Thursday, November 16, 2017

On Geometry And Genomes

Biology concepts – linear chromosomes, circular chromosomes, taxonomy, replication, telomere

Organization is helpful in learning and work,
and apparently in crafts. But there is a fine
line between organization and obsessive
compulsive disorder.
Everyone (teenagers excepted) knows that getting organized helps you to learn and work. When you group tasks, items, or facts, it helps in remembering or working with them. In biology, grouping organisms has a history as old as language.

In the older grouping systems, the name of an organism was a phrase that described some characteristic of the organism. When a new relative was identified, the name phrase had to be lengthened to separate this new organism from those similar to it. As you can imagine, the names got very long very fast.

In the 1750’s, Carolus Linnaeus developed a much easier system of naming. In his “trivial system,” each organism had two descriptors in its name; a binary naming system. Linnaeus’ system (and others) of taxonomy (taxis is Greek for “arrangement”) is based on shared characteristics.

Carolus Linnaeus (he let me call him Carl) had many
names. His knighthood name was Carl von Linne, his
born name was Carl Nilsson Linnaeus. In his naming
system Linne came up with the name mammal, so I guess
he named himself again.
At first, it was the characteristics people could see that were used to group organisms. Then it was the characteristics on the macroscopic and the microscopic levels. Now it is based on molecular characteristics, forming both a taxonomic classification and an evolutionary tree; this is now called the science of phylogenetics.

Molecular characteristics usually mean DNA. Differences in DNA sequence and in the number of mutations that have occurred provide a relationship between organisms. Using these factors, a time line for their divergence can be estimated. We changed the ways we determine similarity, and that changed the rules. With new rules come new exceptions.

Many of the DNA rules start with chromosomes (chromo = color and soma = body, this comes from the dark and light banding pattern of stained DNA). Cellular DNA is very long and very thin, perhaps only 12-22 nanometers wide (about 1/5000 the width of a human hair). In this form, it can only be seen with an electron microscope.

In eukaryotes, this DNA becomes complexed with many proteins during cell division so that all the DNA can be packed up and moved more easily to the daughter cells.  Called chromosomal packaging, the DNA is wound around proteins called histones, then folded many times over, so that the finished chromosome is packed 10,000 times more compact than the original DNA helix. This is the packed DNA that we see as dark and light bands and gives it its name.

DNA packaging with proteins is a eukaryotic characteristic, unless 
I find an exception! The DNA wraps around the histones, then the 
histones line up into a coil, then the coils fold up into the
chromatid. Total packing – about 10,000 fold; it takes a piece of 
DNA 1.5 cm long and makes it 0.0000002 cm long!
By definition, a chromosome is a piece of DNA that contains genes that are essential for the survival and function of the organism. This implies that there may be other pieces of DNA that contain genes that are not necessary for survival.

The molecular rules of biology state that prokaryotes have one chromosome, a single piece of double stranded DNA that contains all the genes that the prokaryote (archaea or bacteria) needs. This is efficient for the organism; it is one stop shopping for replication of all its instructions and only two chromosomes (after replication) need to be segregated to the two daughter cells that are being made.

And here begins our exceptions. There are several prokaryotic organisms that have more than one chromosome. That is to say, their essential genes are located on more than one piece of DNA.

The first identified example of multiple chromosomes in a prokaryote was Rhodobacter sphaeroides, a photosynthetic species of true bacteria that can also break down carbohydrates it takes up. This bacterium was found to have two chromosomes, although one was more than three times the size of the other.

Genes encoding essential products for making proteins and carrying out day-to-day functions are located on each of the two R. sphaeroides circular chromosomes. There are other genes that exist on both of the chromosomes, but appear to be turned on and off via different signals. This implies that the same gene may serve its function at different times in the organism's life, or under different environmental conditions.

R. sphaeroides is by no means the only prokaryote that possesses multiple chromosomes. More than a dozen different groups of bacteria have at least some members with more than one chromosome. This includes Vibrio cholerae, the causative organism of the disease cholera. V. cholerae is responsible for a diarrheal infection that affects more than 3-5 million people per year and causes 130,000 deaths each year.

