by Martian Adam Smyth

Introduction       As with all sciences, microbiology is a field of continual discovery. There are countless species of life forms yet to be discovered in the world, and there will continue to be so for as long as the biosphere survives. Life is not a static thing; new forms are constantly developing and evolving from earlier forms. In this paper, I discuss a relatively recently discovered group of lifeforms that caused a major change in the way biologists classify life. This group, called Archaea - meaning 'ancient ones' - includes creatures living in the most hostile environments on the planet. Originally thought to be a new type of bacteria, analysis of their RNA proved them to be a wholly separate type of life. Archaea are being studied both for their importance as a biological domain - they could help in the discovery of the so-called 'universal ancestor', the precursor to all terrestrial life - and for their potential commercial applications, both in energy production and pollution control. General Description       In the 1970s, Carl Woese and other researchers of the University of Illinois at Urbana-Champaign Life Sciences department were working with rRNA sequences as a method of classification of organisms. 'rRNA' is the ribosomal form of ribonucleic acid. Manufactured from DNA, it is transported to the ribosomes where it embeds itself. Although unsure of its exact function, scientists theorize that rRNA holds the mRNA against the ribosome as it is read to manufacture a protein. 'mRNA' is messenger RNA, and carries the information the ribosome needs for protein synthesis.       During their research, they discovered a group of prokaryotes that differed significantly in their rRNA structures from normal bacteria. Further analysis uncovered the fact that these new species had considerably less in common with bacteria than they did with eukaryotes.       Until this time, the highest-level division of lifeforms was into the groups 'prokaryotes' and 'eukaryotes'. Prokaryotes are unicellular lifeforms with no distinct nucleus. Their genetic material - their DNA - floats freely throughout the cell. Eukaryotes can be either unicellular or multicellular, and their genetic material is contained inside a cell nucleus.       These new prokaryotes were first termed 'archaebacteria', but that term has fallen out of use, and the more accurate name 'archaea' has come into use to describe them. Archaea were first discovered in high-temperature thermal vents - sometimes at temperatures above 100°C - and in extremely saline waters, such as those around salt works. More recently, however, species of archaea have been found in less extreme environments, such as the cold waters of Antarctica and as part of the plankton in the open ocean.       The archaea are unique organisms. While prokaryotes in the cytological sense, they are actually more closely related to eukaryotes than to the bacteria. They are of particular interest for this reason alone - they are simple organisms whose study should provide insights into the nature and evolution of the eukaryotic cell. Their study is also central to an understanding of the nature of the ancestor common to all life. The archaea are, of course, interesting in their own right. The group contains both the methanogens and numerous organisms that grow at extremely high temperatures (in some cases above 100°C). As such, they provide potential insights into mechanisms of thermophilia and methanogenesis. (Woese)       The discovery of organisms that thrive in extreme conditions formerly thought uninhabitable has provoked some scientists to reconsider the possibility of life existing on other planets. For example, the existence of the Sulfolobales phylum would suggest potential viability of a similar form in an environment like the Jovian moon Io.       This ability to exist in harsh conditions, and the ability of some phylums to produce methane or digest sulfur, suggests archaean's use as sources of clean energy and pollution control.       The federal government is so interested in the thermophiles that the Department of Energy recently established the Microbial Genome Initiative to fund genomic sequencing and mapping of microorganisms -- including archaea, also known as archaebacteria -- that may have applications in environmental cleanup, pollution prevention, or energy production. (1.4)       Although they are prokaryotes, archaea are at least as dissimilar from bacteria as they are from eukaryotes. Genetically, archaea are more than two-thirds different from either bacteria or eukaryotes. It is believed that archaea may provide further clues to a common 'universal ancestor'.       