A Brief treatment on the current status of the ArchaeaWithin science and industry

By CM HoutsGeologistMay 6

, 2007Abstract

The acceptance of the Domain Archaea within the past 30 odd years has been greeted with hosannason some fronts and grudging silence on others. Why would a single celled organism physicallyindistinguishable from its bacterial cousins cause such an array of emotions? The media has eagerlytapped into this unexplored territory, because of its strange ability to withstand extreme environments,hence the name,

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Extremophiles.

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The amazing habitats of these creatures are really the leastinteresting thing about them. The questions posed and the controversies raised are of greatersignificance, and may in the end have a far reaching effect, that could not be expected.

Introduction

Archaea are not easily described, without some understanding of their evolution andsignificance. One could claim that all species are significant in their own way, but they cannotclaim an enigmatic presence during the Archaean eon which causes many scientists to believethey may be the LUCA or

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last universal common ancestor.

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The archaea have raisedcompelling questions about the foundation of the Taxonomic and Phylogenic organization inwhich we describe the relationships of organisms. Their physiology and anatomy has instigateda controversy with respect to how they developed, how they have remained virtually

unchanged, and how astoundingly impervious they are to environments, that would kill prettymuch any of your run-of-the-mill Eukaryotes.The aforementioned scientific details are mostly only of interest to microbiologists and the like.On the other hand, the Archaea could prove to be the unsung hero of bioremediation. Theability to thrive in extreme environments provides them with unique biological traits which canbe used to remove pollutants from water, soil, and the atmosphere. They eat nuclear waste,carbon, and the poisonous byproducts of sulfide mining. Their relatively simple genetic codemay be the DNA equivalent of the Rosetta stone for geneticists who are working on sequencingthe genomes of more complex organisms, such as humans. There are theories that excite theimagination, suggesting that Archaea might show how extraterrestrial life survives on planetswith hostile environments or even be the extraterrestrial primogenitor of all living things,catching a lift on a passing comet or meteor.Plausible or not, their differences from other life forms are fascinating and their similarities aredisturbing, on both an evolutionary basis and a philosophical one. In order to clarify this crypticstatement, we must delve into some accepted evolutionary theories. Up until the 1960s or so,there were two kingdoms at the root of the evolutionary tree: the Prokaryotes and theEukaryotes. All known forms of bacteria were divided into one or the other group dependingupon the presence or absence of a cell wall which confined the DNA material. Nobody thoughtto question the traditional taxonomy, as it was sacrosanct and deeply entrenched in thescientific arena. Molecular biology was barely out of its infancy when

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Linus Pauling andEmile Zuckerlandl formalized the idea of using the makeup of biological molecules, their

sequence, as a way to determine phylogenetic relationships.

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It was Dr. Carl Woese and hisassociates who challenged the overtly simplified categorization and offered up a new tri-partitefoundation consisting of eukaryotes, eubacteria, and the archaea. He suggested that, insteadof attempting to completely restructure the taxonomic hierarchy, they create a taxon called

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domains

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that would encompass the kingdoms taxa. Almost everyone hated it. The proposaland evidence was ignored and scoffed at initially, until they gained the approval and support of a well-known German microbiologist.Needless to say, this was not an overnight process. Dr. Woese and his coworkers had notbegun their research with the intent of destroying the assumptions of those within thebiological sciences, nor undermining the framework that had been, reverently, in place sinceDarwin. While working on a methanogen that had been categorized as a prokaryote, they cameacross characteristics that simply did not fit into the accepted definition of that category. Uponfurther tests, they came to the conclusion that it wasn

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t the organism that was the problem; itwas the classification that was giving them trouble. Dr. Ralph Wolfe, who was working with Dr.Woese, insisted that they needed more proof before they could present their findings andhypothesis. They chose to look at an aspect, unknown in methanogens, known in three otherExtremophiles species: halophiles, thermoplasmas, and a thermoacidophile. The methanogenwas found to be the same as the other subjects. They were on a role now, and were able toexperimentally show the strange similarities and differences methanogens had, with both theprokaryote and eukaryotic domains. Despite these and other experimentally proven tests, itwas still years before the archaea were formally acknowledged and Woese

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s phylogeneticrecommendations were integrated.