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Important Groups of Procaryotes (page 1)

(This chapter has 10 pages)

© Kenneth Todar, PhD

The procaryotes (or prokaryotes) consist of millions of genetically-distinct unicellular organisms. They lack structural diversity but have a wide range of genetic and physiological diversity. Sometimes, particular physiological traits unify and distinguish particular groups of procaryotes to microbiologists. In Bergey's Manual of Determinative Bacteriology (1994), the identifiable groups of procaryotes are assembled based on easily-observed phenotypic characteristics such as Gram stain, morphology (rods, cocci, etc.), motility, structural features (e.g. spores, filaments, sheaths, appendages, etc.), and on distinguishing physiological features (e.g. photosynthesis, anaerobiasis, methanogenesis, lithotrophy, etc.).

Nowadays, this type of artificial classification scheme has been abandoned in favor of hierarchical taxonomic schemes based on comparative genetic analysis of the nucleotide sequences of the small subunit ribosomal RNA that is contained in all cellular organisms. In the Second edition of Bergey's Manual of Systematic Bacteriology (2001-2004), as well as the current (3rd) edition of The Prokaryotes, phylogeny dominates the classification schemes. Such an approach generates the Phylogenetic Tree of Life (below) that lands the procaryotes in two Domains, Archaea and Bacteria. At a taxonomic level, organisms at the tips of the archaeal branches represent Orders; the tips of the bacterial branches are Phyla. More information on the taxonomy, phylogeny and classification of procaryotes is given in the references at the bottom of this page. Also, an excellent article online that integrates phylogeny with classification of procaryotes is  Classification and Phylogeny by Gary Olsen.

The Phylogenetic Tree of Life based on comparative ssrRNA Sequencing. The Tree shows the procaryotes in two Domains, Archaea and Bacteria. At a taxonomic level, most organisms at the tips of the Archaeal branches represent a unique Order; most organisms a the tips of the bacterial branches are classified into a unique Phylum. On the Archaeal limb, the three physiological groups are evident in the names: "thermo" and "pyro" for the extreme thermophiles; "methano" for the methanogens; and "halophiles" for the extreme halophiles. The most important, best known, and diverse groups (phyla) branching off of the Bacterial limb are the Cyanobacteria, Proteobacteria and Gram positives.

In the ensuing description of "important groups of procaryotes", groups of organisms are placed under artificial headings based on common structural, biochemical or ecophysiological properties. This does not imply close genetic relatedness among different genera in a group. Sometimes, all of the members of a group do share a close genetic relatedness; in other cases, members of a group are genetically-unrelated, even to an extent that is greater than exists among all members of the Eucaryotic domain. Also herein, some procaryotes are placed in more than one group, and occasionally some groups consist of both Archaea and Bacteria.


On the basis of ssrRNA analysis, the Archaea consist of three phylogenetically-distinct groups: Crenarchaeota, Euryarchaeota and Korarchaeota. However, for the Korarchaeota, only their nucleic acids have been detected, and no organisms have been isolated or cultured.

Based on their physiology, the Archaea can be organized into three types: methanogens (procaryotes that produce methane); extreme halophiles (procaryotes that live at very high concentrations of salt (NaCl); and extreme (hyper) thermophiles (procaryotes that live at very high temperatures). In addition to the unifying archaeal features that distinguish them from Bacteria (i.e., no murein in cell wall, ether-linked membrane lipids, etc.), the Archaea exhibit other unique structural or biochemical attributes which adapt them to their particular habitats. The Crenarchaeota consist mainly of hyperthermophilic sulfur-dependent procaryotes and the Euryarchaeota contains the methanogens and extreme halophiles. ssrRNAs of the Korarchaeota have been obtained from hyperthermophilic environments similar to those inhabited by Crenarchaeota. None of the Korarchaeota have been cultured in the laboratory, although information about them can be inferred from their genome structure.

