Domain Archaea is a Domain in Carl Woese 's three domain classification of living organisms. The domain contains Prokaryotic microorganisms which are ...
ARCHAEA Morphology, Physiology, biochemistry, diversity & Industrial Applications of domain Archaea
B.G. Eranga Thilina Jayashantha B.Sc.(UG) Microbiology (Sp), University of Kelaniya, Sri Lanka
Special Degree, Assignment 1
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Contents
1.) 2.) 3.) 4.) 5.) 6.) 7.) 8.) 9.) 10.) 11.) 12.) 13.) 14.)
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Introduction to Domain Archaea……………………………….02 Fossil records on Archaea………………………………………04 Archaeal Systematics…………………………………………….05 Morphological significances of Archaea……………………...08 Molecular biological significances of Archaea………………15 Viruses of Archaea……………………………………………….17 Significances of Gene Transfer in Archaea…………………...18 Introduction to the Diversity of Archaea………………………20 Euryarchaeota…………………………………………………….24 Thaumarchaeota………………………………………………….32 Nanoarchaeota…………………………………………..32 Korarchaeota……………………………………………………...33 Crenarchaeota…………………………………………………….33 Industrial Applications of Archaea……………………………..35
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1) Introduction to Domain Archaea Domain Archaea is a Domain in Carl Woese ‘s three domain classification of living organisms. The domain contains Prokaryotic microorganisms which are adapted for extreme environments. They show vigorous and stable resistance for extreme and catastrophic environments on Earth. They are most primitive type of organisms on Earth. According to microbiologists, their formation was happened nearly 3.5 billion years ago in early young earth with extreme environments (highly energetic atmosphere, UV, extremely high heat, shock waves due to earthquakes). They have been being evolved for 3.5 billion years. Therefore they are the oldest members in phylogeny. That is why they have adapted for extreme conditions.These organisms are living in both aquatic and terrestrial extreme environments. Majority of aquatic organisms are marine. They are found in hydrothermal vents in basins of oceans, Hot water springs and highly saline environments. Some terrestrial organisms are found in volcanos. These examples show the resistance and adaptations of these organisms to achieve those extreme conditions. There morphological characters are same as other bacteria but some Archaea show exclusively different characteristics than other bacteria. But their Molecular biological, Physiological and Biochemical characteristics are entirely different than other prokaryotes. These different Molecular biological, physiological and Biochemical characteristics serve them resistance for extreme environments. All Archaea can be divided in to three classical groups. They are,
Methanogens Hyper Thermophiles Extreme Halophiles
The scientific community was understandably shocked in the late 1970s by the discovery of an entirely new group of organisms the Archaea. Dr. Carl Woese and his colleagues at the University of Illinois were studying relationships among the prokaryotes using DNA sequences, and found that there were two distinctly different groups. Those "bacteria" that lived at high temperatures or produced methane clustered together as a group well away from the usual bacteria and the eukaryotes. Because of this vast difference in genetic makeup, Woese proposed that life be divided into three domains: Eukaryota, Eubacteria, and Archaebacteria. He later decided that the term Archaebacteria was a misnomer, and shortened it to Archaea. The three domains are shown in the illustration bellow, which illustrates also that each group is very different from the others.
Fig 1: Three Domain Classification system 2|Page
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Fig 2: The hot springs of Yellowstone National Park, USA, were among the first places Archaea were discovered.
Archaea include inhabitants of some of the most extreme environments on Earth. Some live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot springs (such as the ones pictured above), or in extremely alkaline or acid waters. They have been found thriving inside the digestive tracts of cows, termites, and marine life where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean, and even thrive in petroleum deposits deep underground. Some Archaea can survive the desiccating effects of extremely saline waters. However, archaea are not restricted to extreme environments; new research is showing that some archaea are also quite abundant in the plankton of the open sea. One salt-loving group of archaea includes Halobacterium, a well-studied archaea. The light-sensitive pigment bacteriorhodopsin gives Halobacterium its natural specific color and provides it with chemical energy. Bacteriorhodopsin has a lovely purple color and it pumps protons to the outside of the membrane. When these protons flow back, they are used in the synthesis of ATP, which is the energy source of the cell. This protein is chemically very similar to the light-detecting pigment rhodopsin, found in the vertebrate retina. Fig 3 : Clones of Halobacterium salinarum on an agar plate . These contain the information for the production of the modified bacteriorhodopsins.
Fig 4 : Chemiosmotic coupling between the sun energy, Bacteriorhodopsin and phosphorylation by ATP synthase(chemical energy) during metabolism in Halobacterium salinarum.
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2) Fossil records of Archaea Archaea and Bacteria cells may be of similar sizes and shapes, so the shape of a microbial fossil does not usually help in determining its origin. Instead of physical features, micro-paleontologists rely on chemical features. Chemical traces of ancient organisms are called molecular fossils, and include a wide variety of chemical substances. Ideally, a molecular fossil should be A chemical compound that is found in just one group of organisms, It is not prone to chemical decay Decays into predictable and recognizable secondary chemicals. In the case of the Archaea, there is a very good candidate to preserve as a molecular fossil from the cell membrane. Archeal membranes do not contain the same nature of phospholipids that other organisms have; instead, their membranes are formed from Isoprene chains. Because these particular isoprene structures are unique to Archaea, In most Archaea they present as Tetra-ether Monolayer. That is why they are not as prone to decomposition at high temperatures, they make good markers for the presence of ancient Archaea. So they act as Molecular Fossils during the archeological investigations of primitive Archaea in order to reveal the mysterious history of Domain Archaea in the Earth. Molecular fossils of Archaea in the form of isoprenoid residues were first reported from the Messel oil shale of Germany .These are Miocene deposits whose geologic history is well known. Material from the shale was dissolved and analyzed using a combination of chromatography and mass spectrometry. These processes work by separating compounds by weight and other properties, and produce a "chemical fingerprint". The fingerprint of the Messel shale included isoprene compounds identical to those found in some Archaea. Based on the geologic history of the Messel area, thermophiles and halophiles are not likely to have ever lived there, so the most likely culprits to have left these chemical fingerprints behind are archaeal Methanogens. Since their discovery in the Messel shales, isoprene compounds indicative of ancient Archaea have been found in numerous other localities (Hahn & Haug, 1986), including Mesozoic, Paleozoic, and Precambrian sediments. Their chemical traces have even been found in sediments from the Isua district of west Greenland, the oldest known sediments on Earth at about 3.8 billion years old
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Fig 5 : (a) Gas Chromatographic , (b) Mass spectrometric analysis of samples collected from Messel oil shale of Germany to reveal Archaeal molecular fossils.
