Microbial growth

{{biology}}[[File:Auto-and_heterotrophs.png|thumb|right|thumb|The cycle between autotrophs and heterotrophs.]]
There are several types of '''microbial growth'''.

==Autotrophs==
Autotrophs are [[life|organisms]] that are capable of obtaining all the [[carbon]] required from carbon dioxide (CO<sub>2</sub>), the main usable inorganic form of carbon on [[Earth]]. Autotrophs can get their energy either from [[light]] ([[#phototrophs|phototrophs]]) or from chemical reactions ([[#chemotrophs|chemotrophs]]); the latter are almost always [[#lithotrophs|lithotrophs]].

The most familiar autotrophs are the [[oxygen]]-releasing photosynthesizers: [[plants]], algae, and [[cyanobacteria]], but many other [[prokaryote|prokaryotes]] are also autotrophic, being not only phototrophic like plants, but also chemotrophic.

There are a variety of carbon-fixation methods used for obtaining carbon dioxide; some common ones are:
*Calvin-Benson cycle (cyanobacteria/[[chloroplast|chloroplasts]]), purple photosynthetic [[bacteria]] (proteobacteria), etc.
*reductive Krebs cycle (''Chlorobium'', etc.)
*reductive acetyl-CoA pathway (green nonsulfur bacteria like ''Chloroflexus'')
*tapping into the methanogenesis reactions (methanogens)

===Phototroph===
Phototrophs are [[organism]]s whose energy source is sunlight; such organisms are said to practice photosynthesis. The most familiar phototrophs include the oxygen-releasers: plants, algae, and cyanobacteria. These and others, like the purple sulfur bacteria (Chromatiaceae), are [[#autotroph|autotrophic]], but there are some, like the purple nonsulfur bacteria (Rhodospirillaceae), that are [[#heterotroph|heterotrophic]].

Photosynthetic mechanisms vary. The large majority of phototrophs use chlorophyll-carotenoid-protein complexes or "photosystems" to capture light. Cyanobacteria and [[chloroplast|chloroplasts]] have two of them, which operate in series, while other photosynthetic [[bacteria]] have only one. Halobacteria (some archaea that are closely related to methanogens) use bacteriorhodopsin, a reddish pigment related to the vertebrate visual pigment rhodopsin.

Photosynthesis is a [[Chemistry|chemical]] reaction (or more accurately, a chain of chemical reactions) which takes place in green [[plant]]s, some protists (e.g. algae) and some [[prokaryote]]s (e.g. cyanobacteria). Photosynthesis produces glucose, a carbohydrate which can then be broken down to release energy (respiration), or used to synthesize other [[molecule]]s, including [[lipid]]s (fats and oils) and [[protein]]s. Photosynthesis is therefore crucial to all living things (except a few prokaryotes which can synthesize molecules using energy from things like underwater volcanic vents), either directly (plants) or indirectly ([[animal]]s, [[Fungus|fungi]]). 

The reactants (inputs) of photosynthesis are [[water]] and carbon dioxide, and the reaction is powered by [[energy]] from light. Photosynthesis can therefore be simplified to the following reaction:

<center>Carbon Dioxide (6 x CO<sub>2</sub>) + Water (6 x H<sub>2</sub>O) + [[photon]]s → Glucose (C<sub>6</sub>H<sub>12</sub>O<sub>6</sub>) + Oxygen (6 x O<sub>2</sub>)</center>

[[Oxygen]] gas is given off as a waste product of this reaction.  This reaction is the exact reverse of the simplified respiration reaction.

