The Nature of Science

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A Gift Worth Its Weight In Gold

Biology concepts – toxicity, trace elements

Say hello to the Holterman nugget of New South

Wales, Australia, supposedly the largest gold

nugget ever found. Strictly speaking, it isn’t a nugget,

but rather a huge vein of gold in a piece of quartz.

And Bernhardt didn’t find by himself, but he was a

shameless media hound and built himself a legend.

In 2^ndcentury Rome, practitioners of Mithraism, a popular pagan religion of the time, had a feast on December 25 to celebrate the god Mithras, the “Invincible Sun.” This also coincided with other feasts for Saturn and the winter solstice. People gave gifts to one another during these holiday celebrations. This practice of gift giving was adopted by Christians when the pagan and Christian traditions were merged, as they often were.

Today, Christmas presents are most often associated with the gifts of the three kings who came to see the baby wrapped in swaddling clothes (although by the time they arrived, Jesus was already a toddler – camels will never be confused with jet planes). Their gifts were gold – a gift for a king, frankincense – a gift for a priest, and myrrh – a gift for one who was to die (used in burial rights).

These three gifts are not exempt from our search for biologic exceptions and amazement. In terms of biology, they are indeed gifts. This week we will talk about gold, with the others to follow on successive posts, like the ghosts of Christmas past, present, and future.

At December 2012 prices, a 150 lb (69 kg) person has about 37 cents worth of gold in his/her body, excluding any dental work. Hardly worth trying to harvest, but nice to know you’re worth more than you thought. How did the gold get there and is it doing anything?

Living organisms rely on small amounts of some metals and other elements in order to carry out their metabolic reactions. As such, these elements that are needed in small amounts are called trace elements. Examples of important trace elements include selenium, iron, copper, iodine, and zinc. Zinc is probably the king of the trace elements, as it is used in over 200 different reactions in mammalian physiology.

Copper is used in many biochemical pathways,

and it is showing promise as an anti-inflammatory

agent. But NO! people - you can’t get the anti-

inflammatory effects by wearing the copper

bracelets or copper-impregnated compression

wear! On the other hand, copper impregnated

clothes are antimicrobial.

Zincworks to control what genes are activated to make proteins (zinc finger transcription factors), as well as DNA and RNA production and destruction. It is stored in the brain to control just how active some neurons become when stimulated, and plays an important role in neural plasticity – the reordering of neuron connections after experiences and sleep, you may know it as learning and memory. Make sure you take your zinc before studying for that big test!

Because you need only a “trace” of these substances to maintain growth, development and health, they are also called micronutrients. Their functions can be quite diverse. Iron is the oxygen carrier in hemoglobin, but you only need a trace in your diet because you are so good at preserving what you already have. Selenium is contained in a non-traditional amino acid called selenocysteine, which is important for antioxidant proteins (selenium replaces sulphur in the traditional cysteine).

The biologic rule is that gold is not a trace element! Supposedly, no living organism uses gold in its physiology, but you know there has to be an exception. In 2002, Russian scientists investigating a membrane bound enzyme of the aurophilic (au = gold, and philic = loving) bacteria, Micrococcus luteus, showed that the enzyme contained gold in its active site (the area that binds the molecule to be chemical reacted). The gold was important for converting methane to methanol, giving the bacteria a way to produce energy when traditional food sources were scarce.

But we, and presumably ever other organism don’t have this system, so why is there gold in our body? It turns out that we have many things in our body that we don’t use, they just accumulate, things like lead, mercury, cobalt, arsenic. Some are toxic at low levels and some are useful unless we get too much of them. We have discussed the problems associated with having too much iron, and copper excess can be toxic as well. We said zinc is important for many reactions, but too much zinc can hinder copper absorption and you can end up with a copper deficiency. This is just as dangerous as copper excess.

The liver is the site of much detoxification in the body.

Two systems are at work, one to break down or modify

fat soluble toxins, and the other to prepare them and

water soluble toxins for elimination in the bile or urine.

Toxic heavy metals often just get stored in the liver and

cause damage later.