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3) Archaeal Systematics The Archaea constitute one of the three domains into which all known life may be divided. There are two other domains of life. One of these is the Eukaryota, which includes the plants, animals, fungi, and Protists. Except for the Protists, these organisms have been known and studied since the time of Aristotle, and are the organisms with which you are most likely familiar. The second domain to be discovered was the Bacteria, first observed in the 17th century under the microscope by people such as the Dutch naturalist Antony van Leeuwenhoek. Early classifications depended on the shape, colony morphology in laboratory cultures, and other physical characteristics. When biochemistry blossomed as a modern science, chemical characteristics were also used to classify bacterial species, but even this information was not enough to reliably identify and classify the tiny microbes. Reliable and repeatable classification of bacteria was not possible until the late 20th century when molecular biology made it possible to sequence their DNA. Molecules of DNA are found in the cells of all living things, and store the information cells need to build proteins and other cell components. One of the most important components of cells are ribosomes, a large and complex molecule that converts the DNA message into a chemical product (Protein). Most of the chemical composition of a ribosome is ribosomal RNA, which has its own sequence of building blocks. With sequencing techniques, a molecular biologist can take apart the building block of RNA one by one and identify each one. The result is the sequence of those building blocks. Because ribosomes are so critically important is the functioning of living things, they are not prone to rapid evolution. A major change in ribosome sequence can render the ribosome unable to fulfill its duties of building new proteins for the cell. Because of this, we say that the sequence in the ribosomes is conserved, that it does not change much over time. This slow rate of molecular evolution made the ribosome sequence a good choice for unlocking the secrets of bacterial evolution. By comparing the slight differences in ribosome sequence among a wide diversity of bacteria, groups of similar sequences could be found and recognized as a related group. In the 1970s, Carl Woese and his colleagues at the University of Illinois at Urbana-Champaign began investigating the sequences of bacteria with the goal of developing a better picture of bacterial relationships. Their findings were published in 1977, and included a big surprise. Not all tiny microbes were closely related. In addition to the bacteria and eukaryote groups in the analysis, there was a third group of methane-producing microbes. These methanogens were already known to be chemical oddities in the microbial world, since they were killed by oxygen, produced unusual enzymes, and had cell walls different from all known bacteria. Carl Woese’s Research Papers (1977) which included the first findings of Archaea ; An ancient divergence among the bacteria. Balch WE, Magrum LJ, Fox GE, Wolfe RS, Woese CR.J Mol Evol. 1977 Aug 5;9(4):305-11. Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Fox GE, Magrum LJ, Balch WE, Wolfe RS, Woese CR. Proc Natl Acad Sci U S A. 1977 Oct;74(10):4537-4541. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Woese CR, Fox GE. Proc Natl Acad Sci U S A. 1977 Nov;74(11):5088-90.
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The significance of Woese's work was that he showed these bizarre microbes were different at the most fundamental level of their biology. Their RNA sequences were no more like those of the bacteria than like fish or flowers. To recognize this enormous difference, he named the group "Archaebacteria" to distinguish them from the "Eubacteria" (true bacteria). As the true level of separation between these organisms became clear, Woese shortened his original name to Archaea to avoid anyone from thinking that archaea were simply a bacterial group.
Fig 6 : Phylogenic relationships of Domain Archaea according to their molecular biological characteristics ( r-RNA & DNA Sequencing )
Fig 7 : Evolutionary relationships of Archaea with other two domains 6|Page
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Archaea have increasingly become the study of scientific investigation. In many ways, archaeal cells resemble the cells of bacteria, but in a number of important respects, they are more like the cells of eukaryotes. The question arises whether the Archaea are closer relatives of the Bacteria or the Eukarya. One novel approach used in addressing the question is to look at sequences of Duplicated genes in cells. Some DNA sequences occur in more than one copy within each cell, presumably because an extra copy was made at some point in the past, during the evolutionary timeline There are a very few genes known to exist in duplicate copies in all living cells, suggesting that the duplication happened before the separation of the three domains of life. In comparing the two sets of sequences of Duplicated genes, scientists have found that the Archaea may actually be more closely related to Eukaryotes than to the Bacteria.
Fig 8 : The technology behind ribosomal RNA gene phylogenies. 1. DNA is extracted from cells. 2. Copies of the gene encoding rRNA are made by the polymerase chain reaction (PCR). 3, 4. The gene is sequenced and the sequence aligned with sequences from other organisms. A computer algorithm makes pairwise comparisons at each base and generates a phylogenetic tree, 5, that depicts evolutionary relationships.
Fig 9 : Archaea is more closely related with Eukarya than Bacteis
Fig 10 : The three domains of cellular organisms are Bacteria, Archaea, and Eukarya. Archaea and Eukarya diverged long before nucleated cells with organelles (“modern eukaryotes” in part a) appear in the fossil record. LUCA, last universal common ancestor.
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4) Morphological significances of Archaea Even under a high-power light microscope, the largest archaea look like tiny dots. Fortunately, the electron microscope can magnify even these tiny microbes enough to distinguish their physical features. You can see archaea images below, made using a variety of micrographic techniques. Archaeal shapes are quite diverse. Some are spherical, a form known as coccus, and these may be perfectly round or lobed and lumpy. Some are rod-shaped, a form known as bacillus, and range from short bar-shaped rods to long slender hair-like forms. Some oddball species have been discovered with a triangular shape, or even a square shape.
Halococcus salifodinae
Sulfolobus
Methanococcoides burtonii
Methanosarcina rumen
Staphylothermus marinus
Fig 11 : Morphological Diversity of different Archaeal types
Although cell morphology is easily determined, it is a poor predictor of other properties of a cell. For example, under the microscope many rod-shaped Archaea look identical to rod-shaped Bacteria, yet we know they are of different phylogenetic domains With very rare exceptions, it is impossible to predict the physiology, ecology, phylogeny, pathogenic potential, or virtually any other property of a prokaryotic cell by simply knowing its morphology. Individual archaea range from 0.1 micrometers (μm) to over 15 μm in diameter, and occur in various shapes, commonly as spheres, rods, spirals or plates. Other morphologies in the Crenarchaeota include irregularly shaped lobed cells in Sulfolobus, Needle-like filaments that are less than half a micrometer in diameter in Thermofilum Perfectly rectangular rods in Thermoproteus and Pyrobaculum. Haloquadratum walsbyi are flat, Square shaped archaea that live in hypersaline pools. In Thermoplasma and Ferroplasma the lack of a cell wall means that the cells have irregular shapes, Some species form aggregates or filaments of cells up to 200 μm long.These organisms 8|Page
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can be prominent in biofilms. Notably, aggregates of Thermococcus coalescens cells fuse together in culture, forming single giant cells. Archaea in the genus Pyrodictium produce an elaborate multicellular colony involving arrays of long, thin hollow tubes called cannulae that stick out from the cells' surfaces and connect them into a dense bush-like agglomeration. The function of these cannulae is not settled, but they may allow communication or nutrient exchange with neighbors.Multi-species colonies exist, such as the "string-of-pearls" community that was discovered in 2001 in a German swamp. Round whitish colonies of a novel Euryarchaeota species are spaced along thin filaments that can range up to 15 cm long, these filaments are made of a particular bacteria species.
