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 -


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