Figure 1. Phylogenetic tree of Archaea

Methanogens are obligate anaerobes that will not tolerate even brief exposure to air (O2). Anaerobic environments are plentiful, however, and include marine and fresh-water sediments, bogs and deep soils, intestinal tracts of animals, and sewage treatment facilities. Methanogens have an incredible type of metabolism that can use H2 as an energy source and CO2 as a carbon source for growth. In the process of making cell material from H2 and CO2, the methanogens produce methane (CH4) in a unique energy-generating process. The end product (methane gas) accumulates in their environment. Methanogen metabolism created most the natural gas (fossil fuel) reserves that are tapped as energy sources for domestic or industrial use. Methanogens are normal inhabitants of the rumen (fore-stomach) of cows and other ruminant animals. A cow belches about 50 liters of methane a day during the process of eructation (chewing the cud). Methane is a significant greenhouse gas and is accumulating in the atmosphere at an alarming rate. When rain forests are destroyed and replaced by cows, it is "double-hit" on the greenhouse: (1) less CO2 is taken up due to removal of the the autotrophic green plants; (2) additional CO2 and CH4 are produced as gases by the combined metabolism of the animal and symbiotic methanogens. Methanogens represent a microbial system that can be exploited to produce energy from waste materials. Large amounts of methane are produced during industrial sewage treatment processes, but the gas is usually wasted rather than trapped for recycling.

Figure 2. Methanococcus jannaschii (Holger Jannasch). The archaean was originally isolated from a sample taken from a "white smoker" chimney at an oceanic depth of 2,600 meters on the East Pacific Rise. It can be grown in a mineral medium containing only H2 and CO2 as sources of energy and carbon for growth within a temperature range of 50 to 86 degrees. Cells are irregular cocci that are motile due to two bundles of polar flagella inserted near the same cellular pole, making it a rare example of a motile coccus.

Extreme halophiles live in natural environments such as the Dead Sea, the Great Salt Lake, or evaporating ponds of seawater where the salt concentration is very high (as high as 5 molar or 25 percent NaCl). The organisms require salt for growth and will not grow at low salt concentrations (Actually, the cells lyse at low NaCl concentrations). Their cell walls, ribosomes, and enzymes are stabilized by Na+. Halobacterium halobium, the prevalent species in the Great Salt Lake, adapts to the high-salt environment by the development of "purple membrane", formed by patches of light-harvesting pigment in the plasma membrane. The pigment is a type of rhodopsin called bacteriorhodopsin which reacts with light in a way that forms a proton gradient on the membrane allowing the synthesis of ATP. This is the only example in nature of non photosynthetic photophosphorylation. The organisms are heterotrophs that normally respire by aerobic means. The high concentration of NaCl in their environment limits the availability of O2 for respiration so they are able to supplement their ATP-producing capacity by converting light energy into ATP using bacteriorhodopsin.

Figure 3. Halobacterium salinariumis an extreme halophile that grows at 4 to 5 M NaCl and does not grow below 3 M NaCl. This freeze etched preparation shows the surface structure of the cell membrane and reveals smooth patches of "purple membrane" (bacteriorhodopsin) imbedded in the plasma membrane.

Thermomphiles and extreme thermophiles or "hyperthermophiles" come from several distinct phylogenetic lines of Archaea. These organisms require a very high temperature (80 degrees to 105 degrees) for growth. Their membranes and enzymes are unusually stable at high temperatures. Most of these Archaea require elemental sulfur for growth. Some are anaerobes that use sulfur as an electron acceptor for respiration in place of oxygen. Some are lithotrophs that oxidize sulfur as an energy source. Sulfur-oxidizers grow at low pH (less than pH 2), partly because they acidify their own environment by oxidizing So (sulfur) to SO4 (sulfuric acid). 

Hyperthermophiles are inhabitants of hot, sulfur-rich environments usually associated with volcanism, such as hot springs, geysers and fumaroles in Yellowstone National Park and elsewhere, and thermal vents ("smokers") and cracks in the ocean floor. Sulfolobus was the first hyperthermophilic Archaean discovered by Thomas D. Brock of the University of Wisconsin in 1970. His discovery, along with that of Thermus aquaticus (a thermophilic bacterium) in Yellowstone National Park, launched the field of hyperthermophile biology. (Thermus aquaticus is the source of the enzyme taq polymerase used in the polymerase chain reaction, PCR., The bacterium has an optimum temperature for growth of 70 degrees.) Sulfolobus grows in sulfur-rich, hot acid springs at temperatures as high as 90 degrees and pH values as low as 1. Thermoplasma, also discovered by Brock, is a unique thermophile that is the sole representative of a distinct phylogenetic line of Archaea. Thermoplasma resembles the bacterial mycoplasmas in that it lacks a cell wall. Thermoplasma grows optimally at 55 degrees and pH 2. Interestingly, it has only been found in self-heating coal refuse piles, which are a man-made waste.

