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Archaea Are More Wonderful Than You Know

The views expressed are those of the author and are not necessarily those of Scientific American.


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Thermococcus gammatolerans -- a flagellate archaeon that thrives in hot, oxygen-starved waters. Note the tuft of flagella. This microbe lives in water hotter than about 160F. Creative Commons Angels Tapias. Click image for license and link.

In the 1970s, an obscure scientist named Carl Woese (pronounced “woes”) was working on something apparently rather mundane: finding a way to classify bacteria.

Though that may seem a straightforward task, bacteria had stubbornly resisted all previous attempts. The traditional method — looking at differences in appearance, structure, and metabolism and sort of eyeballing it — had failed. Bacteria often look and act a lot alike regardless of their true evolutionary relationship.

Great names in microbiology had given up on the problem long ago. But Woese had an idea: what if bacteria could be scientifically sorted by using their genetic material, as expressed in the RNA that made up their ribosomes, the protein production units of the cell? Most ribosomal RNA mutations are catastrophic to offspring who inherit them, given ribosomes’ critical importance to keeping a cell alive, and thus changes in ribosomal RNA happen only rarely. But over the several billion years microbial life on Earth has existed, they do happen, making this molecule a promising target for judging relationships that stretch into deep time.

After a decade or so of painstakingly cleaving ribosomal RNA into small bits and staring at these sorted bits on photographic films clipped to light boxes — countless hours of tedium fueled by Dr. Pepper and bouts at a chin-up bar — Woese was well on his way to making a bacterial family tree.

Then, something unexpected happened. A colleague named Ralph Wolfe suggested he try his method on an unusual group of bacteria that made methane. Though they came in a pasta-like variety of shapes, their biochemistry and metabolism seemed alike. This excerpt from a 1997 Science article by Virginia Morell captures the shock of what happened next:

But when Woese studied their sequences, the methanogens did not register as bacteria. “They were completely missing the oligonucleotide sequences that I had come to recognize as characteristic of bacteria,” he explains. Thinking the sample had somehow been contaminated, he ran a fresh one. “And that’s when Carl came down the hall, shaking his head,” says Wolfe. “He told me, ‘Wolfe, these things aren’t even bacteria.’ And I said, ‘Now, calm down, Carl; come out of orbit. Of course, they’re bacteria; they look like bacteria.’ “But, as Woese now knew, morphology in bacteria meant nothing. Only their molecules told the story. And the molecules proclaimed that the methanogens were not like any other prokaryote or eukaryote—they were something unto themselves, a third branch of life.

Carl Woese in 2004. Creative Commons Don Hamerman. Click image for license and source.

“Wolfe, these things aren’t even bacteria.” When I read that sentence, a chill ran up my spine. Only a few people on Earth ever get to experience a kind of veil-lifting moment of that magnitude — Einstein, Newton, Kepler, etc., come to mind — but humble Carl Woese was another. He had stumbled on a brave new world of microbes that looked like bacteria to our eyes, but were in fact so unique biochemically and physically that they have ultimately proved to be more closely related to us than to them. He had stumbled on an entirely new form of life, right here on Earth.

Carl Woese died Dec. 30. Woese remains little known, even among non-microbial biologists but particularly among the public. He endured a decade or more of skepticism, ridicule, and ostracism before his observations were accepted and was deeply hurt by the initial reaction; you can and should read more about that in the Science feature story I excerpted above (pay access required). In recent years, some — including the editorial board at Nature Reviews Microbiology — pushed for Woese to receive the Nobel prize for his contributions. Now, that will never happen*.

But Woese is not the only unsung hero in this story**. The organisms he revealed — the archaea — are fascinating and abundant creatures, yet are hardly ever discussed in depth, even within the confines of microbiology classes. That is a shame. Archaea are everywhere — in deep sea vents, in salt flats, in ice, in sea water, in soil, and in you. And they deserve better publicity.

Consider the following intriguing points about the Third Domain:

 

Archaea Make DNA and RNA in Ways that Look Like Us — Which Implies an Interesting Thing

In many ways, archaea look more like us than bacteria — but you have to look closely to see it. “Us” would be the eukaryotes, the life forms that house their DNA in packets called nuclei (among many other traits). The group includes pretty much everything except archaea and bacteria.

Archaea possess DNA and RNA polymerases — enzymes that replicate DNA and RNA — that look like simpler versions of the ones found in eukaryotes.  And their single circular chromosomes can have more than one origin of replication, like eukaryotes but unlike bacteria.

In order to condense their DNA enough to fit inside a cell, bacteria use a protein called gyrase to twist their DNA into coils. Archaea do this too, but they also wrap their DNA around proteins called histones that, again, look like simpler versions of the histones around which eukaryotes wrap their DNA. As far as I know, bacteria do not possess histones.

