Archean Eon

ntroduction The Archean Eon is the age of the bacteria and it starts with anaerobic forms and finishes with the aerobic forms including cyanobacteria that collectively transform the planet to the oxygen rich aerobic environment we know today. Dont let the simplicity of these little organisms fool you, they are tremendously diverse and very successful, after all they have been on the planet for 3.8 billion years, doing pretty much the same thing over that time, a notable exception being the switch from an anaerobic existence to aerobic at the end of the Archean eon. In a time when morphology was used to organize the living work it was thought that all prokaryotes were the same. But gene sequence studies of the 16S ribosomal subunit shook up the tree of life and the result was prokaryotes were divided in two: The Archea and Bacteria, or Eubacteria as they are sometimes referred to. By the time the proposal of three domains, the third is the Eukaryota, gained acceptance in the 1980s it had also become clear that the Archea and Bacteria Domains included some of the most interesting and complex organisms because of the diversity in their metabolism and horizontal gene transfer, basically gene swapping.

Eubacteria Classification No one knew there were single celled organisms as small as bacteria until the optics of the early microscopes improved. Once bacteria were discovered the first strategy for grouping and classifying these new organisms was to use their appearance their morphology. It was the same method that had been successfully used for animals and plants and initially it worked with the bacteria. In the early stages of bacteriology designations of rod shaped bacilli, rounded cocoid bacteria and mobile spirochetes were enough for grouping and classification. But as more bacteria were identified it became clear there were more types than different morphologies making additional naming criteria necessary. One of these new criteria was the pathogenicity of the bacteria, another relied on the metabolic abilities that were being discovered: methanogens for methane producing forms, sulphur bacteria that were found in sulphur rich hot springs and nitrogen fixing species. As time went by, and more forms were identified by genomic structures and sequences, it became clear that this was an immensely diverse group. Simple genus and species names were not enough and numeric and other abbreviations were added to the names of different, but closely related bacteria, to describe surface proteins and genome structure. As a result, the different variants of the bacterium Escherichia coli

Escherichia coli is a rod shaped bacterium and a normal part of the digestive microflora. There are some types that can cause food poisoning and in some cases death. In 2000, strain O157:H7 got into the water supply of Walkerton Ontaria and resulted in the death of 7 people and about 2500 more who became ill. U.S. National Institure of health, Wikimedia Commons

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include the enterohemoragic E. coli O157:H7, the lab strain of the bacterium E. coli BL21(DE3) and E. coli O104:H4 that caused an outbreak of gastrointestinal illness from contaminated vegetables in Germany in the summer of 2011. The outer limits Bacterial Cell Walls Many of the advances in early microscopy resulted from staining techniques that made it easier to see intracellular structures. Stains that differentiated between proteins, carbohydrate and nucleic acids revealed the organelles and nuclear materials inside cells. Of course, there are no organelles inside a bacterium and staining techniques used with eukaryote cells were not as effective in understanding the internal organization of bacterial cells. But, one staining technique differentiated between two bacterial types: the Gram-negative and Gram positive forms and their different types of cell walls. Gram stained mix of GramIn organisms with a positive cocci (Staphylococcus cell wall, the wall aureus, purple) and Gram-negative consists of simple bacilli (Escherichia coli, red). monomers strung Wikimedia Commons together to form fibres that give the cell wall its strength and rigidity. In plants glucose molecules are strung together to form cellulose; N-acetylglucosamine monomers form the chitin of the fungal cell wall; in bacteria peptidoglycan has the same role. Like its fungal and plant counterparts, peptidoglycan is also composed of a series of repeating units. Unlike them, it does not involve linear repetition of a single monomer. Peptidoglycan is composed of two different sugars that form a dimer and these dimers are then strung together. Structure of peptidoglycan in the Every second sugar, or only one sugar of the dimer, has a bacterial cell wall. NAG: Nfour amino peptide attached to it. This small peptide acetylglucosoamine and NAM: Nchain is the key for allowing two different peptidoglycan acetylmuramic acid. fibres to interact; an enzyme will form covalent linkages Wikimedia Commons between the two terminal amino acids of the small peptide chains belonging to two different peptidoglycan molecules, which repeated multiple times, is the basis for the peptidoglycan layers strength and rigidity. Peptidogylcan is common to both Gram-positive and Gram-negative bacteria but its availability for staining differs. In the Gram-positive bacteria the peptidoglycan layer is thick, and on outermost surface of the bacterium and is stained; and designated Gram-positive. In the Gram-negative bacteria the peptidoglycan layer is a thinner layer sandwiched between an inner and outer plasma membrane; yes Gram-negative bacteria have two plasma membranes, with the periplasm between. The additional outer

