Microbial metabolism 5330368 222831339 2008-07-01T09:36:11Z Slashme 451287 typo '''Microbial metabolism''' is the means by which a [[microbe]] obtains the energy and nutrients (e.g. [[carbon]]) it needs to live and reproduce. [[Microbe]]s use many different types of [[metabolism|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 [[biotechnology|industrial processes]] or responsible for [[biogeochemistry|biogeochemical]] cycles. <!-- The redirect page [[Knallgas]] arrives here. Please consider changing the link if you change the name of this section. Thanks. -->==Types of microbial metabolism== [[Image:Troph flowchart.svg|thumb|350px|right|Flow chart to determine the metabolic characteristics of microorganisms]] {{main|Primary nutritional groups}} All microbial metabolism can be arranged according to three principles: 1. How the organism obtains carbon for synthesising cell mass: * '''[[autotroph]]ic''' – [[carbon]] is obtained from [[carbon dioxide]] (CO<sub>2</sub>) * '''[[heterotroph]]ic''' – [[carbon]] is obtained from [[organic compound]]s * '''[[mixotroph]]ic''' – [[carbon]] is obtained from both [[organic compound]]s and by fixing [[carbon dioxide]] 2. How the organism obtains [[reducing equivalent]]s used either in energy conservation or in biosynthetic reactions: * '''[[lithotroph]]ic''' – reducing equivalents are obtained from inorganic compounds * '''[[organotroph]]ic''' – reducing equivalents are obtained from [[organic compound]]s 3. How the organism obtains energy for living and growing: * '''[[chemotroph]]ic''' – energy is obtained from external [[chemical compound]]s * '''[[phototroph]]ic''' – energy is obtained from light In practice, these terms are almost freely combined. Typical examples are as follows: * '''chemolithoautotrophs''' obtain energy from the oxidation of [[inorganic compound]]s and [[carbon]] from the fixation of [[carbon dioxide]]. Examples: Nitrifying bacteria, Sulfur-oxidising bacteria, Iron-oxidising bacteria, [[Knallgas-bacteria]] * '''photolithoautotrophs''' obtain energy from light and [[carbon]] from the fixation of [[carbon dioxide]], using reducing equivalents from [[inorganic compound]]s. Examples: [[Cyanobacteria]] (water as reducing equivalent donor), [[Chlorobiaceae]], [[Chromaticaceae]] (hydrogen sulfide as reducing equivalent donor), ''[[Chloroflexus]]'' (hydrogen as reducing equivalent donor) * '''chemolithoheterotrophs''' obtain energy from the oxidation of [[inorganic compound]]s, but can not fix [[carbon dioxide]]. Examples: some ''[[Nitrobacter]]'' spp., ''[[Wolinella]]'' (with H<sub>2</sub> as reducing equivalent donor), some [[Knallgas-bacteria]] * '''chemoorganoheterotrophs''' obtain energy, [[carbon]] and reducing equivalents for biosynthetic reactions from [[organic compound]]s. Examples: most bacteria, e. g. ''[[Escherichia coli]]'', ''[[Bacillus]]'' spp., ''[[Actinobacteria]]'' * '''photoorganoheterotrophs''' obtain energy from light, [[carbon]] and reducing equivalents for biosynthetic reactions from [[organic compound]]s. Some species are strictly heterotrophic, many others can also fix [[carbon dioxide]] and are mixotrophic. Examples: ''[[Rhodobacter]]'', ''[[Rhodopseudomonas]]'', ''[[Rhodospirillum]]'', ''[[Rhodomicrobium]]'', ''[[Rhodocyclus]]'', ''[[Heliobacterium]]'', ''[[Chloroflexus]]'' (alternatively to photolithoautotrophy with hydrogen) ==Heterotrophic microbial metabolism== Most microbes are [[heterotrophic]] (more precisely chemoorganoheterotrophic), using [[organic compound]]s as both carbon and energy sources. [[Heterotrophic]] microbes live off of nutrients that they scavenge from living hosts (as [[commensals]] or [[parasite]]s) or find in dead organic matter of all kind ([[saprophage]]s). 