This is a crown gall in a birch tree caused by R. radiobacter.
Like in cancer tumor in animal tissues, a gallis unregulated 
growth. In grape vines, it has been responsible for the ruin 
of entire Kentucky vineyards. Kentucky makes wine?
In addition to these organisms there is Agrobacterium tumefaciens, whose name was recently changed to Rhizobium radiobacter. This is a very interesting two chromosome bacterium. It usually is a pathogen of plants, forming galls (tumors) on several cash crops, such as nut trees and grape vines. This is an important tool in the molecular biologist’s toolbox, since it has been found that R. radiobacter easily transfers DNA between itself and the plants it infects, via lateral gene transfer (a subject we have discussed in depth, When Amazing Isn’t Enough and Evolution of Cooperation). But R. radiobacter goes further, it can also cause disease in humans who have poorly functioning immune systems. For folks battling cancers, HIV, or other diseases that wreak havoc with their ability to fight off infections, R. radiobacter can cause bacteremia (bacteria colonizing the blood) or endopthalmitis (infection of the two hollow cavities of the eye).

The second molecular rule of biology is that prokaryotic chromosomes take the shape of a circle; the DNA forms a single loop. This shape is helpful in terms of replicating the prokaryotic chromosome prior to cell division. Start anywhere, and you can keep going to replicate the entire thing.  In point of fact, they don’t start just anywhere, but one start point (called an origin of replication) leads to complete replication.

There are advantages to having a circular chromosome. Prokaryotic chromosomes do not complex with proteins to become more densely packed, so it remains as a thin, long molecule. This means that fewer proteins are needed to maintain a circular, prokaryotic chromosome. In addition, since replication requires the doubling of just one piece of DNA from one origin of replication, this takes less time and fewer proteins to accomplish. Together, these features of a circular chromosome result in a more efficient and simpler process, with fewer chances for mistakes to be made.

Borrelia burgdorferi, a spirochete (spiral) bacterium was
Named for the researcher who discovered, it in 1982, Willy
Burgdorfer. It is one of the few pathogens that can function
without iron; it uses manganese instead. The ways this bug
gets around the rules is astounding.
However, there are exceptions in which prokaryotes have linear chromosomes. The Borrelia burgdorferi bacterium has a single chromosome, but it has the geometry of eukaryotic chromosomes, a line segment with two ends. This was the first prokaryote found to have a linear genome, way back in 1989. This lyme disease pathogen has one major linear chromosome and other pieces of smaller DNA that are circular or linear (which we will discuss in the next post); you just can’t trust a pathogen to follow the rules. Other prokaryotes that have linear chromosomes include our friend R. radiobacter. Even more interesting, while this pathogen has two chromosomes; one is circular and one is linear. How does that happen?

The previous discussions do not mean that all prokaryotes with multiple chromosomes or linear chromosomes are disease-causing agents, just the interesting ones. Since they cause pathology in animals or crops, they hit us in the wallet. It makes sense that we have studied them in more detail and have discovered their hidden exceptions. There are probably thousands of innocuous prokaryotes that have more than one chromosome or have linear chromosomes, we just don’t have a reason to look at them in that much detail.

There may be more than one way that prokaryotes end up with linear chromosomes. In some cases, the linear chromosomes still have bacterial origins of replication, indicating that they may have evolved from circular chromosomes. There is also evidence that some linear chromosomes might have developed from other linear DNAs in the cell, something we will talk about next time.

The rules of defining prokaryotes and eukaryotes also state that eukaryotes have linear chromosomes. The essential genes are stored on more than one piece of DNA, and these pieces have two ends apiece, like a line segment in geometry.

Linear chromosomes are a disadvantage because it is hard to replicate the ends. Because of the way that DNA replicates, the ends of the chromosomes, called telomeres, end up being shortened every time the DNA is replicated. Over time, this leads to shorter chromosomes that might lose DNA sequences that the cell needs in order to function.

Some lines of evidence suggest that telomere shortening is a direct cause of ageing. The loss of important sequences at the ends of chromosomes cases cells to perform at less than optimal levels, and mistakes and toxic products then build up and lead to larger dysfunctions of cells, organs, and systems, ie. getting old.

This is a very simple cartoon depicting recombination. When
sequences are exchanged, it isn’t necessarily a 1:1 exchange.
Sometimes parts of genes are sent one way but not the other,
So new genetic sequences can result. Some help, some hurt, and
some have no effect until the environmental conditions show
them for what they are. Most exchanges do not increase diversity
to any great degree, but the fact that some do has helped move
evolution along.
On the other hand, linear chromosomes may promote genetic diversity. In eukaryotes, the division of the cell requires each chromosome to be replicated, then the matching chromosomes of a pair (one from mom and one from dad) line up together. This is a prime opportunity for the chromosome to exchange some sequences in a process called homologous recombination; a mixing of genes beyond just getting one from each parent.