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plasma membrane prevents the staining of the peptidoglycan layer; the reason for their designation Gram-negative. But there are additional consequences of the outer membrane other than preventing the Gram-stain. Gram-negative bacteria are often pathogenic and the outer lipid layer contains the endotoxins (complex lipopolysaccharides) that make the bacteria toxic. In addition, the outer lipid layer prevents penicillin from damaging the peptidoglycan layer of Gram-negative bacteria, unlike to Grampositive bacteria, where the thick layer of peptidoglycan is exposed and can be easily damaged. Flagellum Not all bacteria are motile, but those capable of movement have the same molecular motor driving the flagellum consisting of three parts: the flagellum, hook and basal structure or motor. The polymerization of thousands of copies of just one protein forms the flagellum connected to the basal structure or motor using the hook which is a coupling between the flagellum and the motor. The motor includes a series of proteins that, because of their amino acid compositions, span the plasma membrane to form rings. The number of rings depends on the whether the bacterium is Gram-positive or Gram-negative with a pair of rings associated with each membrane. Without getting Detailed view of the bacterial flagellar bogged down in the biochemistry, the bacterial motor is motor in a Gram-positive bacterium. The driven by a proton gradient. Hydrolysis of ATP moves a L, and MS-Rings anchor the motor in the proton across the inner membrane and as they accumulate cell membrane, the P ring the cell wall, a proton gradient from outside to the inside the bacterial The motor consists of the secretory begins to build. Proton gradients are a form of stored system pumping protons in the energy and one you may have already encountered is the periplasmic space that fall back thorough electron transport chain of the mitochondria where the stator proteins of the motor. protons accumulate between the inner and outer Mariana Ruiz Villarrael membrane before falling through the hollow core of the (LadyofHats)Wikimedia Commons ATP synthase. The bacterial motor works the much the same way and the only way for the proton to move down the gradient is to pass through the opening in the motor proteins. As they pass through the motor protein, the energy is used to create a conformational change in the motor proteins that moves the central rotor attached to the hook that spins inside the rings embedded in the plasma membrane. Additionally, switch proteins can change whether the motor is spinning clockwise or counter clockwise and the whole complex is made of only 20 proteins! Odds 'n Ends The outer surface of all bacteria is always covered by some form of mucilaginous outer capsule that forms a glycocalyx over the surface of the bacterial cell. The capsule has a number of potential functions including sticking bacterial cells together to form biofilms and as a defense against bacteriophages and phagocytosis by protists or the immune system of other organisms. The outer surface of many bacteria

