Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

How could the application of archaea be used to solve some of humanities problems?

In 1977 a new ‘species’ was discovered by a man called Carl Woese in the hot springs of Yellowstone National Park, USA.1 The microscopic organisms discovered in volcanic hot springs were thought to be a very old group of bacteria that only lived in extreme conditions (but this has now been rethought). These organisms are called archaea. The word ‘archaea’ comes from the Ancient Greek Áρχαїα which means ‘ancient things’. Archaea are a group of single celled microorganisms closely related to the prokaryotic bacteria and they have no nucleus or any other organelles in their cells. When archaea were first discovered they were called archaebacteria and were thought to be a new type of bacteria.2 After further research into them it was found that archaea had different sequential ribosomal RNA to bacteria and, since sequential ribosomal RNA is a part of the classification system, archaea had to be placed in a different domain. Archaea are classified into three different groups: Crenarchaeota, Euryarchaeota, and Korarchaeota. Crenarchaeota include thermophilic and hyperthermophilic organisms. Euryarchaeota include methanogens (archaea that produce methane), halobacteria (archaea that survive high concentrations of salt) and thermophilic anaerobes (archaea that can survive high temperatures). Korarchaeota are archaea that are only found in high temperatures in a marine environment.3

At first, archaea were only found in extreme conditions and were thus thought of as being an extremophile organism. They were first discovered in hot springs where bacteria and most other organisms couldn’t survive, and have also been found in ocean vents, marshes and salt lakes to name some of the extreme conditions. Archaea were first found in extreme conditions, this is what lead to them being undiscovered for so long. Scientists didn’t think anything could survive in these conditions so there was no need to search for life in them. Archaea were discovered in the hot springs when scientists found a green ‘growth’ on top of the water and couldn’t decide what it was. After further study the ‘growth’ was found to be a new species; archaea.4 This radically changed where scientists thought organisms could live and now, many ‘uninhabitable’ places have been found to support archaeal life. The discovery of archaea has also prompted questions about if there could be life on mars where red ‘growths’ have been seen that are similar to archaeal ‘growths’.

Now archaea have been studied for longer, they have been found to live almost everywhere, from the soil to the intestines of humans. Because of this massive diversity of archaea, there are many different types ranging from thermophiles and halophiles to acidophiles (organisms that thrive in acidic conditions). This massive range of diversity gives an almost unending potential for these microscopic creatures to be useful in places man cannot survive. In some environments of the world archaea are the only creatures that can survive which leads them to be easily found as samples of that environment can be analysed and the archaea easily identified. The fact that archaea are so diverse has made scientists think about how many more undiscovered types of organisms there could be. It also made them think about possible uses for archaea in technology if their unique attributes could be harnessed.

Archaea have the same basic cell structure as bacteria in the way that they both lack membrane bound organelles, they both swim using flagella (small rope like chains at the

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

back of an organism that are used for propulsion) and they both have a single plasma membrane and cell wall.

Although there are some similarities, there are also many differences between archaea and bacteria which makes archaea only distantly related to bacteria but gives evidence that archaea and bacteria were once of the same phylum. Archaea have different chemical bonds that make up their cell membrane called ether bonds, rather than ester bonds that most organisms have. This ether bond is more resistant to extreme conditions than the ester bonds in bacterial cell membranes so this is a reason why archaea can survive in such extreme places when other organisms cannot. The cell membrane is comprised mainly of phospholipids that are made up of a phosphate ‘head’ which is hydrophilic, and a fatty acid ‘tail’ that consists of 2 fatty acid chains that are hydrophobic. This structure means that the ‘tails’ don’t like water so the molecules will arrange themselves into a double structure, where the ‘heads’ are facing out, to the water, and the ‘tails’ are in-between the ‘heads’ thus shielded from the water. In normal organisms, the fatty acid tails are straight chains which have no rings or branches but in archaea they have multiple side chains and many ring structures. This structure stops the phospholipid bilayer from denaturing at high temperatures by keeping the molecules steady when other organism’s molecules would vibrate and split, this also helps archaea to survive in the extreme habitats they have been found in. 5 Scientists were fascinated to learn about this new type of phospholipid structure as before the discovery of archaea only unbranched versions had been seen.

