You may get the impression from studying biochemistry that all organisms can be described in terms of respiration and photosynthesis. However, this is far from true. This course has already looked at fermentation, the partial oxidation of organic molecules in the absence of oxygen. Amongst microbes, there is a wide variety of lifestyles that do not fit under the descriptions of respiration, photosynthesis or fermentation as defined in other portions of this course. The detailed study of these diverse lifestyles is normally covered in courses on Microbiology, but we will examine a few of these.

A visible proof of microbe diversity is the Winogradsky column [local]. When soil or mud is incubated in such a column, organisms will form layers. The pigments in these bacteria make the layers have different colors. The lifestyles in a Winogradsky column are most aerobic near the top and most anaerobic near the bottom. Only organisms near the top are capable of classical respiraton or oxygenic photosynthesis. The bulk of the organisms in the column are able to grow using other processes. These organisms are not merely oddities of nature, but are ecologically important. Such diverse lifestyles are responsible for the global cycles of the elements [local].

Photosynthesis can occur without water as the electron donor. Examples include the purple sulfur bacteria and the purple nonsulfur bacteria [local]. These organisms use light absorbed by bacteriochlorophyll molecules to drive electron transport, but utilize organic molecules or H₂ or H₂S as electron donors.

Another lifestyle that utilizes the energy in photons is that of the halophiles [local]. These bacteria harvest light with retinal, the same isoprenoid molecule that is used as the visual pigment in humans. Absorption of a photon causes a photoisomerization of the rhodopsin and a conformational change in the halorhodopsin chromoprotein in the bacterium's membrane. This process results in a pumping of protons from the cytoplasm to the medium and the bacterium uses this trans-membrane proton gradient to provide the free energy for its growth and division.

Other bacteria have lifestyles that produce biological energy without the use of photons. For example, consider the different forms of the element, nitrogen, which can exist at different oxidation levels. The most abundant form is N₂, comprising the bulk of the gas in the atmosphere.

Every year massive amounts of nitrogen fertilizers are applied to crops, much of it in the form of ammonia, but most of it is utilized by lithotrophic bacteria, rather than crops. Lithotrophs [local] utilize inorganic molecules to drive electron transport. This includes NH₃. Oxygen can still be used as the terminal electron acceptor and the energy produced from this electron transfer is used to fix CO₂ via the Calvin cycle. This process is called nitrification because it causes the accumulation of nitrite and nitrate from NH₃.

NH₃ + 1.5 O₂ --> NO₂^- + H₂O + H⁺

If the production of nitrate and nitrite from ammonia were the end of the transfromation, this would still benefit the plant, since they are able to assimilate these inorganic forms of nitrogen and fix it into amino acids. However, soils also contain organisms capable of anaerobic respiraton [local]. These bacteria use nitrate as a terminal electron acceptor to produce energy. The amount of energy is not as great as using O₂, but it is an ecological niche that offers competitive advantage to these organisms. These organisms reduce nitrate to the level of N₂ in a process that is termed denitrification.

Another lifestyle is exhibited by the methanogenic bacteria [local]. These bacteria produce methane, a reduced form of carbon. Often they live in association with other bacteria that carry out mixed acid fermentation that results in the production of H₂ and CO₂. The production of H₂ by these fermenters is energetically difficult because of its low redox potential, so its removal by the methanogens helps the fermentation to proceed. The methanogens utilize the H₂ as an electron donor [local] and the CO₂ as an electron acceptor; the energy produced by the electron transfer is used for growth and division. They are also unusual in that they use trans-membrane sodium gradients as well as proton gradients. The overall reaction can be represented as

4 H₂ + CO₂ ---> CH₄ + 2 H₂O

In addition to hydrogen, these organisms are capable of using a diverse array of organic molecules as electron donors for the production of methane. For example:

CH₃COOH ---> CH₄ + CO₂

4 HCOOH ---> CH₄ + 3 CO₂ + 2 H₂O

4 CH₃OH ---> 3 CH₄ + CO₂ + 2 H₂O

4 CO + 5 H₂O ---> CH₄ + 3 H₂CO₃

Notice that the organic molecule that is reduced to CH₄ may provide its own electrons and hydrogen atoms for the reduction.

• General reference [local]