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 lysed by cooperating swarms of many single cells of Myxobacteria). Most [[pathogen]]ic bacteria can be viewed as [[heterotrophic]] parasites of humans or whatever other eukaryotic species they affect. [[Heterotrophic]] microbes are extremely abundant in nature and are responsible for the breakdown of large organic [[polymer]]s such as [[cellulose]], [[chitin]] or [[lignin]] which are generally indigestible to larger animals. Generally, the 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 [[Embden-Meyerhoff-Parnas|EMP pathway]]) for sugar metabolism and the [[citric acid cycle]] to degrade [[acetate]], producing energy in the form of [[Adenosine triphosphate|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]] utilise alternative metabolic pathways other than [[glycolysis]] and the [[citric acid cycle]]. A well studied example is sugar metabolism via the [[KDPG pathway|keto-deoxy-phosphogluconate pathway]] (also called [[Entner-Doudoroff|ED pathway]]) in ''[[Pseudomonas]]]'' instead of the [[glycolysis|glycolytic]] pathway. Moreover, there is even a third alternative sugar-catabolic pathway used by some bacteria, the [[PP pathway|pentose-phosphate pathway]]. This metabolic diversity and ability of [[prokaryote]]s to use a huge variety of organic compounds arises from the much deeper evolutionary history and diversity of [[prokaryote]]s, as compared to [[eukaryote]]s. It is also noteworthy that the [[mitochondrion]], the small membrane-bound intracellular organelle that is the site of [[eukaryotic]] 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 [[eukaryote]]s share metabolic properties with these [[Proteobacteria]]. Most microbes [[Cellular respiration|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 acceptor]]s other than [[oxygen]] has important biogeochemical consequences. ==Fermentation== {{main|Fermentation (biochemistry)}} Fermentation is a specific type of [[heterotrophic]] metabolism that uses [[organic compound|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<sup>+</sup> and therefore must have an alternative method of using this reducing power and maintaining a supply of NAD<sup>+</sup> for the proper functioning of normal metabolic pathways (e.g. [[glycolysis]]). As [[oxygen]] is not required, fermentative organisms are [[Anaerobic organism|anaerobic]]. Many organisms can use fermentation under anaerobic conditions and [[Anaerobic respiration|respiration]] when [[oxygen]] is not present. These organisms are [[facultative anaerobe]]s. To avoid the overproduction of [[NADH]] obligately fermentative organisms usually do not have a complete [[citric acid cycle]]. Instead of using an [[ATPase]] as in [[Cellular respiration|respiration]], [[Adenosine triphosphate|ATP]] in fermentative organisms is produced by [[substrate-level phosphorylation]] where a [[phosphate]] group is transferred from a high-energy [[organic compound]] to [[Adenosine diphosphate|ADP]] to form [[Adenosine triphosphate|ATP]]. As a result of the need to produce high energy phosphate-containing [[organic compound]]s (generally in the form of CoA-esters) fermentative organisms use [[NADH]] and other cofactors to produce many different reduced metabolic by-products, often including [[hydrogen]] gas (H<sub>2</sub>). These reduced [[organic compound]]s are generally small organic [[acid]]s and [[alcohol]]s derived from [[pyruvate]], the end product of [[glycolysis]]. Examples include [[ethanol]], [[acetate]], [[lactic acid|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|proton (or sodium) motive force]] and therefore [[Adenosine triphosphate|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 use excess [[NADH]] to produce [[lactate]], although this is not the major form of metabolism as it is in fermentative microorganisms. ==Special metabolic properties== ===Methylotrophy=== Methylotrophy refers to the ability of an organism to use [[C1-compounds]] as energy sources. These compounds include [[methanol]], [[methyl amine]]s, [[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]]''. [[Methanotroph]]s