Photosynthesis, however, is not quite this simple and instead occurs in a multiple step chain reaction.  Each step must be catalyzed by different [[enzymes]].  In plants photosynthesis occurs in organelles called [[chloroplast]]s, and the steps of the reactions are classified into "light dependent reactions" and "light independent reactions" (or "[[carbon]] reactions"). It has been demonstrated that the photosynthesis process exploits [[quantum physics]] to enhance its efficiency.<ref>[http://phys.org/news/2014-01-quantum-mechanics-efficiency-photosynthesis.html Quantum mechanics explains efficiency of photosynthesis] January 9, 2014 ''Phys.org''</ref><ref>[http://www.nature.com/ncomms/2014/140109/ncomms4012/full/ncomms4012.html Non-classicality of the molecular vibrations assisting exciton energy transfer at room temperature] by Edward J. O’Reilly & Alexandra Olaya-Castro ''Nature Communications'' 5, Article number: 3012. doi:10.1038/ncomms4012 (09 January 2014).</ref>

These organelles contain pigments including [[chlorophyll]] (which makes plants green) and carotenids.  These pigments are capable of absorbing [[sun]]light, and the energy absorbed causes the pigment to lose an [[electron]] (energy carrying sub-atomic particle).

====Evolution====
A substantial [[literature]] on origin and [[evolution]] of photosynthesis has recently developed. The conclusion of experts is that photosynthesis similar to that used by modern cyanobacteria developed at least 3.5 billion years ago from an earlier non-oxygen evolving phase. Its evolution likely involved both lateral [[gene]] transfer between organisms and a duplication event resulting in two linked photosystems.

====Creationists' take====
[[Creationism|Creationists]] [[Creationist claims|claim]] that the process of photosynthesis could not have evolved since it is [[Irreducible complexity|irreducibly complex]]. [[Answers in Genesis]] poses the question, "Why would evolution produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product have evolved?" They conclude, "It defies common sense to imagine that the irreducible complexity of photosynthetic systems would have arisen according to evolutionary theory. Rather, the incredible organization and intricacy evident in photosynthesis—a process man has yet to fully understand, let alone copy—shrieks of having been designed."<ref>Swindell, Rick (Dec. 2003). "[http://www.answersingenesis.org/tj/v17/i3/photosynthesis.asp Shining light on the evolution of photosynthesis]." Answers in Genesis.</ref>

Answers in Genesis also challenges the gene duplication event in the evolution of photosynthesis on the grounds that it does not add "[[Information theory#Creationist information theory|information]]." They note, "It is then proposed that a 'simple duplication' of the genes encoding one photosystem occurred, followed by [[mutation]] leading to the formation of another photosystem. What is needed is new information to form another photosystem, not duplication of already present genes followed by mutation."<ref>Purdom, Georgia (May 16, 2007). "[http://www.answersingenesis.org/articles/aid/v2/n1/origin-of-photosynthesis Origin of photosynthesis: A theory out of thin air]." Answers in Genesis.</ref>

===Chemotrophs===
Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. Such organisms are divided into:

*[[#Lithotrophs|Lithotrophs]], utilizing inorganic-chemical reactions.
*[[#Organotrophs|Organotrophs]], utilizing organic-chemical reactions.

====Lithotrophs====
Lithotrophs are a diverse group of organisms using inorganic substrate (usually of mineral origin) to obtain reducing equivalents for use in biosynthesis (such as carbon dioxide fixation) or energy (such as [[ATP]] production) via aerobic or anaerobic respiration.

====Organotrophs====
Organotrophs are [[organism]]s that gets their energy from organic compounds, usually by consuming or breaking down other organisms. Nearly all organotrophs are also [[heterotroph]]s, meaning that they also get their carbon from that source. Organotrophs include all [[animal|animals]] and [[fungi]], and many [[bacteria]] and {{wpl|Protist|protists}}.

Organotrophs' energy extraction can be either anaerobic (fermentation) or aerobic. Anaerobic metabolism involves rearrangement of organic molecules, like:

:Sugars -> Lactate
:Sugars -> Ethanol + CO<sub>2</sub>

By contrast, aerobic metabolism involves transferring electrons from organic compounds to some oxidizer (electron acceptor) like oxygen molecules, nitrate, or sulfate. Carbon is released as carbon dioxide, hydrogen as water, etc.