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may also include small hair like projections called pilli that are important in conjugation, a form of reproduction that will be discussed later. The inner space Like all prokaryotes the cytoplasm in bacteria lacks an endomembrane system or organelles. The bacterial cytoplasm is rich in 70S ribosomes consisting of 50S and 30S subunits and a genome, which is located in a specialized region of cytoplasm referred to as the nucleoid. There are no chromosomes in bacteria and instead the genome consists of a one circular piece of double stranded DNA, or in a few cases a linear piece, that loops, folds and supercoils on itself to form a compact structure suspended in the cytoplasm. How compact? The genome of E. coli is 1.5 mm long when it is unfolded, and 1m in length when folded! The other consequence of this organization is that bacterial cells are haploid: there is no complementary second circular loop of DNA! In eukaryotes, histone proteins protect the folded DNA strand but in the bacteria, the folding pattern of the genome confers the stability. An additional piece of circular DNA, a plasmid, may also be present in the cytoplasm and they duplicate themselves independent of the bacterial cell. Plasmids are important in initiating conjugation by producing pilli and play a role in horizontal gene transfer during transformation. Plasmids have also been implicated in antibiotic resistance and toxin production. Plasmids are the work horse of many techniques in molecular biology where genes or DNA fragments are inserted into the plasmid vector that is used to make copies of the inserted DNA for subsequent analysis. Reproductive Diversity Binary fission As mentioned previously, bacterial cells are always haploid and there is no second copy of the genes like in diploid, eukaryotes with paired homologous chromosomes. In terms of variability any mutations or changes in the DNA sequence of the genome that occur are going to be expressed because there is no second copy of the gene or DNA sequence as in the chromosomes of diploid organisms. The simplest form of reproduction is binary fission and when the bacterial genome is duplicated, each copy links itself to the cell wall and as the cell divides a copy of the genome ends up in each of the daughter cells. Bacteria may also contain a second piece of DNA, the plasmid and when plasmids are in the cytoplasm they replicate independent of the division cycle of the bacterial cell. When the bacterial cell divides the plasmids and other cytoplasmic inclusions, including ribosomes, are partitioned randomly between the two daughter cells. The plasmid may also be incorporated in the genome of the bacterium; if this is the case the plasmid DNA is replicated at the same time as the bacterial genome.

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Conjugation Plasmids are also capable of transferring themselves between bacteria. The presence of a fertility gene on the plasmid produces pilli on the surface of the cell wall. They are referred to as F-positive if they have the fertility factor and F-negative if they do not. If a bacterium with pilli encounters one without, the two become connected and a single stranded copy of the plasmid DNA is transferred from the F-positive bacterium to the other F-negative bacterial cell. The complementary strand is produced and the bacterial cell now contains a plasmid that may include genes for antibiotic resistance or unique metabolic pathways. As mentioned, the plasmid can also incorporate itself into the genome of the During bacterial conjugation the bacterium and remain there for many generations before donor cell builds the pilus (1) that snipping itself out and once again becoming a separate attached to and pulls in the other plasmid in the cytoplasm of the bacterial cell. When this snip bacterium (2). Contrary to what is often occurs it is not uncommon for the original piece of plasmid said, the exchanged strand of DNA DNA and an adjacent part of the bacterial genome to be doesn't pass down the pilus (3). removed as well. This results in a new plasmid with all the Mike Jones, Wikimedia Commons original plasmid gene sequences plus some from the host bacterial cell. When this modified plasmid starts to replicate it produces pilli on the surface of its host and when conjugation occurs it passes all of the DNA contained in the plasmid to the other cell and the recipient cell receives both plasmid and bacterial DNA; a form of horizontal gene transfer. Transduction Bacteria often fall prey to bacteriophages, a virus that takes over the bacterial cell and kills them during the lytic phase of the viral life cycle. As is the case with all viral life cycles the virus takes over the host cells replication, transcription and translation machinery and uses it to replicate its genome and produce the proteins of the viral case that are encoded in the viral genome. Well learn more about these life cycles in the section on viruses. The final stage in the life cycle is to assemble the virus by encapsulating a copy of the viral genome that is floating in the bacterial cytoplasm in the viral case. Normally the DNA of the bacteria disappears during viral infections but occasionally a piece may remain intact and when the assembly step for the new viral particles is initiated, it may be encapsulated instead of the viral copy of the genome. This results in a bacteriophage containing a piece of bacterial DNA, not viral DNA. This bacteriophage is capable of injecting its genetic load into another bacterium but the consequence is the bacterium has a piece of bacterial genome that it may then incorporate it its genome. This is another form of horizontal gene transfer. Transformation Even more unusual is transformation; another form of horizontal gene transfer. In transformation, a bacterium can absorb a DNA strand from the external environment and splice it into their own genome! Sometimes it works and a new gene sequence is inserted and becomes active and sometimes it doesnt and the DNA is degraded and salvaged for its nucleotide building blocks. It is just another example of the

