Nitrosarchaeum haohaiensis sp. Nov. CL1T: Isolation and Characterisation of a Novel Ammonia-Oxidising Archaeon From Aquatic Environments

Abstract

Following a 3.5-year enrichment cultivation period, a novel ammonia-oxidising archaeon (AOA), designated strain CL1^T, was isolated from Yangshan Harbour (East China Sea). Strain CL1^T demonstrates a maximum ammonia tolerance of up to 10 mM. Its optimal growth conditions include a pH range of 7–8, a salinity of 2%–3%, and a temperature range of 20°C–25°C. Under these conditions, strain CL1^T achieved a maximum specific growth rate of 0.87 d⁻¹, with cell yields estimated at 3.92 × 10⁶ cells mL⁻¹ μM ammonia⁻¹. Genomic sequencing revealed that strain CL1^T possesses a genome size of 1.63 megabases with a high completeness of 99.95%. Phylogenetic analysis based on the 16S rRNA gene and whole-genome data placed strain CL1^T within the genus Nitrosarchaeum. The average nucleotide identity (ANI) between the genome of strain CL1^T and its closest relative was 92.01%, confirming that strain CL1^T represents a novel species within Nitrosarchaeum. Metabolic pathway analysis demonstrated that strain CL1^T encodes key enzymes for ammonia oxidation, including ammonia monooxygenase (amoA, amoB, amoC) and copper oxidase, indicating its capacity for ammonia oxidation. Additionally, strain CL1^T likely assimilates ammonia through the GS-GOGAT and GDH pathways. Consistent with the observation of extracellular vesicles (EVs) in strain CL1^T via electron microscopy, genome annotation identified core genes associated with EVs function, such as vps4 and FtsZ. The isolation of strain CL1^T provides a valuable model system for investigating its ammonia metabolism and exploring its ecological interactions with other AOA, ammonia-oxidising bacteria (AOB) and nitrite-oxidising bacteria (NOB), thereby contributing to a deeper understanding of nitrogen cycling mechanisms in aquatic environments.