Bayer, Barbara

Abstract Ni.tro.so.pe.la'gi.cus. N.L. masc. adj. nitrosus nitrous; L. masc. adj. pelagicus of the open sea; N.L. masc. n. Nitrosopelagicus a nitrite producer of the open sea. The genus Candidatus Nitrosopelagicus is composed of marine ammonia‐oxidizing archaea, almost all of which are uncultivated. They are found in shallow waters (<200 m depth) of the oligotrophic tropical, subtropical, and temperate open oceans. A single species has been described, Candidatus Nitrosopelagicus brevis, which couples growth with the oxidation of ammonia to nitrite. One described strain ( Ca . N. brevis U25) is capable of hydrolyzing urea to supply the ammonia required for growth. Cells are obligately aerobic, small, and nonmotile rods. They grow free‐living, not associated with surfaces. No growth enhancement has been observed in the presence of organic carbon compounds; a reduction in the lag phase of growth has been observed with addition of α‐ketoacids, potentially serving as radical oxygen scavengers. Organisms are mesophilic and obligately marine. Lipid composition distinguishes Ca . Nitrosopelagicus from Nitrosopumilus using glycerol dibiphytanyl glycerol tetraether (GDGT) distributions, with lower amounts of GDGT‐2 and higher amounts of GDGT‐0 and GDGT‐1 found in Ca . Nitrosopelagicus. Abundance of Ca . Nitrospelagicus‐like organisms is correlated with nitrification rates, suggesting that these organisms are the dominant ammonia oxidizers in epipelagic and upper mesopelagic environments of the low‐ and mid‐latitude open oceans. DNA G + C content (mol%) : 33.1. Type species : Candidatus Nitrosopelagicus brevis Santoro et al. 2015. Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Candidatus Nitrosopelagicus is: preferred name (not correct name) (last update, February 2025) * . LPSN classification: Archaea / Thermoproteati / Thermoproteota / Nitrososphaeria / Nitrosopumilales / incertae sedis / Candidatus Nitrosopelagicus The genus Candidatus Nitrosopelagicus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Nitrosopelagicus (version v220) ** . GTDB classification: d__Archaea / p__Thermoproteota / c__Nitrososphaeria / o__Nitrososphaerales / f__Nitrosopumilaceae / g__Nitrosopelagicus * 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 Ammonia-oxidizing Archaea (AOA) are ubiquitous throughout the oceanic water column; however, our knowledge on their physiological and ecological diversity in different oceanic regions is rather limited. Here, we report the cultivation and characterization of two novel Nitrosopumilus strains, originating from coastal surface waters of the Northern Adriatic Sea. The combined physiological and genomic information revealed that each strain exhibits different metabolic and functional traits, potentially reflecting contrasting life modes. Strain NF5 contains many chemotaxis-related genes and is able to express archaella, suggesting that it can sense and actively seek favorable microenvironments such as nutrient-rich particles. In contrast, strain D3C is non-motile and shows higher versatility in substrate utilization, being able to use urea as an alternative substrate in addition to ammonia. Furthermore, it encodes a divergent, second copy of the AmoB subunit of the key enzyme ammonia monooxygenase, which might have an additional catalytic function and suggests further metabolic versatility. However, the role of this gene requires further investigation. Our results provide evidence for functional diversity and metabolic versatility among phylogenetically closely related thaumarchaeal strains, and point toward adaptations to free-living versus particle-associated life styles and possible niche differentiation among AOA in marine ecosystems.