are a specific type of methylotroph that are also able to use [[methane]] (CH<sub>4</sub>) as a carbon source by oxidizing it sequentially to [[methanol]] (CH<sub>3</sub>OH), [[formaldehyde]] (CH<sub>2</sub>O), [[formate]] (HCOO<sup>-</sup>) and finally [[carbon dioxide]] CO<sub>2</sub> initially using the important enzyme [[methane monooxygenase]]. As [[oxygen]] is required for this process, all (conventional) methanotrophs are obligate [[aerobe]]s. Reducing power in the form of [[quinone]]s and [[NADH]] is produced during these oxidations to produce a [[proton motive force]] and therefore [[Adenosine triphosphate|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 oxidised to CO<sub>2</sub> (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 [[methanogen]]ic 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 [[methanogen]]s, strictly [[Anaerobic organism|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. These cofactors are responsible (among other things) for the establishment of a [[proton]] gradient across the outer membrane thereby driving [[Adenosine triphosphate|ATP]] synthesis. Several different types of [[methanogenesis]] occurs, which differ in the starting compounds oxidized. Some methanogens reduce [[carbon dioxide]] (CO<sub>2</sub>) to [[methane]] (CH<sub>4</sub>) using electrons (most often) from [[hydrogen]] gas (H<sub>2</sub>) [[chemolithoautotrophic]]ally. These [[methanogen]]s can often be found in environments containing fermentative organisms. The tight association of [[methanogen]]s and fermentative bacteria can be considered to be syntrophic (see below) because the [[methanogen]]s, 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 [[methanogen]]s use [[methanol]] (CH<sub>3</sub>OH) as a substrate for [[methanogenesis]]. These are chemoorganotrophic, but still autotrophic in using CO<sub>2</sub> as only carbon source. The biochemistry of this process is quite different from that of the [[carbon dioxide]] reducing [[methanogen]]s. Lastly, a third group of [[methanogen]]s produce both [[methane]] and [[carbon dioxide]] from [[acetate]] (CH<sub>3</sub>COO<sup>-</sup>) with the [[acetate]] being literally split between the two carbons. These acetate-cleaving organisms are the only chemoorganoheterotrophic methanogens. All autotrophic[[methanogen]]s use a variation of the [[acetyl-CoA pathway]] to fix CO<sub>2</sub> and obtain cellular carbon. ===Syntrophy=== 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<sup>-5</sup> atm) and thereby shift the [[Chemical equilibrium|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<sup>-5</sup> atm hydrogen and even lower if also the initially produced acetate is further metabolised 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<sup>-5</sup> 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 CO<sub>2</sub>. ==Anaerobic respiration== In [[aerobic]] organisms, [[oxygen]] is used as a [[terminal electron acceptor]] during respiration. This is largely because [[oxygen]] has a very low [[reduction potential]] allowing for [[aerobic]] organisms to utilize their electron transport systems most efficiently. In [[anaerobic organism]]s, [[terminal electron acceptor]]s other than [[oxygen]] are used. These [[inorganic compound]]s have a higher [[reduction potential]] compared to [[oxygen]], meaning that [[Cellular respiration|respiration]] is less efficient in these organisms generally leading to slower growth rates compared to [[aerobe]]s. Many [[facultative anaerobe]]s can use either [[oxygen]] or alternative [[terminal electron acceptor]]s for respiration depending on the environmental conditions. Most respiring [[anaerobe]]s are heterotrophs, although some do live [[autotroph]]ically. 