Schleper, Christa

AbstractAmmonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first cultivated thermophilic representative with a sequenced genome, which allows to search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota.CandidatusNitrosocaldus cavascurensis has been cultivated from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 25h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome ofCa.N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase, genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the importance of this compound for AOA metabolism.Ca.N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.

Abstract Cen.ar.chae'um., Gr. adj. kainos recent, and Gr. adj. koinos common; Gr. adj. archaios ancient; N.L. neut. n. Cenarchaeum = genus of relatively recent (derived nonthermophilic phenotype) and common (non‐“extremophilic”) Archaea. The species Candidatus Cenarchaeum symbiosum of the genus Candidatus Cenarchaeum constitutes the sole archaeal symbiont of the temperate marine sponge Axinella mexicana . It represented the first tractable organism of the so‐called mesophilic crenarchaeota, now Nitrososphaeria, until pure isolates and enrichment cultures became available. It was also the source of the first assembled full genome of the Nitrososphaeria . Physiological and genomic analyses suggest that representatives of this genus are aerobic, psychrophilic, and capable of a chemolithoautotrophic metabolism, by oxidizing ammonia to nitrite. The environmental distribution of the genus so far has been confined to sponge‐associated communities. DNA G + C content (mol%) : 57.74. Type species : Candidatus Cenarchaeum symbiosum Preston, Wu, Molinsky and DeLong 1996, 6246. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Cenarchaeum is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosopumilales / Nitrosopumilaceae / Candidatus Cenarchaeum The genus Candidatus Cenarchaeum can also be recovered in the Genome Taxonomy Database (GTDB) as g__Cenarchaeum (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosopumilaceae / g__Cenarchaeum * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776