However, a study published in 2010 indicates that the geometry of the chromosome doesn’t matter when it comes to recombination rates. Scientists took a circular chromosome organism and linearized its genome (they cut it so it had ends). They also did the reverse experiment, taking a linear chromosome organism and circularizing its DNA.

In both cases, there was no change in the rate that its DNA recombined and produced slightly different offspring (the two circular chromosomes after replication can swap some pieces). So geometry does not appear to affect genetic diversity – so why did each type evolve? Good question – that can be your Nobel Prize project.

Next week we will continue the discussion of exceptions in DNA structures, including DNA that isn’t part of a chromosome, and mitochondrial and chloroplast genomes that don’t look like they should.

Casjens SR, Mongodin EF, Qiu WG, Luft BJ, Schutzer SE, Gilcrease EB, Huang WM, Vujadinovic M, Aron JK, Vargas LC, Freeman S, Radune D, Weidman JF, Dimitrov GI, Khouri HM, Sosa JE, Halpin RA, Dunn JJ, & Fraser CM (2012). Genome stability of Lyme disease spirochetes: comparative genomics of Borrelia burgdorferi plasmids. PloS one, 7 (3) PMID: 22432010

Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, & Muller D (2014). Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Molecular phylogenetics and evolution, 73, 202-7 PMID: 24440816

Suwanto A, & Kaplan S (1989). Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. Journal of bacteriology, 171 (11), 5850-9 PMID: 2808300

For more information or classroom activities on prokaryotic chromosomes or eukaryotic chromosomes, see:

Prokaryotic chromosomes –

Eukaryotic chromosomes –

Thursday, November 9, 2017

The Evolution Of Cooperation

Biology concepts – biological timeline, serial endosymbiosis, endocystosis, evolution

Taxonomy, the placing of species in different
groups based on their characteristics, changes
everyday – literally everyday – organisms are
placed in different groups and groups are created
and eliminated. That better be a temporary tattoo!
If we look at the 3.5 billion year history of life on Earth, we see that out planet was lifeless for almost a quarter of its span, and animals have been around just a short blip of time, a mere 760 million years. Often, it seems that the big numbers to get in the way of understanding the time line as a whole.

If we treat the entire history of earth as one year, we might get a clearer picture. Earth coalesces from space dust on January 1st, but it isn’t until March 22nd that we find the first evidence of life. These most primitive fossils are of the prokaryotes called Archaea (Greek for “ancient”). Not long after this, maybe a week or so, the eubacteria and Archaea separate from one another.

Then we have to wait until August 7th to find a big change; the first eukaryotic organisms are seen. These represent a fundamental change in the organisms, having nuclei and membrane bound organelles. It's amazing that we must travel 3/4 through our one year time line before we see a cell that looks somewhat like ours!

Here is one of the Namibia sponge fossils recently
discovered in Africa. It represents the oldest animal
in the fossil record. Just how that was recognized as a
fossil is beyond me – I think I have six of those in my
Later in the year, around October 30th at noon, we see the first animals. Fossils of Namibia sponges in Africa were first reported in February of 2012. This fossils are 100 million years older than the previously oldest animal remains, so our new data means that animals have been around for an additional week in our time line of a year.

Insects appear about Nov. 26th, while mammals first show up around Dec. 8th. The dinosaurs became extinct sometime in the afternoon of Dec. 26th, so they had very little time to play with their Christmas presents. Homo sapiens (us) didn’t appear on the doorstep looking for holiday cheer until 11:40 pm on New Years Eve, Dec. 31st!

Our time line analogy shows us that prokaryotes are the wise old ancestors; we aren’t even old enough to be rebellious teenagers, although we still think we know everything. The key question is: how did we progress to analogy-makers from single celled Archaea? If we put together several of the topics we have been discussing in the past three weeks, we may come up with an interesting step in the process. Our clues include:

1) Microcompartments exist in bacteria, like organelles, and they also exist in eukaryotic cells, especially in nucleus' function. This links eukaryotes to prokaryotes.

