Bioreactor metagenome Genome sequencing and assembly

The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Furthermore, most available genomic information is derived from metagenomic sequencing and high quality closed genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named “Candidatus Nitrospira kreftii” and performed a detailed genomic and physiological characterization. The closed genome of Ca. N. kreftii allowed reconstruction of its basic metabolic traits. Similar to N. inopinata, the enrichment culture exhibited a very high ammonia affinity , but a higher nitrite affinity , indicating an adaptation to more oligotrophic environments. Furthermore, this adaptation was supported by an unanticipated inhibition of ammonia oxidation at ammonium concentrations. This substrate inhibition of Ca. N. kreftii indicated that differences in ammonium tolerance can be a niche determining factor for different comammox Nitrospira.