Microbial metabolism
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.
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).
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.
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.
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.
These inorganic compounds release less energy in cellular respiration, which leads to slower growth rates than aerobes.
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.
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.
A classic example of a sulfur-oxidizing bacterium is Beggiatoa, a microbe originally described by Sergei Winogradsky, one of the founders of environmental 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 protons to be translocated across the membrane.
[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.
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.
Like sulfur oxidation, reverse electron flow must be used to form the NADH used for carbon dioxide fixation via the Calvin cycle.
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.
[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.
[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.
[19][20][21] 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.
[24] In addition to oxygenic photosynthesis, many bacteria can also photosynthesize anaerobically, typically using sulfide (H2S) as an electron donor to produce sulfate.
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.
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.
Two different reaction centers (photosystems) are used and proton motive force is generated both by using cyclic electron flow and the quinone pool.
In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center.
While extremely common (80% by volume) in the atmosphere, dinitrogen gas (N2) 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 (NH3), which is easily assimilated by all organisms.
