Microbial metabolism
This article's lead section may be too short to adequately summarize the key points. (December 2020) |
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
All microbial metabolisms can be arranged according to three principles:
1. How the organism obtains carbon for synthesizing cell mass:[1]
- autotrophic – carbon is obtained from carbon dioxide (CO2)
- heterotrophic – carbon is obtained from organic compounds
- mixotrophic – carbon is obtained from both organic compounds and by fixing carbon dioxide
2. How the organism obtains
- lithotrophic – reducing equivalents are obtained from inorganic compounds
- organotrophic – reducing equivalents are obtained from organic compounds
3. How the organism obtains energy for living and growing:
- phototrophic – energy is obtained from light[2]
- chemotrophic – energy is obtained from external chemical compounds[citation needed]
In practice, these terms are almost freely combined. Typical examples are as follows:
- chemolithoautotrophs obtain energy from the oxidation of inorganic compounds and carbon from the fixation of carbon dioxide. Examples: Knallgas-bacteria[3]
- photolithoautotrophs obtain energy from light and carbon from the fixation of carbon dioxide, using reducing equivalents from inorganic compounds. Examples: Chloroflexus(hydrogen (H
2) as reducing equivalent donor) - chemolithoheterotrophs obtain energy from the oxidation of inorganic compounds, but cannot fix carbon dioxide (CO2). Examples: some sulfate-reducing bacteria[citation needed]
- chemoorganoheterotrophs obtain energy, carbon, and hydrogen for biosynthetic reactions from organic compounds. Examples: most bacteria, e. g. Escherichia coli, Bacillus spp., Actinomycetota
- photoorganoheterotrophs obtain energy from light, carbon and reducing equivalents for biosynthetic reactions from organic compounds. Some species are strictly heterotrophic, many others can also fix carbon dioxide and are mixotrophic. Examples: Chloroflexus(alternatively to photolithoautotrophy with hydrogen)
Heterotrophic microbial metabolism
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
Biochemically,
Fermentation
Fermentation is a specific type of heterotrophic metabolism that uses
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
Not all fermentative organisms use substrate-level
Special metabolic properties
Methylotrophy
Methylotrophy refers to the ability of an organism to use
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
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,
Syntrophy
Syntrophy, in the context of microbial metabolism, refers to the pairing of multiple species to achieve a
Aerobic respiration
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
While
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
Denitrification is the utilization of
Sulfate reduction – sulfate as electron acceptor
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
Many sulfate reducers are organotrophic, using carbon compounds such as lactate and pyruvate (among many others) as
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
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
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
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
Although ferric iron is the most prevalent inorganic electron acceptor, a number of organisms (including the iron-reducing bacteria mentioned above) can use other
- Manganic ion (Mn4+
) reduction to manganous ion (Mn2+
) - Selenate (SeO2−
4) reduction to selenite (SeO2−
3) and selenite reduction to inorganic selenium (Se0) - Arsenate (AsO3−
4) reduction to arsenite (AsO3−
3) - Uranyl ion (UO2+
2) reduction to uranium dioxide (UO
2)
Organic terminal electron acceptors
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:
- succinate
- Trimethylamine N-oxide (TMAO) reduction to trimethylamine (TMA)
- Dimethyl sulfoxide (DMSO) reduction to Dimethyl sulfide (DMS)
- Reductive dechlorination
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
Hydrogen oxidation
Many organisms are capable of using hydrogen (H
2) as a source of energy. While several mechanisms of anaerobic hydrogen
- 2 H2 + O2 → 2 H2O + energy
In these organisms, hydrogen is oxidized by a membrane-bound
Sulfur oxidation
Sulfur oxidation involves the oxidation of reduced sulfur compounds (such as sulfide H
2S), inorganic sulfur (S), and thiosulfate (S
2O2−
3) to form
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
3) as a terminal electron acceptor and therefore grow anaerobically.
Ferrous iron (Fe2+
) oxidation
Nitrification
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
Anammox stands for anaerobic ammonia oxidation and the organisms responsible were relatively recently discovered, in the late 1990s.
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
In July 2020 researchers report the discovery of
Phototrophy
Many microbes (phototrophs) are capable of using light as a source of energy to produce
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
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
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. 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
- Lipophilic bacteria, a minority of bacteria with lipid metabolism
References
- ISBN 978-1319017637
- ^ Tang, K.-H., Tang, Y. J., Blankenship, R. E. (2011). "Carbon metabolic pathways in phototrophic bacteria and their broader evolutionary implications" Frontiers in Microbiology 2: Atc. 165. http://dx.doi.org/10.3389/micb.2011.00165
- ^ "Chemolithotrophy | Boundless Microbiology".
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- ^ "Bacteria with a metal diet discovered in dirty glassware". phys.org. Retrieved 16 August 2020.
- ^ Woodyatt, Amy. "Bacteria that eats metal accidentally discovered by scientists". CNN. Retrieved 16 August 2020.
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Further reading
- Madigan, Michael T.; Martinko, John M. (2005). Brock Biology of Microorganisms. Pearson Prentice Hall.