In aerobic organisms' energy metabolism, nearly all of the steps are anaerobic. Combination with oxygen is the last step, and one that was apparently developed or transferred several times among [[prokaryote]]s. [[Eukaryote]]s use [[mitochondria]] for aerobic metabolism; the rest of the cell is anaerobic.

Not surprisingly, some organisms are facultative anaerobes, being able to switch between aerobic and anaerobic metabolism as the available oxygen varies. This distinguishes them from obligate anaerobes and aerobes, which are committed to their nonuse or use of oxygen, respectively.

These considerations suggest that anaerobic metabolism was the original form, and that aerobic metabolism was later added in, which is consistent with life being present on Earth before its atmosphere became significantly oxygenated.

==Heterotrophs==
A '''heterotroph''' is an [[organism]] which gets its carbon from organic compounds, usually by consuming or breaking down other organisms.  Many heterotrophs are also [[organotroph|organotrophs]], meaning they also get their energy from organic compounds. These include all [[animals]] and [[fungi]], and many [[bacteria]] and {{wpl|Protist|protists}}.

[[File:Monotropastrum humile.jpg|thumb|right|thumb|''Monotropastrum humile'', a myco-heterotroph.]]
Some parasitic, non-photosynthesizing plants, known as {{wpl|Myco-heterotrophy|myco-heterotrophs}} are heterotrophic but not organotrophic. Myco-heterotrophy has evolved multiple times in different plant families. These plants obtain carbon from soil fungi.

Interestingly, there are photosynthetic bacteria that are heterotrophs, notably the purple nonsulfur bacteria (Rhodospirillaceae).

Organisms have a wide range of degrees of heterotrophy. Many bacteria, like pseudomonads, can use any of a variety of organic compounds as their sole carbon source, while on the opposite extreme, intracellular [[Symbiosis|symbionts]] and parasites are often so dependent on their host cells for nutrition that they are very difficult to grow in lab conditions.

The animal kingdom is somewhat intermediate, sharing the need to consume a variety of biomolecules, but still able to make many others. The "essential" [[amino acid]]s (EAAs), familiar from human nutrition as those that cannot be made by our bodies and therefore must be consumed, are a nutritional need across the animal kingdom. Likewise, the B vitamins are [[enzyme]] cofactors that must be consumed, and for the same reason.

However, many animals have workarounds that enable them to survive on diets that are short on EAAs and vitamins. A common one is gut symbionts, present in many land vertebrates and termites. Ruminants have extra stomachs before the usual vertebrate stomach, with the first one becoming a fermentation vat for the grass and leaves that they eat. A more common solution among land vertebrates, however, is making a pouch toward the rear of the gut for this purpose, the cecum. Also used are intracellular symbionts, like ''Buchnera'' bacteria in aphids. These insects consume plant sap, which is nutritionally very limited; the bacteria supply what the aphids themselves cannot. Sequencing the bacterium's [[genome]] reveals that though ''Buchnera'' is closely related to enteric bacteria like ''Escherichia coli'', it only has biosynthesis enzymes for what its hosts cannot produce, like the "essential" amino acids.

The degree of heterotrophy is correlated with the type of nutrition. The weakest heterotrophy is found in organisms of decay, which live in soil, gut contents, decomposing dead organisms, etc.; these organisms cannot afford to be very choosy. It is stronger in organisms that consume other organisms, because those others can have ready-made biomolecules, though they are broken down into small ones before they get absorbed. And it is strongest in intracellular organisms, because they can acquire the full gamut of biomolecules from their hosts.

==References==
* Taiz, L. & Zeiger, E. 2002.  ''Plant Physiology 3rd ed.''.  Mass: Sinauer.
* "[http://www.ncbi.nlm.nih.gov/pubmed/11538390 Abstract: Origin and early evolution of photosynthesis]."  PubMed.

==Further reading (popular science)==
* King, J.  ''How Plants Work''.  Cambridge University Press.

==References==
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