If the element itself or amount of the element is toxic, then we have to get rid of some; this is the job of the liver. In some cases even gold can be toxic; as we accumulate more and more gold in the liver and kidney, it can disrupt their functions. Poor liver and/or kidney function – you die. The classic form of toxic gold found in nature is called gold chloride or “liquid gold,” which causes organ damage in humans and severe toxic effects in other organisms, but there is an exception.

A microbiologist and a professor of electronic art at Michigan State Universityhave worked with a bacterium that can withstand gold chloride levels that would kill every other known organism. They found that Cupriavidus metallidurans was hundreds of time more resistant to gold chloride than any other organism.

C. metalliduranstakes in the gold chloride and processes it to pure 24 karat gold, and then deposits it in a thin layer as part of the community of proteins and insoluble products that the bacteria builds around its colony. These organized layer of proteins, lipids and carbohydrates are called biofilms, and are being recognized as very important in bacteria ecology and pathology. In the case of C. metallidurans, the biofilm is intrinsically valuable to Wall Street.

Other organisms accumulate gold as well – bacteria, fungi, algae, fish, etc., but as does everything else in biology, it starts with the bacteria. It turns out that some bacteria excrete high levels of acidic amino acids – aspartate and glutamate (atemeans acid). Yes, amino acids that are used to build proteins are organic acids, hence the name.

To dissolve gold out of powdered and broken rock,

many mines like this one in Brazil spray the ore with

sodium cyanide in water. They collect the runoff and

precipitate out the purer gold. I guess they don’t worry

about all the living things contaminated with the

cyanide.

Thebacterium Chromobacteriumviolaceumactually makes and excretes cyanide. Cyanide binds stably to gold and silver, so it is used in gold mining to bind and concentrate very fine gold particles in rocks. Then the gold can be collected and precipitated. These examples show that if gold is in the immediate environment of these various organisms, it can be dissolved by the organic molecules and taken up by the bacteria when they feed.

Once gold is consumed and stored by the bacteria, it enters the food chain; millions of organisms feed on bacteria, and millions of organisms feed on the feeders, and so on. Eventually, we end up eating a little gold as well. This is similar to how fish that ingest food and swim in water contaminated by mercury runoff can end up increasing the human levels of mercury – the difference is that mercury is much more toxic than gold.

The accumulation of gold in sedentary organisms may provide someone with a gold rush. A 2010 study showed that the saprobicfungi (those that feed on decaying material) around an existing gold mine contain much higher levels of gold than ectomycorrhizalfungi (those that are parasitic) in the same area. The accumulation of gold in soil bacteria and fungi may be able to provide scientifically astute miner with clues as to where they should dig the next mine!

The blue toadstool (Entoloma hochstetteri) is an

example of a saprobic fungus. It gains all the

nutrients it needs from the soil and from decaying

organic material. Therefore, it picks up and

accumulates other things in the soil – like gold maybe.

Bacteria may prove even more important to miners. December 2012 evidence indicates bacteria that dissolve and ingest gold in the rocks and soil purify it to some degree. When they form biofilms, the gold becomes insoluble again, and nuggets or flakes are formed. Veins of gold may be due to bacterial byproducts and corpses flowing into cracks in the rocks. Makes you look at your gold ring differently, doesn’t it.

We might be able to thank gold-loving bacteria for more than our jewelry – gold is finding its way into medical treatments and tests these days. Because gold was rare, pure, inert, and costly, early physicians thought it just had to be good for you. Many remedies had gold incorporated into them, including a popular cure for alcoholism called the Keely cure.

The cure was so widely accepted (and patented by Dr. Keely) that even Theodore Roosevelt himself sent his brother, Elliott, to Dr Keely’s clinic in Dwight, IL to be cured of his addiction. It didn’t work, Elliott drank to the point of depression, and died from injuries that resulted from his jumping from a window.

More recent uses of gold include as an anti-inflammatory agent rheumatoid arthritis, including a compound called aurothiomalate. Just how this works remains a mystery, but a 2010 study in chondrocytes (the cells that make cartilage and are present in joints) showed that this drug down-regulates a signaling enzyme (MAP kinase phosphatase 1) that is important for expression of several inflammatory proteins, including cyclooxygenase, p38 MAP kinase, matrix metalloproteinase-3 and interleukin-6.

