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A Microbial Biorealm page on the genus Cenarchaeum


Domain: Archaea; Phylum: Thaumarchaeota; Order: Cenarchaeales; Family: Cenarchaeaceae; Genus: Cenarchaeum

An important species is Cenarchaeum symbiosum.

Description and significance

The genus Cenarchaeum is named from the Greek kainos (recent) and koinos (common) as well as archaeo (ancient) to be a genus of relatively recent (meaning nonthermophilic, as archea are postulated to have evolved from hyperthermophiles) and common (not living in a very specific niche extremophile environment) archaea.

The species Cenarchaeum symbiosum is a psychrophilic archaeon that lives in in a specific symbiosis with an Axinella species of sponge--this single phylotype of archaea is associated with a lone species of sponge. This type of archaeon was very important in the early development of the domain archaea as the first non-thermophylic crenarchaeote and the first crenarchaeote and non-methanogen to be found in a symbiotic relationship.

Genome structure

Cenarchaeum symbiosum has a single circular chromosome 2,045,086 bp in length. On average, the genome has 57.74% G/C content. The origin(s) of replication are not known. 2,017 protein-encoding genes were predicted and for 65% of these, homology searches showed functional or conserved roles. 47 RNA genes were found in the genome, including 1 operon for a linked small subunit-large subunit ribosomal rRNA, 1 copy of a 5S rRNA, and 45 genes predicted to encode transfer RNAs.

This genome contains most of the core genes generally expected of Archaea. All genes necessary for functional chromosomal replication are also present. Two distinct DNA polymerases are coded for in the genome, one related to those in the thermophilic Crenarchaeota and one similar to euryarchaeotal DNA polymerase II. A eukaryal-like H3-H4 histone was also found in the genome of C. symbiosum, the first crenarchaeote in which this was found.

The genome of C. symbiosum is postulated to contain introns (in 10 of the 45 tRNA genes).

Cell structure, metabolism & life cycle

Cenarchaeum symbiosumexists as rod-shaped cells averaging 0.8 microns long and 0.5 microns wide.

In terms of metabolism, genetic analysis suggests that C. symbiosum uses at least an incomplete TCA cycle. The genome also indicates an intact Embden-Meyerhof-Parnas pathway, although without glucokinase or pyruvate kinase, which suggests that it may form glucose through this pathway rather than breaking it down. However, genes were also found to encode carbohydrate kinases of unknown specificity. Many Entner-Douodoroff pathway components were missing from the genome, indicating that this archaeon does not use the ED pathway for catabolism. However, a nonoxidative pentose phosphate pathway was identified, which could provide NADPH and ribose sugars for anabolism. Homologous genes that could be associated with ammonia oxidation occur in the genome of C. symbiosum, but between missing homologues and identified potential cytochrome replacements for mobile electron carrying, energy derived from ammonia oxidiation is likely obtained through different mechanisms than those of most nitrifying bacteria.

C. symbiosum has an active life cycle in symbiotic association with a sponge, and is seen to actively divide in such samples.

Ecology (including pathogenesis)

Cenarchaeum symbiosum is psychrophilic, with a natural habitat ~8-18 degrees Celcius. This archaeon forms a symbiosis with an Axinella species (potentially Axinella mexicana, but there were small differences). It was found associated with these sponges at depths of 10-20 meters in the ocean just offshore of Santa Barbara, California. This species is abundant and actively divides when associated with the sponge, and remains associated with the sponge over long periods, which suggests that this is truly a symbiotic relationship.

Interesting feature

Cenarchaeum symbiosum was the first crenarchaeote discovered to be psychrophilic, rather than a thermophile or extreme thermophile, showing the wide range of temperatures inhabited by archaea. This made clear the ecological importance of archaea as abundant and ubiquitous rather than existing only in extreme niche environments.

The symbiosis of C. symbiosum with the Axinella species is also the first incidence of Crenarchaeota being involved in a symbiotic relationship. Previously, only two euarchaeal subgroups of methanogens had been described in symbiotic relationships. C. symbiosum was the first non-methanogenic archaeon described in a symbiotic relationship.


Euzeby, J.P. "Classification of domains and phyla - Hierarchical classification of prokaryotes (bacteria)". List of Prokaryotic names with Standing in Nomenclature. Last major update October 06, 2011. Accessed October 19, 2011.

Hallam, S.J., K.T. Konstantinidis, N. Putnam, C. Schleper, Y. Watanabe, J. Sugahara, C. Preston,J. de la Torre, P.M. Richardson, and E.F. DeLong. "Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum". Proceedings of the National Academy of Sciences of the United States of America. 2006. Volume 103. p. 18296-18301.

Preston, C.M., K.Y. Wu, T.F. Molinski, and E.F. DeLong. "A psychrophilic crenarchaeon inhabits a marine sponge: Cenarchaeum symbiosum gen. nov., sp. nov.". Proceedings of the National Academy of Sciences of the United States of America. 1996. Volume 93. p. 6241-6246