2) Sometimes cells will engulf objects, parts of other cells, or other cells. Depending on the size of the particle or cell, we may call this endocytosis or phagocytosis, and is similar to how we saw keratinocytes take up melanosomes.

3) Three eukaryotic organelles, the nucleus, the mitochondria, and the chloroplast have double membranes, and they each have their own DNA.

4) There are two different types of prokaryotes, archaea and bacteria.

Bacterial microcompartments give prokaryotes some compartmentalization in order to carry out necessary chemical reactions. Eukaryotes also have some prokaryotic microcompartment remnants, like the nuclear vault complex. This shows crossover between prokaryotes and eukaryotes, and gives us clues about eukaryotic origins. In fact, the currently accepted theory about the evolution of organelles - the very thing that makes cells eukaryotic - has to do with both types of prokaryotes - archaea and bacteria.

There are three types of endocytosis (with exceptions).
Endocystosis of large objects and cells is called phagocytosis.
Internalization of very small molecules and fluid is called
pinocytosis. Other molecules of various sizes have specific
receptors that recognize them on the cell surface. They are
brought in by receptor-mediated endocytosis. Notice that no
matter what method is used, the internalized particle ends up
surrounded by part of the cell membrane.
The key to their interrelationship has to do with endocytosis (endo = into, cyto = cell). Most prokaryotic and eukaryotic cells eat other cells; they do it all the time – it is how heterotrophic organisms (those that can't make their own carbohydrates, ie. non-plants) gain their nutrients. We do it too, just on a larger scale; we eat millions of cells at a time; often these millions of cells can take the shape of a steak or a carrot.

When a cell, protein, other molecule is engulfed by another cell, it is wrapped in a portion of the aggressor cell’s membrane. The naked molecule is now contained in a vesicle, a membrane bound sac, like the melanosome. If the endocytosed material is an entire cell, something that has its own membrane, then it ends up with two membranes, just like the mitochondrion, chloroplast, and nucleus.

Most often, when one prokaryote phagocytoses another, the story is over….gulp, yum, digest. But scientists believe that long ago (sometime in the first week of August in our time line) an endocytosed cell did not go gentle into that good night. Instead, it took up residence in the cell that ate it. In this rare case, it turned out that both cells gained from the situation.

The endocytosed cell was protected from other predators and had a ready supply of nutrients from the parent cell. The captured cell made lots of ATP, but it didn’t need much because it was being supplied with everything it needed; it didn't need to make energy to move or hunt or escape. Most of its ATP production went unused. Perhaps it moved this excess ATP out into the parent cell. So the parent cell gained a source of ATP production. This was mutualism, a type of symbiosis in which both parties benefit.

Clownfish clean the sea anemone and keep it
parasite free. The poisonous anemone provides
a safe environment for the clown fish; no
unwanted house guests! This is a good example of
mutualistic symbiosis. Bet you didn’t know you
learned things from Finding Nemo.
Imagine if the same thing happened with a cyanobacterium, a cell that could perform photosynthesis. The same sort of symbiosis might be set up, with the endocystosed cell providing carbohydrates and the parent cell providing protection.

Now imagine that these captured cells, the photosynthesizer and the ATP maker, replicated themselves inside their parent cells just as they would if they were outside, living on their own. They could easily do this since they still retained their own DNA and cell division mechanisms.

This is in fact what scientists believe happened. The endocytosed cells that produced extra ATP evolved into our mitochondria. Endocytosed cells that could do photosynthesis became the chloroplasts of plants. Not all cells are plants because not all cells with an ancestral mitochondria also ate a cyanobacterium. The fact that plants cells have mitochondria as well as chloroplasts tells us that plant cells developed AFTER cells with mitochondrial ancestors.

But the nucleus may be a tougher nut to crack. It may be that an endocytosed cell good at keeping DNA safe and producing ribosomes became the nucleus, by endocytosis. The data suggests that our DNA is closer to archaeal DNA than bacterial DNA, so it would have been a eubacteria endocytosing an archaea. Or perhaps the archaea invaded the bacterium rather than being endocytosed. The nucleus does have a double membrane and uses some prokaryotic microcompartments to this day, so this could make sense.

But other theories also exist, including one that says an intermediate eukaryotic cell, theoretically called a chronocyte, had developed some organelles on its own or by endocytosis, including a cytoskeleton. This internal structure allowed the cell become bigger, and engulf a cell large enough to evolve into the nucleus.