The aquatic or semi-aquatic plant Bacopa caroliniania can

be loaded with gold nanoparticles and made to give off

light. Depending on the energy of the UV light shone on

it, it can glow from green to gold to red. Someday, maybe

our tree lined streets will have natural streetlights.

Gold isfinding a home as a treatment in other conditions as well including in cancer, viral infections, and parasitic diseases. But gold is being used most often as a carrier. Because gold is practically inert, nanoparticles of gold can be used to carry drugs to specific targets or to be used as imaging agents to illuminate very small structures.

Most spectacularly, gold may help light a dark world. Plants can now be grown with gold nanoparticles that are small enough to be taken up into the leaf cells. When exposed to UV light, the gold releases energy at a wavelength that stimulates chlorophyll to bioluminesce. The plants actually give off light like natural street lights.

That’s a lot of biology for a hunk of metal used for wedding rings and retirement watches – a way cool gift for any biologist. Next week, the biology of frankincense.

Nieminen, R., Korhonen, R., Moilanen, T., Clark, A., & Moilanen, E. (2010). Aurothiomalate inhibits cyclooxygenase 2, matrix metalloproteinase 3, and interleukin-6 expression in chondrocytes by increasing MAPK phosphatase 1 expression and decreasing p38 phosphorylation: MAPK phosphatase 1 as a novel target for antirheumatic drugs Arthritis & Rheumatism, 62 (6), 1650-1659 DOI: 10.1002/art.27409

Levchenko, L., Sadkov, A., Lariontseva, N., Koldasheva, E., Shilova, A., & Shilov, A. (2002). Gold helps bacteria to oxidize methane Journal of Inorganic Biochemistry, 88 (3-4), 251-253 DOI: 10.1016/S0162-0134(01)00385-3

Antibiotics Are Going Viral

Biology concepts – bacterial immunity, bacteriophage, antibiotics

There are recognized characteristics that all living organisms

share. However, they are not black and white; take a look at

these characteristics and think about fire. Fire grows,

consumes energy, gives off energy, metabolizes, reproduces.

So if fire can be fit into some of these, maybe an argument

can be made for viruses?

Manyscientists do not consider viruses a form of life, but that doesn’t mean the idea is universal. Even virologists can’t agree. Viruses do blur the lines between life and non-life, and it gives us something to debate when parties get quiet. It makes for a great debate in Biology classes too, if you don't have a party to go to.

For many, it comes down to this - viruses don’t react to changes in their environment, grow, or metabolize, so they can’t be alive. They lack all these characteristics because these processes take energy, and viruses themselves don’t make or consume energy. This is a big sticking point for anyone trying to make an argument for including viruses as life.

But they seem to do O.K. at making their way in the world, and are becoming quite the model for immune stimulation. A 2011 study at the Emory Vaccine Center used virus-sized nanoparticles to try to induce life-long immunity as natural viruses do. It is hypothesized that virus particles bind to several different types of innate immune receptors (called Toll-like receptors, TLRs) and this diverse stimulation by one antigen is responsible for longer immunity.

The nanoparticles were composed of a synthetic polymer particle complexed with two stimulators. One is similar to a part of the bacterial cell wall, and the other mimics viral mRNA. The particles also stimulated several different TLRs in mice, and it is hoped they will do similar in humans. Nice to see we can take advantage of viruses, since they take advantage of us so often. Important to our topic today, viruses can even take advantage of bacteria.

What a great image of a T2 bacteriophage. What

look like layers are …. layers. Each is a protein and

what is more, they self assemble! The head carries

the nucleic acid, the legs attach to the bacterium, and

the shaft creates the hole and injects the nucleic acid.

Since bacteria are prokaryotes, it would be right to assume that the viruses that infect them look and act differently than the viruses that infect eukaryotic cells. They even have a different name – bacteriophages (backtron = small rod, and phage = to feed on). Infection of a bacterium by a virus may seem a trivial event - we have our own problems to deal with. But there are several ways in which this infection affects animals.

Bacteriophages insert their nucleic acid into the bacteria from the outside; the virus doesn’t enter the cell. Similar to the bacteriocin delivery system recently discovered in bacteria, bacteriophage also use a spike system to punch a hole in the target cell. Scientists in Switzerland, Russia, and Indiana collaborated in 2011 to show that the bacteriophage spike has a single iron atom at the tip, and it punches, not drills, a hole in the target bacterium.

