de la Torre, José R.

AbstractAmmonia-oxidizing archaea (AOA) within the phylumThaumarchaeaare the only known aerobic ammonia oxidizers in geothermal environments. Although molecular data indicate the presence of phylogenetically diverse AOA from theNitrosocaldusclade, group 1.1b and group 1.1aThaumarchaeain terrestrial high-temperature habitats, only one enrichment culture of an AOA thriving above 50 °C has been reported and functionally analyzed. In this study, we physiologically and genomically characterized a novelThaumarchaeonfrom the deep-branchingNitrosocaldaceaefamily of which we have obtained a high (∼85 %) enrichment from biofilm of an Icelandic hot spring (73 °C). This AOA, which we provisionally refer to as “CandidatusNitrosocaldus islandicus”, is an obligately thermophilic, aerobic chemolithoautotrophic ammonia oxidizer, which stoichiometrically converts ammonia to nitrite at temperatures between 50 °C and 70 °C.Ca.N. islandicus encodes the expected repertoire of enzymes proposed to be required for archaeal ammonia oxidation, but unexpectedly lacks anirKgene and also possesses no identifiable other enzyme for nitric oxide (NO) generation. Nevertheless, ammonia oxidation by this AOA appears to be NO-dependent asCa.N. islandicus is, like all other tested AOA, inhibited by the addition of an NO scavenger. Furthermore, comparative genomics revealed thatCa.N. islandicus has the potential for aromatic amino acid fermentation as its genome encodes an indolepyruvate oxidoreductase(iorAB)as well as a type 3b hydrogenase, which are not present in any other sequenced AOA. A further surprising genomic feature of this thermophilic ammonia oxidizer is the absence of DNA polymerase D genes - one of the predominant replicative DNA polymerases in all other ammonia-oxidizingThaumarchaea.Collectively, our findings suggest that metabolic versatility and DNA replication might differ substantially between obligately thermophilic and other AOA.

Abstract Ni.tro.so.cal'dus. N.L. adj. nitrosus nitrous; L. masc. adj. caldus hot; N.L. masc. n. Nitrosocaldus a nitrite producer at thermophilic growth temperatures. Thermophilic, neutrophilic, autotrophic, and aerobic ammonia‐oxidizing archaea. Urea can be used as a source of energy for growth. Cells fix CO 2 via a modified 3‐hydroxypropionate/4‐hydroxybutyrate carbon fixation pathway. Cells are irregular cocci between 0.65 and 0.75 microns in diameter. Cells reproduce by binary fission. Cell membrane lipids consist mainly of acyclic and cyclized glycerol trialkyl glycerol tetraethers (GTGTs) and glycerol dibiphytanyl glycerol tetraethers (GDGTs), with acyclic GTGT and crenarchaeol as the dominant components. Quinone systems include menaquinones with fully saturated and monounsaturated side chains that comprised six isoprenoid units. The members of the genus Ca . Nitrosocaldus can be found in neutral or slightly alkaline terrestrial geothermal environments at temperatures ranging from 65 to 85°C. Phylogenetic analysis on the basis of both 16S rRNA and amoA genes supports the monophyletic genus Ca . Nitrosocaldus within the family Ca . Nitrosocaldaceae. DNA G + C content (mol%) : 37.1. Type species : Ca . Nitrosocaldus yellowstonensis (Nitrosocaldus yellowstonii) de la Torre, Walker, Ingalls, Könneke and Stahl 2008, 815. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nitrosocaldus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / incertae sedis / Candidatus Nitrosocaldales / Candidatus Nitrosocaldaceae / Candidatus Nitrosocaldus The genus Candidatus Nitrosocaldus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nitrosocaldus (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosocaldaceae / g__Nitrosocaldus * 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

Abstract Ni.tro.so.cal.da'les. N.L. masc. n. Nitrosocaldus type genus of the order; ‐ ales ending to denote order; N.L. fem. pl. n. Nitrosocaldales the Nitrosocaldus order. Coccoid cells reproduce by binary fission. Thermophilic and neutrophilic. Obligately aerobic. Chemolithoautotrophic growth by ammonia oxidation to nitrite using CO 2 as carbon source. Some members can also use urea as an alternative source of energy for growth. Cell membrane is composed of isoprenoid tetraether lipids, including large amounts of acyclic and cyclized glycerol trialkyl glycerol tetraethers (GTGTs) and crenarchaeol (a unique glycerol dibiphytanyl glycerol tetraether (GDGT) containing one cyclohexane ring and four cyclopentane rings). Fully saturated and monounsaturated menaquinones with six isoprenoid units are present. They are globally distributed in various geothermal environments. Phylogenetic analyses of 16S rRNA and amoA gene sequences place the monophyletic order Ca . Nitrosocaldales as a basal lineage within the phylum Thaumarchaeota . This order can be distinguished from the closest order Nitrososphaerales by a lower mol% G + C content, a higher growth temperature (>60°C), and a higher relative abundance of GTGT. The order Ca . Nitrosocaldales is currently represented by a single family Ca . Nitrosocaldaceae. Type genus : Ca . Nitrosocaldus de la Torre, Walker, Ingalls, Könneke and Stahl 2008, 815. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the order Candidatus Nitrosocaldales is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / incertae sedis / Candidatus Nitrosocaldales The order Candidatus Nitrosocaldales can also be recovered in the Genome Taxonomy Database (GTDB) as o__Nitrososphaerales (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales * 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

Abstract Ni.tro.so.cal.da.ce'ae. N.L. masc. n. Nitrosocaldus type genus of the family; ‐ aceae ending to denote family; N.L. fem. pl. n. Nitrosocaldaceae the Nitrosocaldus family. Cells are irregular cocci and divide by binary fission. Strictly aerobic. Thermophilic, neutrophilic, and lithoautotrophic archaea that are able to gain energy via ammonia oxidation to nitrite. Membrane lipids contain glycerol dibiphytanyl glycerol tetraethers (GDGTs) bound to monoglycosidic, diglycosidic, phosphohexose, and hexose‐phosphohexose headgroups. Like other described Thaumarchaeota , members of this family contain crenarchaeol as a major membrane core lipid. However, their membrane lipids are characterized by the presence of the high abundances of acyclic and cyclized glycerol trialkyl glycerol tetraethers (GTGTs). Respiratory lipoquinones are saturated and monounsaturated menaquinones with six isoprenoid units. Cells and molecular markers have been found in neutral or slightly alkaline geothermal environments, such as hot springs and subsurface gold mines. At present, the family Ca . Nitrosocaldaceae only harbors a single genus, which is so far represented by only one species. Therefore, future phylogenetic analysis of additional cultivated representatives may reveal further subdivisions within the family. DNA G+C content (mol%):36.8–41.7%. Type genus: Candidatus Nitrosocaldus de la Torre, Walker, Ingalls, Könneke and Stahl 2008, 815. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the family Candidatus Nitrosocaldaceae is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / incertae sedis / Candidatus Nitrosocaldales / Candidatus Nitrosocaldaceae The family Candidatus Nitrosocaldaceae can also be recovered in the Genome Taxonomy Database (GTDB) as f__Nitrosocaldaceae (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosocaldaceae * 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