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=== {{main|Denitrification}} Denitrification is the utilization of [[nitrate]] (NO<sub>3</sub><sup>-</sup>) as a [[terminal electron acceptor]]. It is a widespread process that is used by many members of the [[Proteobacteria]]. Many [[facultative anaerobe]]s use denitrification because [[nitrate]], like [[oxygen]], has a low [[reduction potential]]. Many denitrifying [[bacteria]] can also use ferric [[iron]] (Fe<sup>3+</sup>) and some [[organic compound|organic]] [[electron acceptor]]s. Denitrification involves the stepwise reduction of [[nitrate]] to [[nitrite]] (NO<sub>2</sub><sup>-</sup>), [[nitric oxide]] (NO), [[nitrous oxide]] (N<sub>2</sub>O) and di[[nitrogen]] (N<sub>2</sub>) by the enzymes nitrate reductase, [[nitrite reductase]], nitric oxide reductase and nitrous oxide reductase, respectively. [[Proton]]s are transported across the membrane by the initial [[NADH]] reductase, [[quinone]]s 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 gas]]es 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]]. ===Sulfate reduction=== [[Sulfate]] reduction is a relatively energetically poor process used by many Gram negative [[bacteria]] found within the δ-[[Proteobacteria]], Gram positive organisms relating to ''[[Desulfotomaculum]]'' or the archaeon ''[[Archaeoglobus]]''. [[Hydrogen sulfide]] (H<sub>2</sub>S) is produced as a metabolic end product. Many [[sulfate]] reducers are [[heterotrophic]], using [[carbon]] compounds such as [[lactate]] and [[pyruvate]] (among many others) as [[electron donor]]s while others are [[autotrophic]], using [[hydrogen]] gas (H<sub>2</sub>) as an [[electron donor]]. Some unusual [[autotrophic]] [[sulfate]] reducing-bacteria can use [[phosphite]] (HPO<sub>3</sub><sup>-</sup>) as an [[electron donor]] (e.g. ''[[Desulfotignum phosphitoxidans]]'') or are capable of [[sulfur]] disproportionation (splitting one compound into two different compounds, in this case an [[electron donor]] and an [[electron acceptor]]) using [[thiosulfate]] (S<sub>2</sub>O<sub>3</sub><sup>2-</sup> e.g. ''[[Desulfovibrio sulfodismutans]]''). All [[sulfate]] reducing-organisms are strict [[anaerobe]]s. 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 [[Adenosine triphosphate|ATP]]. The APS is then reduced by the enzyme APS reductase to form [[sulfite]] (SO<sub>3</sub><sup>2-</sup> and [[Adenosine monophosphate|AMP]]. In organisms that use [[carbon]] compounds as [[electron donor]]s, the [[Adenosine triphosphate|ATP]] consumed is accounted for by fermentation of the [[carbon]] substrate. The [[hydrogen]] produced during fermentation is actually what drives respiration during [[sulfate]] reduction. [[Electron]]s are passed from the [[hydrogenase]] enzyme eventually to the APS reductase, which along with sulfite reductase completes the reduction of [[sulfate]] to [[hydrogen sulfide]]. A [[proton motive force]] is established due to a fact that the [[hydrogenase]], which converts H<sub>2</sub> to 2H<sup>+</sup> is located in the [[periplasm]] (or extracellularly in Gram positive [[bacteria]]). ===Acetogenesis=== {{main|Acetogenesis}} Acetogenesis is a type of microbial metabolism that uses [[hydrogen]] (H<sub>2</sub>) as an [[electron donor]] and [[carbon dioxide]] (CO<sub>2</sub>) as an [[electron acceptor]] to produce [[acetate]]. This is similar to [[methanogenesis]] (see above) in having the same [[electron donor]]s and [[electron acceptor|acceptors]]. [[Bacteria]] that can [[autotrophic]]ally synthesize [[acetate]] are called homoacetogens. [[Carbon dioxide]] [[Redox|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 [[methanogen]]s. 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. ===Inorganic electron acceptors=== [[Ferric]] [[iron]] (Fe<sup>3+</sup>) is a widespread [[Hypoxia (environmental)|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|Geobacter metallireducens]]''. Since some ferric iron-reducing [[bacteria]] (e.g. ''[[Geobacter|G. metallireducens]]'') can use toxic [[hydrocarbon]]s such as [[toluene]] as a carbon source there is significant interest in using these organisms as [[bioremediation]] agents in ferric iron-rich contaminated [[aquifer]]s. 