The Thaumarchaeota: an emerging view of their phylogeny and ecophysiology

Abstract

Thaumarchaeota range among the most abundant archaea on Earth. Initially classified as 'mesophilic Crenarchaeota', comparative genomics has recently revealed that they form a separate and deep-branching phylum within the Archaea. This novel phylum comprises in 16S rRNA gene trees not only all known archaeal ammonia oxidizers but also several clusters of environmental sequences representing microorganisms with unknown energy metabolism. Ecophysiological studies of ammonia-oxidizing Thaumarchaeota suggest adaptation to low ammonia concentrations and an autotrophic or possibly mixotrophic lifestyle. Extrapolating from the wide substrate range of copper-containing membrane-bound monooxygenases, to which the thaumarchaeal ammonia monooxygenases belong, the use of substrates other than ammonia for generating energy by some members of the Thaumarchaeota seems likely.

Figure 1

Phylogeny of ammonia-oxidizing Thaumarchaeota. (a) Schematic phylogeny of Archaea redrawn after a rooted maximum likelihood tree of 53 concatenated ribosomal proteins of Archaea (4853 deduced amino acid positions), with permission from Spang et al. [19^•]. The scale bar represents 10% estimated sequence divergence. (b) Majority consensus trees based on the 16S rRNA gene (1067 nucleic acid positions conserved in >50% of all Archaea) and archaeal amoA gene (592 nucleic acid positions) as inferred by maximum likelihood, distance, and maximum parsimony methods. ‘Nanoarchaeota’ have been shown to represent a fast evolving lineage of the Euryarchaeota (reviewed by Brochier-Armanet et al. in this issue and (a)) and are misplaced in 16S rRNA-based trees as a sister group of the Crenarchaeota. The shadowed area highlights a region of the 16S rRNA tree with unstable branching order and low bootstrap support. The bars represent 10% Jukes-Cantor corrected sequence divergence. Dots (●) indicate in all trees bootstrap support above 80% as inferred by maximum likelihood. Abbreviations: N. yellowstonii, Nitrosocaldus yellowstonii; N. gargensis, Nitrososphaera gargensis; N. maritimus, Nitrosopumilus maritimus; C. symbiosum, Cenarchaeum symbiosum; N. limnia, Nitrosoarchaeum limnia, SAGMCG-1, South African Gold Mine Crenarchaeotic Group 1.