Archaea also use exactly opposite enzymes to bacteria and animals. For example, where an enzyme in bacteria would have a tail that kinks right, an archaeal enzyme would be exactly the same enzyme as the bacteria but the tail would kink to the left, these types of mirror images are called enantiomers (optical isomers). Even this small change can dramatically affect the archaeas metabolism and also shows how the archaea split early from the other animal domains.6,7

Example of enantiomers

Man, being the most dominant species on the planet, has shaped the world to our needs but in doing so has created many disasters that would never have happened if we weren’t here.

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

A recent catastrophe is the Gulf of Mexico oil leak caused by the energy company BP. This was caused by a faulty well control, to which several workers expressed their concerns about before the explosion. Methane, kept under high pressure, shot up through the drill column, reached the surface of the oil rig, and then ignited causing the oil rig to explode. The oil rig is pumping out up to 6,000 gallons of oil a day and around 39 million gallons of oil have escaped and the costs of cleaning it up have reached $11.2 billion.8

The oil spill in the Gulf of Mexico caused by BP has leaked millions of gallons of oil into the ocean, causing devastation in the water and on the coast. Birds that are covered in oil cannot fly as the oil breaks down the insulating capability of their feathers, fish ingest the oil which either kills them or poisons other animals up the food chain, and the shores are thick with oil which kills land animals and burrowing creatures on the beach such as crabs. BP are trying to spray dispersants on the oil to help it break up but this is at a massive cost to them. Archaea are being used naturally at the moment, BP have said that ‘Almost three-quarters of the nearly five million barrels of spilled oil in the Gulf of Mexico have been cleaned up or broken down by natural forces’. 9 These natural forces in the ocean consist of bacteria and archaea found at natural levels in the sea that break down oil. If we were to add more of these to the affected ocean then the breakdown of oil could be sped up so much it could be cleared within a week if conditions were right.

Oleophilic archaea (archaea with an affinity for oil) effectively ‘eat’ oil and break it down into natural substances such as carbon, carbon dioxide, water and some fatty lipids, all of which are not only non toxic but are also beneficial to marine organisms. They can be sprayed onto the oil much like the dispersants already being used, in fact the exact method for spraying dispersants used and the same machinery could be used but the dispersant could be substituted for oleophilic archaea. The archaea are non toxic and would clear up the spill in a smaller amount of time, thus saving BP a lot of money.10 It has also been found that the dispersants break the oil into tiny droplets that adhere themselves to plankton. This greatly affects the population of marine animals because, since many of them are plankton eaters, consuming the oil adhered onto the plankton will kill the animal. This is called bioaccumulation, when the oil may not affect the smallest organism, larger animals eat these small organisms and the concentration of oil increases going up the food chain. Because the larger mammals and fish eat the smaller fish the whales will consume the most concentrated dosage of oil and become very ill as they eat lots of the second most concentrated dosage fish. One possibility of disposing of the archaea is that since the oleophilic archaea live off the oil, when they have ‘eaten’ it all there will be no oil to live off so the archaea will just die, which also provides nutrients and energy to other marine animals.

Another possibility is that the archaea will just reduce down to the natural levels in the sea; this would also have no effect on ocean life as there would be no change in the end number of archaea. Because the archaea produce no ‘foreign’ chemicals, and archaea are naturally found in the ocean in small quantities anyway, there are no foreseeable effects on the food web in the ocean and so would be a viable way of clearing the Gulf of Mexico oil spill. Proof of this is the major oil spill in Prince William Sound, Alaska, where bacteria were used to successfully clean up the oil without harming the environment.11

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

While the same machinery used for spraying dispersants could be used to spray archaea, certain conditions inside the machinery where the archaea are stored must be kept constant or the archaea could die. A certain amount of oil must be kept in the sprayers to keep the archaea alive and this oil will also be sprayed onto the ocean but, along with the other oil in the ocean, will be ‘eaten’ by the archaea. They also grow best in warm temperatures (around 32oC) so to avoid having heating systems, the spray tank could be attached near the engine to absorb some of its heat.