Specific Characteristics in Archaea cellular membranes The most striking chemical differences between Archaea and other living things lie in their cell membrane. There are four fundamental differences between the archaeal membrane and those of all other cells: (1) Chirality of glycerol, (2) Ether linkage, (3) Isoprenoid chains, (4) Branching of side chains. (1) Chirality of glycerol : The basic unit from which cell membranes are built is the phospholipid. This is a molecule of glycerol which has a phosphate added to one end, and two side chains attached at the other end. When the cell membrane is put together, the glycerol and phosphate end of the molecules hang out at the surface of the membrane, with the long side chains sandwiched in the middle. This layering creates an effective chemical barrier around the cell and helps maintain chemical equilibrium. The glycerol used to make archaeal phospholipids is a stereoisomer of the glycerol used to build bacterial and eukaryotic membranes. There are two possible forms of the molecule that are mirror images of each other. It is not possible to turn one into the other simply by rotating it around. While bacteria and eukaryotes have D-glycerol in their membranes, Archaea have L-glycerol in theirs. This is more than a geometric difference. Chemical components of the cell have to be built by enzymes, and the chirality of the molecule is determined by the shape of those enzymes. A cell that builds one form will not be able to build the other form.
Fig 12 : Stereoisomeric difference of glycerol molecules in phospholipids between (a) Archaea and (b)other organisms ( Bacteria , Eukaryotes ) (a)
This suggests that archaea use entirely different enzymes for synthesizing phospholipids than do bacteria and eukaryotes. Such enzymes developed very early in life's history, suggesting an early split from the other two domains (b) 9|Page
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(2) Ether linkage : When side chains are added to the glycerol, most organisms bind them together using an Ester linkage. The side chain that is added has two oxygen atoms attached to one end. One of these oxygen atoms is used to form the link with the glycerol, and the other protrudes to the side when the bonding is done. By contrast, archaeal side chains are bound using an Ether linkage, which lacks that additional protruding oxygen atom. This gives the resulting phospholipid different chemical properties from the membrane lipids of other organisms. Ether bonds are chemically more resistant than Ester bonds. This stability might help archaea to survive extreme temperatures and very acidic or alkaline environments. (3) Isoprenoid chains : The side chains in the phospholipids of bacteria and eukaryotes are fatty acids, chains of usually 16 to 18 carbon atoms. Archaea do not use fatty acids to build their membrane phospholipids. Instead, they have side chains of 20 carbon atoms built from isoprene. Only Archaea use Isoprenoid chains to make phospholipids in their cell membranes. (4) Branching of side chains : Not only are the side chains of Archaeal membranes built from different components, but the chains themselves have a different physical structure. Because isoprene is used to build the side chains, there are side branches off the main chain. The fatty acids of bacteria and eukaryotes do not have these side branches (the best they can manage is a slight bend in the middle), and this creates some interesting properties in archaeal membranes. These branched chains may help prevent archaeal membranes from leaking at high temperatures. (5) Arranging phospholipids as Tetra ethers to form Monolayer of cell membrane In some Archaeal species, isoprene side chains are joined together to form Tetra ether structures. This can mean that the two side chains of a single phospholipid can join together, or they can be joined to side chains of another phospholipid on the other side of the membrane. The chemical nature of these types of molecules can be describe as “Bolaamphiphile”. No other group of organisms can form such transmembrane phospholipids. So in this case Lipid bilayer is replaced by a monolayer. This arrangement may make their membranes more rigid and better able to resist harsh environments. For example, the lipids in Ferroplasma are of this type, which is thought to aid this organism's survival in its highly acidic habitat. (6) Formation of Cyclopropane and Cyclohexane Carbon rings by Isoprenoid side chains Side branches is their ability to form carbon rings. This happens when one of the side branches curls around and bonds with another atom down the chain to make a ring of five carbon atoms. Such rings are thought to provide structural stability to the membrane, since they seem to be more common among species that live at high temperatures. They may work in the same way that cholesterol does in eukaryotic cells to stabilize membranes. 10 | P a g e
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Fig 13: Membrane structures. Top, an archaeal phospholipid: 1, isoprene chains; 2, ether linkages; 3, L-glycerol moiety; 4, phosphate group. Middle, a bacterial or eukaryotic phospholipid: 5, fatty acid chains; 6, ester linkages; 7, D-glycerol moiety; 8, phosphate group. Bottom: 9, lipid bilayer of bacteria and eukaryotes; 10, lipid monolayer of some archaea
The cytoplasmic membrane of Archaea is formed from either glycerol diethers, which have 20-carbon side chains (the 20-C unit is called a phytanyl group composed of 5 isoprene units), or diglycerol tetraethers, which have 40-carbon side chains (Fig 14). In the tetraether lipid, the ends of the phytanyl side chains that point inward from each glycerol molecule are covalently linked. This forms a lipid monolayer instead of a lipid bilayer membrane (Fig 14 d, e). In contrast to lipid bilayers, lipid monolayer membranes are extremely resistant to heat and are therefore widely distributed among hyperthermophilic Archaea, organisms that grow best at temperatures above 80°C. Membranes with a mixture of bilayer and monolayer character are also possible, with some of the opposing hydrophobic groups covalently bonded and others not. Many archaeal lipids contain rings within the hydrocarbon side chains. For example, crenarchaeol, a lipid widespread among species of Thaumarchaeota, a major phylum of Archaea, contains four 5-carbon (cyclopentyl) rings and one 6-carbon (cyclohexyl) ring (Fig 14c). Rings in the hydrocarbon side chains affect the chemical properties of the lipids and thus overall membrane function. Sugars can also be present in archaeal lipids. For example, the predominant membrane lipids of many Euryarchaeota, a major group of Archaea that includes the methanogens and extreme halophiles, are glycerol diether glycolipids. Despite the differences in chemistry between the cytoplasmic membranes of Archaea and organisms in the other domains, the fundamental construction of the archaeal cytoplasmic membrane, inner and outer hydrophilic surfaces and a hydrophobic interior, is the same as that of membranes in Bacteria and Eukarya. Evolution has selected this design as the best solution to the main function of the cytoplasmic membrane permeability.
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Fig 14: Major lipids of Archaea and the architecture of archaeal membranes. (a, b) Note that the hydrocarbon of the lipid is bonded to the glycerol by an ether linkage in both cases. The hydrocarbon is phytanyl (C20) in part and biphytanyl (C40) in part b. (c) A major lipid of Thaumarchaeota is crenarchaeol, a lipid containing 5- and 6-carbon rings. (d, e) Membrane structure in Archaea may be bilayer or monolayer (or a mix of both).