These compelling similarities — of which there are more deeper in the biochemical weeds that I am omitting for space — between archaeal and eukaryotic cells has led some to suggest that in addition to the bacterial engulfment/symbiosis that created mitochondria and chloroplasts, some other more mysterious symbiosis or chimerism may have occurred between an ancient archaeon and bacterium to produce the first proto-eukaryotic cell. Or it may suggest that eukaryotes, in fact, evolved from archaea. This is a hotly debated idea, and one for which you will see further evidence below.

Archaeal Exterior Coatings Are Unlike Anything Else on Earth

Bacterial and eukaryotic membrane lipids share the same general structure (second from top molecule below): a phosphate group (green) attached to a glycerol (red) form the head of the lipid, while two fatty acids from the tail (pink). Further, like bacteria, our lipids’ glycerol heads are linked to their fatty acid tails with ester linkages (yellow).

Archaeal membrane lipids look very, very different from both bacteria and from eukaryotes (top molecule, above). Archaea have tails built of units of the branched chemical isoprene instead of fatty acids, and their 20-carbon tails are called phytanyl groups (I nominate phytanyl for Vowel Efficient Word of the Week). These lipid tails can be branched in even more complex ways than shown above or even incorporate rings(see below) — crazy shapes that bacterial and eukaryotic membrane lipids never take on, as far as I know.

Crenarchaeol, a ringed, branched monolayer membrane lipid from an archaeon. Public domain.

Their phytanyl tails are primarily hooked to their glycerols using ether, not ester, linkages (see 2, above), which resist destruction better than esters. And their glycerols have opposite handedness to the glycerols in our membrane lipids (note mirror orientation in the bacterial and archaeal lipids in figure).

Molecular handedness — chirality in chemistry-speak — is not a thing changed easily by evolution. For instance, the vast majority of protein building blocks called amino acids used by life on Earth are exclusively “left-handed”. Why? No one really knows, although some have guesses. Once lefty amino acids took over, though, there was no going back biochemically — the enzymes were set up a certain way and that was that. Thus, that archaeal and bacterial enzymes use glycerols with opposite handedness implies that bacteria and archaea parted ways long, long ago.

Some archaeal lipids have a property that is rarely or never seen in bacteria or eukaryotes. Bacteria and eukaryotes have membranes made of lipid bilayers that flow past one another (#9). But archaeal phytanyl tails can be covalently bonded to each other to form a lipid monolayer (see #10 and the image of crenarchaeol above).Two heads; one body — a membrane hydra.

The branched and reticulate phytanyl tails and the lipid monolayers all seem to be adaptations to scalding temperatures. They may help prevent membrane leakage or the peeling apart of a bilayer in the watery and often acidic infernos in which hyperthermophilic archaea live.

You may also observe that unlike most of our genetic and protein manufacturing machinery, our lipids resemble bacteria much more than archaea. Is that, too, evidence of an ancient chimerism?

The Mysterious Absence of Archaeal Parasites and Pathogens

No obviously parasitic or pathogenic archaea have ever been found. That is not to say they don’t exist. Archaea existed long before we found them, and now we see that they are everywhere. More on that in a minute.

But this is a point worth pondering (a Talmudic Question, a la Small Things Considered?): why do there seem to be no obvious parasites or pathogens in the domain? Bacteria and eukaryotes have spawned countless nasty parasites from syphillis to bedbugs to mistletoe to Nigerian Craigslist scammers, and to me it seems very odd that an entire domain should be devoid of them.

Is archaeal chemistry so unique that they are ill-equipped to live inside higher organisms? No, that certainly does not seem to be the case, as we will see below. So why have they never crossed to the dark side? Is it something fundamental about their metabolism or chemistry?

The closest thing we have found to a potentially pathogenic or parasitic archaeon is Nanoarchaeum equitans, one of the world’s smallest cells. It‘s found in hydrothermal vents everywhere from the tops of continents — like the Obsidian Pool at Yellowstone — to the depths of the oceans — like the Mid-Ocean Ridge near Iceland and under the Arctic Ocean, a distribution that is in itself worth pondering for what it implies.

Wherever it is found, it lives exclusively on the surface of a much larger archaeon, Ignicoccus. Up to 10 N. equitans may coat the surface of an individual Ignicoccus. Nanoarcheum cannot synthesize lipids, most nucleotides (the building blocks of DNA and RNA) or amino acids. It must take them (steal them? exchange them?) from Ingnicoccus.

But unlike other microbial parasites, N. equitans does have everything necessary to repair its own DNA and carry out DNA, RNA and protein synthesis. Though it clearly cannot live without Ignicoccus, whether it is a symbiont or a parasite is still unclear.

