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The discovery of complete ammonia-oxidizing (comammox)  Nitrospira  has added an important new process to the microbial nitrogen cycle. While comammox  Nitrospira  have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox  Nitrospira  in a urine-fed membrane bioreactor in less than 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 ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox  Nitrospira  were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and  amoA -based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox  Nitrospira , and support the diversity and versatility of their metabolism.

Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor