Nitrosarchaeum haohaiensis sp. Nov. CL1: Isolation and Characterisation of a Novel Ammonia-Oxidising Archaeon From Aquatic Environments.

Following a 3.5-year enrichment cultivation period, a novel ammonia-oxidising archaeon (AOA), designated strain CL1, was isolated from Yangshan Harbour (East China Sea). Strain CL1 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 achieved a maximum specific growth rate of 0.87 d, with cell yields estimated at 3.92 × 10 cells mL μM ammonia. Genomic sequencing revealed that strain CL1 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 within the genus Nitrosarchaeum. The average nucleotide identity (ANI) between the genome of strain CL1 and its closest relative was 92.01%, confirming that strain CL1 represents a novel species within Nitrosarchaeum. Metabolic pathway analysis demonstrated that strain CL1 encodes key enzymes for ammonia oxidation, including ammonia monooxygenase (amoA, amoB, amoC) and copper oxidase, indicating its capacity for ammonia oxidation. Additionally, strain CL1 likely assimilates ammonia through the GS-GOGAT and GDH pathways. Consistent with the observation of extracellular vesicles (EVs) in strain CL1 via electron microscopy, genome annotation identified core genes associated with EVs function, such as vps4 and FtsZ. The isolation of strain CL1 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.