Question

• Many Archaeal lineages are extremophilic. Briefly discuss a fundamental character of Archaea that supports the emergence of extremophiles, in comparison to bacteria or eukaryotes.

Answer 1

Archaebacteria are a type of single-cell organism which are so different from other modern life-forms that they have challenged the way scientists classify life. Until the advent of sophisticated genetic and molecular biology studies allowed scientists to see the major biochemical differences between archaebacteria and “normal” bacteria, both were considered to be part of the same kingdom of single-celled organisms. “Kingdoms,” a way of organizing life forms based on their cell structure, traditionally included Animalia, Planitia, Fungi, Protista (for single-celled eukaryotes), and Monera (which was once considered to hold all forms of prokaryotes).

However, genetic and biochemical studies of bacteria soon showed that one class of prokaryotes was very different from “modern” bacteria, and indeed from all other modern life forms. Eventually named “archaebacteria” from “archae” for “ancient,” these unique cells are thought to be modern descendants of a very ancient lineage of bacteria that evolved around sulfur-rich deep sea vents.

Sophisticated genetic and biochemical analysis has led to a new “phylogenetic tree of life,” which makes use of the concept of “domains” to describe divisions of life that are bigger and more basic than that of “kingdom.” The most modern version of this system shows all eukaryotes – animals, plants, fungi, and protists – constituting the domain of “Eukaryota,” while the more common and modern branching of bacteria constitutes “Prokarya,” and archaebacteria constitute their own domain altogether – the domain of “Archaea.

Another remarkable trait of archaebacteria is their ability to survive in extreme environments, including very salty, very acidic, and very hot surroundings. Archaebacteria have been recorded surviving temperatures as high as 190° Fahrenheit, which is only twenty-two degrees shy of the boiling point of water, and acidities as high as 0.9 pH.

Archaebacteria have even challenged scientist’s ideas about how to define a species, since they practice a lot of horizontal gene transfer – where genes are transferred from one individual to another during their lifetimes – making it difficult to determine how closely different cells are related, or even if archaebacteria cells have the sort of stable combinations of traits that scientists typically use to define a species.

The domain of Archaea include both aerobic and anaerobic species, and can be found living in common environments such as soil as well as in extreme environments.

So what biochemical characteristics make scientists so excited about archaebacteria? Well…

Archaebacteria Characteristics

Archaebacteria have a number of characteristics not seen in more “modern” cell types. These include:

1. Unique cell membrane chemistry.

Archaebacteria have cell membranes made of ether-linked phospholipids, while bacteria and eukaryotes both make their cell membranes out of ester-linked phospholipids

Archaebacteria use a sugar that is similar to, but not not the same as, the peptidoglycan sugar used in bacteria cell membranes.

2. Unique gene transcription.

Archaebacteria have a single, round chromosome like bacteria, but their gene transcription is similar to that which occurs in the nuclei of eukaryotic cells.

This leads to the strange situation that most genes involving most life functions, such as production of the cell membrane, are more closely shared by Eukarya and Bacteria – but genes involved in the process of gene transcription are most closely shared by Eukarya and Archaea.

This has led some scientists to propose that eukaryotic cells arose from a fusion of archaebacteria with bacteria, possibly when an archaebacteria began living endosymbiotically inside a bacterial cell.

Other scientists believe that eukaryotes descended directly from archaebacteria, based on the findings of archaebacteria species, Lokiarcheota, which contains some found only in eukaryotes, which in eukaryotes code for genes with uniquely eukaryotic abilities.

It is thought that Lokiarcheota may be a transitional form between Archaea and Eukaryota.

3. Only archaebacteria are capable of methanogenesis – a form of anaerobic respiration that produces methane.

Archaebacteria who use other forms of cellular respiration also exist, but methane-producing cells are not found in Bacteria or Eukarya.

4. Differences in ribosomal RNA that suggest they diverged from both Bacteria and Eukarya at a point in the distant past

Types of Archaebacteria

There are three main types of archaebacteria. These are classified based on their phylogenetic relationship (how closely related they are to each other), and members of each type tend to have certain characteristics. The major types are:

1. Crenarchaeota – Crenarchaeota are extremely heat-tolerant.

They have special proteins and other biochemistry that can continue to function at temperatures as high as 230° Fahrenheit! Many Chrenarchaeota can also survive in very acidic environments.