Figure 4. Sulfolobus acidocaldarius (T.D. Brock). Sulfolobus is an extreme thermophile that has been found in geothermally-heated acid springs, mud pots and surface soils with temperatures from 60 to 95 degrees C, and a pH of 1 to 5. Left: Electron micrograph of a thin section (85,000X). Under the electron microscope the organism appears as irregular spheres which are often lobed. Right: Fluorescent photomicrograph of cells attached to a sulfur crystal. Fimbrial-like appendages have been observed on the cells attached to solid surfaces such as sulfur crystals.

The Korarchaeota represent what could be one of the least evolved lineages of modern life that has been detected in nature so far. Barns et al. discovered the Korarchaeota in Yellowstone's Obsidian Pool over a decade ago. The group has been subsequently defined only by 16S ribosomal RNA sequences obtained from a variety of marine and terrestrial hydrothermal environments. The 16S-rRNA-based phylogeny of the Korarchaeota suggests that this group forms a very deep, kingdom-level, major lineage within the archaeal domain.

To date, there are no representatives of the Korarchaeota in pure culture, and nothing is known about their properties.  However, in recent years, a robust, continuous enrichment culture that harbors these organisms in significant densities has been established. The enrichment community has been phylogenetically characterized and is known to comprise a relatively low diversity of other hyperthermophilic archaea and bacteria. It is thought to be a potential source for DNA that will provide a complete genome sequence for a member of this unique group of procaryotes

Although the Archaea are often inhabitants of extreme environments, there may be corresponding species of Bacteria, and even eucaryotes, in these habitats as well. No bacterium can produce methane, but in many anaerobic environments Bacteria are found in association with methanogens. With regard to acid tolerance, a bacterium, Thiobacillus, has been observed growing at pH near 0. A eucaryotic alga, Cyanidium, has also been found growing near pH 0. In superheated environments (greater than 100 degrees), Archaea may have an exclusive hold, but Bacteria have been isolated from boiling hot springs in Yellowstone National Park and other parts of the world. No bacterium grows at the highest salt concentration which supports the growth of the halobacteria, but osmophilic yeasts and fungi can grow at correspondingly low water activities where sugar is the solute in high concentration.

Archaeal Cell Envelopes

Archaea possess a broader range of cell envelope structural formats than Bacteria, and their cell walls never contain murein. Some archaea have only a single protein or glycoprotein S-layer as their cell wall (e.g. Methanococcus jannaschii and Sulfolobus acidocaldarius), whereas others have multiple layers (e.g. Methanospirillum hungatei). One archaean has a type of peptidoglycan called pseudomurein (because it lacks N-acetylmuramic acid). Sometimes, there can also be a high proportion of tetraether lipids in membranes, which render the cells more resistant to environmental stresses.

Are Archaea Gram-positive or Gram-negative?

Although the Gram reaction depends on both the structural format and the chemical composition of the cell envelope in bacteria, most archaea stain Gram-negative, independent of their basic cell envelope structure or chemical composition. An interesting exception is Methanobacterium formicicum that stains Gram-positive, since its cell wall contains pseudomurein, a type of peptidoglycan that lacks muramic acid. In one study, all other archaea stained Gram-negative because their cell walls were so disrupted during staining, that the crystal violet-mordant complex could not be retained by the cells. Methanococcus jannaschii was grown at both 50 degrees C and 70 degrees C, which increases the tetraether lipids in its plasma membrane from 20% (50 degrees C) to 45% (70 degrees C) of the total lipids; in both cases the cells stained Gram-negative. One conclusion from these observations is that in a Gram stain preparation of a mixed microbial population containing archaea and bacteria, the archaea are among the Gram-negative cells, and the Gram-positive cells are probably bacteria.

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Kenneth Todar has taught microbiology to undergraduate students at The University of Texas, University of Alaska and University of Wisconsin since 1969.

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