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Hallam, SJ, Mincer, TJ, Schleper, C, Preston, CM, Roberts, K, Richardson, PM and DeLong, EF (2006) Pathways of carbon assimilation and ammonia oxidation suggested by environmental genomic analyses of marine Crenarchaeota. PLoS Biol. 4:e95


Marine Crenarchaeota represent an abundant component of oceanic microbiota with potential to significantly influence biogeochemical cycling in marine ecosystems. Prior studies using specific archaeal lipid biomarkers and isotopic analyses indicated that planktonic Crenarchaeota have the capacity for autotrophic growth, and more recent cultivation studies support an ammonia-based chemolithoautotrophic energy metabolism. We report here analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism. Genes predicted to encode multiple components of a modified 3-hydroxypropionate cycle of autotrophic carbon assimilation were identified, consistent with utilization of carbon dioxide as a carbon source. Additionally, genes predicted to encode a near complete oxidative tricarboxylic acid cycle were also identified, consistent with the consumption of organic carbon and in the production of intermediates for amino acid and cofactor biosynthesis. Therefore, C. symbiosum has the potential to function either as a strict autotroph, or as a mixotroph utilizing both carbon dioxide and organic material as carbon sources. From the standpoint of energy metabolism, genes predicted to encode ammonia monooxygenase subunits, ammonia permease, urease, and urea transporters were identified, consistent with the use of reduced nitrogen compounds as energy sources fueling autotrophic metabolism. Homologues of these genes, recovered from ocean waters worldwide, demonstrate the conservation and ubiquity of crenarchaeal pathways for carbon assimilation and ammonia oxidation. These findings further substantiate the likely global metabolic importance of Crenarchaeota with respect to key steps in the biogeochemical transformation of carbon and nitrogen in marine ecosystems.


PubMed PMC1403158 Online version:10.1371/journal.pbio.0040095


Acetyl-CoA Carboxylase/genetics; Ammonia/metabolism; Carbon/metabolism; Citric Acid Cycle; Crenarchaeota/genetics; Crenarchaeota/metabolism; DNA, Archaeal/genetics; Databases, Genetic; Genome, Archaeal/genetics; Isoenzymes/genetics; Isoenzymes/metabolism; Lactic Acid/analogs & derivatives; Lactic Acid/metabolism; Marine Biology; Molecular Sequence Data; Oceans and Seas; Operon/genetics; Oxidation-Reduction; Oxidoreductases/genetics; Oxidoreductases/metabolism; Phylogeny; Seawater/microbiology



Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status


GO:0004497: monooxygenase activity


PMID:15001713[1] PMID:18793310[2]


Figure 4 (B) Shows the similarity of the C. symbiosum ammonia monooxygenase (acc) gene cluster and unlinked amoC3 locus to the bacterial operon from N. europaea.

CACAO 2435



GO:0004497: monooxygenase activity

ECO:0000317: genomic context evidence used in manual assertion


Seeded From UniProt

Missing: with/from

See also


See Help:References for how to manage references in GONUTS.

  1. Venter, JC et al. (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304 66-74 PubMed GONUTS page
  2. Martínez-García, M et al. (2008) Ammonia-oxidizing Crenarchaeota and nitrification inside the tissue of a colonial ascidian. Environ. Microbiol. 10 2991-3001 PubMed GONUTS page