Once inside, the nucleic acid can have different fates. In many cases, the phage DNA is inserted into the bacterial chromosome and stays there for a while, not harming anyone, but also not making new virus particles. This is called lysogeny. Lysogens (cells infected with lysogenic phage) will then pass on the prophage (the phage nucleic acid that is integrated) on to their daughter cells.

Other bacteriophages don’t have the patience to just hang out in the bacterial genome; they take over the cell, make many copies of themselves and then destroy the bacterium by lysing it (breaking it open). These are the lytic bacteriophages.

You might recognize that lysogenic phage DNA, just sitting there in the chromosome, would die out with the cell (or daughter), so they must have another side to themselves. These phages can be lysogenic if the environment suits them, or lytic if they have the right signals, and they can switch from lysogenic to lytic if the environment changes, so they are called temperate bacteriophage. Do I have to point out that they can’t go the other direction (lytic to lysogenic); how could you insert yourself into the bacterial genome if you have already caused bacterial destruction?!

There are 19 recognized bacteriophage types (probably

more now). They have different kinds of head proteins, and

some are filamentous. Cystovirus (cytovirus) is the only

virus with RNA for a nucleic acid instead of DNA. Tectivirus

is the only phage that infects both archaea and bacteria.

There are currently 19 different classes of bacteriophage that infect bacteria and archaea. That’s a bunch of different ways that a bacterium would have to defend itself, but it can. Bacteria have several different ways to prevent bacteriophage infection. In some cases, the bacteria will produce cell wall molecules to prevent phage binding or nucleic acid injection.

In other cases, the bacteria will identify its own nucleic acid, usually by adding methyl groups to DNA. In some cases, the bacteria will methylate its own DNA, and then cut up (called restriction, this is where the restriction enzymes used in molecular biology come from) any DNA that isn't methylated. In other cases, the bacteria will methylate the incoming viral DNA and target all methylated DNA for restriction.

Recent evidence show that bacteria even have a version of adaptive immunity. The CRISPR systemtakes spacer DNA (short repeats outside genes) from the bacteriophage and places them in specific CRISPR spots in its own chromosome. These serve as a memory in case that bacteriophage is encountered again. If it is, the appropriate spacer can be turned in to a piece of RNA that will target the phage DNA for destruction (called RNAi, the “i” stands for interfering, the process for another discussion).

Finally, bacteria can oppose phage by giving up. Like the apoptosis in our cells or the plant hypersensitive reactionwe have discussed, bacteria can kill themselves in order to prevent themselves from becoming virus factories. In the case of bacteriophage-infected bacteria, the process is called high frequency of lysogeny. This system prevents the bacterium from carrying the prophage and passing it on to daughter cells by having the cell die before it replicates.

So bacteria infected by phage can defend themselves, but in some cases, they don’t need to. In fact, it may help them out. Consider a lysogenic phage of one type and lytic phage of another type. Which would a bacterium consider living with – certainly not the lytic phage. But many viruses, including phage have mechanisms to prevent superinfection (infection with a second virus); phage of one type cannot survive in a bacterium infected with a phage of another type. If the lysogenic phage got there first, it could actually protect the bacterium from a death by a lytic phage.

Cholera toxin is carried by the CTX bacteriophage.

The phage needs TCP, a type IV pillus to infect the

V. cholerae. Once the bacterium is growing on the

intestinal surface, the phage is activated, reproduces,

infects other bacteria, and the cholera toxin is

produced. So to cause disease, the bacteria must

undergo horizontal gene transfer to gain the pillus,

and be infected by the CTX phage.

We maychuckle at the idea of bacteria getting infected – in many cases it serves them right – but it can also affect us. Certain bacteriophages possess DNA that can make an infected bacterium even better at causing humans distress. The cholera toxin of Vibrio cholerae is carried by the CTX bacteriophage, and the diphtheria toxin gene of Cornybacterium diphtheriae is also transferred from bacterium to bacterium by a phage.