Much of the oil (around 26%) has sunk from the top of the ocean to varying depths, while the archaea can still clean this up they will work around 10 times slower than if they were on the top of the ocean due to lower temperatures.12 The lower temperature affects the archaeas rate of metabolism and greatly slows it down.13 Even with the archaea moving slower, they are still faster at clearing the oil than dispersants. Although below the ocean surface there could be a slight problem. The archaea used would be aerobic respirators and so would require oxygen in order for their metabolisms to work. In the ocean there is not much oxygen and what there is gets used by the fish. If the archaea were introduced below the surface of the ocean then they would use up some of the oxygen in the sea to help them break down the oil. While this would dispose of the oil, it would also mean that there is less oxygen for the fish to use which could mean the possibility of them dying of oxygen deprivation. The oleophilic archaea are only moderate aerobes so the oxygen depletion may not be enough to cause a large effect in the oceans however either chemicals would need to be added that produce oxygen, or in-depth testing would be needed to discover how much of an effect the archaea would have on marine populations.

Cell division for bacteria (to which archaea are closely related) takes about 20 minutes to divide via binary fission but could be adapted to have a hyperactive reproduction cycle that would massively speed up the amount of archaea that could be produced. Scientists have managed to increase the rate of reproduction up to 50 times the normal time taken so this means that the archaea would divide every 24 seconds. Within an hour a single archaeon could divide over 120 times resulting in approximately 1.33x1036 archaea. Archaea range from 0.1µm (micrometers) - 15µm in size so taking an average of 7µm (7x10 -6m), when placed next to each other, would measure 931,000,000,000,000,000,000,000,000 km2! Scientists have found that 108 organisms per cm3 of oil is the optimum amount of archaea for the bioremediation (the process that involves the use of microorganisms to return the natural environment altered by contaminants to its original condition14) of oil so an area of 8,620,370,370,370,370,370,370,370 km of oil can be covered with the optimum amount of archaea. Obviously you would not want this amount of archaea so the hyperactive reproduction cycle must be able to be turned off under certain conditions. This hyperactive cycle means the archaea need a lot of food for energy, so leaving only enough food to live on would cut off the cycle while keeping the archaea alive to be used. To reproduce quickly archaea also need optimum temperatures for their enzymes to work (around 32oC), so reducing the temperature would reduce their metabolism which would decrease reproduction rate.

Many oil ships already have minor spillage kits that contain these archaea for if there are any small oil leaks. It uses exactly the same principle as the one I am suggesting but on a smaller scale that is in industrial use already.

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

Another catastrophe that archaea may be able to help with is radiation control. With uranium being used in making energy, the waste products produced are all radioactive and are hard to dispose of, currently being buried deep underground until they have decayed so much they are deemed safe. With increasing energy consumption, more uranium must be used and so more radioactive waste products are being made. The problem comes here that there is not enough storage space to fit all the radioactive waste into.15 Waste products from these energy plants can take up to 15 million years to reach acceptable levels of radiation (Iodine 129) and 4 waste products taking over 1 million years to decay. Archaea can not only be used in radioactive disposal but can also be used in helping to clear up radioactive sites contaminated with actinides (elements above the atomic number 89) and other heavy metals.16

The radiation and toxic substances that we have produced are making many places uninhabitable and with the current growth of the world’s population, we need all the living area we can get. Radiation and toxins make places uninhabitable as they kill everything in the area and, because of their long half lives, damage everything that enters an area for a long time.

Deinococcus radiodurans means ‘strange berry that withstands radiation’; it is called this because of its tetrad structure and the fact it can withstand such high levels of radiation. Deinococcus radiodurans is a polyextremophile which means it can survive many different extreme conditions. It can survive 1,000 times the amount of radiation that can kill a human (instantaneous dose of 5,000 Gy) without losing any cell functions, it can survive severe heat and coldness, live without oxygen and water and in very acidic conditions. 17 This makes it perfect for use in radioactive sites particularly where there is a large amount of radioactive waste which can make the surroundings very hot.

Radiation damages cells by breaking the double stranded DNA in the cell by oxidising either one strand or two strands of the DNA. The single stranded breaks can be repaired easily by using the other undamaged strand as a template, but when there is a double break it is much harder to repair because of the lack of template DNA. When a double strand repair takes place, this is where mutations can occur, although this process used by Deinococcus radiodurans produces no more mutations than our own system of repairing DNA.