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 [[radionuclide|radionuclides]] are used as electron acceptors. Examples include: * [[Manganese|Manganic ion]] (Mn<sup>4+</sup>) reduction to [[Manganese|manganous ion]] (Mn<sup>2+</sup>) * [[Selenium|Selenate]] (SeO<sub>4</sub><sup>2-</sup>) reduction to [[Selenium|selenite]] (SeO<sub>3</sub><sup>2-</sup>) and selenite reduction to inorganic [[selenium]] (Se<sup>0</sup>) * [[Arsenic|Arsenate]] (AsO<sub>4</sub><sup>3-</sup>) reduction to [[arsenic|arsenite]] (AsO<sub>3</sub><sup>3-</sup>) * [[Uranyl|Uranyl ion]] ion (UO<sub>2</sub><sup>2+</sup>) reduction to [[uranium dioxide]] (UO<sub>2</sub>) ===Organic terminal electron acceptors=== An number of organisms, instead of using [[inorganic compound]]s as [[terminal electron acceptor]]s are able to use [[organic compound]]s to accept [[electron]]s from [[Cellular respiration|respiration]]. Examples include: * [[Fumarate]] reduction to [[succinate]] * [[Trimethylamine N-oxide|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 compound]]s are reduced to form their non-chlorinated endproducts. As chlorinated [[organic compound]]s are often important (and difficult to degrade) environmental polutants, reductive dechlorination is an important process in [[bioremediation]]. ==Chemolithotrophy== [[Chemolithotroph]]y is a type of metabolism where energy is obtained from the oxidation of [[inorganic compounds]]. Most [[chemolithotroph]]ic organisms are also [[autotroph]]ic. There are two major objectives to [[chemolithotroph]]y: the generation of energy ([[Adenosine triphosphate|ATP]]) and the generation of reducing power ([[NADH]]). ===Hydrogen oxidation=== Many organisms are capable of using [[hydrogen]] (H<sub>2</sub>) as a source of energy. While several mechanisms of anaerobic [[hydrogen]] [[oxidation]] have been mentioned previously (e.g. [[sulfate]] reducing- and acetogenic [[bacteria]]) [[hydrogen]] can also be used as an energy source aerobically. In these organisms [[hydrogen]] is oxidized by a membrane-bound [[hydrogenase]] causing [[proton]] pumping via electron transfer to various [[quinone]]s and [[cytochrome]]s. 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]]. ===Sulfur oxidation=== [[Sulfur]] oxidation involves the oxidation of reduced [[sulfur]] compounds (such as [[sulfide]] (H<sub>2</sub>S), inorganic [[sulfur]] (S<sup>0</sup>) and [[thiosulfate]] (S<sub>2</sub>O<sub>2</sub><sup>2-</sup>) ) to form [[sulfuric acid]] (H<sub>2</sub>SO<sub>4</sub>). A classic example of a [[sulfur]] oxidizing [[bacterium]] is ''[[Beggiatoa]]'', a microbe originally described by [[Sergei Winogradsky]], one of the founders of [[microbiology]]. 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 [[proton]]s 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 [[electron]]s against their [[thermodynamic]] gradient to produce [[NADH]]. Biochemically, reduced [[sulfur]] compounds are converted to [[sulfite]] (SO<sub>3</sub><sup>2-</sup>) and subsequently converted to [[sulfate]] by the enzyme [[sulfite oxidase]]. 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 [[Adenosine triphosphate|ATP]] and [[NADH]] production. In addition to aerobic [[sulfur]] [[oxidation]], some organisms (e.g. ''[[Thiobacillus denitrificans]]'') use [[nitrate]] (NO<sub>3</sub><sup>2-</sup>) as a [[terminal electron acceptor]] and therefore grow anaerobically. ===Ferrous iron (Fe<sup>2+</sup>) oxidation=== [[Iron(II) oxide|Ferrous iron]] is a soluble form of [[iron]] that is stable at extremely low [[pH]]s or under anaerobic conditions. Under aerobic, moderate [[pH]] conditions ferrous [[iron]] is oxidized spontaneously to the ferric (Fe<sup>3+</sup>) form and is hydrolyzed abiotically to insoluble [[ferric