Context.The discovery of complete ammonia-oxidizing (comammox) Nitrospirahas added an important new process to the microbial nitrogen cycle.
Gap.While comammox Nitrospira have been detected in various ecosystems, very few study has achieved selective enrichment of comammox Nitrospira over other canonical nitrifiers. The selecting factor for the dominance of comammox Nitrospira is still unclear.
Aim.In this study, we aim to selectively enrich comammox Nitrospira in a urine-fed membrane bioreactor and to verify the potential selecting factor.
Methods. To reveal the potential role of urine in enrichment of comammox Nitrospira, multiple molecular approaches were applied, including quantitative PCR, amplicon sequencing and metagenomics. Afterwards, in-depth genome comparison was performed.
Findings.Here, we obtained a selective enrichment of comammox Nitrospirain a urine-fed membrane bioreactor in 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over AOB and AOA. The complete genomes of three new clade A comammox Nitrospirawere recovered by metagenomics, which were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to genes for ammonia and nitrite oxidation, the three recovered genomes contained complete urea utilization pathway, indicated the supply of urine was likely an important contributor for selectively enriching comammox Nitrospira. Specifically, due to the presence of the nickel-dependent urease (UreABC), accessory proteins (UreDFG) and ATP-dependent ABC-type urea transporter (UrtABCDE), urea can be enzymatically hydrolyzed to ammonia by comammox Nitrospira. Besides its role in assimilation and amino acid biosynthesis, the produced ammonia can also fuel nitrification.
Utilization. Three new comammox Nitrospira were enriched and identified. The urea present in the urine media played a significant role in the selective enrichment of comammox Nitrospira, and support the diversity and versatility of their metabolism.
