In 1977 Carl Woese and George Fox expanded our appreciation of microbial diversity by analyzing the genetic sequence of a
molecule (ribosomal RNA) found in all cells. They discovered that species previously classified as bacteria, called methanogenic bacteria, possessed unique enzymes and an unusual
metabolism based on reducing carbon dioxide to methane. These traits were foreign to both uber domains of life, Eurkaryota and Bacteria, prompting Woese to create a new category, which he called Archaebacteria (
archae means ancient in Greek), acknowledging a metabolism that would have suited the putative conditions on earth over 3 billion years ago.
Archaeal groups have been found in a wide array of habitatsfrom boiling sulfur pits, salt marshes, and hydrothermal vents to frosty Antarctic surface waters, mud flats, and freshwater habitatsyet less than 0.1% of expected species have been characterized.
In a new study, genetic analysis offers clues to the fundamentals of archaeal life and some insight into how these organisms can exist in such diverse environments. Steven Hallam, Edward DeLong, and their colleagues enlist genomics techniques to identify the pathways used by the marine sponge symbiont
Cenarchaeum symbiosum to accomplish lifes most essential processes: energy metabolism and carbon
assimilation. And by comparing the
C. symbiosum genome sequence with sequences extracted from environmental samples collected from diverse ocean habitats, they show that planktonic Crenarchaeota share many of the same genetic components.
Many archaeal species can use inorganic compounds (rather than sunlight, like plants) as an energy source for carbon synthesis, earning them the unwieldy name of chemolithoautotroph. Several lines of evidence suggest that planktonic Crenarchaeota, significant components of the marine ecosystem, assimilate carbon in this way and that they might use ammonia (NH3) as an energy source, since they inhabit ammonia-rich Antarctic waters and are associated with high nitrite concentrations. (Nitrite is a by-product of ammonia oxidation.)
To search for genetic clues to carbon and energy metabolism in Crenarchaeota, the researchers extracted
C. symbiosum DNA from its host sponge and constructed a DNA library for sequencing the symbionts genome. Hallam et al. then searched for representative genes linked to pathways associated with autotrophic carbon assimilation. They found many components of two pathways: the 3-hydroxypropionate cycle and the reductive tricarboxylic acid (citric acid) pathway (TCA). Both cycles involve a multistep series of chemical reactions that convert inorganic compoundsin this case, carbon dioxideinto organic carbon molecules. Though some components of the 3-hydroxypropionate cycle were missing in
C. symbiosum, enough elements (including core proteins) were found to support a modified version of this pathway for carbon assimilation, using carbon dioxide.
In eukaryotes, the TCA cycle links the oxidative breakdown of carbon compounds with biosynthesis and energy metabolism. In prokaryotes, the process is reversed, with the oxidation of inorganic compounds (such as carbon dioxide) providing the means for carbon assimilation. Again, though some TCA components were missing, Hallam et al. found evidence suggesting that
C. symbiosum could use partial TCA reactions to produce biosynthetic precursors. Its possible that other genes take the place of the missing components or that the TCA and 3-hydroxypropionate pathways overlap.
The researchers next searched for genes that might play a role in generating energy from ammonia oxidation (also called nitrification because ammonia is converted to nitrite). The
C. symbiosum genome contains many genes associated with nitrification in bacteria, including genes that encode the subunits of ammonia monooxygenase, which catalyzes the first step in converting ammonia to nitr