. This metabolic strategy supports microbial survival and activity in O₂-fluctuating niches, contributing to biogeochemical cycles like nitrogen and sulfur transformations. From an evolutionary perspective, anaerobic respiration likely predated aerobic respiration, emerging in the ancient anoxic to harness energy from diverse couples before the increased atmospheric O₂ levels around 2.4 billion years ago. This ancestral capability allowed prokaryotes to colonize varied gradients and persist in modern microoxic or anoxic zones. The process exhibits remarkable diversity, with microbes employing more than 10 inorganic (e.g., , SO₄²⁻, Fe³⁺, CO₂) and organic (e.g., fumarate, ) acceptors, often coupled to heterotrophic growth on organic carbon or autotrophic fixation via pathways like the Wood-Ljungdahl route in acetogens. Specific processes, such as using , highlight this versatility but are elaborated in dedicated contexts.

Specific anaerobic processes

Denitrification

Denitrification is a dissimilatory process in which certain microbes use (NO₃⁻) as a terminal , reducing it stepwise to dinitrogen gas () and thereby generating energy through electron transport phosphorylation. This process is prevalent in oxygen-limited environments such as sediments, soils, and aquatic systems, where it serves as a key mechanism for removal from ecosystems. Unlike assimilatory nitrate reduction, is primarily catabolic, coupling the reduction to organic carbon oxidation for ATP production. The denitrification pathway involves a sequence of four enzymatic reductions: (NO₃⁻) to (NO₂⁻) catalyzed by (Nar), (NO₂⁻) to (NO) by nitrite reductase (Nir), NO to (N₂O) by nitric oxide reductase (Nor), and N₂O to N₂ by nitrous oxide reductase (Nos). These reductases are typically membrane-bound (Nar, Nor) or periplasmic (Nir, Nos), facilitating a total transfer of five electrons per reduced to 1/2 N₂. Electrons are donated from organic substrates via quinones and , generating a proton motive force that drives ATP synthesis. The overall stoichiometry of denitrification, using simplified (CH₂O) as the , is represented by the equation:
5CH2O+4NO3−→2N2+4HCO3−+CO2+3H2O5 \mathrm{CH_2O} + 4 \mathrm{NO_3^-} \rightarrow 2 \mathrm{N_2} + 4 \mathrm{HCO_3^-} + \mathrm{CO_2} + 3 \mathrm{H_2O}
This reaction yields approximately 3 ATP equivalents per reduced, supporting microbial growth under anaerobic conditions. Prominent denitrifying microbes include heterotrophic bacteria such as species (e.g., P. stutzeri) and Paracoccus denitrificans, which are facultative anaerobes capable of switching from aerobic to . These organisms contribute to environmental cycling by facilitating the loss of fixed as N₂, accounting for 10-20% of global loss, particularly in oxygen minimum zones of oceans and anoxic soils. Regulation of is primarily induced under anaerobic conditions in the presence of or , mediated by global regulators like FNR (fumarate and nitrate reduction) homologs and two-component systems such as NarXL. Oxygen represses expression, while N-oxides activate specific operons for reductases, ensuring coordinated pathway activation. Incomplete , often due to limitation or genetic truncation, can lead to accumulation of N₂O, a potent with 300-fold the warming potential of CO₂. This variation highlights 's dual role in attenuation and climate impact.