hydroxide]] (Fe(OH)<sub>3</sub>). There exists, therefore, three distinct types of ferrous iron-oxidizing microbes. The first are [[acidophile (organisms)|acidophile]]s, such as the [[bacteria]] ''[[Acidithiobacillus ferooxidans]]'' and ''[[Leptospirrillum 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 neutral [[pH]] along oxic-anoxic interfaces. Both these [[bacteria]], such as ''[[Gallionella ferruginea]]'' and ''[[Sphaerotilus natans]]'', and the acidophilic iron oxidizing-bacteria are aerobes. The third type of iron-oxidizing microbes are [[Anaerobic organism|anaerobic]] [[photosynthetic]] [[bacteria]] such as [[Chlorobium]], which use ferrous [[iron]] to produce [[NADH]] for [[autotroph]]ic [[carbon dioxide]] fixation. Biochemically, aerobic [[iron]] reduction 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 during [[sulfur]] [[oxidation]] [[reverse electron flow]] must be used to form the [[NADH]] used for [[carbon dioxide]] fixation via the [[Calvin cycle]]. ===Nitrification=== Nitrification is the process by which [[ammonia]] (NH<sub>3</sub>) is converted to [[nitrate]] (NO<sub>3</sub><sup>-</sup>). Nitrification is actually the net result of two distinct processes: oxidation of [[ammonia]] to [[nitrite]] (NO<sub>2</sub><sup>-</sup>) 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 poor energetically leading to very slow growth rates for both types of organisms. Biochemically, [[ammonia]] [[oxidation]] occurs by the stepwise oxidation of [[ammonia]] to [[hydroxylamine]] (NH<sub>2</sub>OH) 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]] [[Redox|reduction]] 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. In both [[ammonia]]- and [[nitrite]]-[[oxidation]] [[oxygen]] is required, meaning that both nitrosifying and nitrite-oxidizing [[bacteria]] are [[aerobe]]s. 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. ===Anammox=== Anammox stands for anaerobic [[ammonia]] [[oxidation]] and is a relatively recently (late 1990’s) discovered process. It occurs in members of the [[Planctomycetes]] (e.g. Candidatus ''[[Brocadia anammoxidans]]'') and involves the coupling of [[ammonia]] [[oxidation]] to [[nitrite]] [[Redox|reduction]]. As [[oxygen]] is not required for this process these organisms are strict [[anaerobe]]s. Amazingly, [[hydrazine]] (N<sub>2</sub>H<sub>4</sub>-rocket fuel) is produced as an intermediate during anammox metabolism. To deal with the high toxicity of [[hydrazine]], anammox [[bacteria]] contain an [[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 [[autotroph]]s although the mechanism for [[carbon dioxide]] fixation is unclear. Because of this property, these organisms have been applied industrially to remove [[nitrogen]] in [[wastewater treatment]] processes. Anammox has also been shown have widespread occurrence in anaerobic aquatic systems and has been speculated to account for approximately 50% of [[nitrogen]] gas production in some marine environments. == Phototrophy == Many microbes are capable of using light as a source of energy ([[phototroph]]y). Of these, [[algae]] are particularly significant because they are oxygenic, using water as an [[electron donor]] for electron transfer during [[photosynthesis]].{{Fact|date=August 2007}} Phototrophic bacteria are found in the phyla [[Cyanobacteria]], [[Chlorobi]], [[Proteobacteria]], [[Chloroflexi]] and [[Firmicutes]].<ref>{{cite journal |author=D.A. Bryant & N.