But phage may also be turned from the dark side and used to help mankind. In the spirit of our recent discussions on when it is beneficial to be infected, how about letting your doctor infect you with bacteriophage to kill off your bacterial infection?

It is no secret that antibiotic resistance is becoming a large problem in medicine. If we know that viruses can infect bacteria, why don’t we use them as a type of antibiotic? This may very well be a good idea, but it isn’t a new one.

Before the advent of penicillin and other traditional antibiotics, bacteriophages were used to treat bacterial infections in the Soviet Union and Eastern Europe. However, the 1920-30's trials were not without their flaws, mostly because scientists didn’t have a good idea of how phages worked. For many years the West remained behind, because Soviet research was not widely distributed.

To kill bacteria, lytic phages would be the tools of choice. But there is a downside, we use bacteria to stay alive. You wouldn’t want to kill of your gut flora, you need them to digest food and absorb vitamins. So, bacteriophage must be delivered to the site of the infection only, replicate there but not travel, and kill only the target bacteria. This is a tall order, but trials are in progress for bacteriophage as antibiotics against drug resistant Staphylococcus and others. Bacteriophages are even being tested in bacterially-infected plants.

The SOS system is one way a bacterium can repair

DNA damage. The damage stimulates RecA protein

function. This is an important protein. It works in

many forms of DNA repair, as well as being responsible

for homologous recombination. The SOS repair genes

are controlled by RecA degrading the protein that

represses their production. They go on to fix the DNA

problem.

On another front, research at MIT and Boston University from 2010 suggests that it may be possible to inhibit bacterial antibiotic resistance mechanisms, and once again making the resistant bacteria susceptible to conventional antibiotics. In this case, bacteriophage were engineered to target the bacterial DNA repair system in the target cells. The SOS system (see picture to right) is induced when bacteria are treated with antibiotics, but the bacteriophage-treated cells were more susceptible to the antibiotic. This could prevent resistance from developing, but may also be useful in strains that have developed some other antibiotic resistance mechanism.

Another potential bacteriophage aid to humanity has nothing to do with disease. May 2012 work from the University of California has made use of the mechanical energy of the bacteriophage inside bacteria, turning it into electrical energy (piezoelectricity, piezo = to press or squeeze). While this is a very small amount of power per cell, it is hoped that this may soon be harnessed to run your smart phone and iPad.

Next week we will start a three-part series of Christmas posts, the biology of gold, frankincense, and myrrh.

Browning, C., Shneider, M., Bowman, V., Schwarzer, D., & Leiman, P. (2012). Phage Pierces the Host Cell Membrane with the Iron-Loaded Spike Structure, 20 (2), 326-339 DOI: 10.1016/j.str.2011.12.009

Lu, T., & Collins, J. (2009). Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy Proceedings of the National Academy of Sciences, 106 (12), 4629-4634 DOI: 10.1073/pnas.0800442106

For more information or classroom activities, see:

Bacteriophage –

http://jmbe.asm.org/index.php/jmbe/article/view/63/html_33

https://sites.google.com/a/tjc.sg/wow-attachment/home/bacteriophage-class

http://jc-schools.net/ce/virus.html

http://www.sciencebuddies.org/science-fair-projects/project_ideas/MicroBio_p029.shtml

http://www.cellsalive.com/phage.htm

http://www.k8science.org/slides/slide01.cfm?tk=42&pg=2

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=16&ved=0CDoQFjAFOAo&url=http%3A%2F%2Fwonderstruck.co.uk%2Ffiles%2FStudent-Resource-Sheet-2.2-Building-Viruses.pdf&ei=yNJlUNGiHMepyAGW4oFw&usg=AFQjCNGbRS00EnRS7kafEbcmHli_2hAabw

www.wsfcs.k12.nc.us/cms/lib/.../3021/Attack_of_the_Viruses.pdf

https://sites.google.com/site/coralandphage/phage-outreach

http://vimeo.com/8313889

http://www.ted.com/talks/lang/en/angela_belcher_using_nature_to_grow_batteries.html