Sulfate reduction

Sulfate reduction is a form of in which (SO₄²⁻) serves as the terminal , enabling certain microorganisms to generate in oxygen-depleted environments such as anoxic sediments and wetlands. This process, known as dissimilatory reduction, reduces to (H₂S), which is released as a metabolic end product rather than being incorporated into cellular . It plays a critical role in the biogeochemical cycling of and carbon, particularly in marine and freshwater sediments where is abundant. The pathway begins with the activation of to 5'-phosphosulfate (APS) by the enzyme (encoded by sat genes), which consumes one ATP molecule and reflects the high energy cost of the process. APS is then reduced to (SO₃²⁻) by APS reductase (encoded by aprA and aprB genes), transferring two electrons. Finally, is reduced to H₂S by dissimilatory reductase (encoded by dsrA, dsrB, and dsrC genes), requiring six additional electrons in an eight-electron transfer overall. The overall reaction, using as the , is represented as: SO42−+2CH2O→H2S+2HCO3−\text{SO}_4^{2-} + 2 \text{CH}_2\text{O} \rightarrow \text{H}_2\text{S} + 2 \text{HCO}_3^- Due to the initial ATP investment for activation (equivalent to two ATP when considering hydrolysis) and electron transport limitations, the net yield is low, typically approximately 1 ATP per reduced, making it less efficient than aerobic respiration. Common electron donors include (H₂), lactate, and , which are oxidized to provide the necessary electrons via menaquinone-dependent transport chains. The process is strictly anaerobic and inhibited by oxygen, as O₂ competes for electrons and inactivates key enzymes like reductase. Sulfate-reducing microorganisms include diverse bacteria such as species (e.g., Desulfovibrio vulgaris and Desulfovibrio piger) and archaea like Archaeoglobus fulgidus. These organisms thrive in anoxic environments, where H₂S production leads to the formation of black sediments through precipitation of iron sulfides (e.g., FeS), a characteristic feature of sulfate-rich reducing zones. Globally, dissimilatory sulfate reduction processes approximately 11 Tmol of sulfate per year in marine sediments alone, equivalent to about 350 Tg S annually, oxidizing 12–29% of the organic carbon reaching the seafloor and contributing to long-term carbon burial by limiting further oxidation of .

Methanogenesis

Methanogenesis is a unique metabolic process performed exclusively by methanogenic archaea, which reduces or to under strictly anaerobic conditions, serving as a key terminal electron sink in anoxic ecosystems. This process is essential for the degradation of in environments lacking alternative electron acceptors like oxygen or , thereby facilitating the complete mineralization of . Methanogens couple this reduction to , primarily generating a sodium motive force that drives ATP synthesis via a sodium-translocating . The two primary pathways of methanogenesis are hydrogenotrophic and acetoclastic. In the hydrogenotrophic pathway, serves as the and is reduced by hydrogen gas through a series of enzymatic steps involving unique cofactors. The overall reaction is given by: CO2+4H2→CH4+2H2O\mathrm{CO_2 + 4 H_2 \rightarrow CH_4 + 2 H_2O} This pathway proceeds via the fixation of CO₂ onto methanofuran to form formylmethanofuran, followed by transfer to tetrahydromethanopterin (H₄MPT), where it is sequentially reduced to methylene-H₄MPT and then to methyl-H₄MPT using coenzyme F₄₂₀ as an carrier. The final step involves methyl transfer to coenzyme M (2-mercaptoethanesulfonate), forming methyl-coenzyme M, which is reductively demethylated to using coenzyme B as the in a reaction catalyzed by methyl-coenzyme M reductase. In terms of electron balance, the process can be expressed as: CO2+8H++8e−→CH4+2H2O\mathrm{CO_2 + 8 H^+ + 8 e^- \rightarrow CH_4 + 2 H_2O} Energy conservation in hydrogenotrophic methanogenesis yields approximately one ATP per mole of methane produced, primarily through the translocation of sodium ions during the methyl transfer step via the multi-subunit complex Mtr, generating a sodium motive force (Δμ_Na⁺). Coenzyme F₄₂₀, a deazaflavin derivative with a low redox potential, facilitates hydride transfers analogous to NAD(P)H but is specific to methanogens and certain bacteria. Coenzyme M acts as the terminal methyl carrier, essential for all methanogenic pathways. The acetoclastic pathway, utilized by specialized methanogens such as those in the genus , directly converts to and . The reaction is: CH3COOH→CH4+CO2\mathrm{CH_3COOH \rightarrow CH_4 + CO_2} is activated to by acetate kinase and phosphotransacetylase, followed by cleavage into methyl and carbonyl branches; the methyl group is transferred to the corrinoid protein and then to coenzyme M, while the carbonyl is oxidized to CO₂ with electrons funneled to for reduction of the methyl group to . This pathway also conserves energy via a sodium motive force, yielding about one ATP per , and predominates in many anaerobic digesters and sediments where accumulates. Methanogens are obligate anaerobes classified within the domain , primarily in the phylum Euryarchaeota, with some representatives in Bathyarchaeota and Verstraetearchaeota. Notable examples include Methanococcus maripaludis, a mesophilic hydrogenotroph used in genetic studies, and thermophilic species like Methanothermobacter thermoautotrophicus that thrive in hot environments such as hydrothermal vents. These organisms maintain partial pressures at or below thresholds of approximately 1–10 Pa through consumption and are inhibited by oxygen, , and antibiotics targeting . Ecologically, methanogenesis contributes significantly to the global methane budget, producing approximately 0.4 Gt of annually, with roughly 0.2 Gt from wetlands and 0.2 Gt from in like and sheep. Wetlands, including marshes and paddies, support diverse methanogenic communities that thrive on H₂ and CO₂ or produced by fermentative . In digestive systems, methanogens such as Methanobrevibacter consume H₂ from , mitigating stress but releasing as a , which is a potent with a 100-year 28–34 times that of CO₂. This process underscores methanogens' role in carbon cycling and their impact on .