-U. Frigaard |month=Nov |year=2006 |title=Prokaryotic photosynthesis and phototrophy illuminated |journal=Trends Microbiol. |volume=14 |issue=11 |pages=488 |doi=10.1016/j.tim.2006.09.001 }}</ref> Along with [[plant]]s these microbes are responsible for all biological generation of [[diatomic]] [[oxygen]] on [[Earth]]. Because [[chloroplasts]] were derived from a lineage of the Cyanobacteria, the general principles of metabolism in these [[endosymbiont]]s can also be applied to [[chloroplast]]s. In addition to oxygenic [[photosynthesis]], many [[bacteria]] can also photosynthesize anaerobically, typically using [[sulfide]] (H<sub>2</sub>S) as an [[electron donor]] to produce [[sulfate]]. Inorganic sulfur (S<sup>0</sup>), thiosulfate (S<sub>2</sub>O<sub>3</sub><sup>2-</sub>) and ferrous iron (Fe<sup>2+</sup>) can also be used by some organisms. Phylogenetically, all oxygenic photosynthetic [[bacteria]] are [[Cyanobacteria]], while anoxygenic photosynthetic [[bacteria]] belong to the purple bacteria ([[Proteobacteria]]), [[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. This type of metabolism is not considered to be [[photosynthesis]] but rather [[photophosphorylation]], since it generates energy, but does not directly fix carbon. As befits the large diversity of photosynthetic [[bacteria]], there exist many different mechanisms by which light is converted into energy for metabolism. All photosynthetic organisms locate their [[photosynthetic reaction center]]s within a membrane, which may be invaginations of the [[cytoplasmic membrane]] (purple bacteria), [[thylakoid membrane]]s ([[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 [[chlorophyll]]s and [[carotenoids]] allowing them to take advantage of different portions of the [[electromagnetic spectrum]] and thereby inhabit different [[ecological niche|niche]]s. Some groups of organisms contain more specialized light-harvesting structures e.g. [[phycobilisome]]s in [[Cyanobacteria]] and chlorosomes in Green sulfur and non-sulfur bacteria, allowing for increased light utilization efficiency. Biochemically, anoxygenic photosynthesis is very different from oxygenic [[photosynthesis]]. [[Cyanobacteria]] (and by extension [[chloroplasts]]) use the [[Z scheme]] of [[electron]] flow in which [[electron]]s eventually are used to form [[NADH]]. Two different [[photosynthetic reaction center|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 [[electron]]s 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 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 centre. In all cases, however, a [[proton motive force]] is generated and used to drive [[Adenosine triphosphate|ATP]] production via an [[ATPase]]. Most photosynthetic microbes are [[autotroph]]ic, fixing [[carbon dioxide]] via the [[Calvin cycle]]. Some photosynthetic bacteria (e.g. [[Chloroflexus]]) are photoheterotrophs, meaning that they use [[organic compound|organic carbon compounds]] as a carbon source for growth. Some photosynthetic organisms also fix [[nitrogen]] (see below). ==Nitrogen fixation== {{main|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<sub>2</sub>) is generally biologically inaccessible due to its high [[activation energy]]. Throughout all of nature, only specialized [[bacteria]] are capable of nitrogen fixation, converting dinitrogen gas into [[ammonia]] (NH<sub>3</sub>), which is easily assimilated by all organisms. These [[bacteria]], therefore are very important ecologically and are often essential for the survival entire ecosystems. This is especially true in the ocean, where nitrogen-fixing [[cyanobacteria]] are often the only sources or fixed [[nitrogen]] and in soils where specialized symbioses exist between [[legume]]s 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 fixed [[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 [[nitrogenase]]s is very highly regulated, both because nitrogen fixation is an extremely energetically expensive process (16-24 [[Adenosine triphosphate|ATP]] are used per N<sub>2</sub> fixed) and due to the extreme sensitivity of the [[nitrogenase]] to [[oxygen]]. ==See also== *[[lipophilic bacteria]], a minority of bacteria with [[lipid metabolism]] ==References== {{reflist}} *Madigan, M. T., Martinko, J. M. "Brock Biology of Microorganisms, 11th Ed." (2005) Pearson Prentice Hall, Upper Saddle River, NJ. [[Category:Metabolism]] [[es:Metabolismo microbiano]]