Specific Characteristics in Archaea Cell Wall There are lack of Peptidoglycan present in Archaea cell wall. Instead of Peptidoglycan, There is a chemical compound called Pseudomurein and it is the major compound in Archaeal Cell wall. The cell walls of certain methanogenic Archaea contain a molecule that is remarkably similar to peptidoglycan, a polysaccharide called pseudomurein. The backbone of pseudomurein is formed from alternating repeats of N-acetylglucosamine (also present in peptidoglycan) and acetyltalosaminuronic acid; the latter replaces the N-acetylmuramic acid of peptidoglycan. Pseudomurein also differs from peptidoglycan in that the glycosidic bonds between the sugar derivatives are β-1,3 instead of β-1,4, and the amino acids are all of the L-stereoisomer . It is thought that peptidoglycan and pseudomurein either arose by convergent evolution after Bacteria and Archaea had diverged or, more likely, by 12 | P a g e
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evolution from a common polysaccharide present in the cell walls of the common ancestor of the domains Bacteria and Archaea. Cell walls of some other Archaea lack pseudomurein and instead contain other polysaccharides. For example, Methanosarcina species have thick polysaccharide walls composed of polymers of glucose, glucuronic acid, galactosamine uronic acid, and acetate. Extremely halophilic Archaea such as Halococcus, which are related to Methanosarcina, have similar cell walls that are also highly sulfated. The negative charges on the sulfate ion (SO4 2-) bind Na+ present in the habitats of Halococcus salt evaporation ponds and saline seas and lakes at high levels. The sulfate sodium complex helps stabilize the Halococcus cell wall in such strongly ionic environments. S-Layers The most common type of cell wall in Archaea is the paracrystalline surface layer, or S-layer as it is called. S-layers consist of interlocking molecules of protein or glycoprotein. The paracrystalline structure of S-layers can form various symmetries, including hexagonal, tetragonal, or trimeric, depending upon the number and structure of the subunits of which it is composed. S-layers have been found in representatives of all major lineages of Archaea and also in several species of Bacteria. The cell walls of some Archaea, for example the methanogen Methanocaldococcus jannaschii, consist only of an S-layer. Thus, S-layers are sufficiently strong to withstand osmotic pressures without any other wall components. Besides serving as protection from osmotic lysis, S-layers may have other functions. For example, as the interface between the cell and its environment, it is likely that the S-layer functions as a selective sieve, allowing the passage of low-molecular-weight solutes while excluding large molecules or structures (such as viruses). The S-layer may also function to retain proteins near the cell surface, much as the outer membrane does in gram-negative bacteria. Because they lack peptidoglycan, Archaea are naturally resistant to Lysozyme and the antibiotic Penicillin, agents that either destroy peptidoglycan or interrupt its biosynthesis.
Fig 15: The S-layer. Transmission electron micrograph of a portion of an
S-layer No Archaea have been shown to form Endospores, suggesting that the capacity to produce endospores evolved sometime after the prokaryotic lineages diverged about 3.5 billion years ago 13 | P a g e
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Specific Characteristics in Archaeal Flagella Motility is important for microorganisms because the ability to move allows cells to explore new habitats and exploit their resources. In Archaea, Major genera of methanogens, extreme halophiles, Thermosacidophiles, and Hyperthermophiles are all capable of swimming motility. Archaeal flagella are roughly half the diameter of bacterial flagella, but impart movement to the cell by rotating, as do flagella in Bacteria. However, unlike Bacteria, in which a single type of protein makes up the flagella filament, several different flagellin proteins are known from Archaea, and their amino acid sequences and genes that encode them bear little relationship to those of bacterial flagellin. Studies of swimming cells of the extreme halophile Halobacterium show that they swim at speeds only about one-tenth that of cells of Escherichia coli. Whether this holds for all Archaea is unknown, but the significantly smaller diameter of the archaeal flagellum compared with the bacterial flagellum would naturally reduce the torque and power of the flagella motor such that slower swimming speeds are not surprising. Moreover, from biochemical experiments with Halobacterium it appears that archaeal flagella are powered directly by ATP rather than by the proton motive force, the source of energy for the flagella of Bacteria If this holds for the flagella of all motile Archaea, it would mean that the flagella motors of Archaea and Bacteria employ fundamentally different energy-coupling mechanisms. Combined with the clear differences in flagellar protein structure between Archaea and Bacteria. This suggests that, as for endospores, flagellar motility evolved separately as prokaryotes diverged over 3.5 billion years ago. Microbiologists recently zeroed in on the movements of swimming Archaea and showed that Halobacterium was the slowest of all species examined. By contrast, cells of the archaeon Methanocaldococcus swam nearly 50 times faster than cells of Halobacterium and 10 times faster than cells of E. coli. Astonishingly, it is the fastest organism on Earth! Research report ; Herzog, B., and R. Wirth. 2012. Swimming behavior of selected species of Archaea. Appl. Environ. Microbiol. 78: 1670–1674. 25
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5) Molecular Biological significances of Archaea Molecular biological characters of Archaea is more closely related with Eukarya than Bacteria. But there are few similarities between Bacteria and Archaea. One similarity is, Genes of Archaea are located as Operons in the Chromosome as same as in Bacteria. 1.) Transcription factor proteins are similar in Archaea and Eukarya. 2.) During the initiation of Transcription process, TATA-binding protein has bound to the TATA box and Transcription factor protein B has bound to the B recognition element, then archaeal RNA polymerase can bind and initiate transcription. 3.) Some archaeal genes have inverted repeats followed by an AT-rich sequence similar to those found in many bacterial transcription terminators. 4.) One other type of suspected transcription terminator lacks inverted repeats, but contains repeated runs of Thymine. 5.) No Rho-like proteins are involved for the transcription process in Archaea. 6.) Archaeal RNA Polymerase is complex than bacterial one and it is more similar than Eukaryotic RNA Polymerases. Archaea contain only a single RNA polymerase that most closely resembles eukaryotic RNA polymerase II. Both Archaea and Eukarya have RNA polymerase which have 11 or 12 subunits. But Bacterial RNA Polymerase have only 5 subunits ( including sigma factor )
Fig 16: Structure of Bacterial, Archaeal and Eukaryotic RNA Polymerase enzyme complexes.
7.) Structures of Archaeal promoters are resemble to Eukaryotic Promoters. 8.) There are Introns inside the genes in Archaea. But there are no Introns in Bacteria. Archaeal introns are excised during Transcription by a specific ribonuclease that recognizes exon–intron junctions. In a few cases, t-RNA s in Archaea are assembled by splicing together segments from two or three different primary transcripts. 15 | P a g e
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9.) Normally non sense codons (eg: Stop codons) do not code for any amino acids in genetic code. Normally there are 20 amino acids are involved to build life. It is a very uncommon thing that encoding an amino acid from Stop codons. This is very rare incident but it happens in some higher Eukaryotes as well as in certain Archaea. Pyrrolysine is an amino acid which can only found in certain Archaea, coded by UAG stop codon. (It is 22nd amino acid that is known as an uncommon amino acid which is involved to make the life, among 2 uncommon amino acids. 21st is selenocysteine which can be only found in Higher Eukaryotes). Pyrolysine was first found in Methanogenic Archaea. 10.) Starting amino acid (which is encoded by the Start codon) in Archaea is Methionine. It is same as in Eukarya. But in bacteria, Formyl-methionine is the starting amino acid. 11.) Archaea is highly resistant for Chloramphenicol and Streptomycin which are translation inhibiting antibiotics for Bacteria. 12.) Few repressor or activator proteins from Archaea have yet been characterized in detail, but it is clear that Archaea have both types of regulatory proteins. Archaeal repressor proteins either block the binding of RNA polymerase itself or block the binding of TBP (TATA-binding protein) and TFB (transcription factor B), proteins that are required for RNA polymerase to bind to the promoter in Archaea .At least some archaeal activator proteins function in just the opposite way, by recruiting TBP to the promoter, thereby facilitating transcription.