Acetogenesis

Acetogenesis is a form of microbial metabolism in which obligately anaerobic , known as acetogens, reduce (CO₂) to using the Wood-Ljungdahl pathway as the primary mechanism for energy conservation and carbon fixation. This process distinguishes acetogenesis from other anaerobic metabolisms by its reliance on CO₂ and (H₂) or (CO) as substrates, producing as the end product without the formation of or other reduced compounds. The Wood-Ljungdahl pathway operates through two interconnected branches: the methyl branch and the carbonyl branch. In the methyl branch, CO₂ is sequentially reduced to a via intermediates bound to tetrahydrofolate (H₄folate), starting with formation by , followed by conversions to 10-formyl-H₄folate, 5,10-methenyl-H₄folate, 5,10-methylene-H₄folate, and finally methyl-H₄folate; this is then transferred through a corrinoid iron-sulfur protein to the alpha subunit of synthase (ACS). In the carbonyl branch, CO₂ is reduced to CO by CO /ACS (CODH/ACS), a bifunctional complex; the CO binds to the beta subunit of ACS, where it combines with the incoming and (CoA) to form . is then cleaved to and CoA by phosphotransacetylase and kinase, yielding approximately 1 ATP per via . The overall reaction for homoacetogenic growth is 4 H₂ + 2 CO₂ → CH₃COOH + 2 H₂O. Prominent acetogens include Clostridium aceticum, Moorella thermoacetica (formerly Clostridium thermoaceticum), and Acetobacterium woodii, which are capable of homoacetogenesis from H₂/CO₂ or CO, utilizing the Wood-Ljungdahl pathway exclusively for autotrophic growth. Ecologically, acetogens are key players in anaerobic environments such as animal guts (e.g., in ruminants and ), where they ferment and contribute to nutrient cycling by producing as an energy source for the host. Globally, acetogenesis accounts for about 10% of anaerobic carbon flow, producing over 10¹³ kg of acetic acid annually and facilitating the degradation of in sediments and bioreactors. The energy yield of acetogenesis is notably low, typically 0.3–1 ATP per mole of , due to the thermodynamic challenges of reducing CO₂ at low potentials, which requires (E₀' ≈ -450 to -500 mV) as an electron carrier in the carbonyl branch and other reductions. This limitation often necessitates syntrophic associations with hydrogen-producing microbes, where acetogens act as H₂ sinks to maintain favorable and enable mutualistic carbon and energy exchange in anaerobic consortia.