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gene swapping that occurs in bacteria; a key strategy in creating genetic variations in these small little organisms. Metabolic diversity In addition to their reproductive diversity bacteria, and this includes the Archea, are well known for their metabolic diversity. Metabolism, in its simplest sense, is the ability to harness energy and use it to build. Because we are talking about building living things, carbon is the basic building block and energy is in the form of high energy electrons. By themselves these high energy electrons dont do much but when they are combined in a redox pair where the electron is passed between two compounds there is the possibility to harness the energy. In a redox pair the recipient of the electron is reduced, with a reduced positive charge, and the donor is oxidized. The classic example of this is the mitochondrial electron transport chain where the energy of a series of redox reactions is used to pump protons in the space between the inner and outer mitochondrial membranes. So, metabolism is all about passing electrons and building with carbon. Carbon exists in two forms, either organic or inorganic. Organic carbon is incorporated into carboncarbon bonds and although there are various forms of pure inorganic carbon, graphite and diamonds for example, one of the most abundant and is the oxidized version of carbon - atmospheric carbon dioxide. These are the only two forms that carbon can have, but they are linked to each other and, with the exception of the small organic compounds we saw in the prebiotic soup, most complex carbon-carbon bonds are built by living organisms. If a metabolic process is capable of building organic carbon by using atmospheric carbon dioxide we refer to it as autotrophic and the complex carbon that is characteristic of living systems comes from the gaseous form of the element. The opposite of an autotroph is a heterotroph and these organisms build using carbon that already exists as part of an organic carboncarbon bond. The link between the two is autotrophs supply the organic carbon that heterotrophs build with. So based on the source of the carbon building blocks we can divide the varied metabolism into two groups; autotrophs and heterotrophs. We can divide metabolism based on its energy requirements. Your first thoughts about energy supplies may be ATP or others like GTP, NADH+ etc. But, each of these cellular energy sources has one thing in common. They are products of redox pairs that involved a transfer of high energy electrons. The question then becomes how do we energize this electron so that we can trap that energy later? Photons are the basic unit of electromagnetic radiation, including light, and photonic energy can be harnessed to create high energy electrons. In solar energy cells the energy of the photon knocks electrons off silicon and the flow of electrons results in electricity. Plants do the same thing and the photonic energy knocks electrons into a higher energy state and as they are transferred through redox pairs the energy is transferred into the chemical bonds of glucose. All organisms that use lights energy to build carboncarbon bonds use the prefix photo-, and are called phototrophs. Carbon bonds can be a source for energized electrons when these high energy bonds are broken down in a gradual, controlled and step wise manner so that all the energy is not released at once. (Be careful though, we are only discussing a source of potential energy that exists in the organic carbon and the energy released when the bonds are broken - not what happens to carbon.) We refer to metabolisms that use high energy organic bonds with the prefix Chemoorgano- and chemoorganotrophs use covalent bonds in organic chemicals as their energy source. There is a third ways to generate high energy electrons. Many elements and compounds found in the inorganic world have oxidized or reduced states. A classic example is iron, which is oxidized

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to iron oxide, and other examples include ammonia, sulphur gases and even nitrogen which can move between their oxidized and reduced states. If a redox pair exists there is the potential to trap the high energy electron and use it. This is what our third metabolic type does. Because many of these inorganic redox pairs are a part of the earths crust, the lithosphere, we prefix this form of metabolism with lithoand organisms with this type of metabolism are referred to as lithotrophs. So, there are two ways to obtain carbon and three ways to get the energy to build and we have a 3x2 matrix with six possibilities and for each there is a term that describes that type of metabolism. Source of high energy electrons Carbon source Carbon dioxide Organic carbon Light Phototroph Photoheterotroph Organic Carbon Chemoorganotroph Minerals Chemolithotroph