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/lytlc.html

http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit3/viruses/lysolc.html

http://www.blackwellpublishing.com/trun/artwork/Animations/t4attacht/t4attacht.html

http://www.blackwellpublishing.com/trun/artwork/Animations/Lambda/lambda.html

http://www.mcb.uct.ac.za/tutorial/virusentbacteria.htm

http://www.phages.org/PhageInfo.html

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=18&ved=0CE0QFjAHOAo&url=http%3A%2F%2Fjournals.cambridgemedia.com.au%2FUserDir%2FCambridgeJournal%2FArticles%2F11%2520ackermann244.pdf&ei=MdFlUJ74ForpygGms4GgAg&usg=AFQjCNEwUOraC4hUtRNSHU-_G6plMmV6Vw

phage therapy –

http://www.bacteriophagetherapy.info/ECF40946-8E2F-4890-9CA6-D390A26E39C1/Pros%20and%20cons%20of%20phage%20therapy.html

http://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&ved=0CCQQFjAA&url=http%3A%2F%2Fsciencecases.lib.buffalo.edu%2Fcs%2Ffiles%2Fphage_therapy_notes.pdf&ei=DdZlUIGnI6GDywGc9oB4&usg=AFQjCNF74o32r66cr-brYHBS_yFKZHzcbg

http://www.phagetherapycenter.com/pii/PatientServlet?command=static_phagetherapy&language=0

http://blogs.evergreen.edu/phage/

http://blogs.discovermagazine.com/loom/2011/05/20/eaters-of-bacteria-is-phage-therapy-ready-for-the-big-time/

http://www.youtube.com/watch?v=mrBSZaHuyTI

http://www.popsci.com/category/tags/phage-therapy

http://www.popsci.com/science/article/2011-04/bleaching-threatens-coral-phage-therapy-could-prevent-ghost-coral

Extremophiles Are Key, Or Archaea

Biology concepts – archaea, bacteria, domains of life, hydrothermal vent ecosystem, chemosynthesis

What is a bigger mistake – to overestimate or to underestimate? If you overestimate someone, you may be disappointed with the result. If you underestimate, you may never realize what they are capable of accomplishing. What is more, your underestimation may cause you to miss incredible things already taking place.

Underestimate the power and importance of

wee small things at your peril. The atom holds

extreme amounts of energy, and we depend on

the tiniest of prokaryotes for our survival on Earth.

It would be a mistake to underestimate the grit and power of some of nature’s smallest organisms. We could talk about this for months, but why don’t we stick to the discussion of prokaryotes and their ability to get along without conventional organelles that we began last week.

We can go farther in praise of the prokaryote by looking at how some of them manage to live in the most inhospitable environments; places that would kill us in seconds, or at least we hope they would. These are the “extremophiles;” the name makes them sound like Saturday morning cartoon superheroes. For example, Thermococcus gammatolerans is the most radiation tolerant organism on Earth. It can laugh at gamma radiation levels 100x higher than other resistant organisms, even though it lives at the bottom of the sea.

As a result of the molecular biology revolution, many of the extremophiles are now called Archaea (Greek for “ancient”) or archaeabacteria, a completely group of organisms. Archaea are older than bacteria, and but they have some similarities to bacteria. Archaea are generally smaller than bacteria, but the cell wall of most archaea looks just like that of Gram⁺ bacteria. This is a thicker cell wall than that of Gram^- bacteria, and takes up the Gram stain, hence the name Gram⁺.

The archaea cell wall is thick, and is contiguous with the cell membrane,

like that of Gram⁺ bacteria. Gram^- bacteria have thinner walls and

they have a periplasmic space between the wall and the membrane.

Just looking at archaea and bacteria through a microscope makes it hard to tell the difference between these two distant relatives. It is at the molecular level that most of their differences become apparent. The way that archaea make RNAs is more eukaryotic than bacterial and while they both have cell walls, the lipids that make up archaeal membranes are quite different. Archaea lipids are hydrocarbon based, not fatty acid based like those of eukaryotes and bacteria. Also, archaeal cell walls lack the peptidoglycan that is characteristic of bacterial cell walls. Peptidoglycan synthesis is a common target of antibiotics, like penicillins, cephalosporines, and vancomycin.