Chemolithotrophy

Hydrogen and sulfur oxidation

Hydrogen oxidation in microbes involves the chemolithotrophic utilization of molecular hydrogen (H₂) as an electron donor, enabling autotrophic growth through the generation of reducing power and ATP. The process is catalyzed by hydrogenase enzymes, which facilitate the reaction H₂ → 2 H⁺ + 2 e⁻, transferring electrons into the respiratory chain. In aerobic species, such as the Knallgas bacterium Ralstonia eutropha H16 (also known as Cupriavidus necator), a membrane-bound [NiFe]-hydrogenase (MBH) oxidizes H₂ and couples electron transport to O₂ reduction via the cytochrome bc₁ complex and terminal oxidases, yielding energy for ATP synthesis. Some hydrogen-oxidizing bacteria, including certain denitrifying species, can alternatively couple H₂ oxidation to NO₃⁻ reduction under anaerobic conditions, supporting chemolithoautotrophic growth. The overall reaction for aerobic oxidation is 2 H₂ + O₂ → 2 H₂O, with a standard free energy change (ΔG°') of approximately -474 kJ/mol, providing a high energy yield equivalent to about 2–3 mol ATP per mol H₂ oxidized, depending on the electron transport chain efficiency (P/O ratio ≈ 1–1.5 per electron pair). A soluble [NiFe]-hydrogenase in R. eutropha further reduces NAD⁺ to NADH, supporting CO₂ fixation via the Calvin–Benson–Bassham cycle. Sulfur oxidation by chemolithotrophs targets reduced inorganic sulfur compounds like (H₂S) and elemental (S⁰), oxidizing them to (SO₄²⁻) for . This process begins with the oxidation of H₂S to S⁰ by flavocytochrome c, as in the reaction H₂S + 2 cyt c (ox) → S⁰ + 2 cyt c (red) + 2 H⁺, generating electrons for the respiratory chain. Subsequent oxidation of S⁰ or (S₂O₃²⁻) to SO₄²⁻ occurs via the sulfur oxidation () system, a periplasmic multi-enzyme complex including SoxXA (sulfur-binding), SoxYZ (carrier), SoxB (sulfatase), and SoxCD (). In Thiobacillus species (reclassified as Acidithiobacillus or similar), the Sox pathway enables complete oxidation: S₂O₃²⁻ + H₂O + 8 cyt c (ox) → 2 SO₄²⁻ + 8 cyt c (red) + 2 H⁺, with electrons entering the pool for ATP production through . These are typically obligate autotrophs but can exhibit mixotrophic growth when organic substrates are available, enhancing biomass yields in nutrient-variable environments. Hydrogen- and sulfur-oxidizing thrive in diverse extreme environments, including geothermal hot springs and anoxic sediments, where they drive and sulfur cycling. In acidic hot springs (pH ~3, 50–60°C), thermoacidophilic genera like Hydrogenobaculum (Aquificota) and Acidithiobacillus () dominate, oxidizing and reduced sulfur compounds under microaerobic conditions to fix CO₂ at rates up to ~2.7 nmol/mL/day. In marine or freshwater sediments, these microbes facilitate the reoxidation of biogenic H₂S from sulfate reduction, maintaining balance. Sulfur oxidizers, particularly Thiobacillus and Halothiobacillus, are key players in (AMD) sites, where they accelerate pyrite oxidation, generating acidity (pH <4) and elevated levels through incomplete Sox pathways under low-O₂ conditions, exacerbating metal mobilization in mining-impacted waters. Mixotrophic variants of sulfur oxidizers, enriched by organic amendments, improve desulfurization efficiency in bioreactors by combining lithotrophic and heterotrophic .

Iron and manganese oxidation

Microbial iron oxidation is a chemolithotrophic process in which certain bacteria derive energy by oxidizing ferrous iron (Fe²⁺) to ferric iron (Fe³⁺), often under acidic or microoxic conditions. This reaction is mediated by specialized electron transport chains that couple Fe²⁺ oxidation to the reduction of oxygen as the terminal electron acceptor. The overall reaction is given by: 4Fe2++O2+4H+→4Fe3++2H2O4 \mathrm{Fe}^{2+} + \mathrm{O_2} + 4 \mathrm{H}^+ \rightarrow 4 \mathrm{Fe}^{3+} + 2 \mathrm{H_2O} In acidophilic bacteria such as Acidithiobacillus ferrooxidans, Fe²⁺ is oxidized at the cell surface or , with electrons transferred via proteins including the blue copper protein rusticyanin and c-type cytochromes like Cyc2 and Cyc1. These components form a respiratory supercomplex that spans the inner and outer membranes, enabling efficient through proton translocation and ATP synthesis. This process is highly exergonic under acidic conditions, providing a key energy source for these extremophiles. Manganese oxidation involves the microbial conversion of soluble Mn²⁺ to insoluble manganese oxides such as MnO₂, primarily through enzymatic in aerobic or microoxic environments. This is achieved by multicopper oxidases (MCOs), which facilitate the two-electron oxidation of Mn²⁺ to Mn³⁺/Mn⁴⁺, often in a two-step single-electron transfer process coupled to O₂ reduction. Representative organisms include sheathed like Leptothrix discophora, where enzymes such as MofA or the Mnx complex (e.g., MnxG) are localized on the cell surface, leading to the deposition of biogenic Mn oxides as sheaths or aggregates. These oxides exhibit high reactivity and play roles in mineral formation and pollutant remediation. Ecologically, iron- and manganese-oxidizing microbes thrive in niches such as , hydrothermal vents, and freshwater sediments, where they contribute to biogeochemical cycling and . In iron-rich deposits like flocculent mats, prokaryotic cell densities can reach 10⁸ to 10⁹ cells per gram (wet weight), dominated by iron oxidizers such as Zetaproteobacteria. These processes have practical applications in , where A. ferrooxidans regenerates Fe³⁺ to solubilize metals from ores, accounting for a significant portion of global production, and in , where Mn oxidizers remove from via biofiltration. Despite their utility, iron and oxidation face challenges including slow kinetics, particularly in neutral environments where abiotic rates are minimal, and product inhibition by accumulated Fe³⁺ or Mn oxides, which can precipitate and limit substrate access. For biofilters, start-up times extend weeks to months due to the need for accumulation, and co-occurring iron can dissolve Mn oxides, exacerbating secondary . These limitations necessitate optimized conditions, such as control and pre-treatment, to enhance in applied settings.