The archaea Deinococcus radiodurans is able to withstand such massive amounts of radiation because it has multiple copies of its DNA sequence as well as very rapid repair mechanisms so even if some of the DNA copies get damaged there are still many more to become templates. Also, any damage to the DNA can be quickly and properly repaired.18 When a break occurs in the DNA, Deinococcus radiodurans can repair the chromosomes via a process called single-strand annealing and in this process two strands of DNA are fused together. If a double break occurs, it can be fixed with homologous recombination.19 This involves parts of the DNA being exchanged with the non-damaged DNA copies, the damaged part of a chromosome is removed and then the non damaged copy is cut off of the template DNA and takes its place, resulting in a strand of DNA that is a perfect copy of the damaged counterpart. Because of these features, this particular archaea can be most useful

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

in very radioactive environments and can be genetically engineered to dissolve, oxidise, or reduce the radioactivity of material by adding proteins.20

A bacterium called Shewanella oneidensis has recently been discovered that can detoxify elements like uranium and other radioactive actinides. It has been found to secrete two proteins both in its cell wall and in sticky liquid that comes out of the cell. It is these two proteins that can digest harmful materials and turn them into something non-toxic.21

Genetically removing these proteins and transferring them into Deinococcus radiodurans with enzymes should be a simple process which will then enable the radiation resistant archaea to detoxify materials that are complementary to its new proteins.

To genetically engineer the archaea, the plasmid method of engineering must be used as archaea have plasmids (small rings of DNA) rather than normal DNA. The plasmid of the bacteria with the desired protein is removed and added to restrictive enzymes that cut the plasmid in specific places so the proteins can be removed. These enzymes are also used on the archaea to ‘cut’ out their plasmid so the protein can be inserted. The proteins that have been ‘cut’ out are treated with other enzymes that create ends for the proteins that will fuse together when added with other DNA strands.

The plasmids from the archaea are added to the DNA proteins and more enzymes are added to help the fusion of the proteins into the plasmids. The plasmids are then separated by weight; the heaviest ones have successfully fused with the DNA and so are kept and the others are disposed of.

These plasmids are then added into a culture of live Deinococcus radiodurans, some of these will then take up the plasmids and begin to show characteristics of the new proteins. In order to make these identifiable, the plasmids usually also include some antibiotic resistance so antibiotics can be used to kill the archaea that did not take up the proteins. These archaea are then allowed to grow on their own so not only will they have the new proteins, because of natural selection, the new generations that survive will be the best of the previous generations and so would perform better.

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

When the archaea Deinococcus radiodurans it added to the radioactive environment there should be no effects on the food chain and the environment because nothing would be able to withstand the radiation/toxicity of the surroundings. When the place has been cleaned there is an area of uncertainty as to how the added archaea would affect these new organisms. There are a few possible scenarios as to what could happen, this type of archaea are found in small quantities everywhere in the world so the increased number may just spread out further into the surrounding areas which should have no adverse affect on the communities as we live with this archaea anyway. Another possibility is that, because of its new proteins, it could mutate these proteins to eat other materials such as brick which would cause massive problems if the area was to be repopulated by humans. Another complication to this is that because Deinococcus radiodurans is a polyextremophile, it would be very hard to kill if a problem did arise. The only way to kill this type of archaea would be to either boil it as it cannot survive at above 75oC, or to somehow disable its DNA repair mechanisms so it is susceptible to radiation that would kill normal archaea. Neither of these ways would be feasible because to heat to over 75oC you would need to either catch every last archaeon and heat them, or incinerate the surrounding area, and to irradiate them you would also have to irradiate the surrounding area which would cause lasting damage to the environment. These drawbacks make using Deinococcus radiodurans still a possibility but much more research would need to be carried out with properly predicted outcomes and tests in environmental simulators to be sure what affects Deinococcus radiodurans would have on different areas.