This last difference might work out O.K. for us as humans. Not a single disease can be attributed to an archaea – yet. This is a big exception. Every other group of organisms on Earth has at least some members that can do humans harm, even if only inadvertently. Fungi, protozoa, bacteria, even plants can all cause us harm. One study says it is unlikely that we have just missed disease-causing archaea. About 0.38% of bacterial species cause disease, so if diversity in archaea is similar to that in bacteria, we should have found about 20 disease causing archaea by now.

Gum disease (periodontitis) has an outside chance of having an archaeal cause, but the evidence is sketchy. In a couple of studies, the presence of archaea in the mouth has correlated with gum disease; if archaea were present, then there was disease. Also, higher archaea number correlated to more severe disease. But archaea were only present in 1/3 of all cases of periodontitis – this is not good evidence to say archaea are the cause of periodontitis. This is the closest we have come to finding an archaeon with an anti-human bent.

Some archaea are thermophiles (heat loving); they don’t just like it hot, some require it really hot. Many thermophiles live in near undersea hydrothermal vents, where heat from the Earth’s mantle and core escapes into the ocean; basically ocean volcanoes.

The hydrothermal vent is an ecosystem that one

would be hard pressed to call home. Varies from 700˚C

to 4˚C, it is acidic, toxic, and radioactive. Yet many unique

prokaryotic and eukaryotic organisms live nowhere else.

To each his own.

Near a thermal vent, the temperature can reach 400-410˚C (700-720˚F) . The water doesn’t boil because of the great pressure exerted on it by all the water above it. No eukaryotic organism can survive at these temperatures, but thermophiles like T. gammatolerans do just fine. The hydrothermal vents pour out high levels of gamma type ionizing radiation from deep in the Earth, so it is handy that this archaeon is a multi-extremophile.

Only a few feet away from the vent the temperature of the ocean bottom will remain near freezing, about 4.5˚C. Other archaea (and some true bacteria) thrive in this cold environment. Called psychrophiles, cold tolerant archaea have cell walls that resist stiffening in water that is even below freezing temperature, and can fill there cytoplasm with anti-freeze proteins (AFPs; they create a difference between a solution melting point and its freezing point, called thermal hysteresis).

Between these two extreme environments, you can find quasi-conventional animals. As the hydrothermal vent water gives up its heat to the surrounding ocean, it creates an area that holds a temperature of about 10-15˚C. Many interesting animals have been found in this area, including the yeti crab and tube worms. Data from January 2012 describes a pure white octopus found at a depth of 2,394 meters. At this depth there is no light, so the octopus has no need for the elaborate camouflage mechanisms of color and texture. This octopod may represent a new species, but other white, vent-dwelling octopuses have been described previously, just not this far south.

This is the yeti crab (Kiwa hirsute). It is white because it lives

in the dark. It is furry because……..well, it makes the name

appropriate. Actually, the setae (hairs) contain bacteria that

may act to detoxify the water from the hydrothermal vents

where it lives. And it isn’t really a crab either, but I’m not

going to tell it so.

Ultimately, even these animals depend on the archaea for survival. No photosynthetic producers can survive at these depths, so the food chain starts with the chemosynthesizing prokaryotes, particularly those that use hydrogen sulfide to produce energy. Hydrogen sulfide is a major constituent in the hydrothermal vent output…. and would kill us quickly by binding to the enzymes in our mitochondria that perform ATP synthesis.

Some animals, like snails, eat the chemosynthesizing prokaryotes directly, while others predate the snails, etc. On the other hand, tube worms (Riftia pachyptila) get their energy directly from thermophilic proteobacterium that live inside the worm in a symbiotic relationship.

Other archaea live in high salt environments, like in the Dead Sea or the Great Salt Lake. They must be lonely, because given the high salinity, they are the only things living there (Water, Water Everywhere, But….). On the grosser end of the scale, some archaea thrive in human sewage plants, working well in environments without oxygen and high nitrogen contents.

Archaea have also been found in natural asphalt lakes, like near the La Brea region of Trinidad and Tobago. With toxic gases, high temperature, and practically no water at all, it was surprising that scientists found so many different kinds of prokaryotes, including several types of archaea. These 2010 findings suggest that life on other planets might not necessarily depend on water – that would be one heck of an exception!