Nitrification and anammox

is a key chemolithotrophic process in the microbial , involving the stepwise aerobic oxidation of (NH₃) or (NH₄⁺) to (NO₂⁻) and then to (NO₃⁻). This oxidation is carried out by distinct groups of autotrophic that derive energy from the coupled to these reactions. The process plays a central role in transforming reduced forms into more oxidized, bioavailable compounds, facilitating cycling in soils, oceans, and engineered systems like . The first step of nitrification converts ammonia to nitrite and is mediated by ammonia-oxidizing bacteria (AOB), such as Nitrosomonas species. Ammonia monooxygenase (AMO), a membrane-bound enzyme containing copper and iron, catalyzes the oxidation of NH₃ to hydroxylamine (NH₂OH), which is then further oxidized to NO₂⁻ by hydroxylamine oxidoreductase (HAO), a periplasmic enzyme that also generates reducing equivalents for energy conservation. This step yields approximately 275 kJ/mol of NH₃ oxidized under standard conditions, supporting CO₂ fixation via the Calvin cycle in these obligate autotrophs. The second step oxidizes nitrite to nitrate, performed by nitrite-oxidizing bacteria (NOB) like Nitrobacter species, using nitrite oxidoreductase (NXR), a molybdenum- and iron-containing enzyme located in the cytoplasmic membrane. This reaction provides about 74 kJ/mol of NO₂⁻ oxidized, again fueling autotrophic growth. Nitrification as a whole is sensitive to environmental factors like pH (optimal 7-8), oxygen levels, and inhibitors such as ammonia analogs. In addition to this classical two-step process requiring syntrophy between AOB and NOB, complete ammonia oxidation (comammox) has been discovered in organisms such as Nitrospira species (as of 2015), where a single bacterium performs both oxidations, yielding an overall approximately 349 kJ/mol of NH₃ oxidized under standard conditions and enabling efficient nitrogen processing in low-ammonia environments. Anaerobic ammonium oxidation (anammox) represents a distinct chemolithotrophic pathway that directly couples the oxidation of ammonium with the reduction of nitrite to dinitrogen gas (N₂) under anoxic conditions, bypassing oxygen as an electron acceptor. Discovered in the mid-1990s during studies of wastewater sludge, anammox was first attributed to novel planctomycete bacteria, revolutionizing understanding of nitrogen loss in anaerobic environments. The overall reaction is: NH4++NO2−→N2+2H2O\mathrm{NH_4^+ + NO_2^- \rightarrow N_2 + 2H_2O} with a standard Gibbs free energy change of , providing sufficient energy for autotrophic CO₂ fixation, though the process is notably slow with a low growth yield. Anammox is catalyzed within a specialized intracellular compartment called the anammoxosome, which maintains a distinct biochemistry and protects the catabolic enzyme complex from the . Key players include Candidatus Brocadia and Candidatus Scalindua species, which are strictly anaerobic autotrophs using a modified involving hydrazine synthase and hydrazine oxidoreductase to form and oxidize the intermediate (N₂H₄). These bacteria thrive in low-oxygen niches and require as an oxidant, often sourced from partial or . Ecologically, anammox contributes significantly to the global , accounting for up to 50% of nitrogen loss in marine oxygen minimum zones and sediments, as well as in soils and freshwater systems. In , it enables efficient, low-energy nitrogen removal by integrating with partial nitritation processes, reducing needs and production compared to traditional methods.