Many species of Crenarchaeota have been discovered living in hot springs and around deep sea vents, where water has been superheated by magma beneath the Earth’s surface.

One theory of the origin of life suggests that life may have originally started around deep sea vents, where high temperatures and unusual chemistries could have led to the formation of the first cells.

2. Euryarchaeota are able to survive in very salty habitats. They are also able to produce methane, which no other life form on Earth is able to do!

Euryarchaeota are the only form of life known to be able to perform cellular respiration using carbon as their electron acceptor.

This gives them an important ecological niche because the breakdown of complex carbon compounds into the simple molecule of methane is the final step in the decomposition of most life forms. Without methanogens, the Earth’s carbon cycle would be impaired.

Wherever methane gas is produced by life, Euryarchaeota are responsible.

Methanogen archaebacteria can be found in marshes and wetlands, where they are responsible for “swamp gas” and part of the marsh’s distinctive smell, and in the stomachs of ruminants such as cows, where they break down sugars found in grass that are undigestible to eukaryotes by themselves. Some methanogens live in the human gut and assist us in the same way.

They can also be found in deep sea sediments, where they produce pockets of methane beneath the ocean floor.

3. Korarchaeota are the least-understood, and thought to be the oldest lineage of archaebacteria. This makes them possibly the oldest surviving organisms on Earth! Korarchaeota can be found in hydrothermal environments much like Crenarchaeota. However, Korarchaeota have many genes found in both Crenarchaeota and Euryarcheaota, and also genes which are different from both groups. To scientists, this suggests that both other types of archaebacteria may have descended from a common ancestor similar to Korarchaeota. Korarchaeota are rare in nature, perhaps because other, newer forms of life are better adapted to survive in modern environments than they are. Still, Korearchaeota can be found in hot springs, around deep sea vents.

Archaea, Bacteria, and Eukarya

All living things can be classified into a place on the Tree of Life. This phylogenetic tree has three major branches, called Archaea, Bacteria, and Eukarya.

Three Major Domains of Life

A phylogenetic tree traces the evolutionary history of organisms, and indicates common ancestors. We already see a major difference between archaea and bacteria from this classification: they have a different evolutionary history as they occupy very different places on the Tree of Life.

How was this Tree of Life composed? The sequence of 16s ribosomal ribonucleic acid (16s rRNA), a fundamental unit of ribosomes, was compared across organisms. This showed that the underlying genetic code for a component of ribosomes differed greatly between archaea, bacteria, and eukarya. Thus, they form three distinct branches of the Tree of Life.

There was a time when archaea weren't understood to be different from bacteria and, in fact, were erroneously named archaebacteria (and the Tree of Life was drawn wrong!). But they are definitely not bacteria, even though archaea and bacteria share some similarities. Archaea deserve their own branch on the Tree of Life.

Similarities Between Them

Archaea and bacteria are both prokaryotes, meaning they do not have a nucleus and lack membrane-bound organelles. They are tiny, single-cell organisms which cannot be seen by the naked human eye called microbes. When we look at them through a microscope, we find that archaea and bacteria resemble each other in shape and size. They exist as rods, cones, plates, and coils. Both archaea and bacteria have flagella, thread-like structures that allow organisms to move by propelling them through their environment.

Differences Between Them

An archaea might be very insulted if you mistook it for a bacteria, however, and vice-versa. The differences between archaea and bacteria are profound. As mentioned, the genetic code of rRNA differs enough to place them in quite different branches of the Tree of Life, reflecting differing evolutionary paths. (This still needs to be confirmed by sequencing the 16s rRNA of more organisms.)

Remember how both move via flagella? Despite this functional similarity, and structural similarity (i.e. they look similar), they have very different genes encoding them and are comprised of different proteins. Genome sequencing of archaea also reveals genes that resemble eukaryotes more than bacteria. This is a big difference between archaea and bacteria.

Another distinction between these two prokaryotes is the composition of the cell wall. For example, all bacteria contain peptidoglycans (a molecule composed of both protein and sugar rings) in their cell walls. However, archaea do not have this compound in their cell walls.