Fig 17: Repression of genes for nitrogen metabolism in Archaea. The NrpR protein of Methanococcus maripaludis acts as a repressor. It blocks the binding of the TFB and TBP proteins, which are required for promoter recognition, to the BRE site and TATA box, respectively. If there is a shortage of ammonia, α-ketoglutarate is not converted to glutamate. The α-ketoglutarate accumulates and binds to NrpR, releasing it from the DNA. Now TBP and TFB can bind. This in turn allows RNA polymerase to bind and transcribe the operon.
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6) Viruses of Archaea Several DNA viruses have been discovered whose hosts are species of Archaea, including representatives of both the Euryarchaeota and Crenarchaeota phyla. Most viruses that infect species of Euryarchaeota, including both methanogenic and halophilic Archaea, are of the “head and tail” type, resembling phages that infect enteric bacteria, such as phage T4. One novel archaeal virus infects a halophile and is unusual because it is both enveloped and contains a single-stranded DNA genome. By contrast, all other characterized archaeal DNA viruses contain double-stranded and typically circular DNA genomes. RNA archaeal viruses have been detected in thermal environments inhabited by Crenarchaeota. These are single-stranded positive sense RNA viruses (positive-strand viruses), but little else is known about them as they await detailed characterization and laboratory culture. However, as for Bacteria and Eukarya, it is clear that at least some Archaea are infected by viruses with RNA genomes. The most distinctive archaeal viruses infect hyperthermophilic Crenarchaeota. For example, the sulfur chemolithotroph Sulfolobus is host to several structurally unusual viruses. One such virus, called SSV, forms spindle-shaped virions that often cluster in rosettes. Such viruses are widespread in acidic hot springs worldwide. Virions of SSV contain a circular DNA genome of about 15 kbp. A second morphological type of Sulfolobus virus forms a rigid, helical rod-shaped structure. Viruses in this class, nicknamed SIFV, contain linear DNA genomes about twice the size of that of SSV. Many variations on the spindle and rod shaped patterns have been seen in archaeal viral isolation studies. A spindle-shaped virus that infects the hyperthermophile Acidianus displays a novel behavior. The virion, called ATV, contains A spindle-shaped virus also infects Pyrococcus (Euryarchaeota). This virus, named PAV1, resembles SSV but is larger and contains a very short tail .PAV1 has a small circular DNA genome and is released from host cells without cell lysis, probably by a budding mechanism similar to that of the Escherichia coli bacteriophage M13 Pyrococcus has a growth temperature optimum of 100°C, meaning that PAV1 virions must be especially heat-stable. Despite their similar morphologies, genomic comparisons of PAV1 and SSV-type viruses show little sequence similarity, indicating that the two types of viruses do not have common evolutionary roots. Replication events in the life cycles of archaeal viruses are not yet clear. However, considering that the genomes of most of these viruses are double-stranded DNA, it is unlikely that any major novel modes of replication will be uncovered. However, important molecular details, such as the extent to which viral rather than host polymerases and other enzymes are used in the replication process, await further work on these remarkably tough viruses.
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7) Significances of Horizontal Gene Transfer in Archaea
Fig 18: Difference between Horizontal gene transfer and Vertical gene transfer
Archaea contain a single circular chromosome like most Bacteria and genome analysis indicates that horizontal transfer of archaeal DNA also occurs in nature, the development of laboratory-based gene transfer systems lags far behind that for Bacteria. Practical problems here include the fact that most well-studied Archaea are extremophiles, capable of growth only under extreme conditions of high salt or high temperature. The temperatures necessary to culture some hyperthermophiles, for example, will melt agar, and alternative materials are required to form solid media and obtain colonies. Another problem is that most common antibiotics do not affect Archaea. For example, penicillins do not affect Archaea because their cell walls lack peptidoglycan. The choice of selectable markers for genetic crosses is therefore often limited. However, Novobiocin (a DNA gyrase inhibitor) and Mevinolin (an inhibitor of isoprenoid biosynthesis) are used to inhibit growth of extreme halophiles, and Puromycin and Neomycin (both protein synthesis inhibitors) inhibit methanogens. Auxotrophic strains of a few Archaea have also been isolated for genetic selection purposes. No single species of Archaea has become a model organism for archaeal genetics, although more genetic work has been done on select species of extreme halophiles (Halobacterium, Haloferax) than on any other Archaea. Instead, individual mechanisms for gene transfer have been found scattered among a range of Archaea. In addition, several plasmids have been isolated from Archaea and some have been used to construct cloning vectors, allowing genetic analysis through cloning and sequencing rather than traditional genetic crosses. Transposon mutagenesis has been well developed in certain methanogen species including Methanococcus and Methanosarcina, and other tools such as shuttle vectors and other in vitro methods of genetic analysis have been developed for study of the highly unusual biochemistry of the methanogens . Transformation works reasonably well in several Archaea although details and conditions vary from organism to organism. One approach requires removal of divalent metal ions, which in turn results in the disassembly of the glycoprotein cell wall layer surrounding many archaeal cells and hence allows access by transforming DNA. However, Archaea with rigid cell walls have proven difficult to transform, although electroporation sometimes works. One exception is in Methanosarcina species, organisms with a thick cell wall, for which high-efficiency transformation systems have been developed that employ DNA-loaded lipid preparations (liposomes) to deliver DNA into the cell. Although viruses that infect Archaea are plentiful. 18 | P a g e
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Transduction is extremely rare. Only one archaeal virus, which infects the thermophilic methanogen Methanothermobacter thermautotrophicus, has been shown to transduce the genes of its host. Unfortunately the low burst size (about six phages liberated per cell) makes using this system for gene transfer impractical When consider about Archaeal Conjugation, Two types of conjugation have been detected in Archaea. Some strains of Sulfolobus solfataricus contain plasmids that promote conjugation between two cells in a manner similar to that seen in Bacteria. In this process, cell pairing is independent of pili formation and DNA transfer is unidirectional. However, most of the genes encoding these functions seem to have little similarity to those in gram-negative Bacteria. The exception is a gene similar to traG from the F plasmid, whose protein product participates in stabilizing mating pairs. It thus seems likely that the actual mechanism of conjugation in Archaea is quite different from that in Bacteria. Some Halobacteria, in contrast, perform a novel form of conjugation. No fertility plasmids are required, and DNA transfer is bidirectional. Cytoplasmic bridges form between the mating cells and probably facilitate inter cell DNA transfer. Neither type of conjugation has been developed to the point of being used for routine gene transfer or genetic analysis. However, these genetic resources will likely be useful for developing more routine genetic transfer systems for these organisms in the future.
Fig 19: Molecular features of the three domains
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8) Introduction to the Diversity of Archaea The domain Archaea consists of seven major phyla, only five of which contain species described on the basis of cultivated strains. Most described species fall within the phyla Crenarchaeota and Euryarchaeota, while only a handful of species have been described for the Nanoarchaeota, the Korarchaeota, and the Thaumarchaeota . Branching close to the root of the universal tree are Hyperthermophilic species of Crenarchaeota, such as Pyrolobus , as well as Thermophilic species of Nanoarchaeota and Korarchaeota. These are followed by the phylum Euryarchaeota, which includes the methanogenic Archaea and the extreme halophiles and extreme acidophiles, such as Thermoplasma. The phylum Thaumarchaeota was first observed in the deep ocean in the 1990s but has subsequently been found in soils and marine systems all over the world. The first species of Thaumarchaeota were shown to be capable of ammonia oxidation. Several different species have since been isolated and all share this physiological trait. As for Bacteria, many lineages of Archaea are known only from SSU rRNA genes recovered from the environment and there remains great opportunity for the discovery of new lineages in the future.