Phototrophy

Oxygenic photosynthesis

Oxygenic photosynthesis is a light-dependent process performed by certain microbes, notably and , that uses as an to generate oxygen, ATP, and NADPH for carbon fixation. This process occurs via two membrane-bound photosystems, (PSII) and (PSI), arranged in a series known as the Z-scheme, which enables efficient driven by absorption. In PSII, excites electrons from the reaction center chlorophyll (P680), creating a strong oxidant that drives oxidation at the (OEC), a cubane-like cluster composed of four s and one calcium (Mn₄CaO₅). The OEC cycles through five states (S₀ to S₄), facilitating the four-electron oxidation of two s to produce one O₂ , four protons, and four electrons, as described by the : 2 H₂O → O₂ + 4 H⁺ + 4 e⁻. The overall light reactions of oxygenic can be summarized by the equation: 2H2O+2NADP++nADP+nPi+light→O2+2NADPH+nATP+2H+2 \mathrm{H_2O} + 2 \mathrm{NADP^+} + n \mathrm{ADP} + n \mathrm{P_i} + \text{light} \rightarrow \mathrm{O_2} + 2 \mathrm{NADPH} + n \mathrm{ATP} + 2 \mathrm{H^+} where electrons from reduce NADP⁺ to NADPH via the Z-scheme, and a proton gradient powers ATP synthesis through the cytochrome b₆f complex. These reducing equivalents (NADPH and ATP) then fuel the Calvin-Benson-Bassham (CBB) cycle in the or chloroplasts, where ribulose-1,5-bisphosphate carboxylase/oxygenase () fixes CO₂ into organic compounds, such as 3-phosphoglycerate, ultimately producing sugars. In microbial systems, this carbon fixation by and algal accounts for approximately 50 Gt C fixed annually, representing a major portion of global and linking oxygenic directly to the . Key microbial performers include unicellular cyanobacteria like , which thrive in marine environments and contribute significantly to oceanic productivity through oxygenic . Fossil evidence, such as —layered structures formed by cyanobacterial mats—dates back to at least 3.5 billion years ago in Archaean rocks, indicating that oxygenic has ancient origins and played a pivotal role in Earth's oxygenation. The process's efficiency in converting to biomass is low, typically 1-2% under natural conditions in cyanobacteria, limited by factors like light saturation and antenna size, yet it sustains roughly 50% of Earth's atmospheric oxygen production through marine microbial contributions.

Anoxygenic photosynthesis

Anoxygenic photosynthesis is a form of phototrophy performed by certain in anaerobic environments, where light energy is captured to drive electron transport without evolving oxygen, using electron donors such as (H₂S) or (H₂) instead of . This process occurs in diverse bacterial groups, including , green sulfur bacteria, and , and represents an ancient metabolic strategy that predates . Purple bacteria, such as those in the genera Rhodobacter and Rhodospirillum, utilize a photosynthetic reaction center analogous to (PSII) in oxygenic phototrophs, employing H₂S as an to reduce NAD⁺ or other acceptors, often depositing elemental (S⁰) extracellularly. In contrast, green sulfur (e.g., Chlorobium ) possess a (PSI)-like reaction center and employ a reverse to generate reducing power from H₂S, as exemplified by the reaction: 2 H₂S + 2 NADP⁺ + light → S⁰ + 2 NADPH + 2 H⁺. , a group of strictly anaerobic phototrophs in the Firmicutes , reduce NAD⁺ directly via a simple PSI-type reaction center using H₂ or reduced sulfur compounds, adapting to low-light anoxic soils. These systems rely on bacteriochlorophylls a or g as primary pigments, which absorb in the spectrum and enable light harvesting without oxygenic . Ecologically, anoxygenic phototrophs thrive in stratified anoxic aquatic environments, such as sediments, hypersaline lakes, and microbial mats, where they form dense blooms utilizing sulfide gradients. Purple non-sulfur bacteria like Rhodospirillum rubrum exhibit metabolic versatility, often functioning photoheterotrophically by assimilating organic compounds alongside light energy in oxygen-limited habitats. Evolutionarily, anoxygenic photosynthesis is inferred to have originated around 3.5 billion years ago, based on fossil evidence of sulfur-rich microbial structures in ancient rocks, preceding the rise of oxygenic photosynthesis and contributing to early Earth's sulfur cycle.

