Abstract
This chapter is divided into two major sections: a brief comparative description of the physiology of ammonia‐oxidizing archaea (AOA) in relation to the better‐characterized ammonia‐oxidizing bacteria (AOB); and a discussion of features that have been gleaned from the genome sequence and its relevance to environmental genomic studies. An understanding of copper homeostasis is fundamental to the understanding of ecological success of the AOA. The genome sequence points to two types of enzyme systems that may be involved in copper handling or response to oxidative stress: genes encoding multicopper oxidases and DsbA‐type proteins. Early metagenomics studies and the genome sequence of the sponge symbiont C. symbiosum provided an indication of a capacity for ammonia oxidation. Genomic and metagenomic studies have now shed initial light on the gene inventory of mesophilic AOA. These studies indicate not only that a tremendous diversity of Crenarchaeota may thrive by ammonia oxidation but also that a distinct biochemistry of ammonia oxidation serves energy conservation in these organisms. Broad temperature range, as well as oligotrophy among AOA, shows that apparently unfavorable thermodynamics of ammonia oxidation and the requirement of reverse electron transport for biosynthetic needs do not pose significant limitations on the competitiveness of archaeal nitrifiers for scarce energy resources such as ammonia.