Fig 20: Major Phyla in domain Archaea
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Archaea members are important to conduct bio-geochemical cycles such as Sulphur Cycle, Nitrogen cycle and etc… They play impotent roles for recycling matter in the enviorenment. Involvement for Sulphur Cycle Involvement for Nitrogen Cycle
Involvement for Iron Cycle
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Dissimilative Sulfate reduction occurs in Archaeoglobus, a genus of the archaeal phylum Euryarchaeota. The sulfur reducing Archaea of which there are many are all genera of Crenarchaeota (e.g., Acidianus, Sulfolobus, Pyrodictium, and Thermodiscus). Sulphur is oxidized by one some members of Crenarchaeota . Phylum Euryarchaeota members contain NifH gene which is responsible for Nitrogenase enzyme. Therefore they show nitrogen fixing ability. Ammonia oxidizers are found in archaeal phylum Thaumarchaeota (Nitrosopumilus, Nitrosocaldus, Nitrosoarchaeum, Nitrososphaera). Archaeal ammonia-oxidizers appear to be most common in habitats where NH3 is present in low concentration. These organisms are thought to be the dominant ammonia oxidizers in the oceans where ammonia levels are very low. Archaeal ammonia-oxidizers are also common in soils, and in some soils they outnumber bacterial ammonia-oxidizers by several orders of magnitude. The availability of NH3 relative to NH4+ declines with pH, and thus acid soils (pH 6 - 6.5), which are common, may favor organisms able to grow at low NH3 concentration. Some members of Archaea do denitrification process. Dissimillative Iron reduction by Crenarchaeota (Pyrobaculum) Two Archaeal phyla involve for Iron Oxidation
ARCHAEA
Archaea and Global Warming Anthropogenic CO2 emissions have significantly affected global climate. However, Archaea and Bacteria have also profoundly affected our planet, including its climate. One example comes from the Arctic, where soil is frozen as permafrost. Permafrost can be 100 meters deep and it encompasses 25% of the terrestrial surface of the Earth. Within permafrost is stored an enormous mass of organic carbon, most of which has been locked away in ice for more than 20,000 years. But this ice is starting to thaw, and the result could have global consequences. The Intergovernmental Panel on Climate Change predicts that Arctic temperatures will increase 7°C by the year 2100. When permafrost melts, it is converted into wetlands, and these are major habitats for Archaea that produce methane (methanogens). Methane is a greenhouse gas with a warming potential 25 times more powerful than CO2. Hence, if Arctic warming continues at its present pace, much permafrost carbon could be converted into methane, significantly accelerating global climate change. At Stordalen Mire in northern Sweden, microbiologists are investigating methanogens in thawed permafrost. Chambers are used to trap and measure methane produced in the wetlands that have replaced thawed permafrost . The source of most of the methane was found to be a novel methanogen, Methanoflorens stordalenmirensis, which grows rapidly in thawed permafrost. M. stordalenmirensis represents a novel order of methanogens previously called “Rice Cluster II.” These methanogens are present in wetlands worldwide but M. stordalenmirensis is the first characterized species of this new taxonomic family, the Methanoflorentaceae. In addition to human impacts on climate, future control of global climate change may well depend in a major way on what is discovered about the ecology of methanogenesis by M. stordalenmirensis.
Archaeal Diversity A phylogenetic tree of Archaea is shown in. The tree, based on comparative sequences of ribosomal proteins, reveals several phyla, including the,
Euryarchaeota, Thaumarchaeota Nanoarchaeota Nanoarchaeota Crenarchaeota,
The exact ancestry of these groups remains a contentious issue, and phylogenetic trees constructed from 16S ribosomal RNA gene sequences often conflict with those made using other genomic loci The evolutionary history of the Archaea is ancient and complex, involving horizontal gene transfers within and between phyla. Common traits shared by all Archaea include their ether linked lipids, their lack of peptidoglycan in cell walls, and their structurally complex RNA polymerases, which resemble those of Eukarya . But beyond this, Archaea show enormous phenotypic diversity. Archaea include species that carry out chemoorganotrophic or chemolithotrophic metabolisms, and both aerobic and anaerobic species are common. 22 | P a g e
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Chemoorganotrophy is widespread among Archaea, and fermentations and anaerobic respirations are common. Chemolithotrophy is also well established in the Archaea, with H2 being a common electron donor, and with ammonia oxidation found among species of Thaumarchaeota. Anaerobic respiration, especially forms employing elemental sulfur (S) as an electron acceptor, is prevalent among the Archaea, especially Crenarchaeota. Aerobic respiration occurs widely in Thaumarchaeota and is common among a few groups of Euryarchaeota but is characteristic of only a few species of Crenarchaeota. Euryarchaeota that conserve energy from the production of methane. Methanogenesis is a globally important process that is uniquely archaeal. Archaea are also well known for containing many species Of Extremophiles, including species that are Hyperthermophiles, Halophiles and Acidophiles . However, a great many species in the Euryarchaeota and most Thaumarchaeota are not extremophiles and are found in soils, sediments, oceans, lakes, in association with animals, and even in the human gut!
Fig 21: Detailed phylogenetic tree of the Archaea based on comparisons of ribosomal proteins from sequenced genomes. Each of the five archaeal phyla is indicated in a different color. The Korarchaeota and Nanoarchaeota are each represented by only a single known species.
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9) Euryarchaeota Euryarchaeota comprise a large and physiologically diverse group of Archaea. This phylum includes Methanogens (Strictly Anaerobes ) , many genera of extreme Halophilic Archaea ( mainly obligate aerobes ), Hyperthermophiles (Thermococcus and Pyrococcus) & Hyperthermophilic methanogen (Methanopyrus).
Extreme Halophilic Archaea Extremely halophilic Archaea, often called the “Haloarchaea” are a diverse group that inhabits environments high in salt. These include naturally salty environments, such as solar salt evaporation ponds and salt lakes, and artificial saline habitats such as the surfaces of heavily salted foods, for example, certain fish and meats. Such salty habitats are called hypersaline. The term extreme halophile is used to indicate that these organisms are not only halophilic, but that their requirement for salt is very high, in some cases at levels near saturation. An organism is considered an extreme halophile if it requires 1.5 M (about 9%) or more sodium chloride (NaCl) for growth. Most species of extreme halophiles require 2–4 M NaCl (12–23%) for optimal growth. Virtually all extreme halophiles can grow at 5.5 M NaCl (32%, the limit of saturation for NaCl), although some species grow very slowly at this salinity. Some phylogenetic relatives of extremely halophilic Archaea, for example species of Haloferax and Natronobacterium, are able to grow at much lower salinities, such as at or near that of seawater (about 2.5% NaCl); nevertheless, these organisms are phylogenetic relatives of other extreme halophiles. Eg: Halobacterium , Haloferax , Natronobacterium
Fig 22: Some genera of extremely halophilic Archaea.