Specialized metabolisms

Nitrogen fixation

Nitrogen fixation is a vital microbial process that converts inert atmospheric dinitrogen (N₂) into bioavailable (NH₃), serving as the primary natural source of fixed nitrogen for ecosystems worldwide. This reaction is exclusively catalyzed by the enzyme in prokaryotes termed diazotrophs, enabling them to synthesize organic essential for growth and supporting broader food webs. The complex comprises two main components: the iron (Fe) protein, which serves as the , and the molybdenum-iron (MoFe) protein, the site of N₂ reduction. The Fe protein transfers electrons from or flavodoxin to the MoFe protein in a process powered by . The of the reaction is given by: N2+8H++8e−+16ATP→2NH3+H2+16ADP+16Pi\text{N}_2 + 8\text{H}^+ + 8\text{e}^- + 16\text{ATP} \rightarrow 2\text{NH}_3 + \text{H}_2 + 16\text{ADP} + 16\text{P}_i A simplified net equation excludes ATP: N2+8H++8e−→2NH3+H2\text{N}_2 + 8\text{H}^+ + 8\text{e}^- \rightarrow 2\text{NH}_3 + \text{H}_2 This process demands substantial energy—equivalent to 16 ATP per N₂ molecule—and is extremely sensitive to oxygen, which inactivates the enzyme through oxidative damage, necessitating anaerobic microenvironments in diazotrophs. Diazotrophs exhibit diverse lifestyles to accommodate nitrogenase activity. Free-living examples include aerobic soil bacteria like Azotobacter vinelandii, which maintain high respiration rates to scavenge oxygen. Symbiotic associations, such as Rhizobium species forming root nodules in legumes, provide a protected, low-oxygen environment via leghemoglobin. In cyanobacteria like Anabaena and Nostoc, nitrogen fixation occurs in specialized heterocysts—differentiated cells with thick walls that restrict oxygen diffusion while allowing N₂ entry, spatially separating it from oxygenic photosynthesis in vegetative cells. Globally, biological nitrogen fixation inputs approximately 140 Tg N per year into terrestrial ecosystems, with significant contributions from both free-living and symbiotic microbes. In , it supplies around 50% of the nitrogen for crops, reducing reliance on synthetic fertilizers and enhancing . Alternative nitrogenases, including vanadium (V)-dependent and iron-only (Fe-only) variants, occur in some and under molybdenum scarcity; these homologous enzymes exhibit lower efficiency but enable fixation in metal-limited environments.

Methylotrophy

Methylotrophy refers to the metabolic capability of certain microorganisms to utilize reduced one-carbon (C1) compounds, such as (CH₄), (CH₃OH), and (HCHO), as their sole sources of carbon and energy. This process is distinct from general heterotrophy, as it involves specialized enzymes for activating and oxidizing these compounds, enabling growth in environments rich in C1 substrates but poor in multi-carbon organics. Methylotrophs are phylogenetically diverse, spanning and , and play crucial roles in global carbon cycling by converting greenhouse gases like into or CO₂. The initial step in methylotrophic metabolism often involves the oxidation of to by methanol dehydrogenase (MDH), a periplasmic enzyme that transfers electrons to the respiratory chain for energy generation. , a toxic intermediate, is then routed to either assimilation pathways for synthesis or pathways for energy production via complete oxidation to CO₂. typically proceeds through tetrahydrofolate (H₄F)- or tetrahydromethanopterin (H₄MPT)-linked pathways, generating reducing equivalents (NADH) and ATP while releasing CO₂. For methanotrophs, a subset of methylotrophs, the pathway begins with activation by (MMO), which catalyzes the reaction: CH4+O2+NADH+H+→CH3OH+NAD++H2O\text{CH}_4 + \text{O}_2 + \text{NADH} + \text{H}^+ \rightarrow \text{CH}_3\text{OH} + \text{NAD}^+ + \text{H}_2\text{O} MMO exists in particulate (pMMO, copper-dependent) or soluble (sMMO, iron-dependent) forms, with pMMO predominant in most aerobic methanotrophs under copper-replete conditions. Subsequent steps mirror methanol oxidation, yielding energy through the full sequence: CH₄ + 2 O₂ → CH₃OH → HCHO → ... → CO₂. Assimilation of C1 units into central occurs via two primary pathways in : the ribulose monophosphate (RuMP) cycle and the serine cycle. The RuMP cycle, prevalent in Type I () methanotrophs, condenses with 1,5-bisphosphate to form hexulose 6-phosphate, which enters for C3-C6 intermediates; it is energetically efficient, requiring three ATP per three C1 units assimilated. In contrast, the serine cycle, used by Type II () methanotrophs, incorporates methylene-tetrahydrofolate into and serine, forming C4 acids like malate; it demands more energy (six ATP per three C1 units) but links to . Anaerobic methylotrophs, such as those performing nitrite-dependent methane oxidation, employ modified pathways, including intra-aerobic respiration where oxygen is generated from to support MMO activity without external O₂. Representative aerobic methanotrophs include Methylococcus capsulatus (, RuMP pathway), which thrives in neutral pH environments and expresses pMMO for high affinity, and Methylosinus trichosporium (, serine cycle), known for sMMO production under copper limitation. Anaerobic examples feature Candidatus Methylomirabilis oxyfera (NC10 phylum), a denitrifying that couples CH₄ oxidation to reduction, producing dinitrogen gas and contributing to nitrogen cycling in anoxic habitats like freshwater sediments. These microbes highlight the modularity of methylotrophy, with pathway choices reflecting phylogenetic and environmental adaptations. Ecologically, methylotrophs serve as a major biological sink for methane, oxidizing 30–90% of CH₄ produced in wetlands and sediments before atmospheric release, thus mitigating approximately 625 Tg CH₄ year⁻¹ globally. This activity occurs in diverse niches, from oxic soils and freshwater systems to anoxic marine sediments, where anaerobic methanotrophs like M. oxyfera enhance . Their bioremediation potential stems from co-metabolizing pollutants (e.g., chlorinated solvents via sMMO) and reducing from landfills or . Evolutionarily, methylotrophy traces to ancient origins, with evidence suggesting a methylotrophic ancestry for in , where C1 metabolism preceded CO₂-reducing pathways and facilitated early divergence of anaerobic multicarbon processes. Independent evolution in bacterial and archaeal lineages, driven by of MMO and assimilation modules, underscores its adaptive significance in primordial C1-rich atmospheres.

