Ammonia‐oxidising archaea living at low pH: Insights from comparative genomics

<jats:title>Summary</jats:title> <jats:p> Obligate acidophilic members of the thaumarchaeotal genus <jats:italic>Candidatus</jats:italic> Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations to acidic environments are still poorly understood, with only a single member of this genus ( <jats:italic>Ca</jats:italic> . N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured <jats:italic>Ca</jats:italic> . Nitrosotalea strains, extracted an almost complete <jats:italic>Ca</jats:italic> . Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four <jats:italic>Ca</jats:italic> . Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four <jats:italic>Ca</jats:italic> . Nitrosotalea strains represent separate species within the genus. The four <jats:italic>Ca</jats:italic> . Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the <jats:italic>Ca</jats:italic> . Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the <jats:italic>Ca</jats:italic> . Nitrosotalea lineage in acidic environments. </jats:p>