Haloarchaea stain gram-negatively, reproduce by binary fission, and do not form resting stages or spores. Cells of the various cultured genera are rod-shaped, cocci, or cup-shaped, but even cells that form squares are known. Cells of Haloquadratum are square in shape and are only about 0.1 μm thick. Haloquadratum also forms gas vesicles that allow it to float in its salty hypersaline habitat, probably as a means to be in contact with air since most extreme halophiles are obligate aerobes.
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Physiological Adaptations of Extremely Halophilic Archaea Many other extremely halophilic Archaea also produce gas vesicles. Most species of extreme halophiles lack flagella, but a few strains are weakly motile by flagella that rotate to propel the cell Forward. The genomes of Halobacterium and Halococcus are unusual in that large plasmids containing up to 30% of the total cellular DNA are present and the GC base ratio of these plasmids (near 60% GC) differs significantly from that of chromosomal DNA (66–68% GC). Plasmids from extreme halophiles are among the largest naturally occurring plasmids known. Most species of extremely halophilic Archaea are obligate aerobes. Most haloarchaea use amino acids or organic acids as electron donors and require a number of growth factors such as vitamins for optimal growth. A few haloarchaea oxidize carbohydrates aerobically, but this capacity is rare; sugar fermentation does not occur. Electron transport chains containing cytochromes of the a, b, and c types are present in Halobacterium, and energy is conserved during aerobic growth via a proton motive force arising from electron transport. Some haloarchaea have been shown to grow anaerobically, as growth by anaerobic respiration linked to the reduction of nitrate or fumarate has been demonstrated in certain species. The Halobacterium cell wall is composed of glycoprotein and is stabilized by Na+. Sodium ions bind to the outer surface of the Halobacterium wall and are absolutely essential for maintaining cellular integrity. When insufficient Na+ is present, the cell wall breaks apart and the cell lyses. This is a consequence of the exceptionally high content of the acidic (negatively charged) amino acids aspartate and glutamate in the glycoprotein of the Halobacterium cell wall. The negative charge on the carboxyl Group of these amino acids is bound to Na+; when Na+ is diluted away, the negatively charged parts of the proteins tend torepel each other, leading to cell lysis.
Fig 24: Electron micrographs of thin sections of the extreme halophile Halobacterium salinarum.
Natronobacterium, Natronomonas, and their relatives differ from other extreme halophiles in being extremely alkaliphilic as well as halophilic. As befits their soda lake habitat natronobacteria grow optimally at very low Mg2+ concentrations and high pH (9–11).
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Water Balance Maintenance To maintain the osmotic balance in a high-solute environment Such as the salt-rich habitats of Halobacterium, organisms must either accumulate or synthesize solutes intracellularly. These solutes are called compatible solutes. These compounds counteract the tendency of the cell to become dehydrated under conditions of high osmotic strength by placing the cell in positive water balance with its surroundings. Cells of Halobacterium, however, do not synthesize or accumulate organic compounds but instead pump large amounts of K+ from the environment into the cytoplasm. This ensures that the concentration of K+ inside the cell Is even greater than the concentration of Na+ outside the cell. This ionic condition maintains positive water balance. The Halobacterium cell wall is composed of glycoprotein and is stabilized by Na+. Sodium ions bind to the outer surface of the Halobacterium wall and are absolutely essential for maintaining cellular integrity. When insufficient Na+ is present, the cell wall breaks apart and the cell lyses. This is a consequence of the exceptionally high content of the acidic amino acids aspartate and glutamate in the glycoprotein of the Halobacterium cell wall. The negative charge on the carboxyl group of these amino acids is bound to Na+ when Na+ is diluted away, the negatively charged parts of the proteins tend to repel each other, leading to cell lysis.
Cytoplasmic Compornents of Extreme Halophiles Like cell wall proteins, cytoplasmic proteins of Halobacterium are highly acidic, but it is K+, not Na+, that is required for activity. This makes sense because K+ is the predominant cation in the cytoplasm of cells of Halobacterium . Besides having a high acidic amino acid composition, halobacterial cytoplasmic proteins typically contain lower levels of hydrophobic amino acids and lysine, a positively charged (basic) amino acid, than proteins of nonhalophiles. This is also to be expected because in a highly ionic cytoplasm, polar proteins would tend to remain in solution whereas nonpolar proteins would tend to cluster and perhaps lose activity. The ribosomes of Halobacterium also require high KCl levels for stability, whereas ribosomes of nonhalophiles have no KCl requirement. Extremely halophilic Archaea are thus well adapted, both internally and externally, to life in a highly ionic environment. Cellular components exposed to the external environment require high Na+ for stability, whereas internal components require high K+. With the exception of a few extremely halophilic members of the Bacteria that also use KCl as a compatible solute, in no other group of prokaryotes do we find this unique requirement for such high amounts of specific cations.
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Bacteriorhodopsin and Light-Mediated ATP Synthesis in Halobacteria Certain species of haloarchaea can catalyze a light-driven synthesis of ATP. This occurs without chlorophyll pigments, so it is not photosynthesis. However, other light-sensitive pigments are present, including red and orange carotenoids primarily C50 pigments called bacterioruberins and inducible pigments involved in energy conservation; we discuss these pigments here. Under conditions of low aeration, Halobacterium salinarum and some other haloarchaea synthesize a protein called bacteriorhodopsin and insert it into their cytoplasmic membranes. Bacteriorhodopsin is so named because of its structural and functional similarity to rhodopsin, the visual pigment of the eye. Conjugated to bacteriorhodopsin is a molecule of retinal, a carotenoid-like molecule that can absorb light energy and pump a proton across the cytoplasmic membrane. The retinal gives bacteriorhodopsin a purple hue. Thus cells of Halobacterium that are switched from growth under high aeration conditions to oxygen limiting growth conditions (a trigger of bacteriorhodopsin synthesis) gradually change color from orange-red to purple-red as they synthesize bacteriorhodopsin insert it into their cytoplasmic membranes. Bacteriorhodopsin absorbs green light around 570 nm. Following absorption, the retinal of bacteriorhodopsin, which normally exists in a trans configuration (RetT), becomes excited and converts to the cis (RetC) form. This transformation is coupled to the translocation of a proton across the cytoplasmic membrane. The retinal molecule then decays to the Trans isomer along with the uptake of a proton from the cytoplasm, and this completes the cycle. The proton pump is then ready to repeat the cycle. As protons accumulate on the outer surface of the membrane, a proton motive force is generated that is coupled to ATP synthesis through the activity of a proton translocating ATPase. Bacteriorhodopsinmediated ATP production in H. salinarum supports slow growth of this organism under anoxic conditions. The light stimulated proton pump of H. salinarum also functions to pump Na+ out of the cell by activity of a Na+,H+ antiport system and to drive the uptake of nutrients, including the K+ needed for osmotic balance. Amino acid uptake by H. salinarum is indirectly driven by light as well, because amino acids are co transported into the cell with Na+ by an amino acid-Na+ symporter removal of Na+ from the cell occurs by way of the light-driven Na+-H+ antiporter.