This lack of obvious nasties also does not mean that archaea are *free* of parasites or pathogens. On the contrary, plenty of things consume archaea, and archaea play host to an entire spectrum of uniquely-shaped (spindles, canes, and teardrops) DNA viruses that thrive in the same hellish environments that can breed archaea.

Here is an archaeon called Sulfolobus from a hot spring in China sporting several spindle-shaped DNA viruses:

The hyperthermoacidophile archaeon Sulfolobus tengchongensis and its spindle-shaped parasite, the virus STSV1

The strange lack of archaeal pathogens may also have contributed to Woese’s difficulty in winning the Nobel. It’s not the Nobel Prize in Biology; it’s the Nobel Prize in Physiology or Medicine. And without any obvious archaeal diseases, the case for his prize would necessarily be indirect.

Archaea are Everywhere

When archaea were unveiled to the world, they were for many years thought of as extremophile weirdos. They lived in places like salt flats, hydrothermal vents, hot acidic pools, and methane-infested bogs. They weren’t like, you know, normal microbes.

And in many cases, that is true, in astoundingly wonderful ways. We have discovered square, flat archaea that divide into sheets like postage stamps living in salt pans. They use proteins called (eroneously, obviously) bacteriorhodopsins that are structurally and functionally similar — though evolved completely independently — to the vertebrate eye protein rhodopsin to make energy from light. Other species of these salt-loving archaea come in a variety of polyhedral shapes in addition to squares, and sometimes shift shapes between generations.

A postage-stamp like sheet of the square cells of Halquadratum walsbyi. Public domain. Click image for source.

And then there’s Strain 121, named for its ability not just to survive, but to reproduce at 121C, the kill temperature of laboratory and medical sterilization equipment. Prior to its discovery, no cells were thought capable of surviving 15 minutes in the 121C holding temperature ring of autoclaves. Strain 121 can survive at temperatures up to 130C and experiments suggest there may be archaeal species that can tolerate temperatures of 140 to 150C. Lest you forget, water boils at 100C.

But archaea are hard to culture in lab (as are the vast majority of microbes). What if there were more out there, hidden, yet again, in plain view?

When we began looking for archaeal DNA and not worrying about finding the bodies, we discovered the microbes practically everywhere we look. That includes “normal” places like seawater and ocean sediment, soil, and the mammalian gut and vagina. They may make up 40% of the microbial biomass in the open ocean (bacteria still outnumber them about 3 to 1) and may make up 20% of Earth’s total biomass. In spite of their heat-loving reputation, Archaea are also turning up in very cold places too, like Arctic seawater and ice.

To our surprise, we have found super-sized filamentous archaea almost big enough to see with the naked eye living on mangrove roots. We have found methanogenic archaea that interact with protozoa in the guts of cows and termites to help these organisms break cellulose down for energy. We’ve even found an archaeon that lives symbiotically with — of all things — a sponge.

No doubt many more strange and wonderful creatures will appear once we start matching microbes with their DNA sequences — if only we care to look.

____________________________________________

*Nobel prizes are not awarded posthumously, although they made an exception last year in a remarkable case.

**In the Carl Woese tribute department, I salute this student of Mark O. Martin, who dressed as Woese in his flannel and floppy white hair for Halloween. (note the tree with the three domains in his hands). Source: Martin’s fine tribute to Woese.

In that same spirit of affectionate fun, I composed this post. We’ll miss you and we thank you, Carl.

Jennifer Frazer About the Author: Jennifer Frazer is a AAAS Science Journalism Award-winning science writer. She has degrees in biology, plant pathology/mycology, and science writing, and has spent many happy hours studying life in situ. Follow on Twitter @JenniferFrazer.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. JonathanEisen 2:00 pm 01/12/2013

    Wonderful tribute. I have been compiling other tributes and related information about Woese here: http://phylogenomics.blogspot.com/2012/12/rip-carl-woese-collecting-posts-notes.html

    Link to this
  2. 2. Jennifer Frazer in reply to Jennifer Frazer 3:16 pm 01/12/2013

    Thanks, Jonathan. I never knew him but I won’t forget him, either. Thanks for the link!

    Link to this
  3. 3. Torbjörn Larsson, OM 10:37 pm 01/12/2013

    “The branched and reticulate phytanyl tails and the lipid monolayers all seem to be adaptations to scalding temperatures.”

    To predict the domain diversification I find it helpful to contrast Valentine’s energy theory on archaea with Lane’s energy theory on eukaryotes.

    Lane puts eukaryotes as high energy density specialists having access to ~ 10^5 the energy density of bacteria by way of mitochondria specialized genomes energy plants. Several ecological niche inventions follows.