Another theory uses an evolutionary exception as its basis. Some aquatic bacteria, called planctomycetes (planktos = drifting and mycete = fungus-like), have an organized interior, with something that looks like a nucleus with pores, called a nucleoid. In fact, when they were first discovered, planctomycetes were mistaken for small fungal cells. However, we know they are prokaryotes by DNA sequencing. I thought prokaryotes didn’t have nuclei! Remember that in biology, there is almost always an exception. The planctomycete nucleoid structure suggests that the nucleus may have evolved on its own, without endocytosis.

The planctomycete species, Pirellula (latin for small pear),
is an exceptional bacterium. It has a primitive nucleus
and a stalk that makes it look like a eukaryotic
fungal cell. It was misidentified for a long time, and is
a prime example of why the tattoo above was a bad
Finally, another theory posits that the nucleus originated from a virus infecting a primitive prokaryote, and this internalized virus forming a nucleus or causing the cell to be predated by another cell. Even though there are different theories for the nucleus, we can see that the three organelles that have double membranes look like they could have been endocytosed cells, that then evolved into the organelles we see today. Endocytosis resulted in symbiosis, so the theory of organelle development is called endosymbiosis.

Endosymbiosis is a cool idea and has lots of support. Besides the double membrane evidence, lets look at how dividing cells get more mitochondria and chloroplasts. These organelles replicate on their own by binary fission, just like bacteria. They can replicate on their own because they have their own DNA. Mitochondrial DNA (mtDNA) and chloroplast DNA (chDNA) are smaller pieces of DNA than nuclear chromosomes, mtDNA and chDNA look much like the small genomes of bacteria. They are also circular pieces of DNA, not linear like our nuclear chromosomes.

By replicating through binary fission, they can be portioned in the dividing cell so that each daughter gets some of these crucial organelles. But it isn’t as if mitochondria and chloroplasts of today look just like the engulfed ancestors. Mitochondrial and chloroplast genomes are greatly reduced from what they used to be.

Serial endocytosis is also called secondary (2˚) endocytosis.
This refers to the movement of DNA from internalized
cells to the nucleus of the endocytosing cell by lateral
gene transfer. This strengthens the symbiotic relationship
between the two organisms until they can be considered
one total organism.
The mitochondria only codes for about thirteen proteins, just enough for it to replicate on its own. The DNA that codes for the rest of the 1500 or so proteins needed for mitochondrial function have been transferred to the nucleus over time. For a discussion of the chloroplast and its horizontal gene transfer to the nucleus, see the posts on C. litorea, the photosynthetic sea slug.

We know that these gene transfers were actual events based on the structure and nucleotide ordering of the mitochondrial and photosynthetic sequences in the eukaryotic chromosomes; they are structured and coded in ways that are typically bacterial. Because of this slow transfer of DNA to the nucleus, endosymbiosis has evolved over time, changing again and again until we got today’s organelles. Therefore, our idea of organelle development is sometimes called serial endosymbiosis theory (SET), because it must have had several different changes through evolution.

Now that we have laid out the evidence and sense for the serial endosymbiosis theory, next week we can talk about some exceptions that show us that that some organisms just can't stick with something that seems to work. Some life just has to take the road less traveled.

Okie JG, Smith VH, & Martin-Cereceda M (2016). Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts. Proceedings. Biological sciences / The Royal Society, 283 (1831) PMID: 27194700

Kostygov AY, Dobáková E, Grybchuk-Ieremenko A, Váhala D, Maslov DA, Votýpka J, Lukeš J, & Yurchenko V (2016). Novel Trypanosomatid-Bacterium Association: Evolution of Endosymbiosis in Action. mBio, 7 (2) PMID: 26980834

Erbilgin O, McDonald KL, & Kerfeld CA (2014). Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Applied and environmental microbiology, 80 (7), 2193-205 PMID: 24487526

For more information or classroom activities on history of life time lines, endocytosis,  serial endosymbiosis theory, evolution of eukaryotes, or planctomycetes, see:

History of life on Earth timelines -

Endocytosis –

Serial endosymbiosis theory –

Evolution of eukaryotes –

Planctomycetes –

Thursday, November 2, 2017

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 –

Hydrothermal vents –

Chemosynthesis –

Domains/kingdoms -