Fig 23: Model for the mechanism of bacteriorhodopsin. Light of 570 nm (hν570nm) converts the protonated retinal of bacteriorhodopsin from the trans form (RetT) to the cis form (RetC), along with translocation of a proton to the outer surfaceof the cytoplasmic membrane, thus establishing a proton motive force. ATPase activity is driven by the proton motive force.
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Methanogenic Archaea Many Euryarchaeota are methanogens, microorganisms that produce methane (CH4) as an integral part of their energy metabolism. They are strictly anaerobic organisms. Eg: Methanobacterium, Methanocaldococcus, Methanosarcina. Their taxonomy is based on both phenotypic and phylogenetic analyses, with several taxonomic orders being recognized. Methanogens show a diversity of cell wall chemistries. These include the pseudomurein walls of Methanobacterium species and relatives, walls composed of methanochondroitin (so named because of its structural resemblance to chondroitin, the connective tissue polymer of vertebrate animals) in Methanosarcina and relatives, the protein or glycoprotein wallsof Methanocaldococcus and Methanoplanus species, respectively, and the S-layer walls of Methanospirillum Fig 25: Characteristics of some methanogenic Archaea
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Methanogens are mesophilic and nonhalophilic, although speciesthat grow optimally at very high or very low temperatures, at very high salt concentrations, or at extremes of pH,have also been described. Several substrates can be converted to CH4by methanogens. Interestingly, these substrates do not include such common compounds as glucose and organic or fatty acids (other than acetate and pyruvate). Compounds such as glucose can be converted to CH4, but only in reactions in which methanogens and other anaerobes cooperate. With the right mixture of organisms, virtually any organic compound, even hydrocarbons, can be converted to CH4 plus CO2. Three classes of compounds make up the list of methanogenic substrates shown in Table 16.5. These are CO2-type substrates, methylated substrates, and acetate. CO2-type substrates include CO2 itself, which is reduced to CH4 using H2 as the electron donor. Other substrates of this type include formate and CO, carbon monoxide. Methylated substrates include methanol and many others. Methanol can be reduced using an external electron donor such as H2, or, alternatively, in the absence of H2, some CH3OH can be oxidized to CO2 to generate the electrons needed to reduce other molecules of CH3OH to CH4 . The final methanogenic process is the cleavage of acetate to CO2 plus CH4. Only a few known methanogens are acetotrophic, although acetate is a major source of CH4 in nature.
Fig 26:
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Fig 27:
Fig 28:
Thermoplasmatales A phylogenetically distinct line of Archaea contains Thermophilic and extremely acidophilic genera: Thermoplasma, Ferroplasma, and Picrophilus. These prokaryotes are among the most acidophilic of all known microorganisms, with Picrophilus being capable of growth even below 30 | P a g e
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pH 0. Most are thermophilic as well. These genera also form their own taxonomic order within the Euryarchaeota, the Thermoplasmatales. Thermoplasma and Ferroplasma lack cell walls, and in this respect they resemble the mycoplasmas.
Thermococcales and Methanopyrus A few euryarchaeotes thrive in thermal environments and some are Hyperthermophiles. We consider here three hyperthermophilic euryarchaeotes that branch very near the root of the Euryarchaeota . Two of these, Thermococcus and Pyrococcus, form a distinct taxonomic order: the Thermococcales. The third organism, Methanopyrus, is a methanogen that closelyresembles other methanogens in its basic physiology but is unusual in its hyperthermophily, lipids, and phylogenetic position .
Archaeoglobales Hyperthermophilic Crenarchaeota catalyze anaerobic respirations in which elemental sulfur (S0) is used as an electron acceptor, being reduced to H2S. One hyperthermophilic euryarchaeote, Archaeoglobus, can reduce sulfate (SO42−) and forms a phylogenetically distinct lineage within the Euryarchaeota . Eg: Archaeoglobus, Ferroglobus
Fig 30 : Shadowed preparation of cells of Thermoplasma volcanium isolated from hot springs.Cells are 1–2 μm in diameter.
Fig 29:
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10) Thaumarchaeota Early surveys of 16S ribosomal RNA genes from open ocean microbial communities resulted in the shocking conclusion that Archaea were abundant and widespread in the oceans. At the time, the archaeal domain was considered to contain only extremophiles and obligate anaerobes, and their presence in oxygen-rich temperate and even polar oceanic environments was something of a mystery. Even more remarkable, these novel Archaea were widespread and common in soils all over the world. Phylogenetic analysis of their 16S ribosomal RNA gene sequences initially suggested that this novel group of Archaea was a deeply divergent lineage of the Crenarchaeota, a group of hyperthermophilic Archaea. It was only after genome sequence analysis of the marine nitrifier Nitrosopumilus maritimus that it became clear that the Thaumarchaeota are a distinct phylum of Archaea. Analyses of genome sequences confirm that Thaumarchaeota constitute a unique phylum of Archaea and that they diverged from the primary line of archaeal descent prior to the divergence of Crenarchaeota and Euryarchaeota. Thaumarchaeota, ubiquitous in soils and found throughout the marine water column from the equator to the polar seas, are one of the most abundant and widespread phyla on our planet. In surveys of soil or marine samples, thaumarchaea are often found to be the dominant group of Archaea. By using fluorescent phylogenetic probes , thaumarchaea have been detected in oxic marine waters worldwide; they thrive even in waters and sea ice near Antarctica . Marine species are planktonic. Nitrosopumilus maritimus grows chemolithotrophically by aerobically oxidizing ammonia (NH3) to nitrite (NO2–), the first step in nitrification. This organism uses CO2 as its sole carbon source (autotrophy), as do nitrifying Bacteria . However, unlike ammonia-oxidizing Bacteria such as Nitrosomonas, N. maritimus is adapted to life under extreme nutrient limitation, as would befit an organism indigenous to open ocean waters.
11) Nanoarchaeota The Nanoarchaeota are represented by a single species, the highly unusual Nanoarchaeum equitans. N. equitans is one of the smallest cellular organisms known and has the smallest genome among species of Archaea (0.49 Mb). The coccoid cells of N. equitans are very small, about 0.4 μm in diameter, and have only about 1% of the volume of an Escherichia coli cell. They cannot grow in pure culture and replicate only when attached to the surface of their host organism, Ignicoccus hospitalis , a hyperthermophilic species of Crenarchaeota whose name means “the hospitable fireball.” N. equitans grows to 10 or more cells per Ignicoccus cell and lives an apparently parasitic lifestyle , making it the only known archaeal symbiont. 32 | P a g e
Fig 31:
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12) Korarchaeota Ribosomal RNA sequences of Korarchaeota have been observed in a range of geothermal habitats, both submarine and terrestrial. However, Korarchaeum cryptofilum, whose name means “the cryptic filament of youth” is the only characterized species in the phylum Korarchaeota. First observed as a 16S ribosomal RNA gene phylotype recovered from the hot spring named Obsidian Pool in Yellowstone National Park, USA, K. cryptofilum has yet to be grown in pure culture, as for N. equitans. However, its genome sequence has been determined from metagenomic analyses of an enrichment culture. K. cryptofilum is an obligately anaerobic chemoorganotroph and a hyperthermophile, growing at 85°C. Cells are long, thin (