    Valentine puts archaeas as low energy density specialists by way of low ion leakage membranes and small genomes. They naturally separate out from bacteria in almost all ecological niches, by temperature but also other characteristics like salinity et cetera.

    I therefore assumed that the absence of parasitism in the form of other specialization (life cycles and what not) could be predicted by the generic niche pressure of minimizing genomes.

    By exclusion, bacterias finds their niches as medium energy generalists.

    Tracing membrane metabolism phylogenetically it looks like the DNA UCA was a non-chiral lipid generalist. With 50 % chance of choosing each chirality as niche specialization happened, I think the resulting 2-1 result is reasonable.

    “No one really knows, although some have guesses.”

    Well and good, but mind that astrobiology texts (which is my interest) lists a lot of similar mechanisms.

    “experiments suggest there may be archaeal species that can tolerate temperatures of 140 to 150C. Lest you forget, water boils at 100C.”

    Mind that these life forms live at ocean pressures where such hot water doesn’t boil. So it is continuous with earlier cellular lifestyles.

    But, 140-150 degC!? That is a teaser, and no references given! No papers yet?

    Link to this
  4. 4. Torbjörn Larsson, OM 10:51 pm 01/12/2013

    As for histones, it seems to this layman that persistent DNA binding proteins are legion. “Histone-like” proteins are found in bacteria and viruses alike: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3326515/ .

    If bacteria dumped their ancestral histones, it wouldn’t be unprecedented. I hear that the reason insects Hox organization is so peculiar is that they, like generic bacteria, rushes their development. It is perhaps more “Hox-like” than Hox proper, as they do everything ‘at once’.

    Link to this
  5. 5. Glendon Mellow 12:48 am 01/13/2013

    This post is epic Jennifer! Enjoyed it like a good novel.

    Link to this
  6. 6. Stuff we linked to on Twitter last fortnight | Highly Allochthonous 10:25 am 01/13/2013

    [...] They’re weird, and they’re *everywhere*: Archaea are more wonderful than you know. Great post by Jennifer Frazer. http://blogs.scientificamerican.com/artful-amoeba/2013/01/12/archaea-are-more-wonderful-than-you-kno... [...]

    Link to this
  7. 7. Another Week of GW News, January 13, 2012 – A Few Things Ill Considered 4:50 pm 01/14/2013

    [...] 2013/01/12: SciAm:TAA: Archaea Are More Wonderful Than You Know [...]

    Link to this
  8. 8. Links 1/16/13 | Mike the Mad Biologist 4:45 pm 01/16/2013

    [...] Archaea Are More Wonderful Than You Know Mouse eats scorpions and howls at the moon The Myth of Tamiflu: 5 Things You Should Know (there’s very little evidence that it actually does much) Termites measure wood from inside using echolocation DSM-5: A Ruse By Any Other Name… Flu Q&A [...]

    Link to this
  9. 9. I’ve got your missing links right here (19 January 2013) – Phenomena: Not Exactly Rocket Science 12:01 pm 01/19/2013

    [...] “These things aren’t even bacteria!” To understand why that quote is so damn amazing, read this by Jennifer Frazer [...]

    Link to this
  10. 10. Enantiomeri « oh tempo le tue piramidi 6:29 pm 01/20/2013

    [...] dalle ultime letture della settimana di Marcoscan segnalo Archaea Are More Wonderful Than You Know, dal blog The Artful Amoeba su Scientific American. Sapevo dell’esistenza degli archea, una [...]

    Link to this
  11. 11. Hollisjeanne 9:41 am 01/21/2013

    Great overview of Archaea, Jennifer, thanks! And a nice tribute to Woese. I wonder … are misnomers common, left over from more ignorant times? I checked the Haloquadratum link and found they are members of the “Halobacteriaceae”.

    Link to this
  12. 12. Мито-свет | Био-блог 6:01 pm 03/1/2013

    [...] Нама не баш толико блиске архебактерије, према неким мишљењима, лепше су него што можемо да помислимо – Scientific American: Archaea Are More Wonderful Than You Know [...]

    Link to this
  13. 13. Genomics of Bacterial and Archaeal Viruses | Pharmaceutical Intelligence 9:07 pm 03/4/2013

    [...] Archaea Are More Wonderful Than You Know (blogs.scientificamerican.com) [...]

    Link to this
  14. 14. Dropping science | Life of refinement 12:27 pm 05/26/2013

    [...] via Archaea Are More Wonderful Than You Know | The Artful Amoeba, Scientific American Blog Network. [...]

    Link to this
  15. 15. Indrani@Banerjee 11:22 am 07/25/2013

    I have read the above facts and they are truely amazing but I have a query to be solved that why are “postage stamp like sheets of cell” of archaea found in red sea?
    I am hoping for a quick reply to this.

    Link to this

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