User:Bee.whyze/Anaerobic organism

An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenated environment. Anaerobes may be unicellular (e.g. protozoans, bacteria ) or multicellular (e.g. plants, animals). Most fungi are obligate aerobes, requiring oxygen to survive, however some species, such as the Chytridiomycota that reside in the rumen of cattle, are obligate anaerobes; for these species, anaerobic respiration is used because oxygen will disrupt their metabolism or kill them. Areas of the human body can house anaerobic organisms, but unwanted anaerobic organisms can cause anaerobic infections. Anoxic environments are areas that lack oxygen and anaerobic organisms can thrive.

First Observation
In his letter of 14 June 1680 to The Royal Society, Antonie van Leeuwenhoek described an experiment he carried out by filling two identical glass tubes about halfway with crushed pepper powder, to which some clean rain water was added. Van Leeuwenhoek sealed one of the glass tubes by using a flame and left the other glass tube open. Several days later, he discovered in the open glass tube 'a great many very little animalcules, of divers sort having its own particular motion.' Not expecting to see any life in the sealed glass tube, Van Leeuwenhoek saw to his surprise 'a kind of living animalcules that were round and bigger than the biggest sort that I have said were in the other water.' The conditions in the sealed tube had become quite anaerobic owing to consumption of oxygen by aerobic microorganisms.

In 1913 Martinus Beijerinck repeated Van Leeuwenhoek's experiment and identified Clostridium butyricum as a prominent anaerobic bacterium in the sealed pepper infusion tube liquid. Beijerinck commented:

'We thus come to the remarkable conclusion that, beyond doubt, Van Leeuwenhoek in his experiment with the fully closed tube had cultivated and seen genuine anaerobic bacteria, which would happen again only after 200 years, namely about 1862 by Pasteur. That Leeuwenhoek, one hundred years before the discovery of oxygen and the composition of air, was not aware of the meaning of his observations is understandable. But the fact that in the closed tube he observed an increased gas pressure caused by fermentative bacteria and in addition saw the bacteria, prove in any case that he not only was a good observer, but also was able to design an experiment from which a conclusion could be drawn.

Classification
Anaerobic.png can be identified by growing them in test tubes of thioglycollate broth:

1: Obligate aerobes need oxygen because they cannot ferment or respire anaerobically. They gather at the top of the tube where the oxygen concentration is highest. 2: Obligate anaerobes are poisoned by oxygen, so they gather at the bottom of the tube where the oxygen concentration is lowest.

3: Facultative anaerobes can grow with or without oxygen because they can metabolise energy aerobically or anaerobically. They gather mostly at the top because aerobic respiration generates more adenosine triphosphate (ATP) than either fermentation or anaerobic respiration. 4: Microaerophiles need oxygen because they cannot ferment or respire anaerobically. However, they are poisoned by high concentrations of oxygen. They gather in the upper part of the test tube but not the very top.

5: Aerotolerant organisms do not require oxygen as they metabolise energy anaerobically. Unlike obligate anaerobes however, they are not poisoned by oxygen. They can be found evenly spread throughout the test tube.]] For practical purposes, there are three categories of anaerobe:


 * Obligate anaerobes, which are harmed by the presence of oxygen . Two examples of obligate anaerobes are Clostridium botulinum and the bacteria which live near hydrothermal vents on the deep-sea ocean floor.
 * Aerotolerant organisms, which cannot use oxygen for growth, but tolerate its presence . Two examples of aerotolerant organisms are lactobacilli and streptococci, which both reside in the oral cavity.
 * Facultative anaerobes, which can grow without oxygen but use oxygen if it is present . A few examples of facultative anaerobes are Escherichia coli and Salmonella.

However, this classification has been questioned by the fact that recent research showed that human "obligate anaerobes" (such as Fineglodia magna or the methanogenic archaea Methanobrevibacter smithii) can be grown in aerobic atmosphere if the culture medium is supplemented with antioxidants such as ascorbic acid, glutathione and uric acid.

Energy Metabolism
Some obligate anaerobes use fermentation, while others use anaerobic respiration. Fermentation is a metabolic process which makes chemical changes to release energy from glucose, since oxygen is absent. Anaerobic respiration is a form of respiration without the need for oxygen. It still utilizes the electron transport chain, however it uses electron acceptors other than oxygen. Aerotolerant organisms are strictly fermentative. In the presence of oxygen, facultative anaerobes use aerobic respiration; without oxygen, some of them ferment; some use anaerobic respiration.

Fermentation
There are many anaerobic fermentative reactions.

Fermentative anaerobic organisms mostly use the lactic acid fermentation pathway:

C6H12O6 + 2 ADP + 2 phosphate → 2 lactic acid + 2 ATP

The energy released in this equation is approximately 150 kJ per mol, which is conserved in regenerating two ATP from ADP per glucose. This is only 5% of the energy per sugar molecule that the typical aerobic reaction generates.

