The Archaea evolved over 3 billion years ago but were only formally proposed as a domain 20 years ago. Today, many of the unique features and many of those that are shared with either the Bacteria or the Eukarya are well understood. Here, Ricardo Cavicchioli describes some of the important events in our appreciation of this fascinating group of organisms. The Archaea evolved as one of the three primary lineages several billion years ago, but the first archaea to be discovered were described in the scientific literature about 130 years ago. Moreover, the Archaea were formally proposed as the third domain of life only 20 years ago. Over this very short period of investigative history, the scientific community has learned many remarkable things about the Archaea — their unique cellular components and pathways, their abundance and critical function in diverse natural environments, and their quintessential role in shaping the evolutionary path of life on Earth. This Review charts the 'archaea movement', from its genesis through to key findings that, when viewed together, illustrate just how strongly the field has built on new knowledge to advance our understanding not only of the Archaea, but of biology as a whole.

Archaea — timeline of the third domain

LBNL-60247 Preprint Title: The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes Author(s): Dennis L. Maeder, Iain Anderson, et al Division: Genomics November 2006 Journal of Bacteriology

The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes

Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass

ABSTRACT The activity of nitrogenase in the nitrogen-fixing bacteriumAzotobacter vinelandii grown diazotrophically under aerobic conditions is generally considered to be protected against O2 by a high respiration rate. In this work, we have shown that a high rate of respiration is not the prevailing mechanism for nitrogenase protection in A. vinelandii grown in phosphate-limited nitrogen-free chemostat culture. Instead, the formation of alginate appeared to play a decisive role in protecting the nitrogenase that is required for cell growth in this culture. Depending on the O2 tension and cell growth rate, the formation rate and composition of alginate released into the culture broth varied significantly. Furthermore, transmission electron microscopic analysis of cell morphology and the cell surface revealed the existence of an alginate capsule on the surface of A. vinelandii. The composition, thickness, and compactness of this alginate capsule also varied significantly. In general, increasing O2 tension led to the formation of alginate with a higher molecular weight and a greater l-guluronic acid content. The alginate capsule was accordingly thicker and more compact. In addition, the formation of the alginate capsule was found to be strongly affected by the shear rate in a bioreactor. Based on these experimental results, it is suggested that the production of alginate, especially the formation of an alginate capsule on the cell surface, forms an effective barrier for O2 transfer into the cell. It is obviously the quality, not the quantity, of alginate that is decisive for the protection of nitrogenase.

Effect of oxygen on formation and structure of Azotobacter vinelandii alginate and its role in protecting nitrogenase

Low pressure and desiccation effects on methanogens: Implications for life on Mars

In vivo expression of CO dehydrogenase/acetyl coenzyme A synthase in Methanosarcina spp. is coordinately regulated in response to substrate by at least two mechanisms: differential transcription initiation and early elongation termination near the 3' end of a 371-bp leader sequence. This is the first report of regulation of transcription elongation in the Archaea.

A 5′ Leader Sequence Regulates Expression of Methanosarcinal CO Dehydrogenase/Acetyl Coenzyme A Synthase

This chapter discusses molecular genetics of Archaea. Gene transfer systems currently exist for species within all three physiological groups of archaea, halophiles, methanogens, and nonmethanogenic hyperthermophiles. The chapter reviews the development of these systems. Colonization of methanogenic and nonmethanogenic hyperthermophiles on solidified medium is equally problematic, as agar is rapidly dehydrated at high temperatures, especially at the concentrations required for it to remain solidified. Therefore, gellan gum (Gelrite) is used as the solidifying agent for growth of thermophiles and hyperthermophiles, which are incubated in a plastic bag or anaerobe jar to minimize dehydration. Haloarchaea are transformed via polyethylene glycol (PEG) mediated transformation, which was first described in Haloferax volcanii. Gene disruption is required to identify and confirm the function of genes within the archaea. Random mutagenesis using chemical and UV radiation has been successfully used for H. volcanii, Methanococcus voltae, Methanococcus maripaludis, and Pyrococcus abyssi. Progress in the development of methodologies for archaeal genetics has rapidly accelerated in the past decade. Additional methods are currently under development for all three archaeal phyla, including additional systems for markerless exchange, gene expression, topological mapping, protein tagging and expression, as well as others. The choice of archaeal genomes for sequencing is now largely driven by the availability of genetic systems, which at present include complete genomes of the halophiles Haloarcula marismortui and Halobacterium sp.

Kimberly L. Anderson

Papers

A 5′ Leader Sequence Regulates Expression of Methanosarcinal CO Dehydrogenase/Acetyl Coenzyme A Synthase

Molecular Genetics of Archaea

Methanosarcina barkeri Mechanism for the Archaeon Desiccation as a Long-Term Survival