Chemoorganoheterotroph Chemolithoheterotroph

What this seemingly simple table shows is that bacteria can get their energy from anything and the carbon in any form. In their two billion years of evolution they have figured out every possible way to live. But one of these combinations will change the earth. This is the use of light and the splitting of water molecules to create the carbon-carbon bonds of glucose and produce oxygen as a metabolic waste. At first the oxygen was dissolved in the water, and forced the anaerobic prokaryotes to take refuge in the deep oceans where the toxic oxygen didnt accumulate. Oxygen started to appear in the atmosphere and it oxidized the minerals of the earth - the earth began to rust. The appearance of oxidized minerals in the earths rocks identifies the end of the Achaean eon and the start of the Proterozoic. But theres more then rusting rocks. Oxygen started to accumulate in the atmosphere where it reacted to from ozone. Ozone filtered out the ultraviolet light that caused damaging mutations in organisms that lived to close the surface of the ancient oceans. Until that happened it was hard to be a phototroph living in the narrow boundary where light penetrated the oceans waters, but not the damaging UV. Those small little bacteria produced the ozone layer we have today and all the initial oxygen that set the stage for the first unicellular eukaryotes the Kingdom Protista. In addition to surviving on their own, these bacterial cells will ultimately become the plastids of the photosynthetic eukaryotes. Light is one of the best sources of high energy electrons and the chemical bonds in glucose store some of the largest amounts of potential energy. The higher energy covalent carbon bonds produced using light are an excellent food for bacteria that can break the bonds. To be able to harness that much energy will require a series of electron transfer steps that will end up producing ATP. There are bacteria that still do this and at some point in the evolution of the eukaryotes a bacterium capable of oxidative phosphorylation will appear in the cytoplasm of these new cell types more on that, and plastids, when we look at the Proterozoic. Archea The Archaea is a group of bacteria that thrive best under extreme conditions such as, high salt, and extreme temperatures. Theyre found in some of the weirdest places: hot water springs, the deep thermal ocean vents, and guts of cows and termites to name a few. They fall into a number of broad

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categories: methanogens (methane producers), extreme halophiles (salt loving), and extreme thermophiles (loving extreme temperatures either hot or cold). One of the more unusual features of the whole group is the unique lipid composition of the plasma membrane and these changes are no doubt the result of the extreme conditions under which these prokaryotes live. The methanogens all live in anaerobic conditions and even a trace of oxygen is toxic to them. Bog fairies, cow flatulence, and swamp gas are all examples of methanogens at work. In their oxygen free environment they carry on lifes processes of combining hydrogen and carbon dioxide to build organic molecules in a unique process resulting in methane as a by-product. It may seem like a trivial thing but these minute little prokaryotes were so abundant in the Archaean world that trapped in the pockets of water in the Earths crust they happily carried on living and filling the spaces with their waste product of methane. In the deep oceans, water pressure has solidified the methane as methane gas hydrates. A less ancient example of their importance is their importance in landfill and garbage disposal. Landfill sites were plagued with the presence of the explosive gases methane that built up under the layers of rotting garbage. This was an anaerobic environment and the methanogens were hard at work recycling organic material! Originally a problem these landfill sites are being mined for their accumulated methane now tapped as fuel. Halophiles love salt and as you might guess youll find them living in some of the saltiest places on earth, the Dead Sea, the Great Salt Lake and the salt flats where ocean water is evaporated to crystalline sea salt. Extreme thermophiles, as their name implies, adore heat or extreme cold. The hotter or colder, the better, if its anything in between theyll stop growing. Some are aerobic and others are anaerobic but most make use of sulphur in their main energy pathways and as a consequence theyre usually found in sulphur rich water. This includes geysers, hot springs and of course those deep thermal vents at the bottom of the oceans. At the opposite extreme there are others that can withstand extremely low temperatures. Changing earth highlights Archean period (3800 - 2500 Ma)

3700 Ma - Photosynthesizing bacteria 3500 Ma - Oldest fossils 3400 Ma - Small continents form 3100 Ma - Continents begin shifting 2700 Ma - First eukaryotes 2600 Ma - Bacteria on land 2500 Ma - Banded iron formations