Plants and fungi (e.g., yeasts) in general use alcohol (ethanol) fermentation when oxygen becomes limiting:

C6H12O6 (glucose) + 2 ADP + 2 phosphate → 2 C2H5OH + 2 CO2↑ + 2 ATP

The energy released is about 180 kJ per mol, which is conserved in regenerating two ATP from ADP per glucose.

Anaerobic bacteria and archaea use these and many other fermentative pathways, e.g., propionic acid fermentation, butyric acid fermentation, solvent fermentation, mixed acid fermentation, butanediol fermentation, Stickland fermentation, acetogenesis, or methanogenesis.

Anaerobic Respiration
Anaerobic respiration is cellular respiration without the presence of oxygen. These processes use organic and inorganic molecules as the final electron acceptor. In anaerobic respiration depending on the electron acceptor the organism will be able to conserve energy as adenosine triphosphate (ATP), or be able to perform processes within the body that require oxygen to function. The process of using organic molecules as the final electron acceptor is referred to as fermentation. In anaerobic respiration, fermentation generates NAD+ from NADH. Anaerobic respiration is used by many species of bacteria and archaea as well as some eukaryotes. A group of Archaea found in the soil and digestive tracts of ruminants called methanogens provide an example of anaerobic respiration. These methanogens reduce carbon dioxide to methane in order to oxidize NADH. There are multiple categories of fermentation including both lactic acid and alcohol fermentation with ethanol being the resulting product.

Anoxic Environments
Anaerobic organisms are normally found in the body and create the microbiome. The areas they can be found include mucous membranes in the mouth, the gastrointestinal tract and the vagina. Other anoxic environments include the subsurface of the seafloor in the ocean and deep hypersaline basins found in the Mediterranean Sea.

Anaerobic Infections
Anaerobic infections are quite common and are caused by anaerobic bacteria. Anaerobic bacteria are flora in the human body and play an important role in infections, some of which are serious with a high mortality rate. These pathogens are commonly missed due to shortages in collection, transport procedures, lack of isolation and susceptibility testing of anaerobes in many clinical microbiology laboratories. Anaerobic infections can arise in all body locations including the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin, and soft tissues. Compared to other infections anaerobic infections are hard to treat due to their slow growth in culture as well as their growing resistance to antimicrobials. Common anaerobic infections include appendicitis, tetanus, sinusitis and pneumonia.

Culturing Anaerobes
Since normal microbial culturing occurs in atmospheric air, which is an aerobic environment, the culturing of anaerobes poses a problem. Therefore, a number of techniques are employed by microbiologists when culturing anaerobic organisms. The first known technique to grow and maintain anaerobic bacteria is called Hungate technique and is still used today. This technique utilizes a gas tight tube that does not allow any oxygen to enter. The Hungate technique boils culture medium to get rid of any oxygen. Tubes are run under cold water which produces a thin layer of solid agarose medium. For the first time anaerobes were able to be cultured and maintained using a constant flow of anoxic gas. A more recent technique is handling the bacteria in a glovebox filled with nitrogen or the use of other specially sealed containers, or techniques such as injection of the bacteria into a dicot plant, which is an environment with limited oxygen. The GasPak System is an isolated container that achieves an anaerobic environment by the reaction of water with sodium borohydride and sodium bicarbonate tablets to produce hydrogen gas and carbon dioxide. Hydrogen then reacts with oxygen gas on a palladium catalyst to produce more water, thereby removing oxygen gas. The issue with the Gaspak method is that an adverse reaction can take place where the bacteria may die, which is why a thioglycollate medium should be used. The thioglycollate supplies a medium mimicking that of a dicot, thus providing not only an anaerobic environment but all the nutrients needed for the bacteria to thrive.

Recently, a French team evidenced a link between redox and gut anaerobes based on clinical studies on severe acute malnutrition. These findings led to the development of aerobic culture of "anaerobes" by the addition of antioxidants in the culture medium.

The upcoming of metagenomics revealed that the majority of the microbial biodiversity remained uncultured, which inspired new culture techniques. Efforts to identify the human microbiota utilised dilution culturing. Culturomics was developed which is a methodology using hundreds of differing culture conditions, prolonged incubation periods, and MALDI-TOF spectrometry. Ribosomal RNA sequencing allowed identification of new gut bacteria.

Multicellularity
Few complex multicellular life forms are anaerobic. Exceptions include three species of anaerobic Loricifera and the 10-cell Henneguya zschokkei.

In 2010 three species of anaerobic loricifera were discovered in the hypersaline anoxic L'Atalante basin at the bottom of the Mediterranean Sea. They lack mitochondria which contains the oxidative phosphorylation pathway, which in all other animals combines oxygen with glucose to produce metabolic energy, and thus they consume no oxygen. Instead these loricifera derive their energy from hydrogen using hydrogenosomes.

See Also:
Aerobic organism

Fermentation

Anoxic Waters