Syntrophy

Syntrophy refers to an obligately mutualistic interaction in microbial communities where two or more cooperate metabolically to enable the degradation of substrates that neither could utilize alone, often under thermodynamically constrained conditions such as anaerobiosis. This process is fundamental to anaerobic global carbon cycling, serving as an intermediary step in the conversion of complex to by maintaining low concentrations of inhibitory intermediates like (H₂) or . In syntrophic consortia, one microbe (the syntroph) performs or oxidation reactions that produce energy-poor intermediates, which a partner microbe (often a or sulfate reducer) consumes, shifting the overall from endergonic to exergonic. The energetics of syntrophy hinge on interspecies hydrogen transfer (IHT), where the of H₂ is kept below 10⁻⁴ atm to favor oxidation reactions like butyrate breakdown, which would otherwise yield only about -15 kJ/mol ATP. Seminal studies revealed this through the isolation of "Methanobacillus omelianskii," later identified as a co-culture of Syntrophobacter wolinii (ethanol oxidizer) and Methanospirillum hungatei (H₂ consumer), demonstrating how syntrophy enables conversion to , CO₂, and CH₄. Reverse electron transport and flavin-based electron bifurcation in syntrophs further conserve by generating low-potential electrons for , as elucidated in genomic analyses of Syntrophus aciditrophicus. Key mechanisms of syntrophy include indirect interspecies electron transfer (IET) via diffusible carriers like H₂ or , and direct IET through conductive structures such as microbial nanowires or multiheme , which bypass the need for H₂ and enhance in dense aggregates. For instance, flagella-mediated recognition in Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus consortia facilitates specific pairing and activates , improving propionate oxidation rates by up to 33% when supplemented with conductive . These adaptations underscore syntrophy's role in stable community formation, often involving physical proximity or extracellular mediators. Prominent examples occur in anaerobic digestion of fatty acids and aromatics. Syntrophomonas wolfei oxidizes butyrate to in partnership with methanogens, contributing to ~70% of production in . In hydrocarbon degradation, syntrophic like Syntrophus species couple benzoate oxidation to , processing aromatic pollutants in sediments. Anaerobic methane oxidation (AOM) represents a reverse syntrophy, where consortia of ANME and sulfate-reducing consume via direct IET, mitigating ~90% of oceanic . These interactions highlight syntrophy's ecological impact, driving nutrient recycling in anoxic environments like wetlands and the gut microbiome.

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