The most easily noticeable differences among the three domains are in their physical structure. The cell wall, for instance, differs between Eukaryal kingdoms - plants have a polysaccharide cell wall to give them more rigid support, while animals have none, allowing them flexibility. Bacteria have a cell wall composed of a combination of proteins and polysaccharides. Archaean cell walls are protein only. The cell membranes show even greater difference. Bacterial and eukaryal cell membranes are composed of straight-chain fatty acids linked by ester molecules to polysaccharides. Archaeal membranes, however, contain no fatty acids. Instead, they use branched-chain hydrocarbon molecules linked to the polysaccharides by ether bonds. Classification       Until 1977, it was taken as an axiom that all organisms could be placed into one of two groups: prokaryotes or eukaryotes. Then, Carl Woese and Ralph Wolfe called for a change in the way biologists classify organisms. They argued that the archaea were different enough to warrant a new system of grouping. They called for a new level of taxonomy above the 'Kingdom'. To be termed the 'Domain', there would be three: the Bacteria, the Archaea, and the Eukaryota. (25woese) (Entrez)       Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. [...] Archaea is formally subdivided into the two kingdoms Euryarchaeota [...] and Crenarchaeota. (Entrez) Current classification recognizes three "Domains" (Lect10) Archaea - few present survivors retain ancestral characteristics, the adaptations to conditions of the early earth. Methanogens - obtain energy by reducing CO2 to methane and sulfur to H2S. Extreme halophiles - Aerobic species, living in high salt concentrations Crenarchaeota (Eocytes) - Thermacidophiles - Inhabit hot sulfur springs & deep ocean volcanic vents; can stand 110°C, pH 2. Eubacteria - great diversity of prokaryotic organisms adapted to essentially all environments. Photosynthesis evolved several times using different types of chlorophyll, e.g. purple photosynthetic bacteria reduce H2S rather than H2O; cyanobacteria use chlorophyll A. Eukaryota - Complex cells; nuclear genome related to Archaea. Most descended from unicellular ancestors which evolved symbiotic relationships with Eubacteria - mitochondria and chloroplasts derived from such endosymbionts. Most Eukaryotes have genomes of hybrid ancestry. Biochemistry       Archaea are best known for their ability to thrive in hostile environments. The different types of archaea have specialized characteristics which enable them to survive in these environments:       Thermophilia, the preference for environments with very high temperatures, is the most common trait among archaea. Species have been found living in thermal vents such as those in Yellowstone, and in volcanic fissures in the ocean floor. Some have been found living in temperatures as high as 113°C. Few non-archaean species can survive in environments hotter than 80°C. Most thermophilic archaea are methanogens. The chemicals they depend on for energy are usually found in these high-temperature environments.       Acidophiles are lifeforms that exist in highly acidic environments. Until recently, there were only 4 organisms known that could grow at extremely low pH levels; all were eukaryotes. At least two groups of archeans have been added to this group, both of which are also thermophiles.       Halophiles exist in places with very high salt content. Several of the archaeal families have adapted for life in hypersaline environments, especially in the waste-output ponds of salt works. This picture shows an immense bloom of a halophilic archaean species - Halobacterium - in a waste-output pool at a salt works near San Quintin, Baja California Norte, Mexico. Halobacterium, also lives in enormous numbers in highly saline ponds near the south end of San Francisco Bay. (archaea)       The euryarchaeota kingdom of archaea is comprised largely of methanogens, which - instead of using oxygen as the chemical substrate for energy production - use carbon dioxide and hydrogen. The result is methane, which many would like to use as an alternative fuel. Although they are not unique in being anaerobic, the only known lifeforms to generate methane directly are archaeans.       Methanogens are used to convert biomass to the useful fuel methane (natural gas), and to degrade and detoxify agricultural, municipal and industrial wastes. Understanding their basic biochemistry, and identifying the mechanisms that regulate microbial methane production, therefore have direct applications in improving the world-wide exploitation of this biotechnology for energy production and for environmental pollution control. (JNR)       Archaea are already being used for some commercial purposes, and more are constantly under development. Enzymes derived from some species will be used for improved DNA sequencing and as biocatalists in industrial applications. Conclusion       The discovery of a new class of lifeforms caused a notable upheaval in microbiology. Our increasing knowledge of archaea has caused biologists to drastically restructure their classification systems, as well as their assumptions about what conditions are necessary to produce life. As we begin to gain greater understanding of archaea and their place in the natural world, implications of their potential as pollution controllers and clean energy producers manifest. The importance of discoveries such as these can not be underemphasized. Industry will become increasingly dependent on biotechnological solutions as non-renewable resources are exhausted and anti-pollution laws are enacted. Archaea, the 'ancient ones' of the organic world, bring promising secrets from their hostile homes, and may provide clues to the evolution of the eukaryal nucleus, as well as revolutionizing biotechnology and expanding the horizons of our understanding.