Rhee, Sung‐Keun

Summary Obligate acidophilic members of the thaumarchaeotal genus Candidatus 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 ( Ca . N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca . Nitrosotalea strains, extracted an almost complete Ca . Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca . Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca . Nitrosotalea strains represent separate species within the genus. The four Ca . 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 Ca . 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 Ca . Nitrosotalea lineage in acidic environments.

Summary The ammonium‐oxidizing microbial community was investigated in a granular sludge anaerobic ammonium‐oxidizing (anammox) reactor that was operated for about 1 year with high anaerobic ammonium oxidation activity (up to 0.8 kg NH 4 + ‐N m −3  day −1 ). A Planctomycetales ‐specific 16S rRNA gene library was constructed to analyse the diversity of the anaerobic ammonium‐oxidizing bacteria (AnAOB). Most of the specifically amplified sequences (15/16) were similar to each other (> 99%) but were distantly related to all of the previously recognized sequences (< 94%), with the exception of an unclassified anammox‐related clone, KSU‐1 (98%). An ammonia monooxygenase ( amoA ) gene library was also analysed to investigate the diversity of ‘aerobic’ ammonium‐oxidizing bacteria (AAOB) from the β‐ Proteobacteria . Most of the amoA gene fragments (53/55) clustered in the Nitrosomonas europaea–Nitrosococcus mobilis group which has been reported to prevail under oxygen‐limiting conditions. The quantitative results from real‐time polymerase chain reaction (PCR) amplification showed that the dominant AnAOB comprised approximately 50% of the total bacterial 16S rRNA genes in the reactor, whereas the AAOB of β‐ Proteobacteria represented only about 3%. A large fragment (4008 bp) of the rRNA gene cluster of the dominant AnAOB (AS‐1) in this reactor sludge was sequenced and compared with sequences of other Planctomycetales including four anammox‐related candidate genera. The partial sequence of hydrazine‐oxidizing enzyme ( hzo ) of dominant AnAOB was also identified using new designed primers. Based on this analysis, we propose to tentatively name this new AnAOB Candidatus ‘Jettenia asiatica’.