Archaea could also help in the discovery of new antibiotics. Bacteria are building up resistance to all of the conventional antibiotics currently being used. For example, MRSA (Methicillin-resistant Staphylococcus aureus). This occurs by mutations in bacteria when exposed to antibiotics. A bacterium can spontaneously mutate and this mutation could make it resistant to a certain antibiotic. This bacterium would then reproduce while the other bacteria would die so only the resistant bacteria were left. These would then keep reproducing and eventually the whole colony of bacteria would be resistant, making the antibiotics used against them useless.22

Out of all of the archaea found on the earth, so far none of them have been found to be pathogens. This means that none of the archaea can do humans any harm and, sometimes indeed quite the opposite. Antibodies extracted from archaea can be made into antibiotics, are called archaeocins and could be used to kill the resistant bacteria as the bacteria would never have come across these antibodies before and thus would have no resistance. This would be of great help in hospitals which are suffering from multiple resistant bacteria such as Vancomycin Resistant Enterococci. At the moment there is a threat from a new multi antibiotic resistant ‘super bug’ that produces an enzyme called NDM-1. NDM-1 can survive inside other bacteria and makes them resistant to all current forms of the most powerful antibiotic type, carbapenems, and some outbreaks of NDM-1 are resistant to all known antibiotics.23 The new antibiotics found in archaea could be extremely helpful in killing these bacteria as it is the only set of antibiotics that nothing is currently resistant to. Without new antibiotics this bug could spread to something easily transferrable between patients and could cause infections that are untreatable.

Karl Yeadon How could the application of archaea help fix some of humanities biggest problems?

Since there are so many different types of archaea there could be infinite different antibiotics that are yet to be discovered. The most abundant source of possible archaeocins is within the haloarchaea group as many of their family produce antibiotics naturally without the need of stimulation. Currently 4 antibiotics have been synthesised from haloarchaea with more currently in progress.

A few items made by archaea are already commercially available such as the antibiotics mentioned earlier but also, many ships carry small oil spillage cleanup kits that have oleophilic archaea in them.

In conclusion, I believe that archaea could one day play a big part in helping solve global disasters although more research would need to be conducted in order to ensure the safety of the archaea to humans and animals. For each of the research topics I have described, possible scenarios would need to be enacted with the help of digital constructions. This would help make sure the archaea were safe to use and could be used to show any unforeseen problems to the environment. Such problems could be, like with the oleophilic archaea, that their metabolism doesn’t make the products desired and while some tests have found that the archaea produce the end products desired, more tests would be needed to determine any long term effects.

1 www.earthlife.net/prokaryotes/archaea.html by Gordon Ramel.2 www.wisegeek.com/what-are-archaea.htm by Michael Anissimov. Last updated 08 September 2010.3 www.ucmp.berkeley.edu/archaea/archaea.html by Brian Speer. Last updated 20 April 2001.4 www.ucmp.berkeley.edu/archaea/archaea.html by Brian Speer. Last updated 20 April 2001.5 http://www.differencebetween.net/science/difference-between-archaea-and-bacteria/ 6 http://en.wikipedia.org/wiki/Archaea. Last updated 28 September 2010.7 http://zipcodezoo.com/Key/Archaea/Archaea_Kingdom.asp. Last updated 26 April 2010.8 http://www.bp.com/genericarticle.do?categoryId=2012968&contentId=7065280 Last updated 1 October 2010.9 http://www.bbc.co.uk/news/world-us-canada-10877060 by Steve Kingstone. Last updated 5 August 2010.10 http://www.helium.com/items/1863816-oil-eating-bacteria-an-introduction 11 http://science.howstuffworks.com/environmental/green-science/cleaning-oil-spill.htm by Josh Clark.12 http://www.csmonitor.com/Science/2010/0428/Gulf-of-Mexico-oil-spill-How-bad-is-it 13 http://www.liveoilvideo.com/archives/3067

14 http://www.edvotek.com/pdf/956.pdf 15 http://en.wikipedia.org/wiki/Radiation 16 http://en.wikipedia.org/wiki/Radioactive_decay 17 http://www.absoluteastronomy.com/topics/Deinococcus_radiodurans.18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC178572/ by H J Agostini, J D Carroll and K W Minton.19 http://www.daviddarling.info/encyclopedia/D/D_radiodurans.html Last updated 18 December 2007.20 http://en.citizendium.org/wiki/Deinococcus_radiodurans. Journal of Molecular Microbiology and Biotechnology p.64 under heading Beneficial Bacteria and Bioremediation by Milton H. Saier, Jr.21 http://www.asknature.org/strategy/1ee340b8e77682d012ce1f61ab65df68.

22 http://www.drreddy.com/antibx.html by Dr. Reddy. Last updated 17th July 2008.23 http://www.bbc.co.uk/news/health-10925411 by Michelle Roberts. Last updated 11 August 2010.