But not all archaea are extremophiles, and they turn out to be much more common than we had thought. This isn’t just a numbers game, it turns out that we have been underestimating their effects on our lives all along. For instance, nitrogen fixation is crucial for crop production. A 2006 study by Schleper et al. in Norway suggests that there are many more ammonia oxidizing archaea in the soil than there are nitrogen fixing bacteria.

Archaea are responsible for much of the primary production that

occurs in the soil and in the water. Just the methanogenic

archaea alone are responsible for nearly 2% of all the carbohydrates

produced on Earth. Archaea contribute to the primary production

of every ecosytem.

Further, current evidence suggests that archaea may represent 25-84% of all primary production (creation of carbohydrates and other organic compounds from inorganic carbon sources, whether by photosynthesis or chemosynthesis) in the upper layers of seawater. Primary production is the beginning of every food chain, so ultimately all of our food depends on archaea as well. To bad that we have been underestimating our dependence on these oldest of life forms. Who knows what our effects our life choices have been having on them all these years.

On the other hand, not all extremophiles are archaea either. Thermus aquaticus is a bacterium that lives in hot sulfur springs and geysers. It is a chemosynthesizing bacterium that has become important in molecular biology. Since its enzymes can tolerate high temperatures, it is useful for replicating DNA sequences in the lab using the polymerase chain reaction. One step in this reaction requires high temperature and would kill most other enzymes.

Amazingly, this PCR technology and T. aquaticus polymerase has been crucial for helping us see how important the archaea have been in our evolution. In 1977, scientists Carl Woese and George Fox began DNA sequencing of some the extremophiles. They recognized that archaea were very different from eubacteria. The two groups must have diverged long long ago.

The three domains of life are shown here. The length of line shows

the evolutionary distance between domains. You can see that

Archaea are more like us than are the bacteria. You can’t tell from

this chart, but Archaea are older too. They are the roots

of our family tree.

It turns out that Archaea are as closely related to eukaryotes as they are to eubacteria. This stood science on its ear. Up to this point, scientists had been arguing as to whether there were four, or five, or six kingdoms. Now they had to impose a higher classification which superseded all the kingdoms.

Woese’s evidence has led us define to the three domains of life. One domain is the eukaroytes, all the cells with a nucleus (with exceptions, but we can talk about those later), with linear chromosomes instead of one circular piece of DNA (again with exceptions), and with organelles. The second domain is the archaea and the third domain is the bacteria. Six kingdoms follow from these domains; archaea, bacteria, protista, fungi, plantae, and animalia.

Archaea, bacteria, and eukaryotes; we have shown that they are all different, and yet they all developed from some single precursor cell. Next time we will see if our discussion to this point gives us a roadmap to get from that ancient first cell to us.

Rogers, A., Tyler, P., Connelly, D., Copley, J., James, R., Larter, R., Linse, K., Mills, R., Garabato, A., Pancost, R., Pearce, D., Polunin, N., German, C., Shank, T., Boersch-Supan, P., Alker, B., Aquilina, A., Bennett, S., Clarke, A., Dinley, R., Graham, A., Green, D., Hawkes, J., Hepburn, L., Hilario, A., Huvenne, V., Marsh, L., Ramirez-Llodra, E., Reid, W., Roterman, C., Sweeting, C., Thatje, S., & Zwirglmaier, K. (2012). The Discovery of New Deep-Sea Hydrothermal Vent Communities in the Southern Ocean and Implications for Biogeography PLoS Biology, 10 (1) DOI: 10.1371/journal.pbio.1001234

For more information and classroom activities on archaea, hydrothermal vents, chemosynthesis, and domain/kingdoms, see:

Archaea and extremophile bacteria –

http://www.ucmp.berkeley.edu/archaea/archaea.html

http://www.lessonsnips.com/lesson/extremophile

http://euarch.blogspot.com/

www.sinauer.com/pdf/Staley2e_Ch17.pdf

http://www.windows2universe.org/earth/Life/archaea.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.html

http://www.ucmp.berkeley.edu/archaea/archaeamm.html

http://serc.carleton.edu/microbelife/extreme/extremophiles.html

http://science.nasa.gov/science-news/science-at-nasa/2008/07feb_cloroxlake/

http://www.bath.ac.uk/cer/